Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 136 of 168
Found at i:39797262 original size:33 final size:32
Alignment explanation
Indices: 39797223--39797335 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 32
39797213 CTTTCCTTTT
39797223 CTTTCCTTCTTTTTCTTTCTTTTTCTTCTTCTC
1 CTTTCCTTCTTTTTCTTTC-TTTTCTTCTTCTC
39797256 CTTTCCTTCTTTTTCTTTC-TTTC--C-TCTC
1 CTTTCCTTCTTTTTCTTTCTTTTCTTCTTCTC
*
39797284 CTTTCCTTTCCTTTTCTTTCCTTTTCTTTCTT-T-
1 CTTTCC-TTCTTTTTCTTT-CTTTTC-TTCTTCTC
* *
39797317 CTTTCTTTCTTCTTCTTTC
1 CTTTCCTTCTTTTTCTTTC
39797336 CCTCTCATTC
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
28 10 0.14
29 12 0.17
30 1 0.01
31 9 0.13
32 10 0.14
33 24 0.35
34 2 0.03
35 1 0.01
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (32 bp):
CTTTCCTTCTTTTTCTTTCTTTTCTTCTTCTC
Found at i:39799254 original size:10 final size:9
Alignment explanation
Indices: 39799227--39799287 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 9
39799217 TATATTTATT
39799227 TTTTTAAT-
1 TTTTTAATA
**
39799235 TTTAAAATA
1 TTTTTAATA
39799244 TTTTTACATA
1 TTTTTA-ATA
39799254 TTTTTAA-A
1 TTTTTAATA
*
39799262 TTTTTAAAA
1 TTTTTAATA
*
39799271 TTTTAAAATA
1 TTTT-TAATA
39799281 TTTTTAA
1 TTTTTAA
39799288 AATCTTAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
8 14 0.33
9 12 0.29
10 16 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAATA
Found at i:39799257 original size:27 final size:27
Alignment explanation
Indices: 39799227--39799350 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 27
39799217 TATATTTATT
*
39799227 TTTTTAATTTTAAAATATTTTTACATA
1 TTTTTAATTTTAAAATATTTTTAAATA
* *
39799254 TTTTTAAATTTTTAAA-ATTTTAAAATA
1 TTTTT-AATTTTAAAATATTTTTAAATA
*
39799281 TTTTTAAAATCTTAATTTAAATACTTTTTTAAA-A
1 TTTTT--AA--TT--TTAAAATA--TTTTTAAATA
39799315 TTTTTTAATTTTAAAATATTTTTAAAATA
1 -TTTTTAATTTTAAAATATTTTT-AAATA
39799344 TTTTTAA
1 TTTTTAA
39799351 AATACTTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
27 24 0.30
28 22 0.28
29 8 0.10
30 2 0.03
31 2 0.03
32 6 0.08
33 3 0.04
34 1 0.01
35 12 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTTAATTTTAAAATATTTTTAAATA
Found at i:39799287 original size:11 final size:11
Alignment explanation
Indices: 39799234--39799385 Score: 95
Period size: 11 Copynumber: 14.8 Consensus size: 11
39799224 ATTTTTTTAA
39799234 TTTTAAAATAT
1 TTTTAAAATAT
*
39799245 TTTT-ACATAT
1 TTTTAAAATAT
39799255 TTTT--AA-AT
1 TTTTAAAATAT
39799263 TTTT-AAA-A-
1 TTTTAAAATAT
39799271 TTTTAAAATAT
1 TTTTAAAATAT
*
39799282 TTTTAAAATCT
1 TTTTAAAATAT
39799293 TAATTT-AAATACTT
1 T--TTTAAAATA--T
39799307 TTTTAAAAT-T
1 TTTTAAAATAT
39799317 TTTT---A-A-
1 TTTTAAAATAT
39799323 TTTTAAAATAT
1 TTTTAAAATAT
39799334 TTTTAAAATAT
1 TTTTAAAATAT
39799345 TTTTAAAATACTT
1 TTTTAAAATA--T
**
39799358 TTTTTTAAT-T
1 TTTTAAAATAT
39799368 TTTTAAAA-A-
1 TTTTAAAATAT
39799377 TTTTAAAAT
1 TTTTAAAAT
39799386 TAAAATGGGC
Statistics
Matches: 114, Mismatches: 8, Indels: 39
0.71 0.05 0.24
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 10 0.09
9 16 0.14
10 23 0.20
11 36 0.32
12 7 0.06
13 15 0.13
14 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39799326 original size:52 final size:50
Alignment explanation
Indices: 39799234--39799373 Score: 160
Period size: 52 Copynumber: 2.8 Consensus size: 50
39799224 ATTTTTTTAA
* * * **
39799234 TTTTAAAATATTTTT-ACATA-TTTTTAAATTTTTAAAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAATAT
*
39799282 TTTTAAAATCTTAATTT-AAATACTTTTTTAAAATTTTTTAATTTTAAAATAT
1 TTTTAAAATATT--TTTAAAATACTTTTTT-AAATTTTTTAATTTTAAAATAT
*
39799334 TTTTAAAATATTTTTAAAATACTTTTTTTTAATTTTTTAA
1 TTTTAAAATATTTTTAAAATAC-TTTTTTAAATTTTTTAA
39799374 AAATTTTAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
48 11 0.14
50 10 0.13
51 21 0.27
52 36 0.46
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (50 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTAATTTTAAAATAT
Found at i:39799328 original size:16 final size:17
Alignment explanation
Indices: 39799307--39799339 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39799297 TTAAATACTT
39799307 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
39799323 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
39799340 AATATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:39800085 original size:13 final size:14
Alignment explanation
Indices: 39800056--39800085 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39800046 CTTACAATCA
*
39800056 TTTATTAATATTTT
1 TTTATAAATATTTT
39800070 TTTATAAATATTTT
1 TTTATAAATATTTT
39800084 TT
1 TT
39800086 CAGCATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATAAATATTTT
Found at i:39802180 original size:14 final size:14
Alignment explanation
Indices: 39802161--39802190 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39802151 AATAAGATTA
39802161 AATTAATTAAACTT
1 AATTAATTAAACTT
*
39802175 AATTAATTAAAGTT
1 AATTAATTAAACTT
39802189 AA
1 AA
39802191 ACTAAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (14 bp):
AATTAATTAAACTT
Found at i:39805501 original size:14 final size:12
Alignment explanation
Indices: 39805482--39805515 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
39805472 GAGAAAACTG
39805482 AAGAAAAATAGAGA
1 AAGAAAAATA-A-A
39805496 AAGAAAAATAAA
1 AAGAAAAATAAA
39805508 AAGAAAAA
1 AAGAAAAA
39805516 GTGAAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 1 0.05
14 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (12 bp):
AAGAAAAATAAA
Found at i:39805583 original size:17 final size:17
Alignment explanation
Indices: 39805561--39805602 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
39805551 AATTCTTTAG
39805561 TAAAATAATAATAAAAT-
1 TAAAATAA-AATAAAATA
39805578 TAAAATTAAAATAAAATA
1 TAAAA-TAAAATAAAATA
39805596 TAAAATA
1 TAAAATA
39805603 TAAGAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAAAATAAAATA
Found at i:39805602 original size:12 final size:12
Alignment explanation
Indices: 39805561--39805602 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
39805551 AATTCTTTAG
39805561 TAAAATAATAATA
1 TAAAATAA-AATA
*
39805574 -AAATTAAAAT-
1 TAAAATAAAATA
39805584 TAAAATAAAATA
1 TAAAATAAAATA
39805596 TAAAATA
1 TAAAATA
39805603 TAAGAAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 13 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAATAAAATA
Found at i:39807573 original size:70 final size:70
Alignment explanation
Indices: 39807458--39807607 Score: 196
Period size: 70 Copynumber: 2.1 Consensus size: 70
39807448 AACACACCAT
* * * *
39807458 TTTCATTAAATGGTATTGACTCAAAATGAATCGTTTTGAATACGACTCAGA-CCTTAGCTACGAC
1 TTTCATTAAACGGTATTGACTCAAAATCAATCATTTTGAACACGACTCAGATCC-TAGCTACGAC
*
39807522 GCATTG
65 GCACTG
* **
39807528 TTTCATTAAACGGTATTGACTCAAAA-CAAGTCATTTTGAACACGACTTAGATCCTAGCTGTGAC
1 TTTCATTAAACGGTATTGACTCAAAATCAA-TCATTTTGAACACGACTCAGATCCTAGCTACGAC
39807592 GCACTG
65 GCACTG
39807598 TTTCATTAAA
1 TTTCATTAAA
39807608 GTTTCTAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
69 2 0.03
70 66 0.94
71 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (70 bp):
TTTCATTAAACGGTATTGACTCAAAATCAATCATTTTGAACACGACTCAGATCCTAGCTACGACG
CACTG
Found at i:39809589 original size:5 final size:5
Alignment explanation
Indices: 39809581--39809606 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39809571 AAAAAAAAAA
39809581 CGCCT CGCCT CGCCT CGCCT CGCCT C
1 CGCCT CGCCT CGCCT CGCCT CGCCT C
39809607 CATCTCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.19, T:0.19
Consensus pattern (5 bp):
CGCCT
Found at i:39820370 original size:2 final size:2
Alignment explanation
Indices: 39820365--39820389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39820355 AAAGGGGGGA
39820365 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39820390 GTAGAAGGNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39824036 original size:22 final size:22
Alignment explanation
Indices: 39823994--39824037 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39823984 TACACTAAAA
* *
39823994 TAGGTCTTTAGCGGCATTTTTT
1 TAGGCCTTTAGCGGCACTTTTT
*
39824016 TAGGCCTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCACTTTTT
39824038 AACGCCGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCACTTTTT
Found at i:39824173 original size:40 final size:41
Alignment explanation
Indices: 39824087--39824208 Score: 185
Period size: 39 Copynumber: 3.0 Consensus size: 41
39824077 ATTTGCAGCG
* *
39824087 TTTTTCTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGC
1 TTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
*
39824128 GTTTTTTTCTAAGCGTCGCTAAAG-A-ATGGTCTTTAGCGGC
1 -TTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
*
39824168 TTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
1 TTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
39824209 GCTTTTATAC
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
39 22 0.30
40 16 0.22
41 15 0.21
42 20 0.27
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
