Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, 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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 54
Found at i:3344131 original size:29 final size:29
Alignment explanation
Indices: 3344089--3344299 Score: 193
Period size: 29 Copynumber: 7.3 Consensus size: 29
3344079 ACCTGACTCA
3344089 GTGATATTTTGGGAATTATTTTGAAAAAG
1 GTGATATTTTGGGAATTATTTTGAAAAAG
3344118 GTGATATTTTGGGAATTATTTTG-AAAA-
1 GTGATATTTTGGGAATTATTTTGAAAAAG
* *
3344145 GTGATATTTTGGGTATTATTTTGAAAAAT
1 GTGATATTTTGGGAATTATTTTGAAAAAG
* * * *
3344174 GAGACATTTTGGGAATT-TTTTTAAAAATA
1 GTGATATTTTGGGAATTATTTTGAAAAA-G
* * *
3344203 GTGACATTCTGGTAATTACTTTT-AAACAA-
1 GTGATATTTTGGGAATTA-TTTTGAAA-AAG
* * *
3344232 -TGACATTCTGGGAATTATTTAT-AAAATG
1 GTGATATTTTGGGAATTATTT-TGAAAAAG
** *
3344260 GTGATATTTTGATAATTATTTTTAATAAAG
1 GTGATATTTTGGGAATTATTTTGAA-AAAG
3344290 GTGATATTTT
1 GTGATATTTT
3344300 TGTAATTTTC
Statistics
Matches: 155, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
27 26 0.17
28 38 0.25
29 69 0.45
30 16 0.10
31 6 0.04
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (29 bp):
GTGATATTTTGGGAATTATTTTGAAAAAG
Found at i:3344183 original size:56 final size:54
Alignment explanation
Indices: 3344088--3344270 Score: 174
Period size: 56 Copynumber: 3.2 Consensus size: 54
3344078 GACCTGACTC
* * *
3344088 AGTGATATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTGAAA
1 AGTGATATTTTGGGTATTATTTTGAAAAATG-GACATTTTGGGAATTATTTT-AAA
*
3344144 AGTGATATTTTGGGTATTATTTTGAAAAATGAGACATTTTGGGAATTTTTTTAAAAA
1 AGTGATATTTTGGGTATTATTTTGAAAAATG-GACATTTTGGGAATTATTTT--AAA
* * *
3344201 TAGTGACATTCT-GGTAATTACTTTT-AAACAAT-GACATTCTGGGAATTATTTATAAA
1 -AGTGATATTTTGGGT-ATTA-TTTTGAAA-AATGGACATTTTGGGAATTATTT-TAAA
3344257 ATGGTGATATTTTG
1 A--GTGATATTTTG
3344271 ATAATTATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
55 1 0.01
56 50 0.47
57 31 0.29
58 17 0.16
59 7 0.07
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.43
Consensus pattern (54 bp):
AGTGATATTTTGGGTATTATTTTGAAAAATGGACATTTTGGGAATTATTTTAAA
Found at i:3344245 original size:57 final size:57
Alignment explanation
Indices: 3344176--3344284 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
3344166 TGAAAAATGA
* * *
3344176 GACATTTTGGGAATT-TTTTTAAAAATAGTGACATTCTGGTAATTACTTTTAAACAAT
1 GACATTCTGGGAATTATTTAT-AAAATAGTGACATTCTGATAATTACTTTTAAACAAT
* * * *
3344233 GACATTCTGGGAATTATTTATAAAATGGTGATATTTTGATAATTATTTTTAA
1 GACATTCTGGGAATTATTTATAAAATAGTGACATTCTGATAATTACTTTTAA
3344285 TAAAGGTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 40 0.91
58 4 0.09
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (57 bp):
GACATTCTGGGAATTATTTATAAAATAGTGACATTCTGATAATTACTTTTAAACAAT
Found at i:3351505 original size:29 final size:29
Alignment explanation
Indices: 3351463--3351640 Score: 168
Period size: 29 Copynumber: 6.2 Consensus size: 29
3351453 ACCCAGTGAA
* *
3351463 ATTTTGAGAATTATTTTGAAAAAGTTAAC
1 ATTTTGGGAATTATTTTGAAAAAGTTGAC
*
3351492 ATTTTGGGAATTATTTTGAAAAAGGTGAC
1 ATTTTGGGAATTATTTTGAAAAAGTTGAC
3351521 ATTTTGGGAATT-TTTT-AAAATAG-TGAC
1 ATTTTGGGAATTATTTTGAAAA-AGTTGAC
* * * *
3351548 ATTCTGGTAATTATTTTTAAAAAGATGAC
1 ATTTTGGGAATTATTTTGAAAAAGTTGAC
* *
3351577 ATTTTGGGAATTA-TTTGTAAAACGATT-AT
1 ATTTTGGGAATTATTTTG-AAAAAG-TTGAC
* * * *
3351606 ATTTTGGTAATTATTTTTAATAAAGGTGAT
1 ATTTTGGGAATTATTTTGAA-AAAGTTGAC
3351636 ATTTT
1 ATTTT
3351641 TATAATTTTC
Statistics
Matches: 125, Mismatches: 15, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
27 18 0.14
28 15 0.12
29 78 0.62
30 14 0.11
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.44
Consensus pattern (29 bp):
ATTTTGGGAATTATTTTGAAAAAGTTGAC
Found at i:3351561 original size:56 final size:57
Alignment explanation
Indices: 3351458--3351640 Score: 208
Period size: 56 Copynumber: 3.2 Consensus size: 57
3351448 GACCGACCCA
* * * * *
3351458 GTGAAATTTTGAGAATTATTTTGAAAAAGTTAACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTT-AAAAAGATAACATTTTGGTAATTATTTTTAAAAAG
* *
3351516 GTGACATTTTGGGAATT-TTTTAAAATAG-TGACATTCTGGTAATTATTTTTAAAAAG
1 GTGACATTTTGGGAATTATTTTAAAA-AGATAACATTTTGGTAATTATTTTTAAAAAG
* * * *
3351572 ATGACATTTTGGGAATTATTTGTAAAACGATTATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGGAATTATTT-TAAAAAGATAACATTTTGGTAATTATTTTTAA-AAAG
*
3351631 GTGATATTTT
1 GTGACATTTT
3351641 TATAATTTTC
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
56 44 0.41
57 10 0.09
58 41 0.38
59 12 0.11
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (57 bp):
GTGACATTTTGGGAATTATTTTAAAAAGATAACATTTTGGTAATTATTTTTAAAAAG
Found at i:3355068 original size:81 final size:81
Alignment explanation
Indices: 3354937--3355433 Score: 676
Period size: 81 Copynumber: 6.1 Consensus size: 81
3354927 CCAGTTAGAT
* * **
3354937 GATGAACGGTTTAATACCATTGAGTAAAATAATAATAGCCTAACAATGCAATTGGTAGAAAGGTA
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
*
3355002 ACAATTATGCCAGTTA
66 CCAATTATGCCAGTTA
* *
3355018 GATGAAAGGTTTAATACCTTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
*
3355083 CCAATTATGCCATTTA
66 CCAATTATGCCAGTTA
** * * ** * * *
3355099 GATGAACGGTTTAATATTGTTGAGTAAAAGAATGATAGCCTAATTGTAAAATTTGTAGGAAGGTG
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
*
3355164 CCAACTATGCCAGTTA
66 CCAATTATGCCAGTTA
* * *
3355180 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTACAATTTGTAGAAACGTA
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
**
3355245 CCAATTATGTTAGTTA
66 CCAATTATGCCAGTTA
* * *
3355261 GATG-ACGATTTAATACCGTTGAGTAAAAGAATAATAGCCTAATTGTGCAATTGGTAGAAAGGTG
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
3355325 CCAATTATGCCAGTTA
66 CCAATTATGCCAGTTA
* * *
3355341 GATGAACGATTTAATACCGATGAGTAAAGGAATAAT-GCCCTAACTGTGCAATTTGGTAGAAAGG
1 GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAG-CCTAACTGTGCAA-TTGGTAGAAAGG
*
3355405 T-CTCAATTATTCCAGTTA
64 TAC-CAATTATGCCAGTTA
3355423 GATGAACGGTT
1 GATGAACGGTT
3355434 AAACATTATT
Statistics
Matches: 368, Mismatches: 44, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
80 73 0.20
81 258 0.70
82 37 0.10
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (81 bp):
GATGAACGGTTTAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTA
CCAATTATGCCAGTTA
Found at i:3357086 original size:263 final size:258
Alignment explanation
Indices: 3356373--3357324 Score: 1145
Period size: 252 Copynumber: 3.7 Consensus size: 258
3356363 TTTTATATCG
* * * *
3356373 TGTTTGTGAAAATTGAGAAAAGC-AGTTTTCAAAGTTTCTTATTTAATATTTTCGGAAAAATGAT
1 TGTTT-TGAAAAATGAG-AAAGCGA-TTTCCAAAGTTTCTCATTTAATATTTTC--AAAAATGAA
* ** * * *
3356437 TTTTTTGAAAAGTAAGAAAGTGATTTACAAAGTTTCTTACATAGTAAACTATTTCCAATATTGGT
61 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTATTTCAAATATTAGT
* * *
3356502 AAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATAAAATCCTTTGGGTCATCTGTCAG
126 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
* ** *
3356567 TCTTTCGAGCAAGATGATAAGGCCTTCGGGCTGTCTATAAGACCTTTGGGTAGGATGTTTTCACA
191 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
*
3356632 TAA
256 TGA
*
3356635 T-TTTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTC----A-GAAATTTT
1 TGTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAATGAAATTTT
** ** * *
3356694 TGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATTTTCAAA-ACTAGAAAGT
66 TGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTA-TTTCAAATATTAGTAAGT
* * ** * *
3356758 CATTCGGGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTTTAGGTCATCTTTTAGTCTT
130 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTT
* * * *
3356823 TCGAGTAAGATGATAAGTCCTTCGGGCCACCCATAAGACCTTTGGGCAGGATGTTTTCATATGA
195 TCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACATGA
* *
3356887 TGTTTGTGAAAAAAAATGAAAAAGCGATTTCCAAAGTTTCTCACTTAATATTTTCGAAAAATGAA
1 TGTTT-TG---AAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATATTTTC-AAAAATGAA
* *
3356952 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTATTTCGAAATTTTTG
61 ATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTATTTC-AAATATTAG
* * * *
3357017 TAAGTCTTTTGGGCCATCAGTAAGTTTTTCGAGCATGATGATTAAATCCTTCGGGTTATC-GTCA
125 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
* * * * * *
3357081 GTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATATATATGACCTATGGGCAAGATGTTTTCAC
190 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCAC
3357146 ATGA
255 ATGA
* * * *
3357150 -GTTTCG-AAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAACATTTTCAAAAATGAAATGTT
1 TGTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAATGAAATTTT
* * * * *
3357213 TGAAAAGTAAGACAGCAATTTCCATAGTTTCTTACCTCGTAAACTATTTC-ATTACTTAGTAAGT
66 TGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTATTTCAAATA-TTAGTAAGT
** **
3357277 CCTTCAAGCCATCAGTAAGTCTTTCGAGCATGATGGGTAAATCCTTCG
130 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG
3357325 AGTTATATGT
Statistics
Matches: 597, Mismatches: 77, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
252 170 0.28
253 10 0.02
254 4 0.01
255 49 0.08
256 59 0.10
257 80 0.13
259 32 0.05
260 11 0.02
261 4 0.01
262 10 0.02
263 114 0.19
264 54 0.09
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (258 bp):
TGTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAAAAATGAAATTTT
TGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACATAGTAAACTATTTCAAATATTAGTAAGTC
CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTT
CGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACATGA
Found at i:3357482 original size:3 final size:3
Alignment explanation
Indices: 3357461--3357547 Score: 68
Period size: 3 Copynumber: 27.7 Consensus size: 3
3357451 TTCGTCCGGT
* * * *
3357461 TTA TTG TTA TT- TATA TTA TTA TTA ATA TTTA TTA TCA ATA TTTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
* *
3357508 TTA TTA TTA TTA TTTA ATA TTA TTT TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TT
3357548 TATTCTTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 1 0.02
3 54 0.82
4 11 0.17
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3357494 original size:13 final size:12
Alignment explanation
Indices: 3357462--3357545 Score: 82
Period size: 13 Copynumber: 6.9 Consensus size: 12
3357452 TCGTCCGGTT
* *
3357462 TATTGTTATTTA
1 TATTATTATTAA
3357474 TATTATTATTAA
1 TATTATTATTAA
*
3357486 TATTTATTATCAA
1 TA-TTATTATTAA
*
3357499 TATTTATTATTAT
1 TA-TTATTATTAA
3357512 TATTATTATTTAA
1 TATTATTA-TTAA
*
3357525 TATTATT-TTTA
1 TATTATTATTAA
3357536 T-TTATTATTA
1 TATTATTATTA
3357546 TTTATTCTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.08
11 6 0.10
12 18 0.30
13 32 0.52
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:3357495 original size:16 final size:16
Alignment explanation
Indices: 3357474--3357547 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
3357464 TTGTTATTTA
3357474 TATTATTATTAATATT
1 TATTATTATTAATATT
* * *
3357490 TATTATCAAT-ATTTAT
1 TATTATTATTAATAT-T
*
3357506 TATTATTATTATTATT
1 TATTATTATTAATATT
* **
3357522 TAATATTATTTTTATT
1 TATTATTATTAATATT
3357538 TATTATTATT
1 TATTATTATT
3357548 TATTCTTTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
15 3 0.07
16 41 0.89
17 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATTAATATT
Found at i:3357511 original size:19 final size:18
Alignment explanation
Indices: 3357460--3357551 Score: 73
Period size: 19 Copynumber: 4.9 Consensus size: 18
3357450 TTTCGTCCGG
*
3357460 TTTATTGTTATTTATATTA
1 TTTATTATTA-TTATATTA
* *
3357479 TTATTAATATTTATTATCAATA
1 -T-TTATTA-TTATTAT-ATTA
3357501 TTTATTATTATTATTATTA
1 TTTATTATTATTA-TATTA
*
3357520 TTTAATATTATT-T-TTA
1 TTTATTATTATTATATTA
3357536 TTTATTATTATT-TATT
1 TTTATTATTATTATATT
3357552 CTTTTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
16 15 0.25
17 3 0.05
19 20 0.33
20 7 0.12
21 9 0.15
22 6 0.10
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTATTATTATTATATTA
Found at i:3357529 original size:35 final size:32
Alignment explanation
Indices: 3357468--3357547 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
3357458 GGTTTATTGT
3357468 TATTTA-TATTATTATTAATATTTATTATCAA
1 TATTTATTATTATTATTAATATTTATTATCAA
* * *
3357499 TATTTATTATTATTATTATTATTTAATAT-TA
1 TATTTATTATTATTATTAATATTTATTATCAA
*
3357530 TTTTTATTTATTATTATT
1 TATTTA-TTATTATTATT
3357548 TATTCTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 12 0.28
32 31 0.72
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (32 bp):
TATTTATTATTATTATTAATATTTATTATCAA
Found at i:3363092 original size:19 final size:19
Alignment explanation
Indices: 3363068--3363112 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3363058 TATACATGAC
3363068 CATTGATGGGTCTAGTCAT
1 CATTGATGGGTCTAGTCAT
3363087 CATTGATGGGTCTAGTCAT
1 CATTGATGGGTCTAGTCAT
*
3363106 GATTGAT
1 CATTGAT
3363113 ATGGAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (19 bp):
CATTGATGGGTCTAGTCAT
Found at i:3365727 original size:19 final size:18
Alignment explanation
Indices: 3365705--3365750 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3365695 CATTAAATGT
* *
3365705 TATTTAAAATTATAATAAA
1 TATTAAAAATT-TAAGAAA
3365724 TATTAAAAATTTAAGAAA
1 TATTAAAAATTTAAGAAA
*
3365742 TATGAAAAA
1 TATTAAAAA
3365751 CGTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
TATTAAAAATTTAAGAAA
Found at i:3365750 original size:18 final size:19
Alignment explanation
Indices: 3365710--3365750 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3365700 AATGTTATTT
* *
3365710 AAAATTATAATAAATATTA
1 AAAATTATAAGAAATATGA
3365729 AAAATT-TAAGAAATATGA
1 AAAATTATAAGAAATATGA
3365747 AAAA
1 AAAA
3365751 CGTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAGAAATATGA
Found at i:3365906 original size:30 final size:30
Alignment explanation
Indices: 3365870--3365929 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3365860 ATTTTTTAAA
* * *
3365870 TATAAAATATCACATAATTATTTTAAAAAT
1 TATAAAATATCAAAAAATTATTATAAAAAT
*
3365900 TATAAAATATTAAAAAATTATTATAAAAAT
1 TATAAAATATCAAAAAATTATTATAAAAAT
3365930 GTTAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
TATAAAATATCAAAAAATTATTATAAAAAT
Found at i:3365924 original size:21 final size:22
Alignment explanation
Indices: 3365898--3365943 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3365888 TATTTTAAAA
3365898 ATTAT-AAAATATTAAAAAATT
1 ATTATAAAAATATTAAAAAATT
* *
3365919 ATTATAAAAATGTTAAATAATT
1 ATTATAAAAATATTAAAAAATT
3365941 ATT
1 ATT
3365944 TAATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTATAAAAATATTAAAAAATT
Found at i:3367542 original size:29 final size:28
Alignment explanation
Indices: 3367504--3367606 Score: 152
Period size: 29 Copynumber: 3.5 Consensus size: 28
3367494 TTTTCTTTGC
3367504 TTGTAATTTATAAATAGTTTTGGTATTTA
1 TTGTAATTTATAAA-AGTTTTGGTATTTA
*
3367533 TTGTAATTTATAAAAAGTTATGGTATTTA
1 TTGTAATTTAT-AAAAGTTTTGGTATTTA
*
3367562 TTGTAATTTATAGAAAGTTTTGATATTTA
1 TTGTAATTTATA-AAAGTTTTGGTATTTA
3367591 TTGTAATTTATTAAAA
1 TTGTAATTTA-TAAAA
3367607 AAATTGGACT
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.01
29 62 0.91
30 5 0.07
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (28 bp):
TTGTAATTTATAAAAGTTTTGGTATTTA
Found at i:3367619 original size:29 final size:29
Alignment explanation
Indices: 3367529--3367664 Score: 91
Period size: 29 Copynumber: 4.7 Consensus size: 29
3367519 AGTTTTGGTA
**
3367529 TTTATTGTAATTTA-TAAAAAGTTATGGTA-
1 TTTATTGTAATTTATTAAAAAAAT-TGG-AC
* ** * *
3367558 TTTATTGTAATTTA-TAGAAAGTTTTGATA
1 TTTATTGTAATTTATTAAAAAAATTGGA-C
3367587 TTTATTGTAATTTATTAAAAAAATTGGAC
1 TTTATTGTAATTTATTAAAAAAATTGGAC
* * *
3367616 TTTATTATAATAT-TTAAAAAAATTAGAC
1 TTTATTGTAATTTATTAAAAAAATTGGAC
**
3367644 TTTTATAATAATTTATATAAA
1 -TTTATTGTAATTTAT-TAAA
3367665 TATTTATATT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.01
28 16 0.18
29 58 0.65
30 10 0.11
31 4 0.04
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTATTGTAATTTATTAAAAAAATTGGAC
Found at i:3367620 original size:58 final size:58
Alignment explanation
Indices: 3367504--3367626 Score: 162
Period size: 58 Copynumber: 2.1 Consensus size: 58
3367494 TTTTCTTTGC
* **
3367504 TTGTAATTTATAAATAGTTTTGGTATTTATTGTAATTTATAAAAAGTTATGGTATTTA
1 TTGTAATTTATAAATAGTTTTGATATTTATTGTAATTTATAAAAAAATATGGTATTTA
3367562 TTGTAATTTATAGAA-AGTTTTGATATTTATTGTAATTTATTAAAAAAAT-TGG-ACTTTA
1 TTGTAATTTATA-AATAGTTTTGATATTTATTGTAATTTA-TAAAAAAATATGGTA-TTTA
*
3367620 TTATAAT
1 TTGTAAT
3367627 ATTTAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
57 1 0.02
58 48 0.83
59 9 0.16
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (58 bp):
TTGTAATTTATAAATAGTTTTGATATTTATTGTAATTTATAAAAAAATATGGTATTTA
Found at i:3367644 original size:28 final size:28
Alignment explanation
Indices: 3367587--3367658 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3367577 AGTTTTGATA
* * *
3367587 TTTATTGTAATTTATTAAAAAAATTGGAC
1 TTTATTATAATAT-TTAAAAAAATTAGAC
3367616 TTTATTATAATATTTAAAAAAATTAGAC
1 TTTATTATAATATTTAAAAAAATTAGAC
3367644 -TT-TTATAATAATTTA
1 TTTATTATAAT-ATTTA
3367659 TATAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 7 0.18
27 7 0.18
28 14 0.36
29 11 0.28
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (28 bp):
TTTATTATAATATTTAAAAAAATTAGAC
Found at i:3367649 original size:26 final size:29
Alignment explanation
Indices: 3367601--3367658 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3367591 TTGTAATTTA
*
3367601 TTAAAAAAATTGGACTTTATTATAAT-AT
1 TTAAAAAAATTAGACTTTATTATAATAAT
3367629 TTAAAAAAATTAGAC-TT-TTATAATAAT
1 TTAAAAAAATTAGACTTTATTATAATAAT
3367656 TTA
1 TTA
3367659 TATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 7 0.25
27 7 0.25
28 14 0.50
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TTAAAAAAATTAGACTTTATTATAATAAT
Found at i:3367705 original size:15 final size:15
Alignment explanation
Indices: 3367685--3367714 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3367675 TTTATTATAA
3367685 TTTAATAGTTTTTAT
1 TTTAATAGTTTTTAT
*
3367700 TTTAATATTTTTTAT
1 TTTAATAGTTTTTAT
3367715 AATTTTAAAT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATAGTTTTTAT
Found at i:3370808 original size:19 final size:20
Alignment explanation
Indices: 3370784--3370828 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3370774 GCATCTGAGA
*
3370784 AAATAAAATAAAT-GAAATG
1 AAATAAAATAAATAAAAATG
3370803 AAAT-AAATAAATAAAAATG
1 AAATAAAATAAATAAAAATG
3370822 AAATAAA
1 AAATAAA
3370829 GTTTGCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATAAAATAAATAAAAATG
Found at i:3370858 original size:6 final size:6
Alignment explanation
Indices: 3370847--3370889 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3370837 CAAATAAAAC
