Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 26 of 117
Found at i:3446543 original size:16 final size:16
Alignment explanation
Indices: 3446518--3446552 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3446508 GAATTTGTTC
*
3446518 AATTTGAAATAATTTG
1 AATTTAAAATAATTTG
*
3446534 AATTTAAAATGATTTG
1 AATTTAAAATAATTTG
3446550 AAT
1 AAT
3446553 AATTTAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:3447023 original size:20 final size:19
Alignment explanation
Indices: 3446998--3447060 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
3446988 TTTACATTTT
3446998 AATAAAAATAAGAATTAAAA
1 AATAAAAATAA-AATTAAAA
*
3447018 AATAAAAAT-AACTT-AAA
1 AATAAAAATAAAATTAAAA
*
3447035 AATAAATAATAAAA-TATAA
1 AATAAA-AATAAAATTAAAA
3447054 AATAAAA
1 AATAAAA
3447061 GTATGAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.24
18 8 0.22
19 11 0.30
20 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAAATAAAATTAAAA
Found at i:3453429 original size:6 final size:7
Alignment explanation
Indices: 3453413--3453438 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3453403 TGTTTGTAAG
3453413 TTTTTCT
1 TTTTTCT
3453420 TTTTTCT
1 TTTTTCT
3453427 TTTTTCT
1 TTTTTCT
3453434 TTTTT
1 TTTTT
3453439 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:3462299 original size:22 final size:22
Alignment explanation
Indices: 3462247--3462299 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3462237 TTTGTACGAC
3462247 CTTC-GAGCATAATCTTTAAAA
1 CTTCTGAGCATAATCTTTAAAA
* **
3462268 CTTCTAAGCATAATCTTTAAGT
1 CTTCTGAGCATAATCTTTAAAA
3462290 CTTCTGAGCA
1 CTTCTGAGCA
3462300 AGATTCATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (22 bp):
CTTCTGAGCATAATCTTTAAAA
Found at i:3462604 original size:188 final size:189
Alignment explanation
Indices: 3462173--3462943 Score: 906
Period size: 188 Copynumber: 4.1 Consensus size: 189
3462163 ACTTCTGAGT
* * * *
3462173 AAAATATTTTAAATTCTAAAAGTTTTAATGCCTTTGATACAAGGAGCACTCAAAGATGTTGAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTCTGATACAAGAAGCACTCAAAGATGTTGAGAT
** * * *
3462238 TTGTACGACCTTC-GAGCATAATCTTTAAA-AC-TTCTAAGCATAATCTTTAAGTCTTCTGAGCA
66 TTGTAAAACCTTCAGAGCACAATC-TTAAAGACTTTC-AGGCATAATCTCTAAGTCTTCTGAGCA
* * * * * *
3462300 AGATTCATAAGTCTTTC-GAGTTAAATCTATTTTAGATTCAAAATTTGTAGGACCTCCAAG-
129 GGATTCAGAAGT-TTTCTGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCCAAGC
*
3462360 AAAA-A---T--ATTCTCAAAGTTTCAATGCCTCTTATACAAGAAGCACTCAAAGATGTTGAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTCTGATACAAGAAGCACTCAAAGATGTTGAGAT
3462419 TTGTAAAACCTTCAG-GCACAATCTTAAAGACTTTCAGGCATAATCTCTAAGTCTTTCTGA-CAG
66 TTGTAAAACCTTCAGAGCACAATCTTAAAGACTTTCAGGCATAATCTCTAAGTC-TTCTGAGCAG
* * *
3462482 GATTCAGAAGTTTTCTAAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACTTCCAGGC
130 GATTCAGAAGTTTTCTGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCCAAGC
*
3462542 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTCTAATACAAGAAGCACTCAAAGATGTTGAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTCTGATACAAGAAGCACTCAAAGATGTTGAGAT
*
3462607 TTGTAAGACCTTCAG-GCACAATCTTAAAGACTTTCAGGCATAATCTCTAAGTCTTTCTG-GCAG
66 TTGTAAAACCTTCAGAGCACAATCTTAAAGACTTTCAGGCATAATCTCTAAGTC-TTCTGAGCAG
*
3462670 GATTCATAAGTTTT-TCGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCCAAGC
130 GATTCAGAAGTTTTCT-GAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCCAAGC
* * * *
3462730 AAAATATTTTAAATTCTCGAAA-TTTCAATGCCTTTGATACAAGGAGCACTCAAAGATATTAAGA
1 AAAATATTTTAAATTCTC-AAAGTTTCAATGCCTCTGATACAAGAAGCACTCAAAGATGTTGAGA
* * * * * * * * * *
3462794 TTTATAAAAAC-TCTGAGTATAATCTTTAAGACCTTC--GAATGTAATCTCTAAGTCCTCTGAGT
65 TTTGTAAAACCTTCAGAGCACAATCTTAAAGACTTTCAGGCA--TAATCTCTAAGTCTTCTGAGC
* * * *
3462856 AGGATT-TGTAAGTCTTCTGAGCTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCTTC-AGT
128 AGGATTCAG-AAGTTTTCTGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTC--CAAGC
3462919 AAAATATTTTAAATT-T-AAAGTTTCA
1 AAAATATTTTAAATTCTCAAAGTTTCA
3462944 TTACCTATAG
Statistics
Matches: 514, Mismatches: 46, Indels: 48
0.85 0.08 0.08
Matches are distributed among these distances:
180 9 0.02
181 132 0.26
182 14 0.03
183 2 0.00
186 7 0.01
187 17 0.03
188 311 0.61
189 21 0.04
190 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (189 bp):
AAAATATTTTAAATTCTCAAAGTTTCAATGCCTCTGATACAAGAAGCACTCAAAGATGTTGAGAT
TTGTAAAACCTTCAGAGCACAATCTTAAAGACTTTCAGGCATAATCTCTAAGTCTTCTGAGCAGG
ATTCAGAAGTTTTCTGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTCCAAGC
Found at i:3462663 original size:22 final size:22
Alignment explanation
Indices: 3462611--3462652 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3462601 TGAGATTTGT
*
3462611 AAGACCTTCAGGCACAATCTTA
1 AAGACTTTCAGGCACAATCTTA
*
3462633 AAGACTTTCAGGCATAATCT
1 AAGACTTTCAGGCACAATCT
3462653 CTAAGTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (22 bp):
AAGACTTTCAGGCACAATCTTA
Found at i:3463058 original size:40 final size:39
Alignment explanation
Indices: 3462925--3463215 Score: 183
Period size: 40 Copynumber: 7.4 Consensus size: 39
3462915 CAGTAAAATA
* *
3462925 TTTTAAATTTAAAGTTTCATTA-CCTATAGTTAGAAGAGCC
1 TTTTAAATTTAAAGTTTCA-TAGCCTCT-GTTAGAGGAGCC
* *
3462965 TTTTAAATTTTCAAAGTTTCATAGCCTCTATTAAAGGAGCC
1 TTTTAAA-TTT-AAAGTTTCATAGCCTCTGTTAGAGGAGCC
* *
3463006 TTCTGAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCT-GTTAGAGGAGCC
* * * * *
3463046 TTTTAAAGTTAAAGTTTCGTTGCTTCTGTTCAG-GATAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCTGTT-AGAG-GAGCC
* * * *
3463086 TTTTGAATTTAAAGTTT-ATTTGCCTCTAGTCAGA-GA-AC
1 TTTTAAATTTAAAGTTTCA-TAGCCTCT-GTTAGAGGAGCC
** *
3463124 TTTCTAAATTT-TCGTTGTC-T----T-TAGTCAGAGGAGCC
1 TTT-TAAATTTAAAGTT-TCATAGCCTCT-GTTAGAGGAGCC
* * *
3463159 TTTTAAATTTAAAGTTTCATTGCCTCTGGTTAAAGGAGTC
1 TTTTAAATTTAAAGTTTCATAGCCTCT-GTTAGAGGAGCC
*
3463199 TTTTGAATTTAAAGTTT
1 TTTTAAATTTAAAGTTT
3463216 TGTTACCTAT
Statistics
Matches: 197, Mismatches: 33, Indels: 42
0.72 0.12 0.15
Matches are distributed among these distances:
33 8 0.04
34 12 0.06
35 8 0.04
38 8 0.04
39 30 0.15
40 97 0.49
41 21 0.11
42 13 0.07
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (39 bp):
TTTTAAATTTAAAGTTTCATAGCCTCTGTTAGAGGAGCC
Found at i:3463236 original size:40 final size:40
Alignment explanation
Indices: 3463145--3463253 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
3463135 TCGTTGTCTT
* * *
3463145 TAGTCAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCCTC
1 TAGTTAGAGGAGCCTTTTAAATTTAAAGTTTCATTACCTA
* * * * **
3463185 TGGTTAAAGGAGTCTTTTGAATTTAAAGTTTTGTTACCTA
1 TAGTTAGAGGAGCCTTTTAAATTTAAAGTTTCATTACCTA
* *
3463225 TAGTTGGAGGAGCATTTTTAAAATTTAAA
1 TAGTTAGAGGAGC-CTTTT-AAATTTAAA
3463254 AAGTTATTAA
Statistics
Matches: 52, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
40 40 0.77
41 4 0.08
42 8 0.15
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (40 bp):
TAGTTAGAGGAGCCTTTTAAATTTAAAGTTTCATTACCTA
Found at i:3463471 original size:3 final size:3
Alignment explanation
Indices: 3463463--3463495 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3463453 ATATAAATTT
3463463 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3463496 AATACATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3465281 original size:14 final size:14
Alignment explanation
Indices: 3465249--3465286 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
3465239 GTTTTATAAA
3465249 TAAAAATTAAAGTT
1 TAAAAATTAAAGTT
3465263 T-AAAATTAAAGTT
1 TAAAAATTAAAGTT
3465276 TAAAAATTAAA
1 TAAAAATTAAA
3465287 AAAAAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (14 bp):
TAAAAATTAAAGTT
Found at i:3467368 original size:7 final size:7
Alignment explanation
Indices: 3467337--3467362 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3467327 GAGGAGAAAG
3467337 AAAAAAT
1 AAAAAAT
3467344 AAAAAAT
1 AAAAAAT
3467351 AAAAAAT
1 AAAAAAT
3467358 AAAAA
1 AAAAA
3467363 CAAAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:3467504 original size:19 final size:19
Alignment explanation
Indices: 3467477--3467516 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3467467 ATTTGTAAGC
*
3467477 TTTTCTTTTTTCATTTTAT
1 TTTTATTTTTTCATTTTAT
*
3467496 TTTTATTTTTTGATTTTAT
1 TTTTATTTTTTCATTTTAT
3467515 TT
1 TT
3467517 ATTTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTTCATTTTAT
Found at i:3467575 original size:10 final size:10
Alignment explanation
Indices: 3467509--3467581 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
3467499 TATTTTTTGA
*
3467509 TTTTATTTAT
1 TTTTATATAT
*
3467519 TTTTGT-TAT
1 TTTTATATAT
3467528 TTGTT-TAATAT
1 TT-TTAT-ATAT
3467539 TTTTATA-A-
1 TTTTATATAT
3467547 -TTTATA-AT
1 TTTTATATAT
*
3467555 TTATA-ATAT
1 TTTTATATAT
3467564 TTTTATATAT
1 TTTTATATAT
3467574 TTTTATAT
1 TTTTATAT
3467582 TAAAAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
7 7 0.13
8 1 0.02
9 16 0.31
10 22 0.42
11 6 0.12
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3467589 original size:27 final size:25
Alignment explanation
Indices: 3467534--3467589 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3467524 TTATTTGTTT
* *
3467534 AATATTTTTATAATTTATAATTTAT
1 AATATTTTTATAATTTATAATTAAA
*
3467559 AATATTTTTATATATTTTTATATTAAA
1 AATATTTTTATA-ATTTATA-ATTAAA
3467586 AATA
1 AATA
3467590 AATAATTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.46
26 6 0.23
27 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AATATTTTTATAATTTATAATTAAA
Found at i:3476557 original size:188 final size:187
Alignment explanation
Indices: 3476256--3476845 Score: 769
Period size: 188 Copynumber: 3.1 Consensus size: 187
3476246 ACTTCTGAGT
* * * *
3476256 AAAATACTTTAAATTCTTAAAGTTTTAATGCCTTTGATACAATAAGCACTCAAAGATGTTGAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGAAGCACTCAAAGATGTTGAGAT
* * *
3476321 TTGTAAGACCTCCGAGCATAATCTTTAAA-ACTTCTAAGCATAATCTCTAAGTCCTCTGAGTAGG
66 TTGTAAGACCTCAGAGCATAATC-TTAAAGACTTTTAGGCATAATCTCTAAGTCCTCTGAGTAGG
* * * *
3476385 ATTTATAAGTCTTTCGAGCTGAATCTGTTTTAGTTTCAAAATTTGTAAGACCTTCAGGC
130 ATTTATAAGTCTTCCGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTTC-GGC
3476444 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGAAGCACTCAAAGATGTTGAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGAAGCACTCAAAGATGTTGAGAT
* * *
3476509 TTGTAAGACCTTCAG-GCATAATCTTAAAGACTTTTAGGCATAATCTCTAAGTCTTTCTGA-CAT
66 TTGTAAGACC-TCAGAGCATAATCTTAAAGACTTTTAGGCATAATCTCTAAGTC-CTCTGAGTAG
* * * *
3476572 GATTCATAAGTCTTCCAAGTTGAATCAATTTTAGTTTCAAGATTTGTAAGACCTCCGGGC
129 GATTTATAAGTCTTCCGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTTC-GGC
* * * *
3476632 AAAATATTTTAAATTTTCAAAATTTCAATGCCTTTGATACAAGGAGCACTCAAAGATGTTAAGAT
1 AAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGAAGCACTCAAAGATGTTGAGAT
* * * * * * * *
3476697 TTGTAAAACCTCTGAGCATAATCTTTAAGAC-CTTCGAACGTAATCTCTAAGTCCTCTAAGTAGG
66 TTGTAAGACCTCAGAGCATAATCTTAAAGACTTTTAG-GCATAATCTCTAAGTCCTCTGAGTAGG
* * *
3476761 ATTTGTAAGTCTTCCGAGTTGAATCTATTTTAATTTCAAGATTTGTAAGACCTCCTCGGT
130 ATTTATAAGTCTTCCGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCT--TCGGC
3476821 AAAATATTTTAAATT-T-AAAGTTTCA
1 AAAATATTTTAAATTCTCAAAGTTTCA
3476846 TTACCTATAG
Statistics
Matches: 352, Mismatches: 42, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
187 23 0.07
188 303 0.86
189 25 0.07
190 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (187 bp):
AAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGAAGCACTCAAAGATGTTGAGAT
TTGTAAGACCTCAGAGCATAATCTTAAAGACTTTTAGGCATAATCTCTAAGTCCTCTGAGTAGGA
TTTATAAGTCTTCCGAGTTGAATCTATTTTAGTTTCAAGATTTGTAAGACCTTCGGC
Found at i:3476564 original size:22 final size:22
Alignment explanation
Indices: 3476513--3476554 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3476503 TGAGATTTGT
* *
3476513 AAGACCTTCAGGCATAATCTTA
1 AAGACTTTTAGGCATAATCTTA
3476535 AAGACTTTTAGGCATAATCT
1 AAGACTTTTAGGCATAATCT
3476555 CTAAGTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (22 bp):
AAGACTTTTAGGCATAATCTTA
Found at i:3476871 original size:40 final size:39
Alignment explanation
Indices: 3476827--3477004 Score: 187
Period size: 40 Copynumber: 4.4 Consensus size: 39
3476817 CGGTAAAATA
*
3476827 TTTTAAATTTAAAGTTTCATTA-CCTATAGTTAGAAGAGCC
1 TTTTAAATTTAAAGTTTCA-TAGCCTCT-GTTAGAAGAGCC
*
3476867 TTTTAAATTTTCAAAGTTTCATAGCCTCTGTTAAAAGAGCC
1 TTTTAAA-TTT-AAAGTTTCATAGCCTCTGTTAGAAGAGCC
* * *
3476908 TTCTGAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCT-GTTAGAAGAGCC
* * * * * *
3476948 TTTTAAAGTTAAAGTTTCGTTGCTTCTGTTCAGGATAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCTGTT-AGAAGAGCC
*
3476988 TTTTGAATTTAAAGTTT
1 TTTTAAATTTAAAGTTT
3477005 ATTTGCCTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 20 0.17
40 62 0.53
41 21 0.18
42 13 0.11
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (39 bp):
TTTTAAATTTAAAGTTTCATAGCCTCTGTTAGAAGAGCC
Found at i:3476917 original size:41 final size:40
Alignment explanation
Indices: 3476830--3477037 Score: 163
Period size: 40 Copynumber: 5.2 Consensus size: 40
3476820 TAAAATATTT
* *
3476830 TAAATTTAAAGTTTCATTA-CCTATAGTTAGAAGAGCCTTT
1 TAAATTTAAAGTTTCA-TAGCCTCTAGTTAGAAGAGCCTTC
*
3476870 TAAATTTTCAAAGTTTCATAGCCTCT-GTTAAAAGAGCCTTC
1 TAAA-TTT-AAAGTTTCATAGCCTCTAGTTAGAAGAGCCTTC
* * * *