Found at i:39824187 original size:39 final size:42
Alignment explanation
Indices: 39824084--39824214 Score: 196
Period size: 42 Copynumber: 3.2 Consensus size: 42
39824074 AACATTTGCA
* *
39824084 GCGTTTTTCTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCG
1 GCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
*
39824126 GCGTTTTTTTCTAAGCGTCGCTAAAG-A-ATGGTCTTTAGCG
1 GCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
*
39824166 GC-TTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTTTAGCG
1 GCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
*
39824207 GCGCTTTT
1 GCGTTTTT
39824215 ATACAAAAAC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
39 22 0.28
40 16 0.20
41 15 0.19
42 27 0.34
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (42 bp):
GCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCG
Found at i:39824556 original size:21 final size:21
Alignment explanation
Indices: 39824530--39824574 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
39824520 TTTGCTCTGT
*
39824530 TCTGCTTCTCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
*
39824551 TCTGCTTCCCTCGCTGCCGCC
1 TCTGCTTCCCTCGCTGCAGCC
39824572 TCT
1 TCT
39824575 ACTTTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:39828136 original size:7 final size:7
Alignment explanation
Indices: 39828124--39828169 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
39828114 AACCCAATCT
39828124 CTAACCC
1 CTAACCC
39828131 CTAACCC
1 CTAACCC
*
39828138 TTAACCC
1 CTAACCC
* *
39828145 CTGACCT
1 CTAACCC
39828152 CTAACCC
1 CTAACCC
*
39828159 TTAACCC
1 CTAACCC
39828166 CTAA
1 CTAA
39828170 ACCTTATTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.48, G:0.02, T:0.22
Consensus pattern (7 bp):
CTAACCC
Found at i:39828266 original size:7 final size:7
Alignment explanation
Indices: 39828243--39828333 Score: 89
Period size: 7 Copynumber: 13.3 Consensus size: 7
39828233 TAAATTTATA
*
39828243 AACCCTA
1 AACCCTT
39828250 AATCCC-T
1 AA-CCCTT
39828257 AACCCTT
1 AACCCTT
39828264 AACCCTT
1 AACCCTT
*
39828271 AACCCCT
1 AACCCTT
39828278 AA-CC-T
1 AACCCTT
*
39828283 AACCCCT
1 AACCCTT
39828290 AACCCTT
1 AACCCTT
*
39828297 AACCCCT
1 AACCCTT
*
39828304 AACCCCT
1 AACCCTT
39828311 AACCCTT
1 AACCCTT
*
39828318 AACCCAT
1 AACCCTT
*
39828325 AAACCTT
1 AACCCTT
39828332 AA
1 AA
39828334 ATCACATTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
5 3 0.04
6 7 0.10
7 59 0.82
8 3 0.04
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCCTT
Found at i:39828267 original size:21 final size:21
Alignment explanation
Indices: 39828243--39828364 Score: 60
Period size: 21 Copynumber: 5.8 Consensus size: 21
39828233 TAAATTTATA
39828243 AACCCTAAATCCCTAACCCTT
1 AACCCTAAATCCCTAACCCTT
* *
39828264 AACCCTTAACCCCTAA-CC-T
1 AACCCTAAATCCCTAACCCTT
*
39828283 AACCCCT-AA-CCCTTAACCCCT
1 AA-CCCTAAATCCC-TAACCCTT
*
39828304 AACCCCT-AA-CCCTTAACCCATA
1 AA-CCCTAAATCCC-TAACCC-TT
* *
39828326 AACCTTAAATCACATTAACCCTT
1 AACCCTAAATC-C-CTAACCCTT
*
39828349 AAACC-AGAATCCCTAA
1 AACCCTA-AATCCCTAA
39828365 TCCATAATCT
Statistics
Matches: 81, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.04
19 8 0.10
20 8 0.10
21 40 0.49
22 6 0.07
23 9 0.11
24 7 0.09
ACGTcount: A:0.36, C:0.42, G:0.01, T:0.21
Consensus pattern (21 bp):
AACCCTAAATCCCTAACCCTT
Found at i:39828378 original size:14 final size:15
Alignment explanation
Indices: 39828356--39828389 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39828346 CTTAAACCAG
*
39828356 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
39828370 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
39828385 AATCT
1 AATCT
39828390 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:39828844 original size:114 final size:114
Alignment explanation
Indices: 39828623--39829172 Score: 768
Period size: 114 Copynumber: 4.8 Consensus size: 114
39828613 ATTTTAAATC
* * *
39828623 CCTGAGTATTAGTGGCGCTT-CATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTC
1 CCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTCGAAAGCTCAGAAAACGGCGTC
39828687 GTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
66 GTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * ** *
39828736 CTTGAGCATTAGCAGCGCTTACATAAAAACGCCACTAAATCCTTC-TCAGCTCAAAAAACGGCGT
1 CCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCC-TCGAAAGCTCAGAAAACGGCGT
* *
39828800 CGTTGGGCTGAAGTATTCTTGCGGCGCTTTCCCAAAAACACCGCTAAAGA
65 CGTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * **
39828850 CCTGAGCTTTAGCGGCGCCTACATAAAAATGCCACTAAATCCTTC-TCAGCTCAGAAAACGGCGT
1 CCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCC-TCGAAAGCTCAGAAAACGGCGT
* * * * *
39828914 CGTTGGGCTGAAGTATTGTTGTGGTGCTTTCCCATAAACGCCGCTAAAGC
65 CGTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * *
39828964 CCTGAGTATTAGCGGCGCTTTA-ATAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGT
1 CCTGAGCATTAGCGGCGC-TTACATAAAAACGCCACTAAATCCTCGAAAGCTCAGAAAACGGCGT
* * * *
39829028 CGTTGGGCTGAAGAACTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAGGA
65 CGTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
*
39829078 CCTGAGCATTAGCGGCGCTTTCATAAAAACGCCACTAAATCCTCGAAAGC-CAAGAAAACGGCGT
1 CCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTCGAAAGCTC-AGAAAACGGCGT
*
39829142 CGTTGGGCTGAAGTGTTTTTGCGGCGCTTTC
65 CGTTGGGCTGAAGTATTTTTGCGGCGCTTTC
39829173 TGAAATTGAA
Statistics
Matches: 387, Mismatches: 44, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
113 20 0.05
114 364 0.94
115 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (114 bp):
CCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTCGAAAGCTCAGAAAACGGCGTC
GTTGGGCTGAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
Found at i:39832704 original size:27 final size:24
Alignment explanation
Indices: 39832674--39832737 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 24
39832664 ATTTTAAAAA
39832674 TTAAAACAAAAATTAAAAAAAGTATTT
1 TTAAAA-AAAAATT-AAAAAAGTA-TT
*
39832701 TTAAAATTAAAAAATTTAAAAAGTATT
1 TT-AAA--AAAAAATTAAAAAAGTATT
39832728 TTAAAAAAAA
1 TTAAAAAAAA
39832738 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 5 0.15
26 3 0.09
27 6 0.18
28 11 0.33
29 7 0.21
30 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (24 bp):
TTAAAAAAAAATTAAAAAAGTATT
Found at i:39832711 original size:40 final size:39
Alignment explanation
Indices: 39832669--39832799 Score: 135
Period size: 39 Copynumber: 3.3 Consensus size: 39
39832659 AATTTATTTT
*
39832669 AAAAATTAAAACAAAAATTAAAAAAAGTATTTTTAAAATTA
1 AAAAATTAAAA-AAATATTAAAAAAAGTA-TTTTAAAATTA
* *
39832710 AAAAATTTAAAAAGTATTTTAAAAAAA--ATTTTAAAATTTA
1 AAAAA-TTAAAAA-AATATTAAAAAAAGTATTTTAAAA-TTA
**
39832750 AAAAATTAAAAAATATATT-TTAAAAGTATTTTAAAATTA
1 AAAAATTAAAAAA-ATATTAAAAAAAGTATTTTAAAATTA
39832789 AAAAA-TAAAAA
1 AAAAATTAAAAA
39832800 TAAAAATATT
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
38 10 0.13
39 27 0.35
40 18 0.23
41 6 0.08
42 16 0.21
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (39 bp):
AAAAATTAAAAAAATATTAAAAAAAGTATTTTAAAATTA
Found at i:39835748 original size:2 final size:2
Alignment explanation
Indices: 39835741--39835842 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
39835731 ACCTTATCAT
39835741 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39835783 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39835825 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
39835843 CAGTTTTACT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39838968 original size:15 final size:15
Alignment explanation
Indices: 39838943--39838977 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39838933 GACTCTATTT
*
39838943 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
39838957 TAATTAATATTAAGA
1 TAATTAATATTAAGA
39838972 TAATTA
1 TAATTA
39838978 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:39843123 original size:314 final size:313
Alignment explanation
Indices: 39842504--39843135 Score: 1201
Period size: 314 Copynumber: 2.0 Consensus size: 313
39842494 TCTACACTAC
39842504 TAAAGAAATAATCAATAGATTACAAAAGATAAACTAGTTGTTGTTGTTAAAGTTGGTCTTATTAG
1 TAAAGAAATAATCAATAGATTACAAAAGATAAACTAGTTGTTGTTGTTAAAGTTGGTCTTATTAG
39842569 CGTTGGGGTTAATATTTTCTCCCATCACCAACACCACCTAGTTAAAGCACTGTTGAAGTCTAATT
66 CGTTGGGGTTAATATTTTCTCCCATCACCAACACCACCTAGTTAAAGCACTGTTGAAGTCTAATT
*
39842634 TTTGATTGCCGATGTAATGATTAAACTTACCCTACAACTTTAAAAATCCAACTAAAATGTGTAAT
131 TTTGATTGACGATGTAATGATTAAACTTACCCTACAACTTTAAAAATCCAACTAAAATGTGTAAT
39842699 CATGCAGTCTATCATCTCGTCCTTTATCACCATTTCTTTCGTTCCTCTTGGTCAACTTCTTAAAG
196 CATGCAGTCTATCATCTCGTCCTTTATCACCATTTCTTTCGTTCCTCTTGGTCAACTTCTTAAAG
39842764 GCCATTTGTTCTTACAAATCTTTTATTGCAAATGCACCATTAGTTGCAACTTG
261 GCCATTTGTTCTTACAAATCTTTTATTGCAAATGCACCATTAGTTGCAACTTG
39842817 TAAAGAAATAATCAATAGATTACAAAAGATAAACTAGTTGTTGTTGTTAAAGTTGGTCTTATTAG
1 TAAAGAAATAATCAATAGATTACAAAAGATAAACTAGTTGTTGTTGTTAAAGTTGGTCTTATTAG
* *
39842882 CGTTGGGGTTAATCTTTTCTCCCATCACCAGCACCACCTAGTTAAAGCACTGTTGAAGTCTAATT