* *
3370847 AAAATG AAAATG AAAATG AAAAT- AAAAAG AAAAT- AAAACG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA
3370890 TAGGTTGCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:3370873 original size:11 final size:11
Alignment explanation
Indices: 3370838--3370889 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
3370828 AGTTTGCTAC
*
3370838 AAAT-AAAACA
1 AAATGAAAATA
3370848 AAATGAAAATGA
1 AAATGAAAAT-A
3370860 AAATGAAAATA
1 AAATGAAAATA
*
3370871 AAAAGAAAATA
1 AAATGAAAATA
*
3370882 AAACGAAA
1 AAATGAAA
3370890 TAGGTTGCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.11
11 22 0.59
12 11 0.30
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (11 bp):
AAATGAAAATA
Found at i:3376573 original size:7 final size:7
Alignment explanation
Indices: 3376561--3376615 Score: 60
Period size: 7 Copynumber: 7.6 Consensus size: 7
3376551 TAATATATAG
3376561 ATAAAAA
1 ATAAAAA
3376568 ATAAAAA
1 ATAAAAA
3376575 ATAAAAA
1 ATAAAAA
3376582 AT--AAA
1 ATAAAAA
3376587 ATAAAATA
1 ATAAAA-A
3376595 ATAAATAGA
1 ATAAA-A-A
3376604 ATAAAATA
1 ATAAAA-A
3376612 ATAA
1 ATAA
3376616 TTGGAGTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 5 0.12
7 18 0.43
8 12 0.29
9 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (7 bp):
ATAAAAA
Found at i:3376594 original size:17 final size:16
Alignment explanation
Indices: 3376561--3376612 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
3376551 TAATATATAG
3376561 ATAAAAAAT-AA-AAA
1 ATAAAAAATAAATAAA
3376575 ATAAAAAATAAAATAAA
1 ATAAAAAAT-AAATAAA
*
3376592 ATAATAAATAGAATAAA
1 ATAAAAAATA-AATAAA
3376609 ATAA
1 ATAA
3376613 TAATTGGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 9 0.27
16 3 0.09
17 21 0.64
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (16 bp):
ATAAAAAATAAATAAA
Found at i:3376613 original size:17 final size:17
Alignment explanation
Indices: 3376572--3376615 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3376562 TAAAAAATAA
*
3376572 AAAATAAAAAATAAAAT
1 AAAATAATAAATAAAAT
*
3376589 AAAATAATAAATAGAAT
1 AAAATAATAAATAAAAT
3376606 AAAATAATAA
1 AAAATAATAA
3376616 TTGGAGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAATAATAAATAAAAT
Found at i:3377199 original size:24 final size:24
Alignment explanation
Indices: 3377147--3377202 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3377137 TTAGCATCTT
*
3377147 TGAAAAT-AAAACTTAAAATAAAA
1 TGAAAATAAAAACTTAAAAGAAAA
*
3377170 TAAAAATAAAAACTTGAAAAGAAAA
1 TGAAAATAAAAACTT-AAAAGAAAA
3377195 -GAAAATAA
1 TGAAAATAA
3377203 CTTTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 14 0.50
25 8 0.29
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (24 bp):
TGAAAATAAAAACTTAAAAGAAAA
Found at i:3389006 original size:14 final size:14
Alignment explanation
Indices: 3388987--3389016 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3388977 ACATAAAGGA
*
3388987 TTAATGAGTGAATG
1 TTAATGAATGAATG
3389001 TTAATGAATGAATG
1 TTAATGAATGAATG
3389015 TT
1 TT
3389017 TATCCTTTAA
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:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
TTAATGAATGAATG
Found at i:3389129 original size:45 final size:45
Alignment explanation
Indices: 3389060--3389145 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
3389050 ATCCATCATT
* *
3389060 CCTTGTGTGAACATGTTGATTCGGCTACTAGCATGAATTTGGCTC
1 CCTTGTGTGAACATGATGAATCGGCTACTAGCATGAATTTGGCTC
*
3389105 CCTTGTTTGAACATGATGAATCGGCTACTAGCATGAATTTG
1 CCTTGTGTGAACATGATGAATCGGCTACTAGCATGAATTTG
3389146 ATGAATGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (45 bp):
CCTTGTGTGAACATGATGAATCGGCTACTAGCATGAATTTGGCTC
Found at i:3391809 original size:17 final size:16
Alignment explanation
Indices: 3391784--3391820 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3391774 CTTTTAAAAC
3391784 TCTAATTATTATTTTAT
1 TCTAATTATTATTTT-T
*
3391801 TCTATTTATTATTTTT
1 TCTAATTATTATTTTT
3391817 TCTA
1 TCTA
3391821 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTAATTATTATTTTT
Found at i:3409347 original size:46 final size:46
Alignment explanation
Indices: 3409274--3409490 Score: 359
Period size: 46 Copynumber: 4.8 Consensus size: 46
3409264 AAGATAAAAC
*
3409274 CTTACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3409319 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3409365 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACTAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3409411 CTTATCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3409457 CTTTCCA-TT-ATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
3409491 GCCAGTTTAT
Statistics
Matches: 162, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 24 0.15
45 12 0.07
46 126 0.78
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3413684 original size:13 final size:12
Alignment explanation
Indices: 3413668--3413733 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
3413658 TCATCTCTCA
*
3413668 TTTTTTTCTCTT
1 TTTTTTTTTCTT
3413680 TTTTTATTTTCTT
1 TTTTT-TTTTCTT
3413693 TTTATGTTTTTCTT
1 TTT-T-TTTTTCTT
* *
3413707 CTTCTTTTTCTT
1 TTTTTTTTTCTT
* *
3413719 CTTCTTCTTTCTT
1 -TTTTTTTTTCTT
3413732 TT
1 TT
3413734 CGTTTTCTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 15 0.35
13 17 0.40
14 10 0.23
15 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:3419106 original size:44 final size:46
Alignment explanation
Indices: 3418999--3419212 Score: 332
Period size: 46 Copynumber: 4.8 Consensus size: 46
3418989 AAGATAAAAC
*
3418999 CTTACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3419044 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACC-A-ATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3419088 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACTAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3419134 CTTATCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAA-ATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3419179 CTTTCCA-TT-ATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
3419213 GCCAGTTTAT
Statistics
Matches: 157, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
43 24 0.15
44 43 0.27
45 20 0.13
46 70 0.45
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3419116 original size:90 final size:90
Alignment explanation
Indices: 3418999--3419212 Score: 351
Period size: 90 Copynumber: 2.4 Consensus size: 90
3418989 AAGATAAAAC
*
3418999 CTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATAA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATAA
3419064 GCTCGTAAGCTTATTTTACC-AATA
66 GCTCGTAAGCTTATTTTACCAAATA
* * *
3419088 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACTAATATACTTATCATTTAATCCCATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATA
3419153 AGCTCGTAAGCTTATTTTACCAAATA
65 AGCTCGTAAGCTTATTTTACCAAATA
* *
3419179 CTTTCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
3419213 GCCAGTTTAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
89 34 0.29
90 73 0.62
91 10 0.09
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (90 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACCATAA
GCTCGTAAGCTTATTTTACCAAATA
Found at i:3423337 original size:13 final size:13
Alignment explanation
Indices: 3423321--3423384 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 13
3423311 TCATCTCTCA
3423321 TTTTTTTCTCTTT
1 TTTTTTTCTCTTT
3423334 TTTTTTT-TCTTTT
1 TTTTTTTCTC-TTT
*
3423347 TATGTTTTTCTTCTTC
1 T-T-TTTTTC-TCTTT
3423363 TTTTTTTCTCTTCT
1 TTTTTTTCTCTT-T
*
3423377 TTCTTTTC
1 TTTTTTTC
3423385 GTTTTCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 2 0.05
13 15 0.36
14 14 0.33
15 6 0.14
16 3 0.07
17 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:3423340 original size:14 final size:13
Alignment explanation
Indices: 3423321--3423371 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
3423311 TCATCTCTCA
3423321 TTTTTTTCTCTTTT
1 TTTTTTTCT-TTTT
3423335 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
* *
3423348 ATGTTTTTCTTCTTC
1 -TTTTTTTCTT-TTT
3423363 TTTTTTTCT
1 TTTTTTTCT
3423372 CTTCTTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 4 0.12
14 26 0.81
15 2 0.06
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:3423346 original size:20 final size:20
Alignment explanation
Indices: 3423323--3423391 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
3423313 ATCTCTCATT
3423323 TTTTTCTCTTTTTTTTTTTC
1 TTTTTCTCTTTTTTTTTTTC
* *
3423343 TTTTTATGTTTTTCTTCTTCTT-
1 TTTTTCTCTTTTT-TT-TT-TTC
* *
3423365 TTTTTCTCTTCTTTCTTTTC
1 TTTTTCTCTTTTTTTTTTTC
*
3423385 GTTTTCT
1 TTTTTCT
3423392 TATAATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
21 3 0.08
22 12 0.32
23 2 0.05
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTCTCTTTTTTTTTTTC
Found at i:3431333 original size:46 final size:46
Alignment explanation
Indices: 3431260--3431476 Score: 350
Period size: 46 Copynumber: 4.8 Consensus size: 46
3431250 AAGATAAAAT
* *
3431260 CTTACCATTT-ATCCCTTAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3431305 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3431351 CTTACAATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3431397 CTTATCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3431443 CTTTCCA-TT-ATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