3476911 TGAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGCCTTT
1 TAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGCCTTC
* * * * * * *
3476951 TAAAGTTAAAGTTTCGTTGCTTCT-GTTCAGGATAGCCTTT
1 TAAATTTAAAGTTTCATAGCCTCTAGTT-AGAAGAGCCTTC
* * * * * *
3476991 TGAATTTAAAGTTT-ATTTGCCTTTAGTCAGAGGAACCTTC
1 TAAATTTAAAGTTTCA-TAGCCTCTAGTTAGAAGAGCCTTC
3477031 TAAATTT
1 TAAATTT
3477038 TCGTTGTCTT
Statistics
Matches: 134, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
39 20 0.15
40 78 0.58
41 23 0.17
42 13 0.10
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (40 bp):
TAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGCCTTC
Found at i:3477023 original size:80 final size:81
Alignment explanation
Indices: 3476827--3477105 Score: 222
Period size: 80 Copynumber: 3.5 Consensus size: 81
3476817 CGGTAAAATA
* * * *
3476827 TTTTAAATTTAAAGTTTCATTACCTATAGTTAGAAGAGCCTTTTAAATTTTCAAAGTTTCATAGC
1 TTTTGAATTTAAAGTTTCATTGCCTATAGTTAGAGGAGCCTTTTAAATGTTCAAAGTTTCATAGC
3476892 CTCTGTTAAAAGAGCC
66 CTCTGTTAAAAGAGCC
* * * * * *
3476908 TTCTGAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGCCTTTTAAA-GTT-AAAGTTTCGTTGC
1 TTTTGAATTTAAAGTTTCATTGCCTATAGTTAGAGGAGCCTTTTAAATGTTCAAAGTTTCATAGC
* ** *
3476971 TTCTGTTCAGGATAGCC
66 CTCTGTT-AAAAGAGCC
* * * * *
3476988 TTTTGAATTTAAAGTTT-ATTTGCCTTTAGTCAGAGGAACCTTCTAAATTTTC---GTTGTC-T-
1 TTTTGAATTTAAAGTTTCA-TTGCCTATAGTTAGAGGAGCCTTTTAAATGTTCAAAGTT-TCATA
*
3477047 ---T-TGATTAAATGAGCC
64 GCCTCTG-TTAAAAGAGCC
* * * *
3477062 TTTTAAATTTAAAGTTTCATTGCCTCTGGTTAGAGGAGTCTTTT
1 TTTTGAATTTAAAGTTTCATTGCCTATAGTTAGAGGAGCCTTTT
3477106 GAATTTAAAA
Statistics
Matches: 158, Mismatches: 33, Indels: 21
0.75 0.16 0.10
Matches are distributed among these distances:
74 42 0.27
75 4 0.03
79 22 0.14
80 48 0.30
81 42 0.27
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (81 bp):
TTTTGAATTTAAAGTTTCATTGCCTATAGTTAGAGGAGCCTTTTAAATGTTCAAAGTTTCATAGC
CTCTGTTAAAAGAGCC
Found at i:3477097 original size:74 final size:75
Alignment explanation
Indices: 3476893--3477098 Score: 206
Period size: 74 Copynumber: 2.7 Consensus size: 75
3476883 TTTCATAGCC
* * * * *
3476893 TCTGTTAAAAGAGCCTTCTGAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGCCTTTTAAAGTT
1 TCTGTTAAATGAGCCTTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAGGAACCTTCTAAAG-T
3476958 AAAGTTTCGTTGCT
65 --A-TTTCGTTGCT
* * * *
3476972 TCTGTTCAGGAT-AGCCTTTTGAATTTAAAGTTT-ATTTGCCTTTAGTCAGAGGAACCTTCTAAA
1 TCTGTT-A-AATGAGCCTTTTGAATTTAAAGTTTCA-TTGCCTCTGGTTAGAGGAACCTTCTAAA
3477035 -T-TTTCGTTGTCT
63 GTATTTCGTTG-CT
*
3477047 T-TGATTAAATGAGCCTTTTAAATTTAAAGTTTCATTGCCTCTGGTTAGAGGA
1 TCTG-TTAAATGAGCCTTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAGGA
3477099 GTCTTTTGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
73 2 0.02
74 46 0.43
75 6 0.06
78 1 0.01
79 7 0.07
80 43 0.41
81 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (75 bp):
TCTGTTAAATGAGCCTTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAGGAACCTTCTAAAGTA
TTTCGTTGCT
Found at i:3477371 original size:3 final size:3
Alignment explanation
Indices: 3477363--3477407 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3477353 AAATATAAAT
3477363 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3477408 AATACGTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3477975 original size:2 final size:2
Alignment explanation
Indices: 3477970--3478001 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3477960 AAAAGTTAAG
3477970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3478002 TTGGGTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3479521 original size:14 final size:13
Alignment explanation
Indices: 3479500--3479535 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
3479490 TCTTTTTCCA
3479500 TTTTATTTTATTT
1 TTTTATTTTATTT
3479513 TTTTGATTTTATTT
1 TTTT-ATTTTATTT
3479527 TTGTTATTT
1 TT-TTATTT
3479536 GTTTAAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:3479536 original size:19 final size:19
Alignment explanation
Indices: 3479499--3479536 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3479489 TTCTTTTTCC
*
3479499 ATTTTATTTTATTTTTTTG
1 ATTTTATTTTATTTATTTG
3479518 ATTTTATTTT-TGTTATTTG
1 ATTTTATTTTAT-TTATTTG
3479537 TTTAAGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (19 bp):
ATTTTATTTTATTTATTTG
Found at i:3480361 original size:3 final size:3
Alignment explanation
Indices: 3480353--3480386 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3480343 TAAAATATGA
*
3480353 AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3480387 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3485592 original size:16 final size:16
Alignment explanation
Indices: 3485563--3485612 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3485553 TCAAAATCAT
*
3485563 AAAAAA-AAATAAAAC
1 AAAAAAGAAAGAAAAC
* * *
3485578 CAAAAAGAGAGAAAAG
1 AAAAAAGAAAGAAAAC
3485594 AAAAAAGAAAGAAAA-
1 AAAAAAGAAAGAAAAC
3485609 AAAA
1 AAAA
3485613 GTTTTCTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAC
Found at i:3486205 original size:15 final size:15
Alignment explanation
Indices: 3486185--3486224 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
3486175 AGGGACATTC
3486185 GCATTTGCATCACTT
1 GCATTTGCATCACTT
*
3486200 GCATTTGCTTCACTT
1 GCATTTGCATCACTT
*
3486215 GCATGTGCAT
1 GCATTTGCAT
3486225 TATGAGAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (15 bp):
GCATTTGCATCACTT
Found at i:3486284 original size:26 final size:26
Alignment explanation
Indices: 3486254--3486315 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
3486244 TTCACATTAT
3486254 TCGCATCATAACCAAAG-CATTTGCAA
1 TCGCATCATAA-CAAAGACATTTGCAA
* * *
3486280 TCGCATCACAAGAAAGACATTTGCAT
1 TCGCATCATAACAAAGACATTTGCAA
*
3486306 TTGCATCATA
1 TCGCATCATA
3486316 GCATCTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (26 bp):
TCGCATCATAACAAAGACATTTGCAA
Found at i:3487128 original size:188 final size:189
Alignment explanation
Indices: 3486762--3487372 Score: 833
Period size: 188 Copynumber: 3.3 Consensus size: 189
3486752 TAAGACAGTC
* * *
3486762 TGTAAAACTTCTGGGCAAAATATTTTAAATTCTCAAAGTTTCAATGCCATTGATACAAGGAGCAC
1 TGTAAAACCTCTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGGAGCAC
* * * * *
3486827 TCAAAGATGTTAAGATTTGTAAGACCTTCGAGCATAATCTTTAAGATCTCCAAACGTAATCTTTA
66 TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAGATCTTCAAGCGTAATCTCTA
* * ** *
3486892 AGTCTT-TCGAGCAACATTCATAAGTCTTT-TGAGCTAAATTTATTTTAGTTTCAAAATT
131 AGTCTTCTAG-GTAGGATTCATAAGTCTTTCTGAGCTAAATTTATTTTAGTTTCAAGATT
* *
3486950 TGCAAGACCTCTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGGAGCAC
1 TGTAAAACCTCTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGGAGCAC
* * * *
3487015 TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAAACCTTCAGGCATAATCTCTA
66 TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAGATCTTCAAGCGTAATCTCTA
* * * * *
3487080 AGTCTTCTAGGTAGGATTCGTAAGT-TTTCTGAGTTGAATCTGTTTTAGTTTCAAGATT
131 AGTCTTCTAGGTAGGATTCATAAGTCTTTCTGAGCTAAATTTATTTTAGTTTCAAGATT
* * * * *
3487138 TGTAAAACCTCCGGATAAAATATTTTAAATTTTCAAAATTTCAATGCCTTTAATACAAGGAGCAC
1 TGTAAAACCTCTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGGAGCAC
*
3487203 TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAGATCTTCAAGTGTAATCTCTA
66 TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAGATCTTCAAGCGTAATCTCTA
* *
3487268 AGTCTTAC-AGGTAGGATTTATAAATCTTTC-GAGCTAAATTTATTTTAGTTTCAAGATT
131 AGTCTT-CTAGGTAGGATTCATAAGTCTTTCTGAGCTAAATTTATTTTAGTTTCAAGATT
* *
3487326 TGTAAAACCTCCAGG-CAAAATATTTTAAATT-T-AAAGTTTCATTGCCT
1 TGTAAAACCT-CTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCT
3487373 CTAGTTTGAA
Statistics
Matches: 371, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
186 13 0.04
187 4 0.01
188 344 0.93
189 10 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (189 bp):
TGTAAAACCTCTGGACAAAATATTTTAAATTCTCAAAGTTTCAATGCCTTTGATACAAGGAGCAC
TCAAAGATGTTGAGATTTGTAAGACCTCCGAGCATAATCTTTAAGATCTTCAAGCGTAATCTCTA
AGTCTTCTAGGTAGGATTCATAAGTCTTTCTGAGCTAAATTTATTTTAGTTTCAAGATT
Found at i:3487463 original size:40 final size:40
Alignment explanation
Indices: 3487348--3487677 Score: 184
Period size: 40 Copynumber: 8.2 Consensus size: 40
3487338 AGGCAAAATA
* * *
3487348 TTTTAAATTTAAAGTTTCATTGCCTCTAGTTTGAAAAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGCC
* *
3487388 TTTTAAAATTTTAAAGTTTCATAACCT-TTGATTAGAAGAGCC
1 TTTT-AAA-TTTAAAGTTTCATAGCCTCTAG-TTAGAAGAGCC
* *
3487430 TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAGGAGCT
1 TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGCC
* * * *
3487470 TTTTAAATTTAAAGTTTCGTTGCCT-TTGATCAGGGAA-A-CC
1 TTTTAAATTTAAAGTTTCATAGCCTCTAG-TTA--GAAGAGCC
* * *
3487510 TTTTGAATTT----TTGT--TA-CCTCTAGTCAGAGGAGCC
1 TTTTAAATTTAAAGTT-TCATAGCCTCTAGTTAGAAGAGCC
* * * *
3487544 TTTTAAATTTAAAGTTTTATTGCATCTAGTTA-AAGAAACC
1 TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAAG-AGCC
* * *** * *
3487584 TTTTGAATTTAAAGTTTTATTTTCTCTAGTTAGATGAGCAT
1 TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGC-C
* * *
3487625 TTTTAAATTTTTAAAAGTTATCA-AGTCTTTATTTAG-AGTAGCC
1 TTTTAAA--TTT-AAAGTT-TCATAGCCTCTAGTTAGAAG-AGCC
3487668 TTTTAAATTT
1 TTTTAAATTT
3487678 TCTTTCAAAA
Statistics
Matches: 224, Mismatches: 40, Indels: 51
0.71 0.13 0.16
Matches are distributed among these distances:
32 2 0.01
33 1 0.00
34 17 0.08
35 3 0.01
36 2 0.01
37 2 0.01
38 2 0.01
39 5 0.02
40 106 0.47
41 22 0.10
42 31 0.14
43 11 0.05
44 18 0.08
45 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (40 bp):
TTTTAAATTTAAAGTTTCATAGCCTCTAGTTAGAAGAGCC
Found at i:3487582 original size:74 final size:74
Alignment explanation
Indices: 3487452--3487593 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
3487442 AGTTTCATAG
* * * * * **
3487452 CCTCTAGTTAGAGGAGCTTTTTAAATTTAAAGTTTCGTTGCCTTTGATCAGGGAAACCTTTTGAA
1 CCTCTAGTCAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCATTAGATCAAAGAAACCTTTTGAA
3487517 TTTTTGTTA
66 TTTTTGTTA
* *
3487526 CCTCTAGTCAGAGGAGCCTTTTAAATTTAAAGTTTTATTGCATCTAG-TTAAAGAAACCTTTTGA
1 CCTCTAGTCAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCAT-TAGATCAAAGAAACCTTTTGA
3487590 ATTT
65 ATTT
3487594 AAAGTTTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 56 0.97
75 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (74 bp):
CCTCTAGTCAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCATTAGATCAAAGAAACCTTTTGAA
TTTTTGTTA
Found at i:3492531 original size:144 final size:141
Alignment explanation
Indices: 3492383--3492770 Score: 385
Period size: 136 Copynumber: 2.7 Consensus size: 141
3492373 AAGAAGTGCA
* *
3492383 AAATTATCAAATTACCTTATAAGGGTATTTTCATAATTTAGCCTTCATGAGCTCAAATTTTTGTA
1 AAATTATCAAAATACCTTATAAGGGTATTTTCATAATTTAGCCTTC-TGAGCTCAAATTTTTATA
* * ***
3492448 AAACTTTTCAGATCTTAATTTTATAATATTTCATAATTTTTGATGCATTTGAAATTGTAGCAGTG
65 AAACTTTT-A-ATCTAAATTTTATAATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTG
*
3492513 CCCCGAAAAGTGTG
128 CCCCGAAAAGAGTG
* * * ** * * * * * *
3492527 AAATTACCAAAATACCTTTATAGGGGTATTTTCGTAATTTAATCTTTTTAACTCTAATTTTCATG
1 AAATTATCAAAATACC-TTATAAGGGTATTTTCATAATTTAGCCTTCTGAGCTCAAATTTTTATA
* * *
3492592 AAAC-TTT--T-TAAATCTTA-AAT-TTTCATGATTTTTTATTCATTTGAAATCACAGCAGTGCC
65 AAACTTTTAATCTAAATTTTATAATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTGCC
*
3492651 CTGAAAAGAGTG
130 CCGAAAAGAGTG
** *
3492663 AAATTATCAAAATACTCTTATAAGAATATTTTCATAATTT-GACCTTTCCGAGCTCAAATTTTTA
1 AAATTATCAAAATAC-CTTATAAGGGTATTTTCATAATTTAG-CC-TTCTGAGCTCAAATTTTTA
* * *
3492727 CAAAACTTTTTAAATCTCAATTTTATAATATTTTATGATTTTTG
63 TAAAAC-TTTT-AATCTAAATTTTATAATATTTCATGATTTTTG
3492771 GTATTCTAAA
Statistics
Matches: 190, Mismatches: 42, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
136 77 0.41
137 21 0.11
138 7 0.04
139 4 0.02
142 1 0.01
143 10 0.05
144 33 0.17
145 37 0.19
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (141 bp):
AAATTATCAAAATACCTTATAAGGGTATTTTCATAATTTAGCCTTCTGAGCTCAAATTTTTATAA
AACTTTTAATCTAAATTTTATAATATTTCATGATTTTTGATGCATTTGAAATCACAGCAGTGCCC
CGAAAAGAGTG
Found at i:3492598 original size:25 final size:27
Alignment explanation
Indices: 3492570--3492619 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3492560 GTAATTTAAT
*
3492570 CTTTTTAACTC-T-AATTTTCATGAAA
1 CTTTTTAAATCTTAAATTTTCATGAAA
3492595 CTTTTTAAATCTTAAATTTTCATGA
1 CTTTTTAAATCTTAAATTTTCATGA
3492620 TTTTTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (27 bp):
CTTTTTAAATCTTAAATTTTCATGAAA
Found at i:3494310 original size:3 final size:3
Alignment explanation
Indices: 3494302--3494348 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
3494292 AAATTTATGC
*
3494302 ATA ATA ATA ATA ATA TTA ATA ATA AT- ATCA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
3494347 AT
1 AT
3494349 TAAAAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3495141 original size:18 final size:19
Alignment explanation
Indices: 3495104--3495141 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3495094 TGTTGGAGAC
3495104 TTTGAAGATATTTCTTTAA
1 TTTGAAGATATTTCTTTAA
* *
3495123 TTTGAA-ATTTTTTTTTAA
1 TTTGAAGATATTTCTTTAA
3495141 T
1 T
3495142 ATTCCTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTGAAGATATTTCTTTAA
Found at i:3501053 original size:36 final size:36
Alignment explanation
Indices: 3501013--3501083 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
3501003 CACTGAAAAC
*
3501013 ATTTAGGCTTCTTAAGCCTACGC-ATTGTCTTAGGCT
1 ATTTAGGCTTATTAAGCCTACGCTA-TGTCTTAGGCT
*
3501049 ATTTAGGCTTATTGAGCCTACGCTATGTCTTAGGC
1 ATTTAGGCTTATTAAGCCTACGCTATGTCTTAGGC
3501084 GGCGTGTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (36 bp):
ATTTAGGCTTATTAAGCCTACGCTATGTCTTAGGCT
Found at i:3502794 original size:20 final size:21
Alignment explanation
Indices: 3502755--3502796 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3502745 AGACCATCTA
* *
3502755 ATATAAGAATTTTTTGTATTT
1 ATATAAGAATTTTGTATATTT
3502776 ATATAA-AATTTTGTATATTT
1 ATATAAGAATTTTGTATATTT
3502796 A
1 A
3502797 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (21 bp):
ATATAAGAATTTTGTATATTT
Found at i:3504396 original size:177 final size:177
Alignment explanation
Indices: 3503836--3504452 Score: 976
Period size: 176 Copynumber: 3.5 Consensus size: 177
3503826 TTTCTAAGGA
* **
3503836 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAATAATGTCTGGAAAATCCATCTTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
* * *
3503901 GATTCTACCAATCGTGTTTCTTGGGCTCTATTTAATTT-G---G-ACAAGGAAGTGTTTTAATGT
66 GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
* *
3503961 CCATGGTCCAGACTCTTTGATTTGGCTTTCTAAGGACGAACCATAAT
131 CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
* * * * *
3504008 CAAGGCCGAAATTGTCTCAGTTTCGTGAGTACGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
3504073 GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGG-AATGTTTTAATTT
66 GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
*
3504137 CCATAGTCCAGACGCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
131 CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
*
3504184 CAACGCCAAAATTGTTTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
*
3504249 GATTCCACCAATCGTGTTTCTTAGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
66 GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
* *
3504314 CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACTACAAT
131 CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
* * *
3504361 CGACGCCAAAATTGTCTCAATTTCATTAGTATGACAACAATGTCTGGAAAATCCAGATTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
* * *
3504426 GATTCTACCAATTGTGTTTGTTGGGCT
66 GATTCCACCAATCGTGTTTCTTGGGCT
3504453 TTGCCAGACC
Statistics
Matches: 407, Mismatches: 32, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
172 94 0.23
173 1 0.00
176 165 0.41
177 147 0.36
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (177 bp):
CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
Found at i:3511225 original size:50 final size:51
Alignment explanation
Indices: 3511159--3511267 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 51
3511149 ACCCCCACAA
* * *
3511159 AAAAAGAAGAAAACCCACCTTC-CATTCAAACTCAAAAAACTCATTTGAATT
1 AAAAAGAAGAAAACCCACCTTCAAATTCAAACTC-AAAAACCCATTTGAATC
3511210 AAAAAGAAG-AAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
1 AAAAAGAAGAAAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
3511260 AAAAAGAA
1 AAAAAGAA
3511268 AATAAATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 35 0.65
51 19 0.35
ACGTcount: A:0.52, C:0.23, G:0.06, T:0.18
Consensus pattern (51 bp):
AAAAAGAAGAAAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
Found at i:3511830 original size:26 final size:25
Alignment explanation
Indices: 3511780--3511833 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
3511770 TAAAATAAAA
*
3511780 TAATTTTTATATTTGATTATAAATT
1 TAATTTTTATATTTAATTATAAATT
*
3511805 TAATTATTTATATTTTAATT-TTAATT
1 TAATT-TTTATA-TTTAATTATAAATT
3511831 TAA
1 TAA
3511834 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 14 0.56
27 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TAATTTTTATATTTAATTATAAATT
Found at i:3511928 original size:24 final size:24
Alignment explanation
Indices: 3511879--3511929 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
3511869 TAATACGAAT
*
3511879 AAAAATATAAAACTTAAAATTTTA
1 AAAAATATAAAACTTAAAATTATA
3511903 AAAAATATATAAA-TT-AAATTAATA
1 AAAAATATA-AAACTTAAAATT-ATA
3511927 AAA
1 AAA
3511930 TCAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAATATAAAACTTAAAATTATA
Found at i:3515084 original size:29 final size:29
Alignment explanation
Indices: 3515043--3515123 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
3515033 ACAGGAATTG
* *
3515043 AATTCCTTAAAAATAATATTATGATGACTA
1 AATTTCTT-AAAATAATATTATAATGACTA
* * *
3515073 AATTTCTTAAAATAATATTACAATTATTA
1 AATTTCTTAAAATAATATTATAATGACTA
* *
3515102 AATTTTTTTAAATAATATTATA
1 AATTTCTTAAAATAATATTATA
3515124 GGACTAGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 36 0.84
30 7 0.16
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (29 bp):
AATTTCTTAAAATAATATTATAATGACTA
Found at i:3519961 original size:19 final size:19
Alignment explanation
Indices: 3519937--3519975 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3519927 CATAGGATTT
3519937 GAATTGATGTGGCAAGATA
1 GAATTGATGTGGCAAGATA
3519956 GAATTGATGTGGCAAGATA
1 GAATTGATGTGGCAAGATA
3519975 G
1 G
3519976 TACATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (19 bp):
GAATTGATGTGGCAAGATA
Found at i:3522150 original size:26 final size:26
Alignment explanation
Indices: 3522102--3522151 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3522092 GTTTTTGTCG
* **
3522102 TTTATATTTATTTATTAGGTTTAAAT
1 TTTATATTAATTTATTAAATTTAAAT
3522128 TTTATATTAATTTATTAAATTTAA
1 TTTATATTAATTTATTAAATTTAA
3522152 CAAACGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTATATTAATTTATTAAATTTAAAT
Found at i:3523424 original size:14 final size:15
Alignment explanation
Indices: 3523405--3523445 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
3523395 TTAAAAAAAA
3523405 TTTAAATATTAAAT-
1 TTTAAATATTAAATG
3523419 TTTAAA-ATTTAAATG
1 TTTAAATA-TTAAATG
3523434 TATTAAATATTA
1 T-TTAAATATTA
3523446 TCTATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 1 0.04
16 8 0.35
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAAATATTAAATG
Found at i:3525210 original size:37 final size:37
Alignment explanation
Indices: 3525124--3525216 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 37
3525114 TTTTATATAA
*
3525124 AAATAT-ATATAACAATATAAAAATATAAAATATATTT
1 AAATATAAT-TAAAAATATAAAAATATAAAATATATTT
** * ** *
3525161 TTATTTTGTTAAATATATAAAAA-ATAAAATATAATTT
1 AAATATAATTAAAAATATAAAAATATAAAATAT-ATTT
3525198 AAATATAATTAAAAATATA
1 AAATATAATTAAAAATATA
3525217 TGAAATGGAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (37 bp):
AAATATAATTAAAAATATAAAAATATAAAATATATTT
Found at i:3533219 original size:31 final size:33
Alignment explanation
Indices: 3533160--3533222 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
3533150 ATTAATAATT
*
3533160 TATAAAATAATTAAATGTTATTTTATAAAAAAC
1 TATAAAATAATTAAATGTAATTTTATAAAAAAC
3533193 TATAAAAT-A-TAAAT-TAATTTTGATAAAAAA
1 TATAAAATAATTAAATGTAATTTT-ATAAAAAA
3533223 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 13 0.46
32 1 0.04
33 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
TATAAAATAATTAAATGTAATTTTATAAAAAAC
Found at i:3534481 original size:14 final size:14
Alignment explanation
Indices: 3534462--3534488 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3534452 TGTATGCATT
3534462 TATGTATATATGTA
1 TATGTATATATGTA
3534476 TATGTATATATGT
1 TATGTATATATGT
3534489 GCCTATGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TATGTATATATGTA
Found at i:3543460 original size:30 final size:31
Alignment explanation
Indices: 3543406--3543480 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
3543396 TTATCAAATC
* *
3543406 AAAAATTTAATTGAACTGAAAATAAATATTT
1 AAAAATTTAATTGAACTCAAAATAAAAATTT
* *
3543437 AAAAATTTAATT-CATTCAAAATAAAAATTT
1 AAAAATTTAATTGAACTCAAAATAAAAATTT
* *
3543467 AAAATTTTTATTGA
1 AAAAATTTAATTGA
3543481 TTACATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 24 0.67
31 12 0.33
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (31 bp):
AAAAATTTAATTGAACTCAAAATAAAAATTT
Found at i:3546895 original size:180 final size:180
Alignment explanation
Indices: 3546582--3546912 Score: 414
Period size: 179 Copynumber: 1.8 Consensus size: 180
3546572 TATTTAAAAT
* * *
3546582 AAAATAATATTATTTTATTAATATTTTAAAAATTAATAAGCAAGAAATTTAAAAACTAAAGTTAT
1 AAAATAATATTAATTTAATAATATTTTAAAAATTAATAAGCAAGAAATTTAAAAAATAAAGTTAT
** * * **
3546647 TTTTCGAACCAATTCAAATAGTTATGATTATTTGAACAAATATCAATATTAAATCGTTATGGTTT
66 TTACCGAACAAATTCAAATAGTTATGACTATTTGAACAAATATCAATATTAAATCACTATGGTTT
3546712 TTATTTTGTCATAAAACAATTGTTTTTAATCATGCAAACTTATTTGGATA
131 TTATTTTGTCATAAAACAATTGTTTTTAATCATGCAAACTTATTTGGATA
* ** *
3546762 AAAATAATATTAATTTAATAATATTTTAAAAATTAAT-AGTAAGGTATTTAAAAAATGAA-TATA
1 AAAATAATATTAATTTAATAATATTTTAAAAATTAATAAGCAAGAAATTTAAAAAATAAAGT-TA
* * * * ** * * *
3546825 TTTACCGAATAAATTTAAATAGTTATGACTATTTGAATAATTATTTATTTTAAATTACTATGATT
65 TTTACCGAACAAATTCAAATAGTTATGACTATTTGAACAAATATCAATATTAAATCACTATG-GT
* *
3546890 TTTTATTTTGTTATAAAATAATT
129 TTTTATTTTGTCATAAAACAATT
3546913 TTATTTATTT
Statistics
Matches: 125, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
178 1 0.01
179 67 0.54
180 57 0.46
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (180 bp):
AAAATAATATTAATTTAATAATATTTTAAAAATTAATAAGCAAGAAATTTAAAAAATAAAGTTAT
TTACCGAACAAATTCAAATAGTTATGACTATTTGAACAAATATCAATATTAAATCACTATGGTTT
TTATTTTGTCATAAAACAATTGTTTTTAATCATGCAAACTTATTTGGATA
Found at i:3546924 original size:21 final size:22
Alignment explanation
Indices: 3546890--3546930 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3546880 TACTATGATT
3546890 TTTTATTTTGTTATA-AAATAA
1 TTTTATTTTGTTATATAAATAA
3546911 TTTTATTTAT-TTATATAAAT
1 TTTTATTT-TGTTATATAAAT
3546931 TTATTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATTTTGTTATATAAATAA
Found at i:3546948 original size:180 final size:179
Alignment explanation
Indices: 3545509--3546950 Score: 788
Period size: 180 Copynumber: 8.0 Consensus size: 179
3545499 AAATCATATC
* * *
3545509 TTAATATTTTAAAAATTAATGAGTAAAAGATTTAAAAAAATGAATCTATTTATCGAATAAATTCA
1 TTAATATTTTAAAAATTAATAAGT-AAGGATTT-AAAAAATAAATCTATTTATCGAATAAATTCA
* * * * ** * *
3545574 AATAATTATGAGTATTTGAACAATTATTTTATTTCAAATTGCTATAACCTTTTGTTTTATTATAA
64 AATAGTTATGACTATTTGAACAATTA-TTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATAA
* * * * * *
3545639 AACAATTATTTATGTTCATATAAACTTATTCCAAATAAAATAATATAAATTTA
128 AATAATT-TTTTTATTCATACAAACTTATTCTAAATAAAATAATATTAATTTA
* * * * * *
3545692 TTAATATTTCAAAAATTTAA-AAGTAAAAGATTT-AAAAATAACTCTGTTTACCGAGTAAATTCA
1 TTAATATTTTAAAAA-TTAATAAGT-AAGGATTTAAAAAATAAATCTATTTATCGAATAAATTCA
* * * ** *
3545755 AATAATTATGACTGTTTGAATAATTATTTGCTTCAAATAGTTATGA-TTTTTGTTTTGTCATAAA
64 AATAGTTATGACTATTTGAACAATTATTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATAAA
* * ** * ** *
3545819 ATAATTATTTCTATTCACACAAGTTTATTCTGAATAGTATCAT-TATAATTTA
129 ATAATT-TTTTTATTCATACAAACTTATTCTAAATAAAATAATAT-TAATTTA
* * * * *
3545871 TTAATATTCTGAAAATTAATAGGTAAGAGATTTAAAAAATAAATCTGTTTA-CTGAACAAATTCA
1 TTAATATTTTAAAAATTAATAAGTAAG-GATTTAAAAAATAAATCTATTTATC-GAATAAATTCA
* * * * * ** * *
3545935 AATAGTTATG-TTCATTTAAATAATTATCTATTTCAATTTGTTATGACCTTCTGTTTTGTTATAA
64 AATAGTTATGACT-ATTTGAACAATTATTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATAA
* ** * *
3545999 AATAATTGTTTCTA-TCGACGGCAAAATTATTGC-AGAATAAAAT-ATATTGATTTA
128 AATAATT-TTTTTATTC-A-TACAAACTTATT-CTA-AATAAAATAATATTAATTTA
* * ** * * *
3546053 TTTATATTTCGAAAAA-T--TAACCAA-GATTTAAAAACTAAA---ATGTT-TCTAAAACAATTC
1 TTAATATTT-TAAAAATTAATAAGTAAGGATTTAAAAAATAAATCTAT-TTATCGAATA-AATTC
* * * * * *
3546110 AAAATAGTTATGACTATTTGAACAATTATCTATCTGAAATCGTTATGA--TTTTATTTTATCATA
63 -AAATAGTTATGACTATTTGAACAATTATTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATA
* * * * * * * *
3546173 AAATAATTGTTTCCT-TTCACACAAAACTTATTCCAGATTAACTGAACACTAATTTA
127 AAATAATT-TTT-TTATTCATAC-AAACTTATTCTAAATAAAAT-AATATTAATTTA
* * * * * * * * **
3546229 AT-A-ATTTTCAAAATTAATAAGTTAAAAGATTTAAAAGATAAATGTATTTGTTGGAGTCAGTTT
1 TTAATATTTTAAAAATTAATAAG-T-AAGGATTTAAAAAATAAATCTATTT-ATCGAAT-AAATT
* * ** * ** * * **
3546292 AAAATAATTAAAACTATTAGAACAATTATTTATTTCAAATCAATTCTAAATATTTTTGTTAGGTC
62 CAAATAGTTATGACTATTTGAACAATTATTTATTTCAAAT-TGTTAT-GAT-TTTTTGTTTTGTC
** * * *
3546357 ATAAAATAATTAATTTCAATTCAT--AAAGTTAATTCAAAAT-AAATAATACTAATTTA
124 ATAAAATAATT--TTTTTATTCATACAAACTT-ATTCTAAATAAAATAATATTAATTTA
** ** * * * * * ** *
3546413 TTACCATTCAAAAAAATAATGAGTAAGATATTTTAAAAAATAAATCTGTTAATTAAATAAGTTCA
1 TTAATATTTTAAAAATTAATAAGTAAG-GA-TTTAAAAAATAAATCTATTTATCGAATAAATTCA
* * * * * * *
3546478 AATAGATT-TTACTATTTGAATAATTTAATCAATTCAAGTTATTATGGATTGTTTTTGTTTTGTC
64 AATAG-TTATGACTATTTGAACAA-TTATTTATTTCAAATTGTTAT-GA-T-TTTTTGTTTTGTC
* * * *
3546542 ATAAAATAATTATTTTAGTTCATAAAAAATTATT-TAAAATAAAATAATATTATTTTA
124 ATAAAATAATTTTTTTA-TTCATACAAACTTATTCT-AAATAAAATAATATTAATTTA
* * * * **
3546599 TTAATATTTTAAAAATTAATAAGCAAGAAATTTAAAAACTAAAGT-TATTTTTCGAACCAATTCA
1 TTAATATTTTAAAAATTAATAAGTAAG-GATTTAAAAAATAAA-TCTATTTATCGAATAAATTCA
* * ** * * *
3546663 AATAGTTATGATTATTTGAACAAATATCAATATT-AAATCGTTATG-GTTTTTATTTTGTCATAA