66 CGTTGGGGTTAATATTTTCTCCCATCACCAACACCACCTAGTTAAAGCACTGTTGAAGTCTAATT
*
39842947 TTTGATTGACGATGTAATGATTAAAACTTACCCTACAACTTTAAAAATTCAACTAAAATGTGTAA
131 TTTGATTGACGATGTAATGATT-AAACTTACCCTACAACTTTAAAAATCCAACTAAAATGTGTAA
*
39843012 TTATGCAGTCTATCATCTCGTCCTTTATCACCATTTCTTTCGTTCCTCTTGGTCAACTTCTTAAA
195 TCATGCAGTCTATCATCTCGTCCTTTATCACCATTTCTTTCGTTCCTCTTGGTCAACTTCTTAAA
*
39843077 GGCCATTTGTTCTTACAAATCTTTTATTGCAAATGCACCATTAGTTGTAACTTG
260 GGCCATTTGTTCTTACAAATCTTTTATTGCAAATGCACCATTAGTTGCAACTTG
39843131 TAAAG
1 TAAAG
39843136 CAATGTTCTT
Statistics
Matches: 312, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
313 149 0.48
314 163 0.52
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (313 bp):
TAAAGAAATAATCAATAGATTACAAAAGATAAACTAGTTGTTGTTGTTAAAGTTGGTCTTATTAG
CGTTGGGGTTAATATTTTCTCCCATCACCAACACCACCTAGTTAAAGCACTGTTGAAGTCTAATT
TTTGATTGACGATGTAATGATTAAACTTACCCTACAACTTTAAAAATCCAACTAAAATGTGTAAT
CATGCAGTCTATCATCTCGTCCTTTATCACCATTTCTTTCGTTCCTCTTGGTCAACTTCTTAAAG
GCCATTTGTTCTTACAAATCTTTTATTGCAAATGCACCATTAGTTGCAACTTG
Found at i:39849907 original size:21 final size:20
Alignment explanation
Indices: 39849878--39849938 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
39849868 ATTTTTTTAG
* *
39849878 TTATT-TTATTAATATTGCTA
1 TTATTATTATTAACATT-ATA
39849898 TTATTATTA-TAACATTATA
1 TTATTATTATTAACATTATA
39849917 -TATTATTATTATACATATATA
1 TTATTATTATTA-ACAT-TATA
39849938 T
1 T
39849939 ACACGTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
20 15 0.44
21 7 0.21
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTATTATTAACATTATA
Found at i:39849939 original size:21 final size:21
Alignment explanation
Indices: 39849896--39849939 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
39849886 TTAATATTGC
39849896 TATTATTATTATAACATTATA
1 TATTATTATTATAACATTATA
39849917 TATTATTATTAT-ACATATATA
1 TATTATTATTATAACAT-TATA
39849938 TA
1 TA
39849940 CACGTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATTATTATAACATTATA
Found at i:39850158 original size:2 final size:2
Alignment explanation
Indices: 39850151--39850186 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39850141 CACATTTTTA
*
39850151 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39850187 GCACTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39853250 original size:12 final size:12
Alignment explanation
Indices: 39853233--39853257 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39853223 ATATCAACTT
39853233 TAATTTAATATG
1 TAATTTAATATG
39853245 TAATTTAATATG
1 TAATTTAATATG
39853257 T
1 T
39853258 GAAATTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAATTTAATATG
Found at i:39853704 original size:3 final size:3
Alignment explanation
Indices: 39853688--39853721 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
39853678 CCACCGTTAG
* *
39853688 TAC TAC AAC AAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
39853722 TATTATTATT
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:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (3 bp):
TAC
Found at i:39853727 original size:3 final size:3
Alignment explanation
Indices: 39853721--39853770 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
39853711 CTACTACTAC
*
39853721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39853769 TT
1 TT
39853771 TATGTGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39856921 original size:24 final size:24
Alignment explanation
Indices: 39856894--39856940 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39856884 AAACCTAATT
39856894 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
*
39856918 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTCAAATATATTAT
39856941 ATACTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:39861361 original size:24 final size:24
Alignment explanation
Indices: 39861319--39861370 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
39861309 AATCAAAGTC
* *
39861319 AAATATATTGTGCTAATAAA-AGCT
1 AAATATATTATACTAATAAATA-CT
*
39861343 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
39861367 AAAT
1 AAAT
39861371 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:39864083 original size:33 final size:34
Alignment explanation
Indices: 39864022--39864091 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
39864012 AAATTTAATA
*
39864022 ATACAATAATTAATATTATGTACTTATCACAAATG
1 ATACAATAACTAATATTA-GTACTTATCACAAATG
* *
39864057 ATACGATAACTAATATTA-TACTTATCATAAATG
1 ATACAATAACTAATATTAGTACTTATCACAAATG
39864090 AT
1 AT
39864092 TACATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 16 0.50
35 16 0.50
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (34 bp):
ATACAATAACTAATATTAGTACTTATCACAAATG
Found at i:39868781 original size:67 final size:67
Alignment explanation
Indices: 39868673--39868831 Score: 257
Period size: 67 Copynumber: 2.4 Consensus size: 67
39868663 AGAGGAAAAG
* *
39868673 ATTGGTATTTTTCATCTGCAATTTATTTGGTTAGAAATCGATTAACAGGGTTAAGGGTTATA-AA
1 ATTGGTATTTTTCATCTGCAATTTGTTTGGTTAGAAATCGATTAACAAGGTTAAGGGTTA-AGAA
39868737 TCA
65 TCA
39868740 ATTGGTATTTTTCATCTGCAATTTGTTTGGTTAGAAATCGATTAACAAGGTTAAGGGTTAAGAAT
1 ATTGGTATTTTTCATCTGCAATTTGTTTGGTTAGAAATCGATTAACAAGGTTAAGGGTTAAGAAT
*
39868805 CG
66 CA
* *
39868807 ATTGGTATTTTTCATTTACAATTTG
1 ATTGGTATTTTTCATCTGCAATTTG
39868832 CATTTCACTT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
66 1 0.01
67 85 0.99
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (67 bp):
ATTGGTATTTTTCATCTGCAATTTGTTTGGTTAGAAATCGATTAACAAGGTTAAGGGTTAAGAAT
CA
Found at i:39870346 original size:2 final size:2
Alignment explanation
Indices: 39870339--39870373 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39870329 AAGATAAAAT
39870339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39870374 TATCTCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39878968 original size:34 final size:33
Alignment explanation
Indices: 39878896--39878986 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 33
39878886 AGGTTTTTTT
**
39878896 TAAATTAATTAAATTAGGTTTTTGGGTTTTAAA
1 TAAATTAATTAAATTAGGTTTAGGGGTTTTAAA
39878929 TAAATTAATTAAATTAGGATTTAGGGGTTTTTAAA
1 TAAATTAATTAAATTAGG-TTTAGGGG-TTTTAAA
39878964 -AAATTAATTAAATTATGGTTTAG
1 TAAATTAATTAAATTA-GGTTTAG
39878987 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
33 18 0.34
34 26 0.49
35 9 0.17
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (33 bp):
TAAATTAATTAAATTAGGTTTAGGGGTTTTAAA
Found at i:39879443 original size:126 final size:126
Alignment explanation
Indices: 39879048--39879443 Score: 494
Period size: 126 Copynumber: 3.1 Consensus size: 126
39879038 AACTTTGGTT
*
39879048 TTTTTTCTACAATAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCTGAA-AAGATAATGTAAA
1 TTTTTTCTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAA-ATAATGT-AA
* * *
39879112 AAACGCTTCAAGCAGTATGCACTTTCAGCAAAATTACTGAAAAAAGCTCCCACGTGTACGCT-
64 AAACTCTTCAAGCAGGATGCACTTTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* ** * * *
39879174 TTTTTTCTAAAATAGTTATTGAAAAAGTAATTTTGAGAAGACAGTTCTGAACAAATATTGTAAAA
1 TTTTTTCTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAATGTAAAA
* * * * * * *
39879239 AATGCCTCAACCAGGATGCACTGTCAGCAAAATTACTGAAAAAATCACCCACGTGGATGCTC
66 ACT-CTTCAAGCAGGATGCACTTTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * *
39879301 -TTTTTCTACAGTAGTTCCCGAAAAAATAATTTTGAAAAGATGGTTCTGAACAAATAATGTCAAT
1 TTTTTTCTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAATGT-AAA
* * *
39879365 AACTCTTTAAGCAGGATGCACTTTCAACAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
65 AACTCTTCAAGCAGGATGCACTTTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
*
39879427 TTTTTT-TACAGTAGTTC
1 TTTTTTCTACAATAGTTC
39879444 TTGTTTGGCC
Statistics
Matches: 228, Mismatches: 37, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
125 5 0.02
126 211 0.93
127 12 0.05
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (126 bp):
TTTTTTCTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAATGTAAAA
ACTCTTCAAGCAGGATGCACTTTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:39885075 original size:24 final size:24
Alignment explanation
Indices: 39885019--39885075 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
39885009 AAGAACTTCT
39885019 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAATAA
* *
39885043 ATTACTATT-AAAATATTTAAAATAA
1 ATT-TTATTAAAAATA-TAAAAATAA
*
39885068 CTTTTATT
1 ATTTTATT
39885076 TTATTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAATAA
Found at i:39885145 original size:89 final size:90
Alignment explanation
Indices: 39885029--39885210 Score: 330
Period size: 89 Copynumber: 2.0 Consensus size: 90
39885019 ATTTTATTAA
*
39885029 AAATATAAAAATAAATTACTATTAAAATATTTAAAATAACTTTTATTTTATTAAATGAAACAATA
1 AAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAACAATA
*
39885094 TAAAAATAGTTTGTACAAATATATT
66 TAAAAACAGTTTGTACAAATATATT
*
39885119 AAATATATAAA-AAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAACAATA
1 AAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAACAATA
39885183 TAAAAACAGTTTGTACAAATATATT
66 TAAAAACAGTTTGTACAAATATATT
39885208 AAA
1 AAA
39885211 AAATCAATGT
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 79 0.89
90 10 0.11
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (90 bp):
AAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAACAATA
TAAAAACAGTTTGTACAAATATATT
Found at i:39885600 original size:18 final size:18
Alignment explanation
Indices: 39885574--39885616 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39885564 GACTGGGAAA
* * *
39885574 AGGAAACATATAAGGGTT
1 AGGATACATATAAGAGCT
39885592 AGGATACATATAAGAGCT
1 AGGATACATATAAGAGCT
39885610 AGGATAC
1 AGGATAC
39885617 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGAGCT
Found at i:39891435 original size:18 final size:18
Alignment explanation
Indices: 39891382--39891435 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
39891372 ATTCACCTAA
*
39891382 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCAAACCCAATT
* *
39891401 ATCCAACCCAACCCAATT
1 ACCCAACCAAACCCAATT
*
39891419 ACCCAACCTAACCCAAT
1 ACCCAACCAAACCCAAT
39891436 CATAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.41, C:0.44, G:0.02, T:0.13
Consensus pattern (18 bp):
ACCCAACCAAACCCAATT
Found at i:39891467 original size:6 final size:6
Alignment explanation
Indices: 39891456--39891509 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
39891446 ACAAATAATT
* * *
39891456 TAAAAA TAAAAA TAAAATTC TAAAAC TAAAAC TAAAAC TAAAAT TAAAAC
1 TAAAAC TAAAAC TAAAA--C TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC
39891506 TAAA
1 TAAA
39891510 GTCTAAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 38 0.88
8 5 0.12
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAC
Found at i:39891498 original size:18 final size:19
Alignment explanation
Indices: 39891456--39891517 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
39891446 ACAAATAATT
*
39891456 TAAAAATAAAAATAAAATTC
1 TAAAAATAAAACTAAAA-TC
*
39891476 TAAAACTAAAACTAAAA-C
1 TAAAAATAAAACTAAAATC
* *
39891494 TAAAATTAAAACTAAAGTC
1 TAAAAATAAAACTAAAATC
39891513 TAAAA
1 TAAAA
39891518 GTCTAAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 16 0.43
19 6 0.16
20 15 0.41
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAATAAAACTAAAATC
Found at i:39892432 original size:57 final size:57
Alignment explanation
Indices: 39892256--39892503 Score: 297
Period size: 57 Copynumber: 4.4 Consensus size: 57
39892246 ACTGTTTGCT
* *
39892256 TGCTGTCATAAATTGAATTAAAGCTGTTGTTTGAGTGTTTCAAATTGAGCATTTTCA
1 TGCTGTCATAAATTGAATTAAAGCTGCTGTTTTAGTGTTTCAAATTGAGCATTTTCA
* * * * *
39892313 TACTGTCTTAAATTGAA-TCAAGCTACTATTTTAGTGTTTCAAATTGAGCATTTTCA
1 TGCTGTCATAAATTGAATTAAAGCTGCTGTTTTAGTGTTTCAAATTGAGCATTTTCA
* * * *
39892369 TACTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGCATTTTCA
1 TGCTGTCATAAATTGAATTAAAGCTGCTGTTTTAGTGTTTCAAATTGAGCATTTTCA
* * * *
39892426 TGCTGTCTTAAATTAAATT-AAGCTGCTG-TTTAATGTTTCAAATTGAGTATTATT-A
1 TGCTGTCATAAATTGAATTAAAGCTGCTGTTTTAGTGTTTCAAATTGAGCATT-TTCA
* * *
39892481 TGTTGTCCTAAATTAAATTAAAG
1 TGCTGTCATAAATTGAATTAAAG
39892504 TGTTGCTTCA
Statistics
Matches: 164, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
55 38 0.23
56 62 0.38
57 64 0.39
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (57 bp):
TGCTGTCATAAATTGAATTAAAGCTGCTGTTTTAGTGTTTCAAATTGAGCATTTTCA
Found at i:39892537 original size:56 final size:56
Alignment explanation
Indices: 39892256--39892540 Score: 240
Period size: 56 Copynumber: 5.1 Consensus size: 56
39892246 ACTGTTTGCT
* * *
39892256 TGCTGTCATAAATTGAATTAAAGCTGTTGTTTGAGTGTTTCAAATTGAGCATT-TTCA
1 TGCTGTCATAAATTAAATTAAAGCTGCTGTTT-AGTGTATCAAATTGAGCATTATT-A
* * * * * * *
39892313 TACTGTCTTAAATTGAA-TCAAGCTACTATTTTAGTGTTTCAAATTGAGCATT-TTCA
1 TGCTGTCATAAATTAAATTAAAGCTGCT-GTTTAGTGTATCAAATTGAGCATTATT-A
* * * *
39892369 TACTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGCATT-TTCA
1 TGCTGTCATAAATTAAATTAAAGCTGCTG-TTTAGTGTATCAAATTGAGCATTATT-A
* * * *
39892426 TGCTGTCTTAAATTAAATT-AAGCTGCTGTTTAATGTTTCAAATTGAGTATTATTA
1 TGCTGTCATAAATTAAATTAAAGCTGCTGTTTAGTGTATCAAATTGAGCATTATTA
* * * * * * *
39892481 TGTTGTCCTAAATTAAATTAAAG-TGTTGCTTCAGTGTCTCAAAATAAGCATTATTA
1 TGCTGTCATAAATTAAATTAAAGCTGCTG-TTTAGTGTATCAAATTGAGCATTATTA
39892537 TGCT
1 TGCT
39892541 ATTGAAAAAT
Statistics
Matches: 191, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
55 42 0.22
56 83 0.43
57 66 0.35
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (56 bp):
TGCTGTCATAAATTAAATTAAAGCTGCTGTTTAGTGTATCAAATTGAGCATTATTA
Found at i:39899785 original size:18 final size:17
Alignment explanation
Indices: 39899752--39899790 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39899742 TTTTATAAAT
39899752 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39899770 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39899787 TGTG
1 TGTG
39899791 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39900042 original size:23 final size:23
Alignment explanation
Indices: 39900016--39900160 Score: 236
Period size: 23 Copynumber: 6.3 Consensus size: 23
39900006 AGTGTTATTG
39900016 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39900039 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
39900062 TTCAGTGGTGGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
39900085 TTCAGTGGTGGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39900108 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39900131 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39900154 ATCAGTG
1 ATCAGTG
39900161 TGGCACTTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 114 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39900357 original size:36 final size:38
Alignment explanation
Indices: 39900290--39900361 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
39900280 ATGTGTGGAA
* *
39900290 TTGAATTGAATATTGACTTGAAAATGGAAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
39900328 TTGAATTGAAT-GTGA-TT-AAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAA-TGAAAAAGTGAA
39900362 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 4 0.13
36 13 0.42
37 3 0.10
38 11 0.35
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:39901387 original size:2 final size:2
Alignment explanation
Indices: 39901310--39901369 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
39901300 ATTCTGATAA
39901310 AT AT AT AT AT 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 AT AT AT AT AT
39901352 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
39901370 GTGACAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39902287 original size:75 final size:76
Alignment explanation
Indices: 39902190--39902339 Score: 230
Period size: 77 Copynumber: 2.0 Consensus size: 76
39902180 AAAAATCCTC
* * * *
39902190 AAACTTTTTTAAAAAAGCAATTAAGTCCCT-TTTTTTTTGCACTCATTTGGGCACTTGAACTTTC
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTTGCACTCAATTGGGCACTTGAACTTTC
39902254 AAAATGCATTG
66 AAAATGCATTG
* *
39902265 AAACCTTTTCAAAAAAGTAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGTACTTGAACTTT
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTA-TTTTTTTTGCACTCAATTGGGCACTTGAACTTT
39902330 CAAAATGCAT
65 CAAAATGCAT
39902340 AAAAAAGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 26 0.39
77 41 0.61
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (76 bp):
AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTTGCACTCAATTGGGCACTTGAACTTTC
AAAATGCATTG
Found at i:39902425 original size:9 final size:11
Alignment explanation
Indices: 39902393--39902422 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39902383 AGCTTTTATT
*
39902393 AAAAATTAGAA
1 AAAAATTATAA
39902404 AAAAATTATAA
1 AAAAATTATAA
39902415 AAAAATTA
1 AAAAATTA
39902423 AAATCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:39913003 original size:23 final size:23
Alignment explanation
Indices: 39912975--39913029 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
39912965 ATTTGTTAGA
39912975 AAGCATTATTGTTTAATTTGGCG
1 AAGCATTATTGTTTAATTTGGCG
* *
39912998 AAGCATGATTTTTGTTTAATTTTGCG
1 AAGC---ATTATTGTTTAATTTGGCG
39913024 AAGCAT
1 AAGCAT
39913030 GATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.22
26 21 0.78
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (23 bp):
AAGCATTATTGTTTAATTTGGCG
Found at i:39913014 original size:26 final size:26
Alignment explanation
Indices: 39912983--39913033 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39912973 GAAAGCATTA
39912983 TTGTTTAATTTGGCGAAGCATGATTT
1 TTGTTTAATTTGGCGAAGCATGATTT
*
39913009 TTGTTTAATTTTGCGAAGCATGATT
1 TTGTTTAATTTGGCGAAGCATGATT
39913034 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.47
Consensus pattern (26 bp):
TTGTTTAATTTGGCGAAGCATGATTT
Found at i:39919096 original size:6 final size:6
Alignment explanation
Indices: 39919085--39919119 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
39919075 GGTTTTCTCC