3431477 GCCAGTTTAT
Statistics
Matches: 161, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
44 24 0.15
45 12 0.07
46 125 0.78
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3431607 original size:40 final size:40
Alignment explanation
Indices: 3431556--3431661 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
3431546 GTATAGGAGT
* * *
3431556 CAAATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCAC
1 CAAATAATGCACCGTAGTGCTGAGGTCGAGCTTTACTCAC
* * *
3431596 CTAATAATGCACCGTAGTACTGAGGTCGAGTTTTACTCAC
1 CAAATAATGCACCGTAGTGCTGAGGTCGAGCTTTACTCAC
3431636 CAAATAATGCACCGTAGTGCTGAGGT
1 CAAATAATGCACCGTAGTGCTGAGGT
3431662 TGGGATTTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (40 bp):
CAAATAATGCACCGTAGTGCTGAGGTCGAGCTTTACTCAC
Found at i:3431671 original size:40 final size:40
Alignment explanation
Indices: 3431556--3431676 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
3431546 GTATAGGAGT
* * * *
3431556 CAAATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCAC
1 CAAATAATGCACCGTAGTGCTGAGGTCGAGATTTACTCAC
* * *
3431596 CTAATAATGCACCGTAGTACTGAGGTCGAGTTTTACTCAC
1 CAAATAATGCACCGTAGTGCTGAGGTCGAGATTTACTCAC
* * *
3431636 CAAATAATGCACCGTAGTGCTGAGGTTGGGATTTACCCAC
1 CAAATAATGCACCGTAGTGCTGAGGTCGAGATTTACTCAC
3431676 C
1 C
3431677 TAGTACACCG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATAATGCACCGTAGTGCTGAGGTCGAGATTTACTCAC
Found at i:3431932 original size:21 final size:21
Alignment explanation
Indices: 3431907--3431952 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3431897 CATACCCACA
3431907 ATATA-ATTCATGATAAAAATC
1 ATATATATTCATGAT-AAAATC
* *
3431928 ATATATGTTCATGATAACATC
1 ATATATATTCATGATAAAATC
3431949 ATAT
1 ATAT
3431953 GCAAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (21 bp):
ATATATATTCATGATAAAATC
Found at i:3435725 original size:22 final size:21
Alignment explanation
Indices: 3435700--3435774 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 21
3435690 ACCTCTCATT
3435700 TTTTTCTCTTTTTTTTATTTTC
1 TTTTTCTCTTTTTTTT-TTTTC
* *
3435722 TTTTTCTGTTTTTTTCTTCTTC
1 TTTTTCTCTTTTTTT-TTTTTC
*
3435744 TTTTTCTTTTTCTTCTTTCTTTTC
1 TTTTTCTCTTT-TT-TTT-TTTTC
*
3435768 GTTTTCT
1 TTTTTCT
3435775 TATAATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 28 0.64
23 4 0.09
24 12 0.27
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTTCTCTTTTTTTTTTTTC
Found at i:3435733 original size:7 final size:6
Alignment explanation
Indices: 3435700--3435775 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
3435690 ACCTCTCATT
* * * *
3435700 TTTTTC TCTTT- TTTTT- ATTTTC TTTTTC -TGTT- TTTTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
3435744 TTTTTC TTTTTC TTCTTTC -TTTTC GTTTTC TT
1 TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TT
3435776 ATAATATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 18 0.32
6 34 0.61
7 4 0.07
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:3435757 original size:15 final size:15
Alignment explanation
Indices: 3435717--3435761 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3435707 CTTTTTTTTA
*
3435717 TTTTCTTTTTC-TGT
1 TTTTCTTTTTCTTCT
*
3435731 TTTT-TTCTTCTTCT
1 TTTTCTTTTTCTTCT
3435745 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
3435760 TT
1 TT
3435762 CTTTTCGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 11 0.42
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:3435763 original size:35 final size:32
Alignment explanation
Indices: 3435698--3435763 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
3435688 TCACCTCTCA
3435698 TTTTTTTCTCTTTTTTTTATTTTCTTTTTCTG
1 TTTTTTTCTCTTTTTTTTATTTTCTTTTTCTG
3435730 TTTTTTTCTTCTTCTTTTTCT-TTTTCTTCTTTCT
1 TTTTTTTC-TCTT-TTTTT-TATTTTCTT-TTTCT
3435764 TTTCGTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 8 0.27
33 4 0.13
34 12 0.40
35 6 0.20
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (32 bp):
TTTTTTTCTCTTTTTTTTATTTTCTTTTTCTG
Found at i:3435767 original size:18 final size:17
Alignment explanation
Indices: 3435698--3435766 Score: 74
Period size: 16 Copynumber: 4.1 Consensus size: 17
3435688 TCACCTCTCA
3435698 TTTTTTTC-TCTTT-TT
1 TTTTTTTCTTCTTTCTT
*
3435713 TTTATTTTCTT-TTTCTG
1 TTT-TTTTCTTCTTTCTT
3435730 TTTTTTTCTTC-TTCTTT
1 TTTTTTTCTTCTTTC-TT
3435747 TTCTTTTTCTTCTTTCTT
1 TT-TTTTTCTTCTTTCTT
3435765 TT
1 TT
3435767 CGTTTTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
15 3 0.07
16 18 0.40
17 8 0.18
18 13 0.29
19 3 0.07
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTTCTTTCTT
Found at i:3435772 original size:18 final size:17
Alignment explanation
Indices: 3435701--3435775 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 17
3435691 CCTCTCATTT
* *
3435701 TTTTC-TCTTTTTTTTA
1 TTTTCTTCTTTCTTTTC
3435717 TTTTCTT-TTTCTGTTT-
1 TTTTCTTCTTTCT-TTTC
3435733 TTTTCTTC-TTCTTTTTC
1 TTTTCTTCTTTC-TTTTC
3435750 TTTTTCTTCTTTCTTTTC
1 -TTTTCTTCTTTCTTTTC
3435768 GTTTTCTT
1 -TTTTCTT
3435776 ATAATATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
16 22 0.44
17 5 0.10
18 20 0.40
19 3 0.06
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTC
Found at i:3435930 original size:20 final size:19
Alignment explanation
Indices: 3435905--3435942 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3435895 ATCTCGAGCA
3435905 CAGTACAAAGATAGAGCATG
1 CAGTACAAAGATA-AGCATG
3435925 CAGTACAAAGATAAGCAT
1 CAGTACAAAGATAAGCAT
3435943 CATGCTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
CAGTACAAAGATAAGCATG
Found at i:3438960 original size:11 final size:11
Alignment explanation
Indices: 3438941--3439000 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
3438931 TTTAATTATC
*
3438941 TCTCATTTTTT
1 TCTCTTTTTTT
3438952 TCTC--TTTTT
1 TCTCTTTTTTT
3438961 TCT-TTTTTTT
1 TCTCTTTTTTT
*
3438971 TCTATTTTTTT
1 TCTCTTTTTTT
*
3438982 TCTTTTTCTTTT
1 TCTCTTT-TTTT
3438994 TC-CTTTT
1 TCTCTTTT
3439001 CTTCGTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 20 0.47
12 6 0.14
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:3438966 original size:17 final size:16
Alignment explanation
Indices: 3438946--3439000 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
3438936 TTATCTCTCA
3438946 TTTTTTTCTCTTTTTTC
1 TTTTTTT-TCTTTTTTC
3438963 TTTTTTTTTCTATTTTT-
1 -TTTTTTTTCT-TTTTTC
*
3438980 TTTCTTTTTCTTTTTCC
1 TTT-TTTTTCTTTTTTC
3438997 TTTT
1 TTTT
3439001 CTTCGTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 8 0.24
17 13 0.39
18 12 0.36
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:3438989 original size:6 final size:6
Alignment explanation
Indices: 3438957--3439021 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
3438947 TTTTTTCTCT
* *
3438957 TTTTTC -TTTT- TTTTTC TATTT- TTTTTC TTTTTC TTTTTC CTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
3439002 TTCGTTC -TTTTC ATTTTC TT
1 TT-TTTC TTTTTC TTTTTC TT
3439022 ATAATATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
5 15 0.32
6 29 0.62
7 3 0.06
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:3439001 original size:18 final size:18
Alignment explanation
Indices: 3438949--3439021 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
3438939 TCTCTCATTT
*
3438949 TTTTCTCTTTTTTCTTTT-
1 TTTT-TCTTTTTCCTTTTC
3438967 TTTTTCTATTTT--TTTTC
1 TTTTTCT-TTTTCCTTTTC
3438984 TTTTTCTTTTTCCTTTTC
1 TTTTTCTTTTTCCTTTTC
* *
3439002 TTCGTTC-TTTTCATTTTC
1 TT-TTTCTTTTTCCTTTTC
3439020 TT
1 TT
3439022 ATAATATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
16 8 0.17
17 10 0.21
18 27 0.56
19 3 0.06
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTTCCTTTTC
Found at i:3441776 original size:50 final size:50
Alignment explanation
Indices: 3441701--3441802 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
3441691 CCTGATCAAA
3441701 ATGCCATAATCTAGGAACACTAATTGCTTCAATAGTCCCATCAGCATTGC
1 ATGCCATAATCTAGGAACACTAATTGCTTCAATAGTCCCATCAGCATTGC
3441751 ATGCCATAATCTAGGAACACTAATTGCTTCAATAGTCCCATCAGCATTGC
1 ATGCCATAATCTAGGAACACTAATTGCTTCAATAGTCCCATCAGCATTGC
3441801 AT
1 AT
3441803 TGTGTCTTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (50 bp):
ATGCCATAATCTAGGAACACTAATTGCTTCAATAGTCCCATCAGCATTGC
Found at i:3444628 original size:24 final size:24
Alignment explanation
Indices: 3444596--3444651 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3444586 CTATTCTTTC
3444596 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
3444620 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
3444644 GCTTCAAT
1 GCTTCAAT
3444652 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:3444912 original size:30 final size:30
Alignment explanation
Indices: 3444876--3444941 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
3444866 AGTGAACCGG
* **
3444876 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGATTTCCCCGGTTTTCAGC
**
3444906 CGGTTCACCCCGATTTCCCCGGTTTTCAGC
1 CGGTTCAAACCGATTTCCCCGGTTTTCAGC
3444936 CGGTTC
1 CGGTTC
3444942 TTCCGATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.33, G:0.24, T:0.32
Consensus pattern (30 bp):
CGGTTCAAACCGATTTCCCCGGTTTTCAGC
Found at i:3445461 original size:2 final size:2
Alignment explanation
Indices: 3445454--3445506 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3445444 TTCATGTGAA
3445454 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
3445496 AT AT AT AT AT A
1 AT AT AT AT AT A