64 AATAGTTATGACTATTTGAACAATTATTTAT-TTCAAATTGTTATGATTTTTTGTTTTGTCATAA
* * * **
3546726 AACAATTGTTTTTAATCATGCAAACTTATT-TGGATAAAAATAATATTAATTTA
128 AATAATT-TTTTTATTCATACAAACTTATTCTAAAT-AAAATAATATTAATTTA
* * * * *
3546779 ATAATATTTTAAAAATTAAT-AGTAAGGTATTTAAAAAATGAATATATTTACCGAATAAATTTAA
1 TTAATATTTTAAAAATTAATAAGTAAGG-ATTTAAAAAATAAATCTATTTATCGAATAAATTCAA
* * ** * *
3546843 ATAGTTATGACTATTTGAATAATTATTTATTTTAAATTACTATGATTTTTTATTTTGTTATAAAA
65 ATAGTTATGACTATTTGAACAATTATTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATAAAA
* * *
3546908 TAATTTTATTTATTTATATAAATTTATTCTAAATAAAATAATA
130 TAATTTT-TTTATTCATACAAACTTATTCTAAATAAAATAATA
3546951 AAATAATTTA
Statistics
Matches: 953, Mismatches: 238, Indels: 139
0.72 0.18 0.10
Matches are distributed among these distances:
173 4 0.00
174 12 0.01
175 38 0.04
176 24 0.03
177 38 0.04
178 27 0.03
179 156 0.16
180 197 0.21
181 86 0.09
182 58 0.06
183 49 0.05
184 61 0.06
185 98 0.10
186 78 0.08
187 20 0.02
188 7 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (179 bp):
TTAATATTTTAAAAATTAATAAGTAAGGATTTAAAAAATAAATCTATTTATCGAATAAATTCAAA
TAGTTATGACTATTTGAACAATTATTTATTTCAAATTGTTATGATTTTTTGTTTTGTCATAAAAT
AATTTTTTTATTCATACAAACTTATTCTAAATAAAATAATATTAATTTA
Found at i:3551241 original size:181 final size:181
Alignment explanation
Indices: 3550084--3551525 Score: 1027
Period size: 181 Copynumber: 8.0 Consensus size: 181
3550074 CTCTAAACCC
* * ** * * * *
3550084 TAAATTATTTTATTATTTTATTTAGAATAAACTTATATAAATA-AATAAAATTATTTTATAACAA
1 TAAATTA-TATATTATTTTATTCAGAATAAGTTTGTATGAATAGAA-ATAATTATTTTATGACAA
* ** * *
3550148 AATAAAAAATCATAGTAATTTAAAATAAATAATTATTCAAATAGTCATAACTATTTAAATTTATT
64 AACAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATT
* * * * *
3550213 CGGTAAATATATTCATTTTTTAAATAC-CTTACTATTAATTTTTAAAATATTAT
129 CAGTAAACAGATTTATTTTTTAAAT-CTCTTACTATTAATTTTTAAAATATTAA
* * * * * *
3550266 TAAATTA-ATATTATTTTTATCCA-AATAAGTTTGCATGATTAAAAACAATTGTTTTATGACAAA
1 TAAATTATATATTA-TTTTATTCAGAATAAGTTTGTATGAATAGAAATAATTATTTTATGACAAA
* * * ** * * * **
3550329 A-TAAAAACCATAACGATTT-AATATTGATATTTGTTCAAATAATCATAACTATTTGAATTGGTT
65 ACAAAAAATCATAACAATTTGAA-ATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATT
* * * * * *
3550392 C-GAAAAATAGCTTTAGTTTTTAAATTTCTTGCTTATTAATTTTTAAAATATTAA
129 CAG-TAAACAGATTTATTTTTTAAATCTCTTAC-TATTAATTTTTAAAATATTAA
* * * *
3550446 TAAAATA-ATATTATTTTATTTTA-AATAATTTTTTATGAACTA-AAATAATTATTTTATGACAA
1 TAAATTATATATTATTTTA-TTCAGAATAAGTTTGTATGAA-TAGAAATAATTATTTTATGACAA
* * * * ** * *
3550508 AACAAGACATCATAATAACTTGAAATTGATAAATTATTCAAATAGT-AAAATCTATTTGAACTTA
64 AACAAAAAATCATAACAATTTGAAATAAAT-AATTATTCAAATAGTCATAA-CTATTTGAATTTA
* * * * * ** **
3550572 TTTAATTAACAGATTTATTTTTTAAAATATCTTACTCATTATTTTTTTGAATGGTAA
127 TTCAGTAAACAGATTTATTTTTT-AAATCTCTTACT-ATTAATTTTTAAAATATTAA
* ** ** * *
3550629 TAAATTA-GTATTATTTTATTTTGAATAAACTTGTATGAATTGAAATAATTATTTTATGACTAAA
1 TAAATTATATATTATTTTATTCAGAATAAGTTTGTATGAATAGAAATAATTATTTTATGACAAAA
* * * ** * * ** * * * * *
3550693 CAAAATATTAGAATGATTTGAAATAAATAATTGTTCTAATAGTTTTAATTATTTAAACTGATCCA
66 CAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATTCA
** * * * * * *
3550758 ACAAATACATTTATCTTTTAAATCTTTTACTTATTAATTTTTGAAA-ATTAT
131 GTAAACAGATTTATTTTTTAAATCTCTTAC-TATTAATTTTTAAAATATTAA
* * * * * * *
3550809 TAAATTA-GTGTTA-TTTAATCTGAATAAGTTTGTGTGAA-AGGAAACAATTATTTTATGATAAA
1 TAAATTATATATTATTTTATTCAGAATAAGTTTGTATGAATA-GAAATAATTATTTTATGACAAA
* * * *
3550871 A-TAAAAATCATAACGATTT-AAGATAGATAATTGTTCAAATAGTCATAACTATTTGAATTGT-T
65 ACAAAAAATCATAACAATTTGAA-ATAAATAATTATTCAAATAGTCATAACTATTTGAATT-TAT
* * * * * * *
3550933 TTAGAAAACATATTTAGTTTTTAAA--TCTT--TGTTAATTTTCAAAATATAAA
128 TCAGTAAACAGATTTATTTTTTAAATCTCTTACTATTAATTTTTAAAATATTAA
* * * ** * *
3550983 TAAATCA-ATATTATTTTATTCTGAATAATTTTGCGTCG-ATAGAAACAATTATTTTATAACAAA
1 TAAATTATATATTATTTTATTCAGAATAAGTTTGTAT-GAATAGAAATAATTATTTTATGACAAA
* ** * * * * *
3551046 ACAGAAGGTCATAACAAATTGAAATAGATAATTATTTAAAT-GAACATAACTATTTGAATTTGTT
65 ACAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAG-TCATAACTATTTGAATTTATT
* *
3551110 CAGTAAACAGATTTATTTTTTAAATCTCTTACCTATTAATTTTCAGAATATTAA
129 CAGTAAACAGATTTATTTTTTAAATCTCTTA-CTATTAATTTTTAAAATATTAA
* ** ** *
3551164 TAAATTATA-ATGATACTATTCAGAATAAACTTGTGTGAATAGAAATAATTATTTTATGACAAAA
1 TAAATTATATATTATTTTATTCAGAATAAGTTTGTATGAATAGAAATAATTATTTTATGACAAAA
* ** * * *
3551228 CAAAAAATCATAACTATTTGAAGCAAATAATTATTCAAACAGTCATAATTATTTGAATTTACTC-
66 CAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATTCA
* * * *
3551292 GATAAACAGAGTTATTTTTTAAATCTTTTACTTTTAAATTTTTGAAATATTAA
131 G-TAAACAGATTTATTTTTTAAATCTCTTACTATT-AATTTTTAAAATATTAA
** * * * * * *
3551345 TAAATT-TATATTATTTTATTTGGAATAAGTTTATATGAACATAAATAATTGTTTTATAATAAAA
1 TAAATTATATATTATTTTATTCAGAATAAGTTTGTATGAATAGAAATAATTATTTTATGACAAAA
** * * * * *
3551409 CAAAAGGTTATAGCAATTTGAAATAAATAATTGTTCAAATACTCATAATTATTTGAATTTATTC-
66 CAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATTCA
* * *
3551473 GATAAATAGATTCATTTTTTAAATCTTTTACTCATTAATTTTTAAAATATTAA
131 G-TAAACAGATTTATTTTTTAAATCTCTTACT-ATTAATTTTTAAAATATTAA
3551526 GATATGATTT
Statistics
Matches: 989, Mismatches: 229, Indels: 85
0.76 0.18 0.07
Matches are distributed among these distances:
173 12 0.01
174 13 0.01
175 43 0.04
176 71 0.07
177 4 0.00
178 68 0.07
179 113 0.11
180 122 0.12
181 352 0.36
182 95 0.10
183 96 0.10
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (181 bp):
TAAATTATATATTATTTTATTCAGAATAAGTTTGTATGAATAGAAATAATTATTTTATGACAAAA
CAAAAAATCATAACAATTTGAAATAAATAATTATTCAAATAGTCATAACTATTTGAATTTATTCA
GTAAACAGATTTATTTTTTAAATCTCTTACTATTAATTTTTAAAATATTAA
Found at i:3551334 original size:535 final size:533
Alignment explanation
Indices: 3550102--3551467 Score: 1393
Period size: 535 Copynumber: 2.5 Consensus size: 533
3550092 TTTATTATTT
* * * * * * *
3550102 TATTTAGAATAAACTTATATAAATA-AATAAAATTATTTTATAACAAAATAAAAAATCATAGTAA
1 TATTCAGAATAAACTTGTATGAATAGAA-ATAATTATTTTATGACAAAACAAAAAATCATAATAA
* * * *
3550166 TTTAAAATAAATAATTATTCAAATAGTCATAACTATTTAAATTTATTCGGTAAATATATTCATTT
65 TTTGAAATAAATAATTATTCAAATAGTCATAATTATTTAAATTTA-TCGATAAATACATT-ATTT
* * * **
3550231 TTTAAATAC-CTTACTATTAATTTTTAAAATATTATTAAATTAATATTATTTTTATCCAAATAAG
128 TTTAAAT-CTTTTACTTTTAATTTTTGAAATATTATTAAATT-ATATTA-TTTTATCTGAATAAG
* * * * *
3550295 TTTGCATGATTAAAAACAATTGTTTTATGACAAAATAAAAACCATAACGATTTAATATTGATATT
190 TTTGTATGA--AAAAACAATTGTTTTATGATAAAATAAAAATCATAACGATTTAA-ATAGATAAT
*
3550360 TGTTCAAATAATCATAACTATTTGAATTGGTTCGAAAAATAGCTTTAGTTTTTAAATTTCTTGCT
252 TGTTCAAATAATCATAACTATTTGAATTGGTTAGAAAAATA-CTTTAGTTTTTAAA-TTCTT-CT
* * * **
3550425 TATTAATTTTTAAAATATTAATAAAATAATATTATTTTATTTTAAATAATTTTTTATGAACTAAA
314 TATTAATTTTCAAAATATAAATAAAATAATATTATTTTATTCTAAATAATTTTGCATGAACTAAA
* * * * *
3550490 ATAATTATTTTATGACAAAACAAGACATCATAATAACTTGAAATTGATAAATTATTCAAATAGTA
379 ACAATTATTTTATAACAAAACAAGACATCATAACAAATTGAAATAGATAAATTATTCAAATAGTA
* * * * **
3550555 AAATCTATTTGAACTTATTTAATTAACAGATTTATTTTTTAAAATATCTTACTCATTATTTTTTT
444 AAAACTATTTGAACTTATTCAATAAACAGATTTATTTTTTAAAATATCTTACTCATTAATTTTCA
* * **
3550620 GAATGGTAATAAATTAGTATTATTT
509 GAATAGTAATAAATTAGTATGATAC
** * * * * * *
3550645 TATTTTGAATAAACTTGTATGAATTGAAATAATTATTTTATGACTAAACAAAATATTAGAATGAT
1 TATTCAGAATAAACTTGTATGAATAGAAATAATTATTTTATGACAAAACAAAAAATCATAATAAT
* * ** * * * * *
3550710 TTGAAATAAATAATTGTTCTAATAGTTTTAATTATTTAAACTGATCCAACAAATACATTTATCTT
66 TTGAAATAAATAATTATTCAAATAGTCATAATTATTTAAATTTAT-CGATAAATACA-TTATTTT
* *
3550775 TTAAATCTTTTACTTATTAATTTTTGAAA-ATTATTAAATTAGTGTTATTTAATCTGAATAAGTT
129 TTAAATCTTTTACTT-TTAATTTTTGAAATATTATTAAATTA-TATTATTTTATCTGAATAAGTT
* *
3550839 TGTGTGAAAGGAAACAATTATTTTATGATAAAATAAAAATCATAACGATTTAAGATAGATAATTG
192 TGTATGAAA--AAACAATTGTTTTATGATAAAATAAAAATCATAACGATTTAA-ATAGATAATTG
* * *
3550904 TTCAAATAGTCATAACTATTTGAATTGTTTTAGAAAACATA-TTTAGTTTTTAAA-TC-T-TTGT
254 TTCAAATAATCATAACTATTTGAATTG-GTTAGAAAA-ATACTTTAGTTTTTAAATTCTTCTTAT
* *
3550965 TAATTTTCAAAATATAAAT-AAATCAATATTATTTTATTCTGAATAATTTTGCGTCG-A-TAGAA
317 TAATTTTCAAAATATAAATAAAAT-AATATTATTTTATTCTAAATAATTTTGCAT-GAACTA-AA
*
3551027 ACAATTATTTTATAACAAAAC-AGA-AGGTCATAACAAATTGAAATAGAT-AATTATTTAAAT-G
379 ACAATTATTTTATAACAAAACAAGACA--TCATAACAAATTGAAATAGATAAATTATTCAAATAG
* * * *
3551088 -AACATAACTATTTGAATTTGTTCAGTAAACAGATTTATTTTTT-AAATCTCTTAC-CTATTAAT
442 TAA-A-AACTATTTGAACTTATTCAATAAACAGATTTATTTTTTAAAATATCTTACTC-ATTAAT
*
3551150 TTTCAGAATATTAATAAATTA-TAATGATAC
504 TTTCAGAATAGTAATAAATTAGT-ATGATAC
*
3551180 TATTCAGAATAAACTTGTGTGAATAGAAATAATTATTTTATGACAAAACAAAAAATCATAACT-A
1 TATTCAGAATAAACTTGTATGAATAGAAATAATTATTTTATGACAAAACAAAAAATCATAA-TAA
** * * * *
3551244 TTTGAAGCAAATAATTATTCAAACAGTCATAATTATTTGAATTTACTCGATAAACAGAGTTATTT
65 TTTGAAATAAATAATTATTCAAATAGTCATAATTATTTAAATTTA-TCGATAAATACA-TTATTT
* *
3551309 TTTAAATCTTTTACTTTTAAATTTTTGAAATATTAATAAATTTATATTATTTTATTTGGAATAAG
128 TTTAAATCTTTTACTTTT-AATTTTTGAAATATTATTAAA-TTATATTATTTTATCT-GAATAAG
* * * * * * * * *
3551374 TTTATATGAACATAAATAATTGTTTTATAATAAAACAAAAGGTTATAGCAATTTGAAATAAATAA
190 TTTGTATGAA-A-AAACAATTGTTTTATGATAAAATAAAA-ATCATAACGATTT-AAATAGATAA
* *
3551439 TTGTTCAAATACTCATAATTATTTGAATT
251 TTGTTCAAATAATCATAACTATTTGAATT
3551468 TATTCGATAA
Statistics
Matches: 680, Mismatches: 115, Indels: 61
0.79 0.13 0.07
Matches are distributed among these distances:
534 6 0.01
535 167 0.25
536 72 0.11
537 126 0.19
538 45 0.07
539 3 0.00
540 4 0.01
542 109 0.16
543 129 0.19
544 19 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (533 bp):
TATTCAGAATAAACTTGTATGAATAGAAATAATTATTTTATGACAAAACAAAAAATCATAATAAT
TTGAAATAAATAATTATTCAAATAGTCATAATTATTTAAATTTATCGATAAATACATTATTTTTT
AAATCTTTTACTTTTAATTTTTGAAATATTATTAAATTATATTATTTTATCTGAATAAGTTTGTA
TGAAAAAACAATTGTTTTATGATAAAATAAAAATCATAACGATTTAAATAGATAATTGTTCAAAT
AATCATAACTATTTGAATTGGTTAGAAAAATACTTTAGTTTTTAAATTCTTCTTATTAATTTTCA
AAATATAAATAAAATAATATTATTTTATTCTAAATAATTTTGCATGAACTAAAACAATTATTTTA
TAACAAAACAAGACATCATAACAAATTGAAATAGATAAATTATTCAAATAGTAAAAACTATTTGA
ACTTATTCAATAAACAGATTTATTTTTTAAAATATCTTACTCATTAATTTTCAGAATAGTAATAA
ATTAGTATGATAC
Found at i:3553611 original size:30 final size:31
Alignment explanation
Indices: 3553556--3553631 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
3553546 TTTTATTGTA
* * * *
3553556 ATCAATAAAAATTTAAAATTTTTATTTTGA-
1 ATCAATTAAATTTTTAAATATTTATTTTGAG
* *
3553586 ATGAATTAAATTTTTAAATATTTATTTTTAG
1 ATCAATTAAATTTTTAAATATTTATTTTGAG
*
3553617 TTCAATTAAATTTTT
1 ATCAATTAAATTTTT
3553632 GATTTGATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (31 bp):
ATCAATTAAATTTTTAAATATTTATTTTGAG
Found at i:3557099 original size:2 final size:2
Alignment explanation
Indices: 3557092--3557125 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3557082 GTAATAATGA
*
3557092 AT AT AT AT AT AT AT AT AT AT AT AT AG AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3557126 AACTCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3562579 original size:14 final size:14
Alignment explanation
Indices: 3562560--3562586 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3562550 CACATAAGGC
3562560 ACATATATACATAT
1 ACATATATACATAT
3562574 ACATATATACATA
1 ACATATATACATA
3562587 AATGCATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
ACATATATACATAT
Found at i:3563862 original size:31 final size:33
Alignment explanation
Indices: 3563824--3563886 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
3563814 TTAAAAATTA
*
3563824 TTTTTTATCAAAATTA-ATTT-A-TATTTTATAG
1 TTTTTTAT-AAAATAACATTTAATTATTTTATAG
3563855 TTTTTTATAAAATAACATTTAATTATTTTATA
1 TTTTTTATAAAATAACATTTAATTATTTTATA
3563887 AATTATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 12 0.43
32 1 0.04
33 9 0.32
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (33 bp):
TTTTTTATAAAATAACATTTAATTATTTTATAG
Found at i:3564506 original size:31 final size:32
Alignment explanation
Indices: 3564468--3564535 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
3564458 TTATCACATC
3564468 ATTATT-AATAAATTT-AAATTTTAAAATATTT-
1 ATTATTAAAT-AATTTAAAATTTT-AAATATTTA
*
3564499 ATTATTAAATATTTTAAAATTTTAAATATTTA
1 ATTATTAAATAATTTAAAATTTTAAATATTTA
3564531 ATTAT
1 ATTAT
3564536 ATTAAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTATTAAATAATTTAAAATTTTAAATATTTA
Found at i:3564528 original size:24 final size:25
Alignment explanation
Indices: 3564485--3564551 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
3564475 ATAAATTTAA
*
3564485 ATTTTAAAATATTTATTA-TTAAAT
1 ATTTTAAAATATTTAATATTTAAAT
*
3564509 ATTTTAAAAT-TTTAAATATTTAATT
1 ATTTTAAAATATTT-AATATTTAAAT
* *
3564534 ATATTAAAACATATTAAT
1 ATTTTAAAATAT-TTAAT
3564552 GATATAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 3 0.09
24 13 0.37
25 13 0.37
26 4 0.11
27 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTAAAATATTTAATATTTAAAT
Found at i:3571390 original size:11 final size:10
Alignment explanation
Indices: 3571359--3571389 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3571349 ATACATATTT
3571359 ATTAAAAAAA
1 ATTAAAAAAA
*
3571369 GTTAAAAAAA
1 ATTAAAAAAA
3571379 ATTAAAAAAA
1 ATTAAAAAAA
3571389 A
1 A
3571390 AGTCAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:3571704 original size:23 final size:23
Alignment explanation