39919085 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
39919120 TCATTTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:39919129 original size:63 final size:64
Alignment explanation
Indices: 39919034--39919162 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
39919024 GAACAAAATT
*
39919034 AAATAAAAATGGAGAAATAGGAAATATTTGGAAAT-TATGAAGGTTTTCTCCAAAATG-AAAATG
1 AAATAAAAATGGAGAAATA-GAAATATTTGGAAATGAATG-AGGTTTTCTCCAAAATGTAAAATG
39919097 A
64 A
* * *
39919098 AAATGAAAATGGAGAAAT-GAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGTGAAATGA
1 AAATAAAAATGGAGAAATAGAAAT-ATTTGGAAATGAATGAGGTTTTCTCCAAAATGTAAAATGA
39919162 A
1 A
39919163 TTCATTTGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
62 5 0.09
63 26 0.45
64 27 0.47
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (64 bp):
AAATAAAAATGGAGAAATAGAAATATTTGGAAATGAATGAGGTTTTCTCCAAAATGTAAAATGA
Found at i:39919159 original size:44 final size:44
Alignment explanation
Indices: 39919111--39919197 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
39919101 TGAAAATGGA
** * *
39919111 GAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGT
1 GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATGT
*
39919155 GAAATGAATTCATTTGGAAATGAATAAGGATTTCTCAAAAATG
1 GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATG
39919198 ATCGGAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (44 bp):
GAAATGAAATCATTTGGAAATGAATAAGGATTTCTCAAAAATGT
Found at i:39921271 original size:25 final size:25
Alignment explanation
Indices: 39921182--39921267 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
39921172 CACAGCTTTT
* *
39921182 ATGAGCATCCCAATATTTGGCTCTC
1 ATGAGCTTCCCAATAATTGGCTCTC
* * *
39921207 ACGAGCTTCTCAATTAA-TGGCTCTT
1 ATGAGCTTCCCAA-TAATTGGCTCTC
* * *
39921232 ATGAGCTTCTCGATAATTGGCTCGC
1 ATGAGCTTCCCAATAATTGGCTCTC
39921257 ATGAGCTTCCC
1 ATGAGCTTCCC
39921268 GATATACAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.06
25 44 0.90
26 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCAATAATTGGCTCTC
Found at i:39924992 original size:21 final size:21
Alignment explanation
Indices: 39924948--39925041 Score: 127
Period size: 21 Copynumber: 4.4 Consensus size: 21
39924938 TTATATATTA
* * *
39924948 AATATATATTT-AATATACAT
1 AATATATATTTGATTAAAAAT
39924968 AATATATATTTGATTAAAAAT
1 AATATATATTTGATTAAAAAT
39924989 AATATATATTTGATTAAAAAT
1 AATATATATTTGATTAAAAAT
39925010 AAAATATATATTTGATTAAAAAT
1 --AATATATATTTGATTAAAAAT
*
39925033 AAAATATAT
1 AATATATAT
39925042 ATTTAATATA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
20 11 0.16
21 35 0.52
23 21 0.31
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (21 bp):
AATATATATTTGATTAAAAAT
Found at i:39925015 original size:23 final size:23
Alignment explanation
Indices: 39924968--39925045 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
39924958 TAATATACAT
39924968 AATATATATTTGATTAAAAAT--
1 AATATATATTTGATTAAAAATAA
39924989 AATATATATTTGATTAAAAATAA
1 AATATATATTTGATTAAAAATAA
39925012 AATATATATTTGATTAAAAATAA
1 AATATATATTTGATTAAAAATAA
39925035 AATATATATTT
1 AATATATATTT
39925046 AATATATAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.38
23 34 0.62
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AATATATATTTGATTAAAAATAA
Found at i:39927542 original size:15 final size:15
Alignment explanation
Indices: 39927522--39927551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39927512 TTCACTATTA
*
39927522 TGTCTTTTGTGTTTT
1 TGTCTTTTATGTTTT
39927537 TGTCTTTTATGTTTT
1 TGTCTTTTATGTTTT
39927552 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.07, G:0.17, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATGTTTT
Found at i:39931577 original size:18 final size:18
Alignment explanation
Indices: 39931536--39931578 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39931526 TCATTGCAAT
39931536 ATATATAAAAATAATTTA
1 ATATATAAAAATAATTTA
* *
39931554 AAATATAAAAAT-TTATTA
1 ATATATAAAAATAAT-TTA
39931572 ATATATA
1 ATATATA
39931579 TTAATATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATAAAAATAATTTA
Found at i:39932023 original size:11 final size:11
Alignment explanation
Indices: 39932007--39932034 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39931997 GTCGCCTCTT
39932007 CCTTCGTTCTA
1 CCTTCGTTCTA
39932018 CCTTCGTTCTA
1 CCTTCGTTCTA
39932029 CCTTCG
1 CCTTCG
39932035 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:39935556 original size:18 final size:17
Alignment explanation
Indices: 39935528--39935562 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39935518 ATTATTAAGA
*
39935528 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39935545 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39935563 TTAATGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39935712 original size:18 final size:17
Alignment explanation
Indices: 39935684--39935718 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39935674 ATTATTAAGA
*
39935684 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39935701 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39935719 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39935800 original size:156 final size:157
Alignment explanation
Indices: 39935516--39935831 Score: 562
Period size: 156 Copynumber: 2.0 Consensus size: 157
39935506 ATAAGAATAT
*
39935516 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATGATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
39935581 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
39935646 TAATAATTT-ACCAAACAAATTTCTGC
131 TAATAATTTAACAAAACAAATTTATGC
39935672 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
39935737 AAATATGTTTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
39935802 TAATCATTTAACAAAACAAATTTATGC
131 TAATAATTTAACAAAACAAATTTATGC
39935829 TAA
1 TAA
39935832 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 134 0.88
157 18 0.12
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTAACAAAACAAATTTATGC
Found at i:39935962 original size:45 final size:43
Alignment explanation
Indices: 39935864--39935987 Score: 116
Period size: 45 Copynumber: 2.9 Consensus size: 43
39935854 TTTTCCATTA
39935864 TACTATTACACCTCTATT-C---CATTCAACCAAACGCAAGAT
1 TACTATTACACCTCTATTCCATACATTCAACCAAACGCAAGAT
* **
39935903 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAG-TTGATT
1 TACTATTACACCTCTATTCCA-TACATTCAACCAAAC-GCAAGA-T
* *
39935948 TACTATTACACCTCTAATCCAATACA-CCGAACCAAACGCA
1 TACTATTACACCTCTATTCC-ATACATTC-AACCAAACGCA
39935988 CCCTAACTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
39 17 0.25
40 1 0.01
44 17 0.25
45 32 0.47
46 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (43 bp):
TACTATTACACCTCTATTCCATACATTCAACCAAACGCAAGAT
Found at i:39943389 original size:27 final size:27
Alignment explanation
Indices: 39943324--39943382 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
39943314 AGCAGATCAC
* *
39943324 ATATAACCCTATCTGTATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
39943351 ATATTACCCTATCTATATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
39943378 ATATT
1 ATATT
39943383 CTCCTATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATTACCCTATCTATATAGCGTGTAA
Found at i:39950812 original size:2 final size:2
Alignment explanation
Indices: 39950807--39950838 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
39950797 ATGTATGTAT
39950807 AC AC AC AC AC AC AC AC AC AC ATC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC A-C AC AC AC AC A
39950839 TATATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:39952883 original size:39 final size:39
Alignment explanation
Indices: 39952759--39952912 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 39
39952749 AGCGGCATTT
* *
39952759 TTAGCGGCGTTTGT-ATAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGTTT-TCA-AGAAAACGCCGC-AAAAAATGAGCA
* * * * *
39952800 TTAGAGGCGCTTT-ACGTAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTTTCAAG-AAAACGCCGCAAAAAAT-GAGCA
* *
39952840 TTAGCGGCGTTTCCAAGAAAGCGCCGCAAAAAATGAGCA
1 TTAGCGGCGTTTTCAAGAAAACGCCGCAAAAAATGAGCA
39952879 TTAGCGGCGTTTTTCTAA-AAAACGCCGCAAAAAA
1 TTAGCGGCG-TTTTC-AAGAAAACGCCGCAAAAAA
39952913 CCTAAGCCCA
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
39 18 0.20
40 60 0.65
41 14 0.15
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTTCAAGAAAACGCCGCAAAAAATGAGCA
Found at i:39953022 original size:41 final size:41
Alignment explanation
Indices: 39952951--39953228 Score: 342
Period size: 41 Copynumber: 6.8 Consensus size: 41
39952941 CTTTCGAGGA
* * *
39952951 TTTAGCGGCG-TTTTTGAAAAAGTGTCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGTC
* * * *
39952992 TTTAGCGGCGCTTTTCCCAAAACGCAGCTAATGCTCTGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * * * *
39953033 TTCAGCGGCGCTTTTTTACAAGCACCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * * *
39953074 TTTAGCGGCGCTTTGTCAAAATCGCCGCTAAAGCTTGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
* * *
39953115 TTCAGCGGCGCTTTTTCAAAAAGCGCCGCTAATGCTTGGGTT