3445507 ACCAACCACG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3447812 original size:29 final size:31
Alignment explanation
Indices: 3447780--3447842 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 31
3447770 AACGATAATA
3447780 ATATTA-TTATAAAAAATGTT-TTCAAAA-TT
1 ATATTAGTTATAAAAAATGTTCTT-AAAACTT
* *
3447809 ATA-TAGTTTTTAAAAATGTTCTTAAAACTT
1 ATATTAGTTATAAAAAATGTTCTTAAAACTT
3447839 ATAT
1 ATAT
3447843 ATCATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
28 2 0.07
29 19 0.68
30 7 0.25
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
ATATTAGTTATAAAAAATGTTCTTAAAACTT
Found at i:3447909 original size:36 final size:35
Alignment explanation
Indices: 3447808--3448198 Score: 294
Period size: 36 Copynumber: 11.2 Consensus size: 35
3447798 TTTTCAAAAT
3447808 TATATAGTTTTTAAAAATGTTCTT-AAAACT-TATATA
1 TATATA-TTTTTAAAAATGTT-TTAAAAACTATATA-A
* * ** * *
3447844 TCATATAAGTTTTCAAAATAATGTCAAAACTATATAA
1 T-ATAT-ATTTTTAAAAATGTTTTAAAAACTATATAA
* *
3447881 TATATGTGTTTTAAAAATGCTTTAAAAAC----T-A
1 TATATAT-TTTTAAAAATGTTTTAAAAACTATATAA
* * *
3447912 TATATA-TTTTCAAAATGTTTTAAAAATTTTATAA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATAA
* *
3447946 TATATATTTTCAAAAATGCTTTAAAAACTATATATTA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATA--A
*
3447983 TATTTATTTTT-AAAATGTTTTAAAAAC----T-A
1 TATATATTTTTAAAAATGTTTTAAAAACTATATAA
*
3448012 TATATA-TTTTCAAAATGTTTTAAAAACTATATAA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATAA
* *
3448046 TATATATTTTCAAAAATGCTTTAAAAACTATATATTA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATA--A
*
3448083 TATTTATTTTT-AAAATGTTTTAAAAACTATATAA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATAA
* * *
3448117 TATATAAATGTTTGCAAACATGTTTTCAAAACTATATATTA
1 TATAT--AT-TTT-TAAAAATGTTTTAAAAACTATATA--A
* * * *
3448158 TATATAGTTTAAAAAATGTTTT-CAAACTATACAA
1 TATATATTTTTAAAAATGTTTTAAAAACTATATAA
3448192 TATATAT
1 TATATAT
3448199 ATATATATAT
Statistics
Matches: 285, Mismatches: 41, Indels: 60
0.74 0.11 0.16
Matches are distributed among these distances:
28 4 0.01
29 40 0.14
31 6 0.02
32 2 0.01
33 2 0.01
34 26 0.09
35 46 0.16
36 69 0.24
37 55 0.19
38 8 0.03
39 21 0.07
41 6 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATATTTTTAAAAATGTTTTAAAAACTATATAA
Found at i:3447977 original size:100 final size:100
Alignment explanation
Indices: 3447791--3448115 Score: 440
Period size: 100 Copynumber: 3.2 Consensus size: 100
3447781 TATTATTATA
* * * *
3447791 AAAAATGTTTTCAAAATTATATAGT-TTTTAAAAATGTTCTTAAAACTTATAT-ATCATATAAGT
1 AAAAATGTTTTAAAAACTATATA-TATTTTCAAAATGTT-TTAAAAATTATATAAT-ATAT-A-T
** * * * * *
3447854 TTTC-AAAATAATGTCAAAACTATATAATATATGTGTTTT
61 TTTCAAAAATGCTTTAAAAACTATATATTATATTTATTTT
* *
3447893 AAAAATGCTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTTTATAATATATATTTTCA
1 AAAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCA
3447958 AAAATGCTTTAAAAACTATATATTATATTTATTTT
66 AAAATGCTTTAAAAACTATATATTATATTTATTTT
* *
3447993 TAAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCA
1 AAAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCA
3448058 AAAATGCTTTAAAAACTATATATTATATTTATTTT
66 AAAATGCTTTAAAAACTATATATTATATTTATTTT
*
3448093 TAAAATGTTTTAAAAACTATATA
1 AAAAATGTTTTAAAAACTATATA
3448116 ATATATAAAT
Statistics
Matches: 203, Mismatches: 17, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
99 5 0.02
100 148 0.73
101 16 0.08
102 34 0.17
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (100 bp):
AAAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCA
AAAATGCTTTAAAAACTATATATTATATTTATTTT
Found at i:3448019 original size:29 final size:29
Alignment explanation
Indices: 3447981--3448080 Score: 119
Period size: 29 Copynumber: 3.2 Consensus size: 29
3447971 AACTATATAT
*
3447981 TATATTTATTTTTAAAATGTTTTAAAAAC
1 TATATATATTTTTAAAATGTTTTAAAAAC
*
3448010 TATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTTTAAAATGTTTTAAAAAC
*
3448039 TATATAATATATATTTTCAAAAATGCTTTAAAAAC
1 --TAT-ATATAT-TTTT--AAAATGTTTTAAAAAC
3448074 TATATAT
1 TATATAT
3448081 TATATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
29 27 0.44
31 3 0.05
32 10 0.16
33 6 0.10
35 15 0.25
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATATATTTTTAAAATGTTTTAAAAAC
Found at i:3448194 original size:75 final size:72
Alignment explanation
Indices: 3448010--3448197 Score: 245
Period size: 75 Copynumber: 2.6 Consensus size: 72
3448000 TTTTAAAAAC
*
3448010 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATAT-ATTTTCAAAAATGCTTTAAAAAC
1 TATATATATTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTCAAAAATGCTTTAAAAAC
3448074 TATATAT
66 TATATAT
* * * * *
3448081 TATATTTATTTTTAAAATGTTTTAAAAACTATATAATATATAAATGTTTGCAAACATGTTTTCAA
1 TATATATATTTTAAAAATGTTTTAAAAACTATATAATATAT-AAT-TTT-CAAAAATGCTTTAAA
3448146 AACTATATAT
63 AACTATATAT
* * *
3448156 TATATATAGTTTAAAAAATGTTTT-CAAACTATACAATATATA
1 TATATATA-TTTTAAAAATGTTTTAAAAACTATATAATATATA
3448198 TATATATATA
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
71 39 0.38
73 2 0.02
74 4 0.04
75 44 0.43
76 13 0.13
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (72 bp):
TATATATATTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTCAAAAATGCTTTAAAAAC
TATATAT
Found at i:3448198 original size:2 final size:2
Alignment explanation
Indices: 3448191--3448247 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
3448181 AAACTATACA
*
3448191 AT AT AT AT AT AT AT AT AT AT AT AT GT 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
*
3448233 AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT A
3448248 AAAAGACGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3448199 original size:36 final size:35
Alignment explanation
Indices: 3447869--3448200 Score: 260
Period size: 35 Copynumber: 9.6 Consensus size: 35
3447859 AAATAATGTC
* * * *
3447869 AAAACTATATAATATATGTGTTTTAAAAATGCTTT
1 AAAACTATATAATATATATATTTCAAAAATGTTTT
*
3447904 AAAA--A-CT-ATATATAT-TTTC-AAAATGTTTT
1 AAAACTATATAATATATATATTTCAAAAATGTTTT
* * *
3447933 AAAAATTTTATAATATATAT-TTTCAAAAATGCTTTA
1 -AAAACTATATAATATATATATTTCAAAAATG-TTTT
* * **
3447969 AAAACTATATATTATATTTATTTTTAAAATGTTTT
1 AAAACTATATAATATATATATTTCAAAAATGTTTT
*
3448004 AAAA--A-CT-ATATATAT-TTTC-AAAATGTTTT
1 AAAACTATATAATATATATATTTCAAAAATGTTTT
*
3448033 AAAAACTATATAATATATAT-TTTCAAAAATGCTTTA
1 -AAAACTATATAATATATATATTTCAAAAATG-TTTT
* * **
3448069 AAAACTATATATTATATTTATTTTTAAAATGTTTT
1 AAAACTATATAATATATATATTTCAAAAATGTTTT
* *
3448104 AAAAACTATATAATATATAAATGTTTGCAAACATGTTTT
1 -AAAACTATATAATATAT--ATATTT-CAAAAATGTTTT
* *
3448143 CAAAACTATATATTATATATAGTTTAAAAAATGTTTT
1 -AAAACTATATAATATATATA-TTTCAAAAATGTTTT
* *
3448180 CAAACTATACAATATATATAT
1 AAAACTATATAATATATATAT
3448201 ATATATATAT
Statistics
Matches: 237, Mismatches: 39, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
29 19 0.08
30 14 0.06
31 13 0.05
32 3 0.01
33 4 0.02
34 24 0.10
35 59 0.25
36 57 0.24
37 12 0.05
38 7 0.03
39 25 0.11
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAACTATATAATATATATATTTCAAAAATGTTTT
Found at i:3449101 original size:84 final size:83
Alignment explanation
Indices: 3448834--3449546 Score: 669
Period size: 84 Copynumber: 8.6 Consensus size: 83
3448824 ATATAACCTC
* * * *
3448834 GAAGTTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
1 GAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
*
3448899 GCTGCAAATGATGTGCCCTC
65 GCTGCAAATGATGTG-CCTT
** * * * * *
3448919 GAAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTCAAGCTATT
1 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
3448981 CTGCAAATGATGTGCCTT
66 CTGCAAATGATGTGCCTT
* * * * * ** * * *
3448999 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCTTTCTAGCCTTGAGTTATG
1 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * *
3449064 CTGTAAATGTTATGCCCTT
66 CTGCAAATGATGTG-CCTT
* * * *
3449083 GAAGCTGAGTGTAATCGAACT-TAAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 GAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
*
3449144 TCTGCAAATGATGTGCCTT
65 GCTGCAAATGATGTGCCTT
* * *
3449163 CGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
1 -GAAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTA
*
3449228 TGCTGCAAATGATATGCCTT
64 TGCTGCAAATGATGTGCCTT
* ** * *
3449248 GGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
1 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
3449313 GCTGCAAATGATGTGCCGTT
65 GCTGCAAATGATGTGCC-TT
* * * * * *
3449333 G-AGCTGAGCGTAGTCGAACTCGACGGTCTTGTGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* * * * *
3449397 GCTGTAAACGATATAACCTC
65 GCTGCAAATGATGT-GCCTT
* ** * * * * * *
3449417 GAAGTTGAACGTAGTCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATT
1 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
3449479 CTGCAAATGATGTGCCTT
66 CTGCAAATGATGTGCCTT
* * * *
3449497 GGAGCTGAGCT-TAATCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTCT
1 GAAGCTGAG-TGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
3449547 GGCCTTGAGC
Statistics
Matches: 508, Mismatches: 101, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
80 55 0.11
81 132 0.26
82 22 0.04
83 37 0.07
84 164 0.32
85 98 0.19
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATGTGCCTT
Found at i:3449248 original size:249 final size:245
Alignment explanation