Indices: 3571655--3571704 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3571645 TTAATTTCTC
*
3571655 ATATT-TTAAATAAATTATATAA
1 ATATTATTAAATAAAATATATAA
* *
3571677 A-ATTATTCAATAAAATATTTAA
1 ATATTATTAAATAAAATATATAA
3571699 ATATTA
1 ATATTA
3571705 AAGTATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTATTAAATAAAATATATAA
Found at i:3571711 original size:28 final size:28
Alignment explanation
Indices: 3571671--3571729 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3571661 TAAATAAATT
*
3571671 ATATAAAATTATT-CAATAAAATATTTAA
1 ATATAAAAGTATTACAATAAAA-ATTTAA
* * *
3571699 ATATTAAAGTATTACATTAAAAATTTTA
1 ATATAAAAGTATTACAATAAAAATTTAA
3571727 ATA
1 ATA
3571730 AATTATGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATAAAAGTATTACAATAAAAATTTAA
Found at i:3573599 original size:15 final size:15
Alignment explanation
Indices: 3573561--3573607 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3573551 CTTTAATAGA
*
3573561 TAATATTTAATATATT
1 TAATATTTAAAAT-TT
*
3573577 TAAAATTTAAAATTT
1 TAATATTTAAAATTT
*
3573592 TAATATTTATAATTT
1 TAATATTTAAAATTT
3573607 T
1 T
3573608 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATATTTAAAATTT
Found at i:3577073 original size:19 final size:19
Alignment explanation
Indices: 3577049--3577087 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3577039 ACCATATGTA
3577049 CTATCTTGCCACATCAATT
1 CTATCTTGCCACATCAATT
3577068 CTATCTTGCCACATCAATT
1 CTATCTTGCCACATCAATT
3577087 C
1 C
3577088 AAATCCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (19 bp):
CTATCTTGCCACATCAATT
Found at i:3578491 original size:25 final size:24
Alignment explanation
Indices: 3578458--3578533 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
3578448 AGTCGTAGGC
3578458 CAGATATAATCATAAAAATCTCAA
1 CAGATATAATCATAAAAATCTCAA
** * *
3578482 CAGATTATAAAAATGAAACAA-CTGAT
1 CAGA-TATAATCAT-AAA-AATCTCAA
*
3578508 CAGATATAATCATAAAACT-TCAA
1 CAGATATAATCATAAAAATCTCAA
3578531 CAG
1 CAG
3578534 GTAATAGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
23 6 0.15
24 7 0.18
25 14 0.36
26 10 0.26
27 2 0.05
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (24 bp):
CAGATATAATCATAAAAATCTCAA
Found at i:3581338 original size:20 final size:20
Alignment explanation
Indices: 3581299--3581338 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3581289 AATTTTTTAT
*
3581299 TTTTAAATTGTTTAATATAA
1 TTTTAAATTATTTAATATAA
3581319 TTTTAAATATATTTAA-ATAA
1 TTTTAAAT-TATTTAATATAA
3581339 AATTAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTAAATTATTTAATATAA
Found at i:3581960 original size:30 final size:30
Alignment explanation
Indices: 3581908--3581988 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
3581898 TCTAGTTCCT
* * *
3581908 ATAATATTA-TTTAAAAAAATTTAATAATT
1 ATAATATTATTTTTAAGAAATTTAATAATC
* * *
3581937 GTAATATTATTTTTAAGAAATTTAGTCATC
1 ATAATATTATTTTTAAGAAATTTAATAATC
*
3581967 ATAATATTATTTTTAAGGAATT
1 ATAATATTATTTTTAAGAAATT
3581989 CAATTCCTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 8 0.19
30 35 0.81
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (30 bp):
ATAATATTATTTTTAAGAAATTTAATAATC
Found at i:3585227 original size:26 final size:25
Alignment explanation
Indices: 3585196--3585249 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
3585186 TTAAATTTAT
3585196 TTAAA-TTAAAATTAAAATATAAATAA
1 TTAAATTTAAAA-TAAAATATAAA-AA
* *
3585222 TTAAATTTATAATCAAATATAAAAA
1 TTAAATTTAAAATAAAATATAAAAA
3585247 TTA
1 TTA
3585250 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 15 0.60
27 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAATTTAAAATAAAATATAAAAA
Found at i:3585818 original size:50 final size:51
Alignment explanation
Indices: 3585757--3585863 Score: 182
Period size: 50 Copynumber: 2.1 Consensus size: 51
3585747 TCATTTTTTT
*
3585757 TTTTTTGATTCAAATGGGTTTTTGAGTTTGAATTTGAAGGTGGG-TTTCTTC
1 TTTTTTGATTCAAATGGGTTTTTGAGTTTGAA-TGGAAGGTGGGTTTTCTTC
3585808 TTTTTT-ATTCAAATGGGTTTTTGAGTTTGAATGGAAGGTGGGTTTTCTTC
1 TTTTTTGATTCAAATGGGTTTTTGAGTTTGAATGGAAGGTGGGTTTTCTTC
3585858 TTTTTT
1 TTTTTT
3585864 TGGGGGGTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
49 10 0.19
50 38 0.70
51 6 0.11
ACGTcount: A:0.17, C:0.06, G:0.24, T:0.53
Consensus pattern (51 bp):
TTTTTTGATTCAAATGGGTTTTTGAGTTTGAATGGAAGGTGGGTTTTCTTC
Found at i:3592845 original size:175 final size:176
Alignment explanation
Indices: 3592532--3593203 Score: 890
Period size: 175 Copynumber: 3.9 Consensus size: 176
3592522 GGTCTGGCAA
* * * *
3592532 AGCCAACAAACACAATTGGTAGAATCTGAAAGAATCTGGATTTTCCAGACATTGTTGTCATACTA
1 AGCCAAGAAACACGATTGGTAGAATCTGAAAGAACCTGGATTTTCCAGACATTGTTGTCATACTC
* * *
3592597 ATGAAATTGAGACAATTTTGGCGTCGATTGTAGTTCGTCCTTAGAAAACCAAATCAAAGAGTCTG
66 ATGAAATTGAGACAATTTTGGCGTTGATTATGGTTCGTCCTTAGAAAACCAAATCAAAGAGTCTG
3592662 GACTATGGAAATTAAAACATTTCCTTGTTCTTTCCAAATTAAATAG
131 GACTATGGAAATTAAAACATTTCCTTGTTCTTTCCAAATTAAATAG
*
3592708 AGCCTAAGAAA-ACGATTGGTGGAATCTGAAAGAACCTGGATTTT-CAGACATTGTTGTCATACT
1 AGCC-AAGAAACACGATTGGTAGAATCTGAAAGAACCTGGATTTTCCAGACATTGTTGTCATACT
* *
3592771 CATGAAATTGAAACAATTTTGGCGTTGATTATGGTTCGTCCTTAGAAAACCAAATCAAAGCGTCT
65 CATGAAATTGAGACAATTTTGGCGTTGATTATGGTTCGTCCTTAGAAAACCAAATCAAAGAGTCT
3592836 GGACTATGGAAATT-AAACA-TTCCTTGTTCTTTCCAAATTAAATAG
130 GGACTATGGAAATTAAAACATTTCCTTGTTCTTTCCAAATTAAATAG
* * *
3592881 AGCCCAAGAAACACGATTGGTGGAATCTGAAAGAACCTGGATTTTCCAGACATCGTTGTCGTACT
1 AG-CCAAGAAACACGATTGGTAGAATCTGAAAGAACCTGGATTTTCCAGACATTGTTGTCATACT
* * * * *
3592946 CACGAAACTGAGACAATTTCGGCCTTGATTTATGGTTCGTCCTTAGAAAGCCAAATCAAAGAGTC
65 CATGAAATTGAGACAATTTTGGCGTTGA-TTATGGTTCGTCCTTAGAAAACCAAATCAAAGAGTC
* * *
3593011 TGGAACCATGGACATTAAAACACTTCCTTG-----TCC-AATTAAATAG
129 TGG-ACTATGGAAATTAAAACATTTCCTTGTTCTTTCCAAATTAAATAG
* ** *
3593054 AGCCAAGAAACAAGATTGGTAGAATCTGAAAGAAGAT-GATTTTTCCAGACATTATTGTCATACT
1 AGCCAAGAAACACGATTGGTAGAATCTGAAAGAACCTGGA-TTTTCCAGACATTGTTGTCATACT
3593118 CATG-AATTGAGACAATTTTGGC----------GTT-GTCCTTAGAAAA-CAAATCAAAGAGTCT
65 CATGAAATTGAGACAATTTTGGCGTTGATTATGGTTCGTCCTTAGAAAACCAAATCAAAGAGTCT
*
3593170 GGACTAT-GAAATTAAAATATTTCCTTGTTCTTTC
130 GGACTATGGAAATTAAAACATTTCCTTGTTCTTTC
3593204 TACTAAAATA
Statistics
Matches: 446, Mismatches: 36, Indels: 43
0.85 0.07 0.08
Matches are distributed among these distances:
156 17 0.04
157 4 0.01
158 17 0.04
159 11 0.02
160 3 0.01
161 2 0.00
171 18 0.04
172 55 0.12
173 46 0.10
174 43 0.10
175 132 0.30
176 71 0.16
177 15 0.03
178 5 0.01
179 7 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (176 bp):
AGCCAAGAAACACGATTGGTAGAATCTGAAAGAACCTGGATTTTCCAGACATTGTTGTCATACTC
ATGAAATTGAGACAATTTTGGCGTTGATTATGGTTCGTCCTTAGAAAACCAAATCAAAGAGTCTG
GACTATGGAAATTAAAACATTTCCTTGTTCTTTCCAAATTAAATAG
Found at i:3594792 original size:178 final size:177
Alignment explanation
Indices: 3594283--3594898 Score: 956
Period size: 177 Copynumber: 3.5 Consensus size: 177
3594273 TTTCTAAGGA
* **
3594283 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAATAATGTCTGGAAAATCCATCTTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
* * *
3594348 GATTCTACCAATCGTGTTTCTTGGGCTCTATTTAATTT-G---G-ACAAGGAAGTGTTTTAATGT
66 GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
* *
3594408 CCATGGTCCAGACTCTTTGATTTGGCTTTCTAAGGACGAACCATAAT
131 CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
* * * * *
3594455 CAAGGCCGAAATTGTCTCAGTTTCGTGAGTACGAACAACAATGTCTGGAAAATCCAGGTTCTTTC
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATG-ACAACAATGTCTGGAAAATCCAGGTTCTTTC
3594520 AGATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGG-AATGTTTTAATT
65 AGATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATT
*
3594584 TCCATAGTCCAGACGCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
130 TCCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
*
3594632 CAACGCCAAAAATTGTTTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTC
1 CAACGCC-AAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTC
*
3594697 AGATTCCACCAATCGTGTTTCTTAGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATT
65 AGATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATT
* *
3594762 TCCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACTACAAT
130 TCCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
* * *
3594810 CGACGCCAAAATTGTCTCAATTTCATTAGTATGACAACAATGTCTGGAAAATCCAGATTCTTTCA
1 CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
* * *
3594875 GATTCTACCAATTGTGTTTGTTGG
66 GATTCCACCAATCGTGTTTCTTGG
3594899 CTTTGCCAGA
Statistics
Matches: 404, Mismatches: 32, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
172 28 0.07
173 66 0.16
174 1 0.00
177 219 0.54
178 90 0.22
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (177 bp):
CAACGCCAAAATTGTCTCAATTTCATGAGTATGACAACAATGTCTGGAAAATCCAGGTTCTTTCA
GATTCCACCAATCGTGTTTCTTGGGCTCTATTTAATTTGGAAAGAACAAGGAAATGTTTTAATTT
CCATAGTCCAGACTCTTTGATTTGGTTTTCTAAGGACGAACCATAAT
Found at i:3601653 original size:48 final size:51
Alignment explanation
Indices: 3601584--3601687 Score: 169
Period size: 49 Copynumber: 2.1 Consensus size: 51
3601574 ACACCCCCAA
* *
3601584 AAAAAGAAGAAAACCCACCTTC-CATTCAAACTCAAAAACTCATTTGAAT-
1 AAAAAGAAGAAAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
3601633 AAAAAGAAG-AAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
1 AAAAAGAAGAAAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
3601683 AAAAA
1 AAAAA
3601688 AAAAAAATGA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
48 12 0.24
49 34 0.67
50 5 0.10
ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18
Consensus pattern (51 bp):
AAAAAGAAGAAAACCCACCTTCAAATTCAAACTCAAAAACCCATTTGAATC
Found at i:3602247 original size:26 final size:25
Alignment explanation
Indices: 3602197--3602250 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
3602187 TAAAATAAAA
*
3602197 TAATTTTTATATTTGATTATAAATT
1 TAATTTTTATATTTAATTATAAATT
*
3602222 TAATTATTTATATTTTAATT-TTAATT
1 TAATT-TTTATA-TTTAATTATAAATT
3602248 TAA
1 TAA
3602251 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 14 0.56
27 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TAATTTTTATATTTAATTATAAATT
Found at i:3602344 original size:23 final size:24
Alignment explanation
Indices: 3602293--3602345 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3602283 ATATAATACG
3602293 AATAAAAATATAAAACTTAAAATT
1 AATAAAAATATAAAACTTAAAATT
*
3602317 -TTAAAAATATATAAA-TT-AAATT
1 AATAAAAATATA-AAACTTAAAATT
3602339 AATAAAA
1 AATAAAA
3602346 TCAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 5 0.20
23 17 0.68
24 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AATAAAAATATAAAACTTAAAATT
Found at i:3608969 original size:25 final size:24
Alignment explanation
Indices: 3608899--3608974 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
3608889 TTTCTATTAC
*
3608899 CTGTTGA-AGTTTTATGATTATAT
1 CTGTTGAGATTTTTATGATTATAT
* * **
3608922 CTGATCAG-TTGTTTCATTTTTATAAT
1 CTGTTGAGATT-TTT-ATGATTAT-AT
3608948 CTGTTGAGATTTTTATGATTATAT
1 CTGTTGAGATTTTTATGATTATAT
3608972 CTG
1 CTG
3608975 GCCTACGACT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
23 6 0.15
24 8 0.21
25 12 0.31
26 11 0.28
27 2 0.05
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (24 bp):
CTGTTGAGATTTTTATGATTATAT
Found at i:3610370 original size:19 final size:19
Alignment explanation
Indices: 3610346--3610384 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3610336 CATAGGATTT
3610346 GAATTGATGTGGCAAGATA
1 GAATTGATGTGGCAAGATA
3610365 GAATTGATGTGGCAAGATA
1 GAATTGATGTGGCAAGATA
3610384 G
1 G
3610385 TACATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (19 bp):
GAATTGATGTGGCAAGATA
Found at i:3612553 original size:26 final size:26
Alignment explanation
Indices: 3612505--3612554 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3612495 GTTTTTGTCG
* **
3612505 TTTATATTTATTTATTAGGTTTAAAT
1 TTTATATTAATTTATTAAATTTAAAT
3612531 TTTATATTAATTTATTAAATTTAA
1 TTTATATTAATTTATTAAATTTAA
3612555 CAAACGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTATATTAATTTATTAAATTTAAAT
Found at i:3613819 original size:14 final size:15
Alignment explanation
Indices: 3613800--3613840 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
3613790 TTAAAAAAAA
3613800 TTTAAATATTAAAT-
1 TTTAAATATTAAATG
3613814 TTTAAA-ATTTAAATG
1 TTTAAATA-TTAAATG
3613829 TATTAAATATTA
1 T-TTAAATATTA
3613841 TCTATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 1 0.04
16 8 0.35
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTAAATATTAAATG
Found at i:3617076 original size:35 final size:34
Alignment explanation
Indices: 3617037--3617109 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
3617027 TTTTTTTGGG
* * * *
3617037 TATTTTTCATTTTTTTTTGTTTTTATATTTTGTAT
1 TATTTTTCATATTTTTTT-ATTTCATATTTTGTAA
**
3617072 TATTTTTGGTATTTTTTTATTTCATATTTTGTAA
1 TATTTTTCATATTTTTTTATTTCATATTTTGTAA
3617106 TATT
1 TATT
3617110 ATTATTATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 17 0.53
35 15 0.47
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.73
Consensus pattern (34 bp):
TATTTTTCATATTTTTTTATTTCATATTTTGTAA
Found at i:3617598 original size:69 final size:70
Alignment explanation
Indices: 3617506--3617753 Score: 242
Period size: 69 Copynumber: 3.5 Consensus size: 70