1 TTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGTC
*
39953157 TTTAGCGGTGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
*
39953198 TTTAGCGACGCTTTTTCAAAAACGCCGCTAA
1 TTTAGCGGCGCTTTTTCAAAAACGCCGCTAA
39953229 AGCTTTAGCG
Statistics
Matches: 200, Mismatches: 35, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
41 155 0.77
42 45 0.22
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTC
Found at i:39953194 original size:124 final size:123
Alignment explanation
Indices: 39952976--39953233 Score: 347
Period size: 124 Copynumber: 2.1 Consensus size: 123
39952966 GAAAAAGTGT
* * * *
39952976 CGCTAATGCTCGGGTCTTTAGCGGCGCTTTTCCCAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
1 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
* * * * *
39953041 CGCTTTTTTACAAGCACCGCTAATGCTCGGGTCTTTAGCGGCGCTTTGTCAAAATCGC
66 CGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
* * * *
39953099 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTTCAAAAAGCGCCGCTAATGCT-TGGGTTTTTAGC
1 CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAA-CGCAGCTAATGCTCT-GGTCTTCAGC
* * *
39953163 GGTGCTTTTTCAAAAACGCCGCTAATGCTCGGGTCTTTAGCGACGCTTTTTCAAAAACGC
64 GGCGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
39953223 CGCTAAAGCTT
1 CGCTAAAGCTT
39953234 TAGCGGCGTT
Statistics
Matches: 117, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 34 0.29
124 83 0.71
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (123 bp):
CGCTAAAGCTTGGGTCTTCAGCGGCGCTTTTCCAAAAACGCAGCTAATGCTCTGGTCTTCAGCGG
CGCTTTTTCAAAAACACCGCTAATGCTCGGGTCTTTAGCGACGCTTTGTCAAAAACGC
Found at i:39953252 original size:33 final size:35
Alignment explanation
Indices: 39953197--39953262 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
39953187 ATGCTCGGGT
*
39953197 CTTTAGCGACGCTTTTTCAAAAA-CGCCGCTAAAG
1 CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAAAG
* *
39953231 CTTTAGCGGCG-TTTTTGAAAAAGCACCGCTAA
1 CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAA
39953263 TCCCAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (35 bp):
CTTTAGCGACGCTTTTTCAAAAAGCACCGCTAAAG
Found at i:39955352 original size:43 final size:42
Alignment explanation
Indices: 39955298--39955648 Score: 441
Period size: 43 Copynumber: 8.2 Consensus size: 42
39955288 TTTTCGTGAC
* *
39955298 CTTTAGTGGCGTTTTTAGGGAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
** * ** *
39955341 CACTCGCGGCGTTTGTCGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
* *
39955384 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* *
39955427 TTTTAGCGGCGTTTGTTGGCAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* * *
39955470 TTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTCGT
1 CTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGGT
* *
39955513 CTTTAGCGGCGTTCGTGGGGAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCCTGGT
*
39955556 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGT
* **
39955599 CTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTAATGGT
1 CTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGGT
39955642 CTTTAGC
1 CTTTAGC
39955649 AGTGTTTTTT
Statistics
Matches: 272, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
42 6 0.02
43 261 0.96
44 5 0.02
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGT
Found at i:39955410 original size:86 final size:86
Alignment explanation
Indices: 39955298--39955648 Score: 497
Period size: 86 Copynumber: 4.1 Consensus size: 86
39955288 TTTTCGTGAC
* * ** * * *
39955298 CTTTAGTGGCGTTT-TTAGGGAAAGCGCCGCTAAAGGTCCTGGTCACTCGCGGCGTTTGTCGAAA
1 CTTTAGCGGCGTTTGTT-GGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
39955362 AAGCGCCGCTAAAGGTCTTGGT
65 AAGCGCCGCTAAAGGTCTTGGT
* * * *
39955384 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGTTTTTAGCGGCGTTTGTTGGCAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
*
39955449 AGCGCCGCTAAAGGTCCTGGT
66 AGCGCCGCTAAAGGTCTTGGT
* * * * * *
39955470 TTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCCTCGTCTTTAGCGGCGTTCGTGGGGAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
39955535 AGCGCCGCTAAAGGTCTTGGT
66 AGCGCCGCTAAAGGTCTTGGT
39955556 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* **
39955621 AGCGCTGCTAAAGGTAATGGT
66 AGCGCCGCTAAAGGTCTTGGT
39955642 CTTTAGC
1 CTTTAGC
39955649 AGTGTTTTTT
Statistics
Matches: 234, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 232 0.99
87 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (86 bp):
CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCGCTAAAGGTCTTGGT
Found at i:39955493 original size:129 final size:129
Alignment explanation
Indices: 39955298--39955648 Score: 515
Period size: 129 Copynumber: 2.7 Consensus size: 129
39955288 TTTTCGTGAC
* * ** * * *
39955298 CTTTAGTGGCGTTT-TTAGGGAAAGCGCCGCTAAAGGTCCTGGTCACTCGCGGCGTTTGTCGAAA
1 CTTTAGCGGCGTTTGTT-GGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
* * *
39955362 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGGT
65 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * *
39955427 TTTTAGCGGCGTTTGTTGGCAAAGCGCCGCTAAAGGTCCTGGTTTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* * * *
39955492 AGCGTCGCTAAAGGTCCTCGTCTTTAGCGGCGTTCGTGGGGAAAGCGCCGCTAAAGGTCTTGGT
66 AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
39955556 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
* *
39955621 AGCGCTGCTAAAGGTAATGGTCTTTAGC
66 AGCGCCGCTAAAGGTCATGGTCTTTAGC
39955649 AGTGTTTTTT
Statistics
Matches: 198, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 196 0.99
130 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:39955728 original size:22 final size:22
Alignment explanation
Indices: 39955700--39955742 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39955690 TAGCGGCGCT
*
39955700 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
39955722 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
39955743 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:39957456 original size:61 final size:61
Alignment explanation
Indices: 39957353--39957471 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
39957343 TATTCCAGAT
* * *
39957353 GATTTATTTATACCATAAATATATCAGAATCTCCATAGTGTAAGACAACTATTAGAAAGGA
1 GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAAGGA
* ***
39957414 GATTTATTTGTACCATAAAAATATCAGAATCTTTGTACTGTAAGACAACTACTAGAAA
1 GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAA
39957472 AGAGTTATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (61 bp):
GATTTATTTATACCATAAAAATATCAGAATCTCCATACTGTAAGACAACTACTAGAAAGGA
Found at i:39961040 original size:3 final size:3
Alignment explanation
Indices: 39961032--39961106 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
39961022 TTATATATAT
39961032 ATA ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
39961075 ATA AT- ATA AT- ATA AT- ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39961107 TCAAAACATA
Statistics
Matches: 61, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
2 20 0.33
3 38 0.62
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:39961048 original size:5 final size:5
Alignment explanation
Indices: 39961024--39961107 Score: 123
Period size: 5 Copynumber: 15.8 Consensus size: 5
39961014 TTCTTTTGTT
39961024 ATATA TATATA ATAATA ATATA ATATA ATATA ATATA ATATA ATATA TATAATA
1 ATATA -ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA
39961078 ATATA ATATA ATATA ATAATA ATATA ATAT
1 ATATA ATATA ATATA AT-ATA ATATA ATAT
39961108 CAAAACATAC
Statistics
Matches: 74, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
5 52 0.70
6 19 0.26
7 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:39961076 original size:40 final size:43
Alignment explanation
Indices: 39961023--39961107 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
39961013 TTTCTTTTGT
39961023 TATATATATATAATAATAATATAATATAAT-ATAATATAATATAA
1 TATATATA-ATAAT-ATAATATAATATAATAATAATATAATATAA
39961067 TATATATAATAATATAATATAATATAATAATAATATAATAT
1 TATATATAATAATATAATATAATATAATAATAATATAATAT
39961108 CAAAACATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 15 0.38
43 17 0.43
44 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (43 bp):
TATATATAATAATATAATATAATATAATAATAATATAATATAA
Found at i:39971177 original size:25 final size:25
Alignment explanation
Indices: 39971122--39971179 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
39971112 CTCCCAACTG
* *
39971122 ATGTTGAAAAATTTTCAAATCTGAA
1 ATGTTTAAAAATTTCCAAATCTGAA
* *
39971147 ATGTTTAAAAATTTCCAAATTTGGA
1 ATGTTTAAAAATTTCCAAATCTGAA
39971172 ATGTTTAA
1 ATGTTTAA
39971180 TTAGCATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (25 bp):
ATGTTTAAAAATTTCCAAATCTGAA
Found at i:39971732 original size:21 final size:24
Alignment explanation
Indices: 39971699--39971748 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
39971689 CTACGAGCTT
39971699 TTTTAGAATTATTT-AATT-T-AA
1 TTTTAGAATTATTTCAATTATAAA
39971720 TTTT-GAATATATTTCAATTATAAA