Indices: 3448790--3449527 Score: 823
Period size: 249 Copynumber: 3.0 Consensus size: 245
3448780 TTATTGACAA
* * * * ** * *
3448790 ATAACCCTTCTGGCCTTGAGCTATGTTGTAAACGATATAACCTCGAAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT
* *
3448855 CAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCG
66 CAAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCG
* *
3448920 AAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTCAAGCTATTCTGC
126 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
* *
3448985 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCTAACAG
191 AAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGCTAACAG
* *
3449039 ATAACCTTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT
* * * * * *
3449104 TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTCGAAGC
66 CAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TCGAAGC
* * * * * * * *
3449169 TGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
130 TGAGTGTAATCGAACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
* * **
3449234 AAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAG
191 AAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGCTAACAG
* * * * * * * *
3449289 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT
* * * * * * * *
3449353 CGACGGTCTTGTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAACGATATAACCTCG
66 CAAAGGTCTT-TG--G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT-GCCTCG
* ** *
3449418 AAGTTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
126 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
* *
3449483 AAATGATGTGCCTTGGAGCTGAGCTTAATCGAACTCGAAGGTCTT
191 AAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTT
3449528 GGTGGCAGGT
Statistics
Matches: 406, Mismatches: 72, Indels: 22
0.81 0.14 0.04
Matches are distributed among these distances:
244 2 0.00
245 68 0.17
246 1 0.00
248 1 0.00
249 229 0.56
250 45 0.11
252 1 0.00
253 57 0.14
254 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (245 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT
CAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCT
GAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATG
ATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGCTAACAG
Found at i:3453565 original size:15 final size:16
Alignment explanation
Indices: 3453545--3453574 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3453535 TGCGAATGAT
3453545 GAAC-AAAATAAAAGA
1 GAACAAAAATAAAAGA
3453560 GAACAAAAATAAAAG
1 GAACAAAAATAAAAG
3453575 GGTTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (16 bp):
GAACAAAAATAAAAGA
Found at i:3454852 original size:24 final size:23
Alignment explanation
Indices: 3454801--3454852 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
3454791 ATATGAGGTA
3454801 AAAATAATAATAAAAAAAAACAT
1 AAAATAATAATAAAAAAAAACAT
*
3454824 --GATAATAATAAATAAATAAA-AT
1 AAAATAATAATAAA-AAA-AAACAT
3454846 AAAATAA
1 AAAATAA
3454853 GAAGTTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 3 0.13
24 4 0.17
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAATAATAATAAAAAAAAACAT
Found at i:3456151 original size:66 final size:64
Alignment explanation
Indices: 3456088--3456216 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 64
3456078 ATCATATAAG
* * *
3456088 TTTTCAAAATAATGTCAAAACTATATAATATATGTGTTTTAAAAATGCTTTAAAAAACTATATAT
1 TTTTCAAAATAATGTAAAAACTATATAATATATAT-TTTCAAAAATGCTTT-AAAAACTATATAT
3456153 A
64 A
** * *
3456154 TTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCAAAAATGCTTTAAAAACTATATAT
1 TTTTCAAAATAATGTAAAAACTATATAATATATATTTTCAAAAATGCTTTAAAAACTATATAT
3456217 TATATTTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 13 0.23
65 14 0.25
66 29 0.52
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (64 bp):
TTTTCAAAATAATGTAAAAACTATATAATATATATTTTCAAAAATGCTTTAAAAACTATATATA
Found at i:3456196 original size:100 final size:100
Alignment explanation
Indices: 3456027--3456351 Score: 449
Period size: 100 Copynumber: 3.2 Consensus size: 100
3456017 ATTATTATAA
* * * *
3456027 AAAATGTTTTCAAAATTATATAGT-TTTTAAAAATGTTCTTAAAACTTATAT-ATCATATAAGTT
1 AAAATGTTTTAAAAACTATATA-TATTTTCAAAATGTT-TTAAAAATTATATAAT-ATAT-A-TT
** * * * * * *
3456090 TTC-AAAATAATGTCAAAACTATATAATATATGTGTTTTA
61 TTCAAAAATGCTTTAAAAACTATATATTATATTTATTTTT
*
3456129 AAAATGCTTTAAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCA
1 AAAATG-TTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCA
3456194 AAAATGCTTTAAAAACTATATATTATATTTATTTTT
65 AAAATGCTTTAAAAACTATATATTATATTTATTTTT
*
3456230 AAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCAA
1 AAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCAA
3456295 AAATGCTTTAAAAACTATATATTATATTTATTTTT
66 AAATGCTTTAAAAACTATATATTATATTTATTTTT
3456330 AAAATGTTTTAAAAACTATATA
1 AAAATGTTTTAAAAACTATATA
3456352 ATATATAAAT
Statistics
Matches: 204, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
100 119 0.58
101 35 0.17
102 23 0.11
103 27 0.13
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (100 bp):
AAAATGTTTTAAAAACTATATATATTTTCAAAATGTTTTAAAAATTATATAATATATATTTTCAA
AAATGCTTTAAAAACTATATATTATATTTATTTTT
Found at i:3456241 original size:36 final size:36
Alignment explanation
Indices: 3456041--3456415 Score: 295
Period size: 36 Copynumber: 10.7 Consensus size: 36
3456031 TGTTTTCAAA
3456041 ATTATATAGT-TTTTAAAAATGTTCTT-AAAACTTATAT
1 ATTATATA-TATTTTAAAAATGTT-TTAAAAAC-TATAT
* * ** * *
3456078 ATCATATA-AGTTTTCAAAATAATGTCAAAACTATAT
1 ATTATATATA-TTTTAAAAATGTTTTAAAAACTATAT
* * * *
3456114 AATATATGTGTTTTAAAAATGCTTT--AAA--A-A-
1 ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
* *
3456144 ACTATATATATTTTCAAAATGTTTTAAAAA-T-TAT
1 ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
* *
3456178 ATAATATATATTTTCAAAAATGCTTTAAAAACTATAT
1 ATTATATATATTTT-AAAAATGTTTTAAAAACTATAT
* *
3456215 ATTATATTTATTTTTAAAATGTTTTAAAAAC-----
1 ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
*
3456246 --TATATATATTTTCAAAATGTTTTAAAAACTATAT
1 ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
*
3456280 A--ATATATATTTTCAAAAATGCTTTAAAAACTATAT
1 ATTATATATATTTT-AAAAATGTTTTAAAAACTATAT
* *
3456315 ATTATATTTATTTTTAAAATGTTTTAAAAACTATAT
1 ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
* * * *
3456351 AATATATAAATGTTTGCAAACATGTTTTCAAAACTATAT
1 ATTATATATAT-TTT--AAAAATGTTTTAAAAACTATAT
*
3456390 ATTATATATAGTTTAAAAAATGTTTT
1 ATTATATATA-TTTTAAAAATGTTTT
3456416 CCAACTATAC
Statistics
Matches: 270, Mismatches: 43, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
29 27 0.10
30 20 0.07
31 1 0.00
32 4 0.01
33 1 0.00
34 26 0.10
35 35 0.13
36 66 0.24
37 60 0.22
39 29 0.11
40 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (36 bp):
ATTATATATATTTTAAAAATGTTTTAAAAACTATAT
Found at i:3456250 original size:64 final size:63
Alignment explanation
Indices: 3456181--3456317 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 63
3456171 AAATTATATA
* * *
3456181 ATATATATTTTCAAAAATGCTTTAAAAACTATATATTATATTTATTTT-TAAAATGTTTTAAAAA
1 ATATATATTTTC-AAAATGCTTTAAAAACTATATA--ATATATATTTTCAAAAATGCTTTAAAAA
3456245 C
63 C
*
3456246 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCAAAAATGCTTTAAAAAC
1 -ATATATATTTTCAAAATGCTTTAAAAACTATATAATATATATTTTCAAAAATGCTTTAAAAAC
3456310 -TATATATT
1 ATATATATT
3456318 ATATTTATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
62 8 0.12
63 10 0.15
64 15 0.23
65 21 0.32
66 12 0.18
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (63 bp):
ATATATATTTTCAAAATGCTTTAAAAACTATATAATATATATTTTCAAAAATGCTTTAAAAAC
Found at i:3456255 original size:29 final size:29
Alignment explanation
Indices: 3456217--3456316 Score: 119
Period size: 29 Copynumber: 3.2 Consensus size: 29
3456207 AACTATATAT
*
3456217 TATATTTATTTTTAAAATGTTTTAAAAAC
1 TATATATATTTTTAAAATGTTTTAAAAAC
*
3456246 TATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTTTAAAATGTTTTAAAAAC
*
3456275 TATATAATATATATTTTCAAAAATGCTTTAAAAAC
1 --TAT-ATATAT-TTTT--AAAATGTTTTAAAAAC
3456310 TATATAT
1 TATATAT
3456317 TATATTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
29 27 0.44
31 3 0.05
32 10 0.16
33 6 0.10
35 15 0.25
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (29 bp):
TATATATATTTTTAAAATGTTTTAAAAAC
Found at i:3456430 original size:75 final size:72
Alignment explanation
Indices: 3456246--3456433 Score: 236
Period size: 75 Copynumber: 2.6 Consensus size: 72
3456236 TTTTAAAAAC
*
3456246 TATATATATTTTCAAAATGTTTTAAAAACTATATAATATAT-ATTTTCAAAAATGCTTTAAAAAC
1 TATATATATTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTCAAAAATGCTTTAAAAAC
3456310 TATATAT
66 TATATAT
* * * * *
3456317 TATATTTATTTTTAAAATGTTTTAAAAACTATATAATATATAAATGTTTGCAAACATGTTTTCAA
1 TATATATATTTTAAAAATGTTTTAAAAACTATATAATATAT-AAT-TTT-CAAAAATGCTTTAAA
3456382 AACTATATAT
63 AACTATATAT
* ** *
3456392 TATATATAGTTTAAAAAATGTTTT-CCAACTATACAATATATA
1 TATATATA-TTTTAAAAATGTTTTAAAAACTATATAATATATA
3456434 TATATATGTA
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
71 39 0.39
73 2 0.02
74 4 0.04
75 43 0.43
76 13 0.13
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (72 bp):
TATATATATTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTCAAAAATGCTTTAAAAAC
TATATAT
Found at i:3457237 original size:172 final size:175
Alignment explanation
Indices: 3456938--3457295 Score: 686