3617496 ATGATTTTAA
*
3617506 ATTAAAGA-GA-TCGGGATTGAACCGCGAA-TCGA-AGAATAAGAAGATCAGGATTAAACCACGA
1 ATTAAAGATGACT-GGGACTGAACCGC-AAGTCGAGAGAATAAGAAGATCAGGATTAAACCACGA
* *
3617567 ATCAAAT
64 GTCAAAG
* * *
3617574 ATTAACGATGACTGGGACTGAACCGCAAGTCGAGGGAATTAATGAAATGGTC-GAGATTAAACCA
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAA-TAA-G-AA-GATCAG-GATTAAACCA
*
3617638 CGAGCCAAAG
61 CGAGTCAAAG
* *
3617648 ATTAAAGATGACTGGGACTAAACCGCAAGTC-AGAGAATGAA-ATGA-CTAGGATTAAACCACGA
1 ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAAT-AAGAAGATC-AGGATTAAACCACGA
3617710 GTCAAAG
64 GTCAAAG
* * *
3617717 ATTAAAGATGACTGAGATTGAGCCGCAAGTCAGAGAG
1 ATTAAAGATGACTGGGACTGAACCGCAAGTC-GAGAG
3617754 TCAAAGATTA
Statistics
Matches: 149, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
68 10 0.07
69 65 0.44
70 6 0.04
71 7 0.05
72 2 0.01
73 10 0.07
74 49 0.33
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (70 bp):
ATTAAAGATGACTGGGACTGAACCGCAAGTCGAGAGAATAAGAAGATCAGGATTAAACCACGAGT
CAAAG
Found at i:3617694 original size:34 final size:35
Alignment explanation
Indices: 3617650--3618782 Score: 408
Period size: 35 Copynumber: 31.5 Consensus size: 35
3617640 AGCCAAAGAT
*
3617650 TAAAGATGACTGGGACTAAACCGCAAGTCAGAGAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * * *
3617685 TGAA-ATGACTAGGATTAAACCACGAGTCAAAGAT
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * *
3617719 TAAAGATGACTGAGATTGAGCCGCAAGTCAGAGAGTCAAAGA
1 TAAAGATGACTGGGATTAAACCGCAAGTC--AGAG----A-A
* * * * *
3617761 TTAAAGATGATTGGGATTGAACCGTAAGTCAAAAAA
1 -TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* ** * * *
3617797 TTAATGAAATGA-TCGGGATTAAATGGCGAGTCAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * *
3617835 TAAAGATGACTGGGATTGAACCGTAAGTTAGAGAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAG-AA
* *** * *
3617871 TAATGAAATGA-TCGGGATTAAACCTTGAGTCAAAGAT
1 TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * *
3617908 TAAAGATGACTGGGATTGAACCGCAAGTCAAAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * *
3617943 TGAA-ATGA-TCGGGATTAAACCGCAAGTCAAAGAT
1 TAAAGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * *
3617977 TAAAGATGACTGGGATTGAACCGTAAGTCAGAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * * *
3618012 TTAATGAAATGA-TCGAGATTAAACCGCGAGTTAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * * *
3618050 TAAAGATGACTAGGATTGAACCGCAAGTCAAAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * *
3618085 TTAATGAAATGA-TCGGGATTAAATCGCGAGTCAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* *
3618123 TAAAGATGACTGGGATTGAACCGTAAGTCA-AGAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAG-AA
* * * * *
3618158 TTAATGAAATGA-TCGGGATTAAACCACGAGTCAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
** * * * * *
3618196 TAAAGACAATTGAGATTGAACCGCAAGTCAAAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * *
3618231 TGAA-ATGA-TCGGATTAAACCGCGAGTCAAAGAT
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * *
3618264 TAAAGATGACTGGGATTGAATCGCAGGTCAAAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* ** * * * *
3618299 TTAACGAAATGA-TCGGGATTAAATAGCGAGTTAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * * *
3618337 TAAAGATGACTAGGATTGAATCGCAAGTCAGAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * *
3618372 TTAATGAAATGA-TCGGGATTAAACCGCGAGTCAAAGATT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGA-A
* *
3618411 TAAAGATGACTGGGATTGAACCGTAAGTCA-AGAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAG-AA
* * * * *
3618446 TTACTGAA-ATGA-TCGGGATTAAACTGCGAGTTAAAGAT
1 -TA---AAGATGACT-GGGATTAAACCGCAAGTCAGAGAA
3618484 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * *
3618519 TGAA-ATGA-TCGGGATTAAACCACGAGTCA-ATGAT
1 TAAAGATGACT-GGGATTAAACCGCAAGTCAGA-GAA
* * *
3618553 TAAAGATGATTGGGATTGAATCGCAAGTCAG-GAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAG-AA
* * * * * * *
3618588 TAATGAAATGA-TCAGGATTAGACCACGAGTCAAAGAT
1 TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
* * * *
3618625 TAAAGATGAC-GGGATTGAACCGTAAGTCAAAAAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * *
3618659 TTAATGAAATGA-TCGGGATTAAATCGCGAGTCAAAGAT
1 -TAA--AGATGACT-GGGATTAAACCGCAAGTCAGAGAA
*
3618697 TAAAGATGACTGGGATTGAACCGCAAGTCAGAGAA
1 TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
* * * * * * *
3618732 TGAA-ATGA-TCGAGATTAAATCACGAGTCAAAGAT
1 TAAAGATGACT-GGGATTAAACCGCAAGTCAGAGAA
3618766 TAAAGATGACTGGGATT
1 TAAAGATGACTGGGATT
3618783 GAACTGTAAG
Statistics
Matches: 801, Mismatches: 217, Indels: 160
0.68 0.18 0.14
Matches are distributed among these distances:
33 26 0.03
34 132 0.16
35 291 0.36
36 60 0.07
37 64 0.08
38 194 0.24
39 6 0.01
41 3 0.00
43 25 0.03
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (35 bp):
TAAAGATGACTGGGATTAAACCGCAAGTCAGAGAA
Found at i:3617769 original size:43 final size:43
Alignment explanation
Indices: 3617708--3617791 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
3617698 ATTAAACCAC
*
3617708 GAGTCAAAGATTAAAGATGACTGAGATTGAGCCGCAAGTCAGA
1 GAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGA
* * *
3617751 GAGTCAAAGATTAAAGATGATTGGGATTGAACCGTAAGTCA
1 GAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCA
3617792 AAAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.21
Consensus pattern (43 bp):
GAGTCAAAGATTAAAGATGACTGAGATTGAACCGCAAGTCAGA
Found at i:3617835 original size:73 final size:73
Alignment explanation
Indices: 3617751--3618803 Score: 1426
Period size: 73 Copynumber: 14.7 Consensus size: 73
3617741 GCAAGTCAGA
* *
3617751 GAGTCAAAGATTAAAGATGATTGGGATTGAACCGTAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
**
3617816 TAAATGGC
66 TAAACCGC
* * *
3617824 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTTAGAGAAA-TAATGAAATGATCGGGA
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCA-AAAAATTAATGAAATGATCGGGA
**
3617888 TTAAACCTT
65 TTAAACCGC
3617897 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC--AAAA--AATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
3617958 TAAACCGC
66 TAAACCGC
* * * *
3617966 AAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGAAAATTAATGAAATGATCGAGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
3618031 TAAACCGC
66 TAAACCGC
* *
3618039 GAGTTAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
*
3618104 TAAATCGC
66 TAAACCGC
* *
3618112 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
*
3618177 TAAACCAC
66 TAAACCGC
** * *
3618185 GAGTCAAAGATTAAAGACAATTGAGATTGAACCGCAAGTC--AAAA--AATGAAATGATC-GGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
3618245 TAAACCGC
66 TAAACCGC
* * *
3618253 GAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAGGTCAAAAAATTAACGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
**
3618318 TAAATAGC
66 TAAACCGC
* * * *
3618326 GAGTTAAAGATTAAAGATGACTAGGATTGAATCGCAAGTCAGAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
3618391 TAAACCGC
66 TAAACCGC
* * *
3618399 GAGTCAAAGATTTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTACTGAAATGATCGGGA
1 GAGTCAAAGA-TTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGA
*
3618464 TTAAACTGC
65 TTAAACCGC
* * * *
3618473 GAGTTAAAGATTAAAGATGACTGGGATTAAACCGCAAGTC---AGA-GAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
*
3618534 TAAACCAC
66 TAAACCGC
* * * ** *
3618542 GAGTCAATGATTAAAGATGATTGGGATTGAATCGCAAGTCAGGAAA-TAATGAAATGATCAGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
* *
3618606 TAGACCAC
66 TAAACCGC
*
3618614 GAGTCAAAGATTAAAGATGAC-GGGATTGAACCGTAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
*
3618678 TAAATCGC
66 TAAACCGC
* * *
3618686 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC---AGA-GAATGAAATGATCGAGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
* *
3618747 TAAATCAC
66 TAAACCGC
* *
3618755 GAGTCAAAGATTAAAGATGACTGGGATTGAACTGTAAGTCAAAAAATTA
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTA
3618804 TATAAGACTG
Statistics
Matches: 865, Mismatches: 95, Indels: 40
0.87 0.09 0.04
Matches are distributed among these distances:
68 45 0.05
69 191 0.22
70 11 0.01
71 27 0.03
72 100 0.12
73 422 0.49
74 69 0.08
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (73 bp):
GAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
TAAACCGC
Found at i:3618190 original size:361 final size:360
Alignment explanation
Indices: 3617751--3618803 Score: 1515
Period size: 361 Copynumber: 2.9 Consensus size: 360
3617741 GCAAGTCAGA
* *
3617751 GAGTCAAAGATTAAAGATGATTGGGATTGAACCGTAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
*** * *
3617816 TAAATGGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTTAGAGAAATAATGAAATG
66 TAAACCACGAGTCAAAGATTAAAGATGATTGGGATTGAACCGCAAGTTAGAGAAATAATGAAATG
**
3617881 ATCGGGATTAAACCTTGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGA
131 ATC-GGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGA
* * *
3617946 AATGATCGGGATTAAACCGCAAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGAAA
195 AATGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAAA
* * *
3618011 ATTAATGAAATGATCGAGATTAAACCGCGAGTTAAAGATTAAAGATGACTAGGATTGAACCGCAA
260 ATTAATGAAATGATCGAGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAA
3618076 GTCAAAAAATTAATGAAATGATCGGGATTAAA-TCGC
325 GTCAAAAAATTAATGAAATGATCGGGATTAAACT-GC
3618112 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
** * *
3618177 TAAACCACGAGTCAAAGATTAAAGACAATTGAGATTGAACCGCAAG-T-CA-AAA-AATGAAATG
66 TAAACCACGAGTCAAAGATTAAAGATGATTGGGATTGAACCGCAAGTTAGAGAAATAATGAAATG
* * *
3618238 ATCGGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAGGTCAAAAAATTAA
131 ATCGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAA-T--
* * * *
3618303 CGAAATGATCGGGATTAAATAGCGAGTTAAAGATTAAAGATGACTAGGATTGAATCGCAAGTCAG
193 -GAAATGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAG
*
3618368 AAAATTAATGAAATGATCGGGATTAAACCGCGAGTCAAAGATTTAAAGATGACTGGGATTGAACC
257 AAAATTAATGAAATGATCGAGATTAAACCGCGAGTCAAAGA-TTAAAGATGACTGGGATTGAACC
* *
3618433 GTAAGTCAAGAAATTACTGAAATGATCGGGATTAAACTGC
321 GTAAGTCAAAAAATTAATGAAATGATCGGGATTAAACTGC
* * * *
3618473 GAGTTAAAGATTAAAGATGACTGGGATTAAACCGCAAGTC-AG--A-GAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
* * *
3618534 TAAACCACGAGTCAATGATTAAAGATGATTGGGATTGAATCGCAAGTCAG-GAAATAATGAAATG
66 TAAACCACGAGTCAAAGATTAAAGATGATTGGGATTGAACCGCAAGTTAGAGAAATAATGAAATG
* *
3618598 ATCAGGATTAGACCACGAGTCAAAGATTAAAGATGAC-GGGATTGAACCGTAAGTCAAAAAATTA
131 ATC-GGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC--AAAA--A
3618662 ATGAAATGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCA
191 ATGAAATGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCA
* * * *
3618727 G---A-GAATGAAATGATCGAGATTAAATCACGAGTCAAAGATTAAAGATGACTGGGATTGAACT
256 GAAAATTAATGAAATGATCGAGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACC
3618788 GTAAGTCAAAAAATTA
321 GTAAGTCAAAAAATTA
3618804 TATAAGACTG
Statistics
Matches: 623, Mismatches: 54, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
355 37 0.06
356 86 0.14
357 72 0.12
358 4 0.01
359 4 0.01
360 186 0.30
361 226 0.36
362 5 0.01
363 1 0.00
364 2 0.00
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (360 bp):
GAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATGATCGGGAT
TAAACCACGAGTCAAAGATTAAAGATGATTGGGATTGAACCGCAAGTTAGAGAAATAATGAAATG
ATCGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGAA
ATGATCGGGATTAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAGAAAA
TTAATGAAATGATCGAGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAG
TCAAAAAATTAATGAAATGATCGGGATTAAACTGC
Found at i:3618416 original size:288 final size:287
Alignment explanation
Indices: 3617751--3618801 Score: 1594
Period size: 288 Copynumber: 3.7 Consensus size: 287
3617741 GCAAGTCAGA
* * *
3617751 GAGTCAAAGATTAAAGATGATTGGGATTGAACCGTAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
* *
3617816 TAAATGGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTTAGAGAAATAATGAAATG
66 TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCA-AGAAATAATGAAATG
**
3617881 ATCGGGATTAAACCTTGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGA
130 ATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGA
* * *
3617946 AATGATCGGGATTAAACCGCAAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAGAAA
195 AATGATCGGGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAAGTCAGAAA
* *
3618011 ATTAATGAAATGATCGAGATTAAACCGC
260 ATTAATGAAATGATCGGGATTAAACAGC
*
3618039 GAGTTAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
3618104 TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTAATGAAATG
66 TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAA-TAATGAAATG
** * *
3618169 ATCGGGATTAAACCACGAGTCAAAGATTAAAGACAATTGAGATTGAACCGCAAGTCAAAAAATGA
130 ATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGA
* *
3618234 AATGATC-GGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAGGTCAAAAA
195 AATGATCGGGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAAGTCAGAAA
* *
3618298 ATTAACGAAATGATCGGGATTAAATAGC
260 ATTAATGAAATGATCGGGATTAAACAGC
* * *
3618326 GAGTTAAAGATTAAAGATGACTAGGATTGAATCGCAAGTCAGAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
* *