1 TTTTAGAAT-TATTTCAATTATAAA
39971744 TTTTA
1 TTTTA
39971749 TTACACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 4 0.17
23 1 0.04
24 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTAGAATTATTTCAATTATAAA
Found at i:39974685 original size:31 final size:31
Alignment explanation
Indices: 39974647--39974782 Score: 117
Period size: 31 Copynumber: 4.5 Consensus size: 31
39974637 TTCTTGGTCC
39974647 AATTTGGTACAC-AAACTTGACACTTTTTCCT
1 AATTTGGTAC-CTAAACTTGACACTTTTTCCT
*
39974678 AATTTGGTACCTAAACTTGACACTTTTTCTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
* * *
39974709 AAGTTGGTACTTAATA-TT-----TTTTGGGATAC-
1 AATTTGGTACCTAA-ACTTGACACTTTT----TCCT
*
39974738 AATTTGGTACCTAAACTTGACTCTTTTTCCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
39974769 AATTTGGTACCTAA
1 AATTTGGTACCTAA
39974783 TCTTTTTTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
26 4 0.05
28 1 0.01
29 14 0.17
30 4 0.05
31 56 0.67
32 1 0.01
34 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCT
Found at i:39974742 original size:60 final size:60
Alignment explanation
Indices: 39974678--39974790 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
39974668 ACTTTTTCCT
* *
39974678 AATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTTAATATTTTTTGGGATAC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATAC
* * *
39974738 AATTTGGTACCTAAACTTGACTCTTTTTCCTAATTTGGTACCTAATCTTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTT
39974791 TTTGTTCGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (60 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATAC
Found at i:39975748 original size:20 final size:23
Alignment explanation
Indices: 39975689--39975748 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
39975679 ATCTTAGAAA
* *
39975689 TAAATATAATTTATTAAAAGTAT
1 TAAAAATATTTTATTAAAAGTAT
*
39975712 TAAAAATATGTTA--AAAA-TAT
1 TAAAAATATTTTATTAAAAGTAT
39975732 T-AAAAT-TTTTATTAAAA
1 TAAAAATATTTTATTAAAA
39975749 CAAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 4 0.13
19 5 0.16
20 8 0.26
21 4 0.13
23 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAAAATATTTTATTAAAAGTAT
Found at i:39982027 original size:20 final size:20
Alignment explanation
Indices: 39981983--39982028 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
39981973 CCCTTGATTT
*
39981983 TTTTATGAAATATATAGCATA
1 TTTTATGAAATAAATA-CATA
39982004 -TTTATGTAAATAAATA-ATA
1 TTTTATG-AAATAAATACATA
39982023 TTTTAT
1 TTTTAT
39982029 AAAAGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTATGAAATAAATACATA
Found at i:39989257 original size:38 final size:38
Alignment explanation
Indices: 39989215--39989291 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
39989205 AAAATGGTTT
*
39989215 AAAAATTAAAA-ATTAAAAAATGTTCTTAAAAATTCAAA
1 AAAAATTAAAATATTAAAAAAT-ATCTTAAAAATTCAAA
* * *
39989253 AAAAATTAAAATTTTTAAAAATATCTTCAAAATTCAAA
1 AAAAATTAAAATATTAAAAAATATCTTAAAAATTCAAA
39989291 A
1 A
39989292 TATAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (38 bp):
AAAAATTAAAATATTAAAAAATATCTTAAAAATTCAAA
Found at i:39992837 original size:29 final size:28
Alignment explanation
Indices: 39992780--39992836 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
39992770 TATAACACTT
** *
39992780 TTTTATATTTTTAGAGATCAGAGTAAAA
1 TTTTATATTTTTAGAGAAAAGAATAAAA
39992808 TTTTATTATTTTTAGAGAAAAAGAATAAA
1 TTTTA-TATTTTTAGAG-AAAAGAATAAA
39992837 TGTTTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 11 0.46
30 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (28 bp):
TTTTATATTTTTAGAGAAAAGAATAAAA
Found at i:39993134 original size:2 final size:2
Alignment explanation
Indices: 39993127--39993166 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39993117 TAATAACATA
39993127 AT AT AT AT 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 AT AT AT AT
39993167 TCAAACATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39999239 original size:14 final size:14
Alignment explanation
Indices: 39999220--39999254 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39999210 TGACTTTTTT
*
39999220 TTCTAATGATACTA
1 TTCTAACGATACTA
39999234 TTCTAACGATACTA
1 TTCTAACGATACTA
39999248 TTCTAAC
1 TTCTAAC
39999255 ATGTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:39999874 original size:12 final size:12
Alignment explanation
Indices: 39999857--39999890 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39999847 TTGGGGCATA
*
39999857 CGAGCCAGTGCC
1 CGAGCCAGAGCC
39999869 CGAGCCAGAGCC
1 CGAGCCAGAGCC
*
39999881 TGAGCCAGAG
1 CGAGCCAGAG
39999891 TAGAAGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.35, T:0.06
Consensus pattern (12 bp):
CGAGCCAGAGCC
Found at i:40000501 original size:48 final size:48
Alignment explanation
Indices: 40000445--40000536 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
40000435 CAACATTACA
* *
40000445 ACATTACAAGACTAAAACTTGGAACAAATTTTGTAATATAAATTAAAT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
* *
40000493 ACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATT
40000537 TTGTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (48 bp):
ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:40000546 original size:62 final size:62
Alignment explanation
Indices: 40000470--40000720 Score: 416
Period size: 62 Copynumber: 4.1 Consensus size: 62
40000460 AACTTGGAAC
* *
40000470 AAATTTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* *
40000532 AAATTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* * * *
40000594 AAATTTTG-T-TATAAATTAAATATATTATAGCATTAAAAATTGGATCAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
40000654 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
40000716 AAATT
1 AAATT
40000721 AGGTACATTG
Statistics
Matches: 174, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
60 54 0.31
61 2 0.01
62 118 0.68
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (62 bp):
AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
Found at i:40000629 original size:122 final size:123
Alignment explanation
Indices: 40000470--40000720 Score: 423
Period size: 122 Copynumber: 2.0 Consensus size: 123
40000460 AACTTGGAAC
*
40000470 AAATTTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAA
1 AAATTTTGT-ATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAA
40000535 TTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
65 TTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
* * * *
40000594 AAATTTTGT-TATAAATTAAATATATTATAGCATTAAAAATTGGATCAAACTTTGTAATATAAAT
1 AAATTTTGTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
* *
40000658 TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
66 TTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
40000716 AAATT
1 AAATT
40000721 AGGTACATTG
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
122 111 0.93
124 9 0.08
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (123 bp):
AAATTTTGTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
TTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
Found at i:40005172 original size:40 final size:40
Alignment explanation
Indices: 40005126--40005274 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 40
40005116 TATTTTTTTT
* *
40005126 ATTTTTTTAATTTTAAAATACTTTTAAAA-CCTTTTATTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT-TTAA
*
40005166 ATTTTTTAAATTTTAAAAT-TTTTTAAAATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
*
40005205 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAA
*
40005246 TTTTTATTTTAATTTTTAAAATAATTTTT
1 -ATTT-TTTTAA-TTTTAAAAT-ATTTTT
40005275 TGGTATTTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
39 29 0.30
40 35 0.36
41 8 0.08
42 4 0.04
43 6 0.06
44 9 0.09
45 6 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:40022637 original size:20 final size:20
Alignment explanation
Indices: 40022612--40022656 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
40022602 GCAAATTTCG
40022612 GGTAAAATTGAATTAATTCA
1 GGTAAAATTGAATTAATTCA
*
40022632 GGTAAAATTGAATTAATTCG
1 GGTAAAATTGAATTAATTCA
40022652 GGTAA
1 GGTAA
40022657 CAGACCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTAAAATTGAATTAATTCA
Found at i:40036471 original size:18 final size:20
Alignment explanation
Indices: 40036448--40036487 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40036438 TAGAAATAGT
40036448 AATTAAAAT-AT-TTTTTTA
1 AATTAAAATGATATTTTTTA
*
40036466 AATTAAACTGATATTTTTTA
1 AATTAAAATGATATTTTTTA
40036486 AA
1 AA
40036488 AATATATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTAAAATGATATTTTTTA
Found at i:40040151 original size:23 final size:24
Alignment explanation
Indices: 40040125--40040205 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 24
40040115 TTCATAGTTT
40040125 TAAA-ATTATATTATTATATTATG
1 TAAACATTATATTATTATATTATG
*
40040148 TAAA-ATTATATCATGTATTATTATTG
1 TAAACATTATATTAT-TA-TATTA-TG
*
40040174 TAATACATAATA-TATTA-ATTAT-
1 TAA-ACATTATATTATTATATTATG
*
40040196 TAAATATTAT
1 TAAACATTAT