Period size: 172 Copynumber: 2.1 Consensus size: 175
3456928 ATCAAATTGG
3456938 AAATCATGGAAATACTACCCCATGAAATTAAACCATATTGGAATAATTAGGGGAAAATATGCAAA
1 AAAT-ATGGAAATACTACCCCATGAAATTAAACCATATTGGAATAATTAGGGGAAAATATGCAAA
3457003 AAATTCCCTAAGCCTAGAAATGATGTATGAAAGATTCTACATGCTTTGGAATGTGATTTGCA-CG
65 AAATTCCCTAAGCCTAGAAATGATGTATGAAAGATTCTACATGCTTTGGAATGTGATTTGCACCG
3457067 ATTTAAAAGTTTGCACATGTATGGGGATC-AATCACAAATAATGGA
130 ATTTAAAAGTTTGCACATGTATGGGGATCAAATCACAAATAATGGA
3457112 AAATATGGAAA-ACTACCCCATGAAATTAAACCATATTGGAATAATTAGGGGAAAATATGCAAAA
1 AAATATGGAAATACTACCCCATGAAATTAAACCATATTGGAATAATTAGGGGAAAATATGCAAAA
3457176 AATTCCCTAAGCCTAGAAATGATGTATGAAAGATTCTACATGCTTTGGAATGTGATTTGCACCGA
66 AATTCCCTAAGCCTAGAAATGATGTATGAAAGATTCTACATGCTTTGGAATGTGATTTGCACCGA
3457241 TTTAAAAGTTTGCACATGTATGGGGATCAAATCACAAATAATGGA
131 TTTAAAAGTTTGCACATGTATGGGGATCAAATCACAAATAATGGA
3457286 AAATATGGAA
1 AAATATGGAA
3457296 TTTTAAGTGG
Statistics
Matches: 182, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
172 114 0.63
173 38 0.21
174 30 0.16
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (175 bp):
AAATATGGAAATACTACCCCATGAAATTAAACCATATTGGAATAATTAGGGGAAAATATGCAAAA
AATTCCCTAAGCCTAGAAATGATGTATGAAAGATTCTACATGCTTTGGAATGTGATTTGCACCGA
TTTAAAAGTTTGCACATGTATGGGGATCAAATCACAAATAATGGA
Found at i:3460188 original size:24 final size:24
Alignment explanation
Indices: 3460156--3460204 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3460146 CCAAGGTGTT
3460156 GGGACCGTCGACGCACCCCATGGC
1 GGGACCGTCGACGCACCCCATGGC
3460180 GGGACCGTCGACGCACCCCATGGC
1 GGGACCGTCGACGCACCCCATGGC
3460204 G
1 G
3460205 CAACCTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.41, G:0.35, T:0.08
Consensus pattern (24 bp):
GGGACCGTCGACGCACCCCATGGC
Found at i:3475158 original size:13 final size:13
Alignment explanation
Indices: 3475140--3475168 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3475130 CCTTGAGCTT
3475140 TCACTTACTTCTC
1 TCACTTACTTCTC
3475153 TCACTTACTTCTC
1 TCACTTACTTCTC
3475166 TCA
1 TCA
3475169 ATAGAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (13 bp):
TCACTTACTTCTC
Found at i:3476724 original size:27 final size:26
Alignment explanation
Indices: 3476666--3476726 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3476656 AACCCAATCC
* * *
3476666 GACCAGAAAATTATACATCCTCTACCA
1 GACCA-AAAAATATACACCCTCCACCA
*
3476693 GACCAAAAAATATACACCCTCCACCC
1 GACCAAAAAATATACACCCTCCACCA
3476719 GAACCAAA
1 G-ACCAAA
3476727 CCTAACTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.44, C:0.34, G:0.07, T:0.15
Consensus pattern (26 bp):
GACCAAAAAATATACACCCTCCACCA
Found at i:3476794 original size:17 final size:19
Alignment explanation
Indices: 3476762--3476822 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
3476752 ATCTGACCCG
3476762 AAATA-ATATATTTATTAAA
1 AAATATATAT-TTTATTAAA
3476781 AAATAT-T-TTTTATTCAATAA
1 AAATATATATTTTATT--A-AA
*
3476801 AAATATATATTTAATTAAA
1 AAATATATATTTTATTAAA
3476820 AAA
1 AAA
3476823 ATAATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 12 0.34
20 9 0.26
21 1 0.03
22 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATATATTTTATTAAA
Found at i:3476813 original size:21 final size:20
Alignment explanation
Indices: 3476762--3476831 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
3476752 ATCTGACCCG
3476762 AAATAATATATTTATT-AAA
1 AAATAATATATTTATTAAAA
*
3476781 AAAT-AT-TTTTTATTCAATAA
1 AAATAATATATTTATT-AA-AA
3476801 AAAT-ATATATTTAATTAAAA
1 AAATAATATATTT-ATTAAAA
3476821 AAATAATATAT
1 AAATAATATAT
3476832 AGAGCGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 7 0.16
18 2 0.05
19 5 0.12
20 14 0.33
21 12 0.28
22 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAATATATTTATTAAAA
Found at i:3479138 original size:20 final size:20
Alignment explanation
Indices: 3479115--3479177 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
3479105 CTACCTTTTG
* *
3479115 AGTATTGATACCCTATGAAC
1 AGTATCGATACCTTATGAAC
3479135 AGTATCGATACCTTATGAAC
1 AGTATCGATACCTTATGAAC
3479155 AGTATCGATACCTTATGAAC
1 AGTATCGATACCTTATGAAC
3479175 AGT
1 AGT
3479178 TCTACACTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
AGTATCGATACCTTATGAAC
Found at i:3480935 original size:131 final size:131
Alignment explanation
Indices: 3480788--3481052 Score: 496
Period size: 131 Copynumber: 2.0 Consensus size: 131
3480778 AATTTTAATG
3480788 AAATTTACCTTTTTAATTTTTTTAGTTTTATATTAAAGAAAATATATTATGTCAAATATATTTTT
1 AAATTTACCTTTTTAATTTTTTTAGTTTTATATTAAAGAAAATATATTATGTCAAATATATTTTT
*
3480853 ATATTATAAAAA-ATATTACTAAAATATTTATATCAAATTCATCCTTTCAACTGATTAATCAATA
66 ATATTATAAAAATA-AGTACTAAAATATTTATATCAAATTCATCCTTTCAACTGATTAATCAATA
3480917 TA
130 TA
3480919 AAATTTACCTTTTTAATTTTTTTAGTTTTATATTAAAGAAAATATATTATGTCAAATATATTTTT
1 AAATTTACCTTTTTAATTTTTTTAGTTTTATATTAAAGAAAATATATTATGTCAAATATATTTTT
*
3480984 ATATTATAAAAATAAGTACTAAAATATTTATATCAAATTCATCCTTTCAACTGATTAATCGATAT
66 ATATTATAAAAATAAGTACTAAAATATTTATATCAAATTCATCCTTTCAACTGATTAATCAATAT
3481049 A
131 A
3481050 AAA
1 AAA
3481053 GTTTTTTATA
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
131 130 0.99
132 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (131 bp):
AAATTTACCTTTTTAATTTTTTTAGTTTTATATTAAAGAAAATATATTATGTCAAATATATTTTT
ATATTATAAAAATAAGTACTAAAATATTTATATCAAATTCATCCTTTCAACTGATTAATCAATAT
A
Found at i:3486576 original size:138 final size:138
Alignment explanation
Indices: 3486328--3486604 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
3486318 TGTAATTTTT
3486328 TTCATAAATGTTGTGTGACATCTCTAACTCGTATTTGGGGATGAATACGGGAAAGTGGTATTATA
1 TTCATAAATGTTGTGTGACATCTCTAACTCGTATTTGGGGATGAATACGGGAAAGTGGTATTATA
3486393 TTTATTGGTATTAGAGTTGTAGGCTTAGTTGATTCTAGGCCTAAATAGAGTTTATTTTAAAGTGA
66 TTTATTGGTATTAGAGTTGTAGGCTTAGTTGATTCTAGGCCTAAATAGAGTTTATTTTAAAGTGA
3486458 AAAATGTG
131 AAAATGTG
3486466 TTCATAAATGTTGTGTGACATCTCTAACTCGTATTTGGGGATGAATACGGGAAAGTGGTATTATA
1 TTCATAAATGTTGTGTGACATCTCTAACTCGTATTTGGGGATGAATACGGGAAAGTGGTATTATA
3486531 TTTATTGGTATTAGAGTTGTAGGCTTAGTTGATTCTAGGCCTAAATAGAGTTTATTTTAAAGTGA
66 TTTATTGGTATTAGAGTTGTAGGCTTAGTTGATTCTAGGCCTAAATAGAGTTTATTTTAAAGTGA
3486596 AAAATGTG
131 AAAATGTG
3486604 T
1 T
3486605 ACATGTCATT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.39
Consensus pattern (138 bp):
TTCATAAATGTTGTGTGACATCTCTAACTCGTATTTGGGGATGAATACGGGAAAGTGGTATTATA
TTTATTGGTATTAGAGTTGTAGGCTTAGTTGATTCTAGGCCTAAATAGAGTTTATTTTAAAGTGA
AAAATGTG
Found at i:3489499 original size:16 final size:16
Alignment explanation
Indices: 3489478--3489511 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3489468 AAAAAGAGTT
3489478 AGTTAGATGGCTTATC
1 AGTTAGATGGCTTATC
3489494 AGTTAGATGGCTTATC
1 AGTTAGATGGCTTATC
3489510 AG
1 AG
3489512 CTAGCTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (16 bp):
AGTTAGATGGCTTATC
Found at i:3490767 original size:109 final size:108
Alignment explanation
Indices: 3490577--3490793 Score: 425
Period size: 109 Copynumber: 2.0 Consensus size: 108
3490567 ATGTAATGGA
3490577 AGTTCTGGAATCATTTCCATGCATGAAACTTGAATAAACAATTAGAAATGCATTAAGATGAATTC
1 AGTTCTGGAATCATTTCCATGCATGAAACTTGAATAAACAATTAGAAATGCATTAAGATGAATTC
3490642 GACTAAGGTTAGGGCTTATAGAGACGATTGAATTTGGATTTTT
66 GACTAAGGTTAGGGCTTATAGAGACGATTGAATTTGGATTTTT
3490685 AGTTCTGGAATCATTTCCATGCATGAAACTTGAATTAAACAATTAGAAATGCATTAAGATGAATT
1 AGTTCTGGAATCATTTCCATGCATGAAACTTGAA-TAAACAATTAGAAATGCATTAAGATGAATT
3490750 CGACTAAGGTTAGGGCTTATAGAGACGATTGAATTTGGATTTTT
65 CGACTAAGGTTAGGGCTTATAGAGACGATTGAATTTGGATTTTT
3490794 TTATATGGAA
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 34 0.31
109 74 0.69
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (108 bp):
AGTTCTGGAATCATTTCCATGCATGAAACTTGAATAAACAATTAGAAATGCATTAAGATGAATTC
GACTAAGGTTAGGGCTTATAGAGACGATTGAATTTGGATTTTT
Found at i:3494185 original size:16 final size:17
Alignment explanation
Indices: 3494164--3494197 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3494154 ATATATCCGG
*
3494164 ATAATA-AATTGTTGAA
1 ATAATATAATTATTGAA
3494180 ATAATATAATTATTGAA
1 ATAATATAATTATTGAA
3494197 A
1 A
3494198 ATAAATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
ATAATATAATTATTGAA
Found at i:3494429 original size:21 final size:21
Alignment explanation
Indices: 3494376--3494432 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3494366 ACCGTTATGG
* * *
3494376 TGTTGACGTGGCAGTTTACGA
1 TGTTGACGTGGTAGTTAACAA
* *
3494397 TGTTGATGTGGTGGTTAACAA
1 TGTTGACGTGGTAGTTAACAA
3494418 TGTTGACGTGGTAGT
1 TGTTGACGTGGTAGT
3494433 CCATAGTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.09, G:0.35, T:0.37
Consensus pattern (21 bp):
TGTTGACGTGGTAGTTAACAA
Found at i:3494779 original size:22 final size:24
Alignment explanation
Indices: 3494751--3494800 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
3494741 ACCTGATATG
*
3494751 ACCAG-AAAAT-TATACATCCTCC
1 ACCAGAAAAATATATACACCCTCC
3494773 ACCAGAAAAAATATATACACCCTCC
1 ACCAG-AAAAATATATACACCCTCC
3494798 ACC
1 ACC
3494801 CGAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
24 5 0.21
25 14 0.58
ACGTcount: A:0.44, C:0.34, G:0.04, T:0.18
Consensus pattern (24 bp):
ACCAGAAAAATATATACACCCTCC
Found at i:3496599 original size:194 final size:198
Alignment explanation
Indices: 3496245--3496638 Score: 726
Period size: 194 Copynumber: 2.0 Consensus size: 198
3496235 GGCTTAACCT