3618391 TAAACCGCGAGTCAAAGATTTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATTACTGAAAT
66 TAAATCGCGAGTCAAAGA-TTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAA-TAATGAAAT
** * * * *
3618456 GATCGGGATTAAACTGCGAGTTAAAGATTAAAGATGACTGGGATTAAACCGCAAGTCAGAGAATG
129 GATCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATG
* * * *
3618521 AAATGATCGGGATTAAACCACGAGTCAATGATTAAAGATGATTGGGATTGAATCGCAAGTCAGGA
194 AAATGATCGGGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAAGTCAGAA
* *
3618586 AA-TAATGAAATGATCAGGATTAGACCA-C
259 AATTAATGAAATGATCGGGATTA-AACAGC
* *
3618614 GAGTCAAAGATTAAAGATGAC-GGGATTGAACCGTAAGTCAAAAAATTAATGAAATGATCGGGAT
1 GAGTCAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
* *
3618678 TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTC-AG--AGAATGAAATGA
66 TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATAATGAAATGA
* * * *
3618740 TCGAGATTAAATCACGAGTCAAAGATTAAAGATGACTGGGATTGAACTGTAAGTCAAAAAAT
131 TCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAAT
3618802 TATATAAGAC
Statistics
Matches: 695, Mismatches: 64, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
282 61 0.09
283 1 0.00
285 2 0.00
286 29 0.04
287 217 0.31
288 331 0.48
289 54 0.08
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (287 bp):
GAGTCAAAGATTAAAGATGACTAGGATTGAACCGCAAGTCAAAAAATTAATGAAATGATCGGGAT
TAAATCGCGAGTCAAAGATTAAAGATGACTGGGATTGAACCGTAAGTCAAGAAATAATGAAATGA
TCGGGATTAAACCACGAGTCAAAGATTAAAGATGACTGGGATTGAACCGCAAGTCAAAAAATGAA
ATGATCGGGATTAAACCGCGAGTCAAAGATTAAAGATGACTGGGATTGAATCGCAAGTCAGAAAA
TTAATGAAATGATCGGGATTAAACAGC
Found at i:3619865 original size:16 final size:17
Alignment explanation
Indices: 3619845--3619893 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
3619835 TTTTTTCATT
3619845 TTTTTTTATTTTTTTGA
1 TTTTTTTATTTTTTTGA
3619862 TTTTTTTGA--TTTTTGA
1 TTTTTTT-ATTTTTTTGA
3619878 TTTTTTTACTTTTTTT
1 TTTTTTTA-TTTTTTT
3619894 TTAAGCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 7 0.25
18 6 0.21
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTATTTTTTTGA
Found at i:3619883 original size:9 final size:9
Alignment explanation
Indices: 3619824--3619893 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
3619814 TTTCTCATTT
*
3619824 TTTTTTTCA
1 TTTTTTTGA
*
3619833 TTTTTTTTCA
1 -TTTTTTTGA
*
3619843 TTTTTTTTTA
1 -TTTTTTTGA
3619853 TTTTTTTGA
1 TTTTTTTGA
3619862 TTTTTTTGA
1 TTTTTTTGA
3619871 --TTTTTGA
1 TTTTTTTGA
3619878 TTTTTTT-A
1 TTTTTTTGA
3619886 CTTTTTTT
1 -TTTTTTT
3619894 TTAAGCAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
7 7 0.13
8 1 0.02
9 29 0.53
10 18 0.33
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:3619884 original size:10 final size:10
Alignment explanation
Indices: 3619823--3619868 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
3619813 CTTTCTCATT
3619823 TTTTTTTTCA
1 TTTTTTTTCA
3619833 TTTTTTTTCA
1 TTTTTTTTCA
*
3619843 TTTTTTTTTA
1 TTTTTTTTCA
*
3619853 -TTTTTTTGA
1 TTTTTTTTCA
3619862 TTTTTTT
1 TTTTTTT
3619869 GATTTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.09, C:0.04, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:3631638 original size:23 final size:23
Alignment explanation
Indices: 3631612--3631665 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3631602 TTATTATTAT
*
3631612 TAATAACAATTAAATATTTAT-CA
1 TAATAA-AATTAAACATTTATGCA
*
3631635 TAATAAATTTAAACATTTATGCA
1 TAATAAAATTAAACATTTATGCA
*
3631658 TAAAAAAA
1 TAATAAAA
3631666 ACTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
TAATAAAATTAAACATTTATGCA
Found at i:3631652 original size:22 final size:24
Alignment explanation
Indices: 3631612--3631660 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
3631602 TTATTATTAT
*
3631612 TAATAACAATTAAATATTTAT-CA
1 TAATAACAATTAAACATTTATGCA
*
3631635 TAATAA-ATTTAAACATTTATGCA
1 TAATAACAATTAAACATTTATGCA
3631658 TAA
1 TAA
3631661 AAAAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (24 bp):
TAATAACAATTAAACATTTATGCA
Found at i:3632668 original size:25 final size:23
Alignment explanation
Indices: 3632634--3632704 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
3632624 TTGTCTTCTG
3632634 TTTTT-TTTTTTTGGGTATTTTTCA
1 TTTTTATTTTTTT-GGTATTTTT-A
3632658 TTTTTATTTTTTTTGGT-TTTTTA
1 TTTTTA-TTTTTTTGGTATTTTTA
3632681 TTTTGTATTATTTTTGGTATTTTT
1 TTTT-TATT-TTTTTGGTATTTTT
3632705 TTTATTTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.17
24 20 0.48
25 8 0.19
26 7 0.17
ACGTcount: A:0.10, C:0.01, G:0.11, T:0.77
Consensus pattern (23 bp):
TTTTTATTTTTTTGGTATTTTTA
Found at i:3636614 original size:31 final size:31
Alignment explanation
Indices: 3636579--3636645 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
3636569 TCTGTTATGG
*
3636579 AAACCTAACCTTACCATCAGGCTTGTGAGAA
1 AAACCTAACCTTACCATCAGGCTTGTAAGAA
*
3636610 AAACCTAACCTTTCCATCAGGCTTGTAAGAA
1 AAACCTAACCTTACCATCAGGCTTGTAAGAA
3636641 AAACC
1 AAACC
3636646 ACTTCATCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.22
Consensus pattern (31 bp):
AAACCTAACCTTACCATCAGGCTTGTAAGAA
Found at i:3645080 original size:38 final size:35
Alignment explanation
Indices: 3645036--3645105 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 35
3645026 TAGTTTCCAT
3645036 TCTTAGTTTGTCTACGTTTTTTCTCTTTAACCTACTGC
1 TCTTAGTTTGTCTAC-TTTTTT-T-TTTAACCTACTGC
3645074 TCTTAGTTTGTCTACTTTTTTTTTTAACCTAC
1 TCTTAGTTTGTCTACTTTTTTTTTTAACCTAC
3645106 CTCTTATCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 10 0.31
36 1 0.03
37 6 0.19
38 15 0.47
ACGTcount: A:0.14, C:0.21, G:0.09, T:0.56
Consensus pattern (35 bp):
TCTTAGTTTGTCTACTTTTTTTTTTAACCTACTGC
Found at i:3654963 original size:25 final size:25
Alignment explanation
Indices: 3654934--3654987 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3654924 CGGATGAGAA
*
3654934 ATAAGATTCACTAGTTATAGAAAAT
1 ATAAGATTCACTAGTTATAAAAAAT
3654959 ATAAGATTCACTAGTTATAAAAAAT
1 ATAAGATTCACTAGTTATAAAAAAT
3654984 ATAA
1 ATAA
3654988 ACATACATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.31
Consensus pattern (25 bp):
ATAAGATTCACTAGTTATAAAAAAT
Found at i:3655025 original size:20 final size:20
Alignment explanation
Indices: 3654977--3655015 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3654967 CACTAGTTAT
3654977 AAAAAATATAAACATACATA
1 AAAAAATATAAACATACATA
3654997 AAAAAATATAAACATACAT
1 AAAAAATATAAACATACAT
3655016 CAAATCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATATAAACATACATA
Found at i:3661071 original size:23 final size:24
Alignment explanation
Indices: 3661031--3661097 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
3661021 TAGACTTACA
* * *
3661031 TCTTCCCATAGCTTGAACCAT-GC
1 TCTTCCCACATCTCGAACCATAGC
* *
3661054 TCTTCCCACATCTCGAACCTTCAGT
1 TCTTCCCACATCTCGAACCAT-AGC
*
3661079 TCTTCCCACGTCTCGAACC
1 TCTTCCCACATCTCGAACC
3661098 TTCAGTTCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 17 0.47
25 19 0.53
ACGTcount: A:0.19, C:0.40, G:0.10, T:0.30
Consensus pattern (24 bp):
TCTTCCCACATCTCGAACCATAGC
Found at i:3661084 original size:25 final size:25
Alignment explanation
Indices: 3661054--3661124 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
3661044 TGAACCATGC
3661054 TCTTCCCACATCTCGAACCTTCAGT
1 TCTTCCCACATCTCGAACCTTCAGT
*
3661079 TCTTCCCACGTCTCGAACCTTCAGT
1 TCTTCCCACATCTCGAACCTTCAGT
* * *
3661104 TCCTCTCACATATCGAACCTT
1 TCTTCCCACATCTCGAACCTT
3661125 TGACTCTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.20, C:0.39, G:0.08, T:0.32
Consensus pattern (25 bp):
TCTTCCCACATCTCGAACCTTCAGT
Found at i:3662741 original size:52 final size:50
Alignment explanation
Indices: 3662593--3662741 Score: 165
Period size: 52 Copynumber: 2.9 Consensus size: 50
3662583 TACAAACTTG
* *
3662593 CCTATTAAGAATCTCTTTTCTCTTAGAATTCTTTTTTTGCAAATCAAATTTA
1 CCTATTAAGAATCTC-TTTCTTTTAGAATTC-TTTTTTGCAAGTCAAATTTA
* * * *
3662645 TCTATTAAAAAAT-TTTTTCATTTTAGAATTCTTCTCTTGCAAGTCAAATTTA
1 CCTATT-AAGAATCTCTTTC-TTTTAGAATTCTT-TTTTGCAAGTCAAATTTA
*
3662697 CCTATTAAGAATCCTCTTTCTTTTAGAATTCTTTATTTGTAAGTC
1 CCTATTAAGAAT-CTCTTTCTTTTAGAATTCTTT-TTTGCAAGTC
3662742 TTCTTGTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
51 12 0.15
52 58 0.73
53 10 0.12
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (50 bp):
CCTATTAAGAATCTCTTTCTTTTAGAATTCTTTTTTGCAAGTCAAATTTA
Found at i:3663151 original size:31 final size:31
Alignment explanation
Indices: 3663113--3663173 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3663103 TCTTATCCAT
*
3663113 TCAAACATATACATCCATAAAAATGTTAATC
1 TCAAACATATACATCCATAAAAATATTAATC
3663144 TCAAACATATACATCCATAAAAATATTAAT
1 TCAAACATATACATCCATAAAAATATTAAT
3663174 TTCTTATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (31 bp):
TCAAACATATACATCCATAAAAATATTAATC
Found at i:3664572 original size:21 final size:22
Alignment explanation
Indices: 3664536--3664576 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3664526 TCGAAAACTT
*
3664536 GAAGAAAATGTGAATGATCTCA
1 GAAGAAAATCTGAATGATCTCA
3664558 GAAGAAAA-CTGAATGATCT
1 GAAGAAAATCTGAATGATCT
3664577 AAATATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (22 bp):
GAAGAAAATCTGAATGATCTCA
Found at i:3665834 original size:325 final size:320
Alignment explanation
Indices: 3665233--3666131 Score: 1077
Period size: 323 Copynumber: 2.8 Consensus size: 320
3665223 AATACTATGG
* * * * * * *
3665233 AGATCCGCACCCAACCTACGAGATATTGTCCGTTTTGACCCGAAGGTCTTATGATTTTATCTCAC
1 AGATTCGCACCCAACCTACGAGATATTATCC-ATTTGACCCGAAGGTCTCACGATTTTATCCCAT
* ** * *
3665298 AAAAGGTGCCTCATAAGTTTGAATTTAG--TTATATATATATATCATTCCTTATCCACACATTCT
65 AAAAGGTACCTCATAAGTTTGGGTTTAGATTTCTATATATATATCATTCTTTATCCACACATTCT
* ** * *
3665361 TTCAATGTGGGATTAGGGGCGTTACAATCTCTTCATATTTAGAGCTTGATAACCTTGTCAAGTCA
130 TT-AATGTGGGATTA-AGGCGTTACAATCTCTTCACCTTTAGAGCTTGACATCCTTGTCAAGTCA
* * * * * **
3665426 AGTCCAACCACAGGATCAAGATCACACTAGATCACTGTATAACACTTAGTGACTCTTATGATCGC
193 AGTCTAACCACAGGATCAAGATCACAC-AGAT-ACCGTGTAGCACTTAGTGACTCCTACAATCGC
* * ** *
3665491 ACCGTGTAGCATTTAGTGACTCCCA-TGATCGTCGATTAGTAACCTCGCTTTGATATCATTTATA
256 ACCATGTAGCACTTAGTGACTCCCACTG-TAATCGACTAGTAACCTCGCTTTGATATCATTTATA
3665555 A
320 A
* * * *
3665556 AGATTCGCACTCAACCTACAAAATATTATCCACTTTGGCCCGAAGGTCTCACGATTTTATCCCAT
1 AGATTCGCACCCAACCTACGAGATATTATCCA-TTTGACCCGAAGGTCTCACGATTTTATCCCAT
* *
3665621 AAAAGGTACCTCATAAGTTTGGGTTTAGATTTCTACATATATATCATTCTTTATCCACACAATCT
65 AAAAGGTACCTCATAAGTTTGGGTTTAGATTTCTATATATATATCATTCTTTATCCACACATTCT
* * *
3665686 TCTAATGTGGGATTAAGGACGTTACAATCTCTTCACCTTTAGAGTTTGACGTCCTTGTCAAGTTA
130 T-TAATGTGGGATTAAGG-CGTTACAATCTCTTCACCTTTAGAGCTTGACATCCTTGTCAAGTCA
*
3665751 AGTCTAATCACAGGATCAAGATCACATCAGAGTACCGTGTAGCACTTAGTGACTCCTACAATCGC
193 AGTCTAACCACAGGATCAAGATCACA-CAGA-TACCGTGTAGCACTTAGTGACTCCTACAATCGC
* **
3665816 ACCATGTAGCACTTAGTGACTCCCACTGTAATCGACTAGTAACCTCGCTTTGATATCATTTGTGG
256 ACCATGTAGCACTTAGTGACTCCCACTGTAATCGACTAGTAACCTCGCTTTGATATCATTTATAA
** ** * * *
3665881 AGATTCATACCCAACCTGTGAGATATTATCTATTTGATCCGAAGGTCTCACGATTTTATCCTAT-
1 AGATTCGCACCCAACCTACGAGATATTATCCATTTGACCCGAAGGTCTCACGATTTTATCCCATA
* * * *
3665945 AAAGGTACCTCATAAATTTAGGTTTAGATCTCTATATGTATATCATTCTTTATCCACACATTCTT
66 AAAGGTACCTCATAAGTTTGGGTTTAGATTTCTATATATATATCATTCTTTATCCACACATTC-T
* * * * * * *
3666010 TTAATGTGGGATTGGAGGCATTACAATCTCTCCACCTTTAGTGCTTGACTTCCCTGTCAAGCCAA
130 TTAATGTGGGATT-AAGGCGTTACAATCTCTTCACCTTTAGAGCTTGACATCCTTGTCAAGTCAA
* *
3666075 GTCTAACCACAGGACCAAGATCACACCAGACCACCGTGTAGCACTTAGTGACTCCTA
194 GTCTAACCACAGGATCAAGATCACA-CAGA-TACCGTGTAGCACTTAGTGACTCCTA
3666132 TGGCTGTCGA
Statistics
Matches: 493, Mismatches: 73, Indels: 20
0.84 0.12 0.03
Matches are distributed among these distances:
323 238 0.48
324 36 0.07
325 214 0.43
326 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (320 bp):
AGATTCGCACCCAACCTACGAGATATTATCCATTTGACCCGAAGGTCTCACGATTTTATCCCATA
AAAGGTACCTCATAAGTTTGGGTTTAGATTTCTATATATATATCATTCTTTATCCACACATTCTT
TAATGTGGGATTAAGGCGTTACAATCTCTTCACCTTTAGAGCTTGACATCCTTGTCAAGTCAAGT
CTAACCACAGGATCAAGATCACACAGATACCGTGTAGCACTTAGTGACTCCTACAATCGCACCAT
GTAGCACTTAGTGACTCCCACTGTAATCGACTAGTAACCTCGCTTTGATATCATTTATAA
Found at i:3667163 original size:93 final size:93
Alignment explanation
Indices: 3667058--3667241 Score: 350
Period size: 93 Copynumber: 2.0 Consensus size: 93
3667048 CAAAAATAAA
3667058 GAATAAAACATTTATTCATTTAGGAACATACATATATATATTTAAAAACAAGCAAAATATGTGAG
1 GAATAAAACATTTATTCATTTAGGAACATACATATATATATTTAAAAACAAGCAAAATATGTGAG
3667123 ATTCTATTTACCTTCTTTCGATTCCAAG
66 ATTCTATTTACCTTCTTTCGATTCCAAG
* *
3667151 GAATAAAACATTTATTCATTTAGGAATATACATATATATATTTAAAAACAAGCAAAATATGTGAT
1 GAATAAAACATTTATTCATTTAGGAACATACATATATATATTTAAAAACAAGCAAAATATGTGAG
3667216 ATTCTATTTACCTTCTTTCGATTCCA
66 ATTCTATTTACCTTCTTTCGATTCCA
3667242 CCACCTAGTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (93 bp):
GAATAAAACATTTATTCATTTAGGAACATACATATATATATTTAAAAACAAGCAAAATATGTGAG
ATTCTATTTACCTTCTTTCGATTCCAAG
Found at i:3677079 original size:11 final size:10
Alignment explanation
Indices: 3677061--3677143 Score: 51
Period size: 11 Copynumber: 7.7 Consensus size: 10
3677051 TAATGGATGA
*
3677061 AAAAAAAAAC
1 AAAAAAAAAG
*
3677071 AAGAAAAAATG
1 AA-AAAAAAAG
3677082 AAAAAAAAAAG
1 -AAAAAAAAAG
**
3677093 AAAAAAAGGG
1 AAAAAAAAAG
3677103 AAAAAATGAAA-
1 AAAAAA--AAAG
*