40040206 TTTTTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
23 14 0.29
24 6 0.12
25 5 0.10
26 7 0.15
27 3 0.06
28 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TAAACATTATATTATTATATTATG
Found at i:40040170 original size:15 final size:15
Alignment explanation
Indices: 40040133--40040171 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40040123 TTTAAAATTA
*
40040133 TATTATTATATTATG
1 TATTATTATATCATG
**
40040148 TAAAATTATATCATG
1 TATTATTATATCATG
40040163 TATTATTAT
1 TATTATTAT
40040172 TGTAATACAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (15 bp):
TATTATTATATCATG
Found at i:40040980 original size:20 final size:21
Alignment explanation
Indices: 40040940--40041006 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 21
40040930 ATTTTATAAT
40040940 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTGAAA
*
40040964 TTTTTACAAA-TATTTTG-AA
1 TTTTTAAAAATTATTTTGAAA
40040983 -TTTTAAAAATTATTTT-AAA
1 TTTTTAAAAATTATTTTGAAA
40041002 TTTTT
1 TTTTT
40041007 CTGTAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 10 0.26
22 1 0.03
24 9 0.24
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGAAA
Found at i:40042599 original size:18 final size:18
Alignment explanation
Indices: 40042572--40042613 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40042562 TTAAGTCCAT
*
40042572 ATGCCAGTGTGAGCCCAC
1 ATGCCCGTGTGAGCCCAC
40042590 ATGCCCGTGTGAGCCCAC
1 ATGCCCGTGTGAGCCCAC
40042608 ATGCCC
1 ATGCCC
40042614 AGATTGGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (18 bp):
ATGCCCGTGTGAGCCCAC
Found at i:40053078 original size:46 final size:46
Alignment explanation
Indices: 40053011--40053104 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
40053001 CTTGGACTGT
* *
40053011 GTATTCGCCTGATTTGTTCCCTCGCCATATTAGAACATCCGGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
40053057 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
40053103 GT
1 GT
40053105 CCTGCTTACC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (46 bp):
GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
Found at i:40054779 original size:105 final size:101
Alignment explanation
Indices: 40054600--40054797 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 101
40054590 AATTGACGGA
* * * * *
40054600 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGAGCTTTGGCATTTTAA
1 TAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGGCATTCTAA
40054665 TGAACAGACCATAACTGAGTTATGGCACATTGAACG
66 TGAACAGACCATAACTGAGTTATGGCACATTGAACG
* *
40054701 TAAGACCATGGTTGGACCATGACAATATAGATACATGTGTAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGACAATAT--ATA-A-ATGTAAGACCATAGCTGAGCTATGGCATT
* * *
40054766 CTGATGATA-AGACCATAACTGGGTTGTGGCAC
62 CTAATGA-ACAGACCATAACTGAGTTATGGCAC
40054798 TACAAATGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 26 0.32
103 2 0.02
104 1 0.01
105 52 0.63
106 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAATATATAAATGTAAGACCATAGCTGAGCTATGGCATTCTAA
TGAACAGACCATAACTGAGTTATGGCACATTGAACG
Found at i:40054810 original size:33 final size:32
Alignment explanation
Indices: 40054738--40054814 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
40054728 TAGATACATG
* * **
40054738 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
* *
40054770 TGATAAGACCATAACTGGGTTGTGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
40054804 TGTAAGACCAT
1 TGTAAGACCAT
40054815 GGCAGAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:40054826 original size:105 final size:105
Alignment explanation
Indices: 40054633--40054831 Score: 251
Period size: 105 Copynumber: 1.9 Consensus size: 105
40054623 AATGTTTAAA
* * **
40054633 TGTAAGACCATAGCTGAGCTTTGGCATTTTAATGAACAGACCATAACTGAGTTATGGCACATTGA
1 TGTAAGACCATAGCTGAGCTATGGCATTCTAATGAACAGACCATAACTGAGTTATGGCACATCAA
**
40054698 ACGTAAGACCATGGTTGGACCATGACAATATAGATACATG
66 ACGTAAGACCATGGCAGGACCATGACAATATAGATACATG
* * * *
40054738 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATA-AGACCATAACTGGGTTGTGGCAC-TAC
1 TGTAAGACCATAGCTGAGCTATGGCATTCTAATGA-ACAGACCATAACTGAGTTATGGCACAT-C
*
40054801 AAATGTAAGACCATGGCA-GAGCCATGACAAT
64 AAACGTAAGACCATGGCAGGA-CCATGACAAT
40054832 GCATGTAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
104 3 0.04
105 76 0.95
106 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (105 bp):
TGTAAGACCATAGCTGAGCTATGGCATTCTAATGAACAGACCATAACTGAGTTATGGCACATCAA
ACGTAAGACCATGGCAGGACCATGACAATATAGATACATG
Found at i:40063767 original size:26 final size:26
Alignment explanation
Indices: 40063715--40063767 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
40063705 TCCATTGAAT
** *
40063715 ATAATTAAAATATATTAATTTATTTA
1 ATAATTAAAATATATTAATAAAATTA
* *
40063741 ATAATTTAAATATTTTAATAAAATTA
1 ATAATTAAAATATATTAATAAAATTA
40063767 A
1 A
40063768 AGCATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATTAAAATATATTAATAAAATTA
Found at i:40064156 original size:2 final size:2
Alignment explanation
Indices: 40064149--40064173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40064139 AGTTCGCAAT
40064149 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40064174 TAGGAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40068533 original size:3 final size:3
Alignment explanation
Indices: 40068525--40068603 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
40068515 AGGGTAAGAC
40068525 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40068573 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40068604 GTTCGAGAGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40073243 original size:19 final size:19
Alignment explanation
Indices: 40073219--40073257 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40073209 TCAGCAAAGT
40073219 TAGCATTCTCAATCTACCA
1 TAGCATTCTCAATCTACCA
40073238 TAGCATTCTCAATCTACCA
1 TAGCATTCTCAATCTACCA
40073257 T
1 T
40073258 CTTAAGCTCC
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:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (19 bp):
TAGCATTCTCAATCTACCA
Found at i:40074717 original size:3 final size:3
Alignment explanation
Indices: 40074711--40074753 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
40074701 AAAAAAAAAA
40074711 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG
40074754 GGAGACGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40074758 original size:7 final size:7
Alignment explanation
Indices: 40074712--40074758 Score: 50
Period size: 6 Copynumber: 7.4 Consensus size: 7
40074702 AAAAAAAAAA
40074712 AGAAGA-
1 AGAAGAG
40074718 AGAAGA-
1 AGAAGAG
40074724 AGAAGA-
1 AGAAGAG
40074730 AGAAGA-
1 AGAAGAG
40074736 AGAAGA-
1 AGAAGAG
40074742 AGAAGAG
1 AGAAGAG
*
40074749 AGAAGGG
1 AGAAGAG
40074756 AGA
1 AGA
40074759 CGGTAACCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 30 0.77
7 9 0.23
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:40075839 original size:26 final size:26
Alignment explanation
Indices: 40075803--40075858 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40075793 GTTTAATCAA
40075803 AGCATAATTTCGGTCCAAATTCATAC
1 AGCATAATTTCGGTCCAAATTCATAC
40075829 AGCATAATTTCGGTCCAAATTCATAC
1 AGCATAATTTCGGTCCAAATTCATAC
40075855 AGCA
1 AGCA
40075859 AGTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (26 bp):
AGCATAATTTCGGTCCAAATTCATAC
Found at i:40078581 original size:17 final size:16
Alignment explanation
Indices: 40078561--40078605 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
40078551 AGTATTTTAA
40078561 TTTTTTATTTTATCTT
1 TTTTTTATTTTATCTT
* *
40078577 TTTTTAACTTTTTTCTT
1 TTTTTTA-TTTTATCTT
40078594 TTTCTTTATTTT
1 TTT-TTTATTTT
40078606 CCATTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTATCTT
Found at i:40078581 original size:23 final size:24
Alignment explanation
Indices: 40078553--40078605 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
40078543 TCCTTTTGAG
40078553 TATTTTAA-TTTTTTATTTTATCTT
1 TATTTTAACTTTTTTATTTT-TCTT
*
40078577 T-TTTTAACTTTTTTCTTTTTCTT
1 TATTTTAACTTTTTTATTTTTCTT
40078600 TATTTT
1 TATTTT
40078606 CCATTCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (24 bp):
TATTTTAACTTTTTTATTTTTCTT
Found at i:40079619 original size:13 final size:13
Alignment explanation
Indices: 40079601--40079625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40079591 AGAAGAGAAT
40079601 GGGAAAAAAAAAA
1 GGGAAAAAAAAAA
40079614 GGGAAAAAAAAA
1 GGGAAAAAAAAA
40079626 CATAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GGGAAAAAAAAAA
Found at i:40082224 original size:37 final size:37
Alignment explanation
Indices: 40082183--40082331 Score: 262
Period size: 37 Copynumber: 4.0 Consensus size: 37
40082173 GCTGAAGCTA
* **
40082183 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
40082220 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
40082257 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
40082294 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
40082331 C
1 C
40082332 TAAAACTACC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
Done.