3677114 AATAAAATAATG
1 AA-AAAA-AAAG
3677126 AAAAAAAAGAG
1 AAAAAAAA-AG
3677137 AAAAAAA
1 AAAAAAA
3677144 GACTCAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 18 0.32
11 29 0.52
12 9 0.16
ACGTcount: A:0.81, C:0.01, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3677106 original size:19 final size:20
Alignment explanation
Indices: 3677062--3677145 Score: 64
Period size: 19 Copynumber: 4.0 Consensus size: 20
3677052 AATGGATGAA
*
3677062 AAAAAAAACAAGAAAAAATG
1 AAAAAAAACAAGAAAAAAAG
3677082 AAAAAAAA-AAGAAAAAAAGGG
1 AAAAAAAACAAGAAAAAAA--G
* * *
3677103 AAAAAATGAAAAATAAAATAATG
1 AAAAAA--AACAAGAAAA-AAAG
*
3677126 AAAAAAAA-GAGAAAAAAAG
1 AAAAAAAACAAGAAAAAAAG
3677145 A
1 A
3677146 CTCAAATTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
19 13 0.25
20 13 0.25
21 9 0.17
23 9 0.17
24 6 0.12
25 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (20 bp):
AAAAAAAACAAGAAAAAAAG
Found at i:3678659 original size:44 final size:44
Alignment explanation
Indices: 3678588--3678687 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
3678578 ATTGACGAGG
** * * * *
3678588 ATTTACTTTTCTCCAAAGTTGTTAAGCCTCAGCTTGGAGGAGCTTT
1 ATTT-CTTTT-TCCAAAGTCATCAAGCCTCAGCTTAGAAGAGCCTT
**
3678634 ATTTCTTTTTCCAAAGTCATCAAGCCTGTGCTTAGAAGAGCCTT
1 ATTTCTTTTTCCAAAGTCATCAAGCCTCAGCTTAGAAGAGCCTT
*
3678678 ATTTATTTTT
1 ATTTCTTTTT
3678688 TAAAAATTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 36 0.80
45 5 0.11
46 4 0.09
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (44 bp):
ATTTCTTTTTCCAAAGTCATCAAGCCTCAGCTTAGAAGAGCCTT
Found at i:3678767 original size:43 final size:44
Alignment explanation
Indices: 3678665--3678768 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 44
3678655 AAGCCTGTGC
* *
3678665 TTAGAAGAGCCTTATTTATTTTTTAAAAATTGTTAAGCTTCTGT
1 TTAGAAGAGCCTTATTTATTTTTTAAAAATTGTTAAACTTCTAT
* * *
3678709 TTAGAAGAGCTTTATTTATTTTTT-AAAGTTGTTAAACTTTTAT
1 TTAGAAGAGCCTTATTTATTTTTTAAAAATTGTTAAACTTCTAT
3678752 TTA-AATGAGCCTTATTT
1 TTAGAA-GAGCCTTATTT
3678769 TTTAAGTCGT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.04
43 28 0.53
44 23 0.43
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (44 bp):
TTAGAAGAGCCTTATTTATTTTTTAAAAATTGTTAAACTTCTAT
Found at i:3678955 original size:168 final size:167
Alignment explanation
Indices: 3678697--3679089 Score: 427
Period size: 168 Copynumber: 2.4 Consensus size: 167
3678687 TTAAAAATTG
* * * * * * * * * *
3678697 TTAAGCTTCTGTTTAGAAGAGCTTTATTTATTTTT-TAAAGTTGTTAAACTTTTATTTAAATGAG
1 TTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTAGAGGAG
* * *
3678761 C-CTTATTTTTTAAGTCGTTGAGCCTTTGCTTAG-TGAAGCCTTATTTATTTTTCAAAGTTATTG
66 CTC-AATTTTTTAAGTCGTTAAGCCTTTGCTTAGAGGAA-CCTTATTTATTTTTCAAAGTTATTG
** * * * * **
3678824 AGTTTCTGTTTAAATGAGTCTTATTTTTTTTTCAAAAGTTG
129 AGCCTCTATTTAAAGGAGCCTTA-TTTATTTTC-AAAGTCA
* * * *
3678865 TTGAGTCTCTGTTTAGAAGAGTTTTAATTT-TTTTTCAAAA-TTGTTGAGCCTCTGTTTAGAGGA
1 TTAAGCCTCTGATTAGAAGAGTTTT-ATTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTAGAGGA
* ** * *
3678928 GCTCAATTTTTTAAGTTGTTAAGCCTTTGCTTAGAGGAATTTTATTTATTTTTTAAAGTTGTTGA
65 GCTCAATTTTTTAAGTCGTTAAGCCTTTGCTTAGAGGAACCTTATTTATTTTTCAAAGTTATTGA
*
3678993 GCCTCTATTTAAAGGCGCCTTATTTATTTTCAAAGTCA
130 GCCTCTATTTAAAGGAGCCTTATTTATTTTCAAAGTCA
3679031 TTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTA
1 TTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTA
3679090 AAAGAGCTTT
Statistics
Matches: 186, Mismatches: 33, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
165 4 0.02
166 37 0.20
167 25 0.13
168 109 0.59
169 11 0.06
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (167 bp):
TTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTAGAGGAG
CTCAATTTTTTAAGTCGTTAAGCCTTTGCTTAGAGGAACCTTATTTATTTTTCAAAGTTATTGAG
CCTCTATTTAAAGGAGCCTTATTTATTTTCAAAGTCA
Found at i:3678990 original size:81 final size:83
Alignment explanation
Indices: 3678682--3679096 Score: 284
Period size: 81 Copynumber: 5.0 Consensus size: 83
3678672 AGCCTTATTT
* * * * ** * * * *
3678682 ATTTTTTAAAAATTGTTAAGCTTCTGTTTAGAAGAGCTTTATTTATTTTTTAAAGTTGTTAAACT
1 ATTTTTT-AAAGTCGTTAAGCCTCTGCTTAGAAGAATTTTATTTATTTTTCAAAGTTGTTGAGCC
* * * *
3678747 TTTATTTAAATGAGCCT-T
65 TCTGTTTAAAGGAGCCTCA
* * * ** * **
3678765 ATTTTTT-AAGTCGTTGAGCCTTTGCTTAG-TGAAGCCTTATTTATTTTTCAAAGTTATTGAGTT
1 ATTTTTTAAAGTCGTTAAGCCTCTGCTTAGAAGAA-TTTTATTTATTTTTCAAAGTTGTTGAGCC
* * *
3678828 TCTGTTTAAATGAGTCTTA
65 TCTGTTTAAAGGAGCCTCA
* * * * * * *
3678847 TTTTTTTTTCAAAAGTTGTTGAGTCTCTGTTTAGAAGAGTTTTAATTT-TTTTTCAAAATTGTTG
1 --ATTTTTT--AAAGTCGTTAAGCCTCTGCTTAGAAGAATTTT-ATTTATTTTTCAAAGTTGTTG
*
3678911 AGCCTCTGTTTAGAGGAG-CTCA
61 AGCCTCTGTTTAAAGGAGCCTCA
* * * *
3678933 ATTTTTT-AAGTTGTTAAGCCTTTGCTTAGAGGAATTTTATTTATTTTTTAAAGTTGTTGAGCCT
1 ATTTTTTAAAGTCGTTAAGCCTCTGCTTAGAAGAATTTTATTTATTTTTCAAAGTTGTTGAGCCT
* * *
3678997 CTATTTAAAGGCGCCTTA
66 CTGTTTAAAGGAGCCTCA
* * * * *
3679015 TTTATTTTCAAAGTCATTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCAAAAGTTGTTAAG
1 ATT-TTTT-AAAGTCGTTAAGCCTCTGCTTAGAAGAATTTTATTTATTTTTC-AAAGTTGTTGAG
*
3679080 CCTCTGTTTAAAAGAGC
63 CCTCTGTTTAAAGGAGC
3679097 TTTAGCTGTT
Statistics
Matches: 258, Mismatches: 59, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
80 6 0.02
81 107 0.41
82 5 0.02
83 11 0.04
84 12 0.05
85 35 0.14
86 28 0.11
87 48 0.19
88 6 0.02
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (83 bp):
ATTTTTTAAAGTCGTTAAGCCTCTGCTTAGAAGAATTTTATTTATTTTTCAAAGTTGTTGAGCCT
CTGTTTAAAGGAGCCTCA
Found at i:3679109 original size:44 final size:43
Alignment explanation
Indices: 3678602--3679163 Score: 239
Period size: 44 Copynumber: 13.2 Consensus size: 43
3678592 ACTTTTCTCC
* * * * * *
3678602 AAAGTTGTTAAGCCTCAGCTTGGAGGAGCTTTATTTCTTTTTCC
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
** * * * * *
3678646 AAAGTCATCAAGCCTGTGCTTAGAAGAGCCTTATTTATTTTTTA
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
* * *
3678690 AAAATTGTTAAGCTTCTGTTTAGAAGAGCTTTATTTATTTTT-T
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
* * * * *
3678733 AAAGTTGTTAAACTTTTATTTA-AATGAGCCTTA-T-TTTTT--
1 AAAGTTGTTAAGCCTCTGTTTAGAA-GAGCTTTATTATTTTTCA
* * * * * *
3678772 -AAGTCGTTGAGCCTTTGCTTAG-TGAAGCCTTATTTATTTTTC-
1 AAAGTTGTTAAGCCTCTGTTTAGAAG-AGCTTTA-TTATTTTTCA
* * ** *
3678814 AAAGTTATTGAGTTTCTGTTTA-AATGAG-TCTTATTTTTTTTTCA
1 AAAGTTGTTAAGCCTCTGTTTAGAA-GAGCT-TTA-TTATTTTTCA
* * * *
3678858 AAAGTTGTTGAGTCTCTGTTTAGAAGAGTTTTAATTTTTTTTCA
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTT-ATTATTTTTCA
* * *
3678902 AAA-TTGTTGAGCCTCTGTTTAGAGGAGC-TCA--ATTTTT--
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTATTATTTTTCA
* * * * ** *
3678939 TAAGTTGTTAAGCCTTTGCTTAGAGGAATTTTATTTATTTTT-T
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
* * * *
3678982 AAAGTTGTTGAGCCTCTATTTA-AAGGCGCCTTATT-TATTTTC-
1 AAAGTTGTTAAGCCTCTGTTTAGAA-GAGCTTTATTAT-TTTTCA
** * *
3679024 AAAGTCATTAAGCCTCTGATTAGAAGAGTTTTATTTATTTTTCA
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
* * *
3679068 AAAGTTGTTAAGCCTCTGTTTAAAAGAGCTTTAGCTGTTTTTCA
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
* ** * * * * *
3679112 AAAGTTATGGAGCCTTTGCTTAGAGGAGTTTTATTTATTTCTCA
1 AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTA-TTATTTTTCA
*
3679156 AAAATTGT
1 AAAGTTGT
3679164 GGAGTCTCTA
Statistics
Matches: 395, Mismatches: 95, Indels: 56
0.72 0.17 0.10
Matches are distributed among these distances:
37 3 0.01
38 42 0.11
39 7 0.02
40 6 0.02
41 8 0.02
42 38 0.10
43 106 0.27
44 181 0.46
45 4 0.01
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.46
Consensus pattern (43 bp):
AAAGTTGTTAAGCCTCTGTTTAGAAGAGCTTTATTATTTTTCA
Found at i:3679668 original size:19 final size:19
Alignment explanation
Indices: 3679632--3679670 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3679622 ATTTTTTTGG
*
3679632 AGATTTTTTGTTTTAAAAA
1 AGATTTTTTGTTTCAAAAA
3679651 AGATTTTTT-TTCTCAAAAA
1 AGATTTTTTGTT-TCAAAAA
3679670 A
1 A
3679671 TTTGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (19 bp):
AGATTTTTTGTTTCAAAAA
Found at i:3679906 original size:16 final size:18
Alignment explanation
Indices: 3679881--3679914 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3679871 AATTCTAGAG
3679881 AAAAGAAGAGA-AAAAAA
1 AAAAGAAGAGAGAAAAAA
3679898 AAAAG-AGAGAGAAAAAA
1 AAAAGAAGAGAGAAAAAA
3679915 GAGCAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAGAGAAAAAA
Found at i:3680200 original size:4 final size:4
Alignment explanation
Indices: 3680186--3680226 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
3680176 ATTTTTGTTA
*
3680186 TTAT TTA- TTAT TTAT TTAT TTAT TCTAT TTAT TTAG TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT T
3680227 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
5 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:3680216 original size:17 final size:16
Alignment explanation
Indices: 3680186--3680226 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3680176 ATTTTTGTTA
3680186 TTATTTA-TTATTTAT
1 TTATTTATTTATTTAT
3680201 TTATTTATTCTATTTAT
1 TTATTTATT-TATTTAT
*
3680218 TTAGTTATT
1 TTATTTATT
3680227 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 15 0.65
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTATTTAT
Found at i:3683581 original size:21 final size:22
Alignment explanation
Indices: 3683545--3683585 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3683535 CCGAAAACTT
*
3683545 GAAGAAAATGTGAATGATCTCA
1 GAAGAAAATCTGAATGATCTCA
3683567 GAAGAAAA-CTGAATGATCT
1 GAAGAAAATCTGAATGATCT
3683586 AAATATCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (22 bp):
GAAGAAAATCTGAATGATCTCA
Found at i:3692989 original size:3 final size:3
Alignment explanation
Indices: 3692962--3693038 Score: 122
Period size: 3 Copynumber: 25.7 Consensus size: 3
3692952 TTACTTGAAA
3692962 ATT ATT GATT -TT ATT GATT -TT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3693007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3693039 ATCTAATGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.06
3 60 0.86
4 6 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3693893 original size:18 final size:17
Alignment explanation
Indices: 3693857--3693899 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3693847 TTTTAAAGAA
**
3693857 AATATAAATTTATTAAC
1 AATATAAATGAATTAAC
3693874 AATATAAATGAATATAAC
1 AATATAAATGAAT-TAAC
*
3693892 AACATAAA
1 AATATAAA
3693900 ATATCTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
AATATAAATGAATTAAC
Found at i:3695180 original size:8 final size:8
Alignment explanation
Indices: 3695164--3695205 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
3695154 ATAAATCATG
*
3695164 ATTAAAAA
1 ATTATAAA
*
3695172 ATTACAAA
1 ATTATAAA
3695180 ATTATAAA
1 ATTATAAA
3695188 ATTATAAAA
1 ATTAT-AAA
3695197 ATTATAAA
1 ATTATAAA
3695205 A
1 A
3695206 AAAAAAACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 23 0.74
9 8 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
ATTATAAA
Found at i:3695197 original size:17 final size:16
Alignment explanation
Indices: 3695164--3695205 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3695154 ATAAATCATG
* *
3695164 ATTAAAAAATTACAAA
1 ATTATAAAATTAAAAA
3695180 ATTATAAAATTATAAAA
1 ATTATAAAATTA-AAAA
3695197 ATTATAAAA
1 ATTATAAAA
3695206 AAAAAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTATAAAATTAAAAA
Found at i:3695543 original size:216 final size:218
Alignment explanation
Indices: 3695288--3695765 Score: 542
Period size: 216 Copynumber: 2.2 Consensus size: 218
3695278 TAATAGAAAT
* * * * *
3695288 ATAAAAGATATTCATATAACTTCTTATCTTTAAAAGAGATGGAAAACCATAAATTACAAGAAAAT
1 ATAAAAGACACTCATATAAC-TCTTATTTTTAAAAGAGATAGAAAACCATAAATCACAA-AAAAT
* * *
3695353 GAAAAGT-AAAAAAATATAAATGTTACAAACCAAAAGATATGGT-AATAAAATTTTAACAAAAAA
64 GAAAAATAAAAAAAATATAAATGTTACAAAACAAAAGATATGATCAAT-AAATTTTAACAAAAAA
* * * * * * *
3695416 TGATTTTTAA-AAATTG-AT-TAAGAAAATAAAAAATCAATAATTCAAGTAATATAATAAATAAG
128 TG--GTTAAATAAAATGAATATAAAAAAATAAAAAATCAATAATTAAAGTAATATAACAAACAAG
*
3695478 AATTTG-GAGAAAAAAGTG-TAAAAGAGAC
191 AA-TTGAAAGAAAAAAGTGTTAAAA-AGAC
* *
3695506 ATGAAAA-A-ACTCATATAACTCTTATTTTTAAAAGAGATAGAAAATCATAAATCACAAAAAATT
1 AT-AAAAGACACTCATATAACTCTTATTTTTAAAAGAGATAGAAAACCATAAATCACAAAAAATG
** * * * *
3695569 AAAAATAAAAAAAATATAAATGTTACAAAATGAAAGGTTTGATCAATAACTTTTAACAAATAATG
65 AAAAATAAAAAAAATATAAATGTTACAAAACAAAAGATATGATCAATAAATTTTAACAAAAAATG
* * *
3695634 GTTAAATAAAATGAATATAAAAAAATCAAAAATCAATAATTAAAGTAATATGACAAACAATAATT
130 GTTAAATAAAATGAATATAAAAAAATAAAAAATCAATAATTAAAGTAATATAACAAACAAGAATT
*
3695699 GAAAGAAAAAAGTGTTATAAAGAC
195 GAAAGAAAAAAGTGTTAAAAAGAC
* * *
3695723 ATAAAAGACACTAATATAACTCTCATTCTTAAAAGAGATAGAA
1 ATAAAAGACACTCATATAACTCTTATTTTTAAAAGAGATAGAA
3695766 TATTATATAT
Statistics
Matches: 220, Mismatches: 30, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
214 4 0.02
215 15 0.07
216 89 0.40
217 70 0.32
218 38 0.17
219 4 0.02
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (218 bp):
ATAAAAGACACTCATATAACTCTTATTTTTAAAAGAGATAGAAAACCATAAATCACAAAAAATGA
AAAATAAAAAAAATATAAATGTTACAAAACAAAAGATATGATCAATAAATTTTAACAAAAAATGG
TTAAATAAAATGAATATAAAAAAATAAAAAATCAATAATTAAAGTAATATAACAAACAAGAATTG
AAAGAAAAAAGTGTTAAAAAGAC
Done.