3496245 GCCACCAAACAACAGCCCCACGCCCCACGCCATACCCTGCAGCAGCAAGGTCACCATCTCCAACA
1 GCCACCAAACAACAGCCCCACGCCCCACGCCATACCCTGCAGCAGCAAGGTCACCATCTCCAACA
3496310 ATTTATGGCACCTTCAACTGCCAATCATTTTTTAATTTCATTTTCAGATTGTAATGGGTATAAAA
66 ATTTATGGCACCTTCAACT-CCAA-CATTTTTTAATTTCATTTTCAGATTGTAATGGGTATAAAA
3496375 CTAGAGAAAACAAACAATGTAAGGGATTTTTCAGCAATAAATATTTTTCTCAGCACTAGAAATTT
129 CTAGAGAAAACAAACAATGTAAGGGATTTTTCAGCAATAAATATTTTTCTCAGCACTAGAAATTT
3496440 ACGAG
194 ACGAG
3496445 GCCACCCAAACAACAG-CCC-CGCCCCACGCCATACCCTGCAGCAGCAAGGTCACCATCTCCAAC
1 GCCA-CCAAACAACAGCCCCACGCCCCACGCCATACCCTGCAGCAGCAAGGTCACCATCTCCAAC
3496508 AATTTATGGCACCTTCAACT-C-A-ATTTTTTAATTTCATTTTCAGATTGTAATGGGTATAAAAC
65 AATTTATGGCACCTTCAACTCCAACATTTTTTAATTTCATTTTCAGATTGTAATGGGTATAAAAC
3496570 TAGAGAAAACAAACAATGTAAGGGATTTTTCAGCAATAAATATTTTTCTCAGCACTAGAAATTTA
130 TAGAGAAAACAAACAATGTAAGGGATTTTTCAGCAATAAATATTTTTCTCAGCACTAGAAATTTA
3496635 CGAG
195 CGAG
3496639 CAAAGAGAAT
Statistics
Matches: 193, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
194 109 0.56
196 1 0.01
197 1 0.01
199 64 0.33
200 7 0.04
201 11 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (198 bp):
GCCACCAAACAACAGCCCCACGCCCCACGCCATACCCTGCAGCAGCAAGGTCACCATCTCCAACA
ATTTATGGCACCTTCAACTCCAACATTTTTTAATTTCATTTTCAGATTGTAATGGGTATAAAACT
AGAGAAAACAAACAATGTAAGGGATTTTTCAGCAATAAATATTTTTCTCAGCACTAGAAATTTAC
GAG
Found at i:3497745 original size:26 final size:26
Alignment explanation
Indices: 3497714--3497770 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3497704 TTTATGTTTT
3497714 TTTACTTAAGTAATTTAATTTCTTTA
1 TTTACTTAAGTAATTTAATTTCTTTA
*
3497740 TTTACTTAAGTACTTTAATTTCTTTA
1 TTTACTTAAGTAATTTAATTTCTTTA
3497766 TTTAC
1 TTTAC
3497771 ATTTGTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTACTTAAGTAATTTAATTTCTTTA
Found at i:3499276 original size:20 final size:20
Alignment explanation
Indices: 3499251--3499298 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3499241 TGGAACGTGG
3499251 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
3499271 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
3499291 GGGGAATC
1 GGGGAATC
3499299 AGTTTCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:3501954 original size:20 final size:22
Alignment explanation
Indices: 3501908--3501954 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
3501898 TTCCCCTGTG
*
3501908 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCAGTTCCCCTTCAA
*
3501930 -AGGGAATCAGTT-CCC-TCAA
1 GGGGGAATCAGTTCCCCTTCAA
3501949 GGGGGA
1 GGGGGA
3501955 TCGATTCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.19
Consensus pattern (22 bp):
GGGGGAATCAGTTCCCCTTCAA
Found at i:3509488 original size:20 final size:20
Alignment explanation
Indices: 3509463--3509500 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3509453 TCCCTTTTTT
*
3509463 GCATCTTTGCATTTGCATGA
1 GCATCTTTGCATTAGCATGA
3509483 GCATCTTTGCATTAGCAT
1 GCATCTTTGCATTAGCAT
3509501 CTATACATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
GCATCTTTGCATTAGCATGA
Found at i:3512957 original size:31 final size:31
Alignment explanation
Indices: 3512850--3512961 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
3512840 TCTCTGCTCT
* * *
3512850 GACTGGTAATTCCTTGTATAGGTTCTGCACC
1 GACTGGTAATTCCTTTTATAGGTTCAGCATC
* **
3512881 GACTGGTAATTTCTATCTCTGGCAGGTTCAG--TC
1 GACTGGTAATTCCT-T-T-T-ATAGGTTCAGCATC
* *
3512914 GCTATTGATAATTCCTTTTATAGGTTCAGCATC
1 G--ACTGGTAATTCCTTTTATAGGTTCAGCATC
3512947 GACTGGTAATTCCTT
1 GACTGGTAATTCCTT
3512962 ATGGACCTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
31 33 0.55
32 2 0.03
33 6 0.10
34 2 0.03
35 17 0.28
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
GACTGGTAATTCCTTTTATAGGTTCAGCATC
Found at i:3515229 original size:28 final size:28
Alignment explanation
Indices: 3515193--3515260 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
3515183 GGGATGGTTG
*
3515193 AAATA-CCCTGGATCTATAAAAT-ACCCA
1 AAATACCCCTGGATCAATAAAATGA-CCA
*
3515220 AAATACCCCTAGATCAATAAAATGACCA
1 AAATACCCCTGGATCAATAAAATGACCA
*
3515248 AAATACCACTGGA
1 AAATACCCCTGGA
3515261 ATGTAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.14
28 29 0.83
29 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.09, T:0.19
Consensus pattern (28 bp):
AAATACCCCTGGATCAATAAAATGACCA
Found at i:3516351 original size:19 final size:19
Alignment explanation
Indices: 3516327--3516371 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3516317 GTGGGTGCTT
3516327 ACCGGCTGAACTGGTCTAG
1 ACCGGCTGAACTGGTCTAG
3516346 ACCGGCTGAACTGGTCTAG
1 ACCGGCTGAACTGGTCTAG
3516365 ACCGGCT
1 ACCGGCT
3516372 TGACCGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.20
Consensus pattern (19 bp):
ACCGGCTGAACTGGTCTAG
Found at i:3516380 original size:19 final size:19
Alignment explanation
Indices: 3516327--3516381 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3516317 GTGGGTGCTT
*
3516327 ACCGGCTGAACTGGTCTAG
1 ACCGGCTGAACCGGTCTAG
*
3516346 ACCGGCTGAACTGGTCTAG
1 ACCGGCTGAACCGGTCTAG
3516365 ACCGGCTTG-ACCGGTCT
1 ACCGGC-TGAACCGGTCT
3516382 GGTATGAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 32 0.94
20 2 0.06
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (19 bp):
ACCGGCTGAACCGGTCTAG
Found at i:3516514 original size:66 final size:67
Alignment explanation
Indices: 3516395--3516522 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
3516385 ATGAAGATTG
* * * * * *
3516395 TGGCAGGTTCAGTCGTTGTGGGTTATTTCTTTGTATAGGTTCTGTATCGACTGGTAATTCCTATC
1 TGGCAGGTTCAGTCGCTGTGGATAATTCCTTTGTATAGGTTCAGTAACGACTGGTAATTCCTATC
3516460 TC
66 TC
*
3516462 TGGCAGGTTCAGTCGCTGTTGATAATTCCTTT-TATAGGTTCAG-AACGGACTGGTAATTCCT
1 TGGCAGGTTCAGTCGCTGTGGATAATTCCTTTGTATAGGTTCAGTAAC-GACTGGTAATTCCT
3516523 TATAGACCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.04
66 24 0.45
67 27 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (67 bp):
TGGCAGGTTCAGTCGCTGTGGATAATTCCTTTGTATAGGTTCAGTAACGACTGGTAATTCCTATC
TC
Found at i:3517385 original size:17 final size:16
Alignment explanation
Indices: 3517357--3517443 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 16
3517347 AAAAAGACGT
*
3517357 AAAAAGATAGAAAAGA
1 AAAAAAATAGAAAAGA
3517373 AAGAAAAATAGAAAA-A
1 AA-AAAAATAGAAAAGA
**
3517389 AAAAAGGTAGAAAAAAGA
1 AAAAAAATAG--AAAAGA
3517407 AAAAAAATA-AAAA-A
1 AAAAAAATAGAAAAGA
*
3517421 ATAAAAAT-GAAGAAGA
1 AAAAAAATAGAA-AAGA
3517437 AAGAAAA
1 AA-AAAA
3517444 CCGATCAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.18
15 12 0.21
16 7 0.12
17 19 0.34
18 8 0.14
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (16 bp):
AAAAAAATAGAAAAGA
Found at i:3517391 original size:30 final size:31
Alignment explanation
Indices: 3517357--3517443 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 31
3517347 AAAAAGACGT
3517357 AAAAAGATAGAAAAGAAAGAAAAATAGAAAAA
1 AAAAAGATAGAAAAGAAAGAAAAATA-AAAAA
*
3517389 AAAAAGGTAGAAAAAAGAAA-AAAAATAAAAAA
1 AAAAAGATAG--AAAAGAAAGAAAAATAAAAAA
3517421 ATAAAA-AT-GAAGAAGAAAGAAAA
1 A-AAAAGATAGAA-AAGAAAGAAAA
3517444 CCGATCAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
29 2 0.04
30 6 0.12
31 5 0.10
32 16 0.33
33 11 0.23
34 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (31 bp):
AAAAAGATAGAAAAGAAAGAAAAATAAAAAA
Found at i:3517393 original size:23 final size:22
Alignment explanation
Indices: 3517367--3517413 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
3517357 AAAAAGATAG
3517367 AAAAGAAAGAAAAATAGAAAAAA
1 AAAAGAAAGAAAAA-AGAAAAAA
**
3517390 AAAAGGTAGAAAAAAGAAAAAA
1 AAAAGAAAGAAAAAAGAAAAAA
3517412 AA
1 AA
3517414 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAAGAAAGAAAAAAGAAAAAA
Found at i:3517405 original size:34 final size:34
Alignment explanation
Indices: 3517367--3517443 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
3517357 AAAAAGATAG
* *
3517367 AAAAGAAAGAAAAATAGAAAAA-AAAAAGGTAGAA
1 AAAAGAAA-AAAAATAAAAAAATAAAAAGGAAGAA
*
3517401 AAAAGAAAAAAAATAAAAAAATAAAAATGAAGAA
1 AAAAGAAAAAAAATAAAAAAATAAAAAGGAAGAA
*
3517435 GAAAGAAAA
1 AAAAGAAAA
3517444 CCGATCAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 12 0.32
34 26 0.68
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (34 bp):
AAAAGAAAAAAAATAAAAAAATAAAAAGGAAGAA
Found at i:3519579 original size:53 final size:53
Alignment explanation
Indices: 3519496--3519702 Score: 301
Period size: 53 Copynumber: 3.9 Consensus size: 53
3519486 TTTCTTGACA
*
3519496 AAATGAATTT-AAAGAAGTTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
1 AAATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
* * *
3519548 AAATGAATTTGAAAGCAA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
1 AAATGAATTTGAAAG-AAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
* *
3519601 AAATGAATTTGAAAAAAGCTAAGCTTGATTTTCAGGAGTTTCTTGATGTTTTC
1 AAATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
* * *
3519654 AAATGAAATTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATG
1 AAATG-AATTTGAAAGAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATG
3519703 ATAATTGTAA
Statistics
Matches: 137, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
52 12 0.09
53 85 0.62
54 40 0.29
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (53 bp):
AAATGAATTTGAAAGAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
Found at i:3519636 original size:106 final size:106
Alignment explanation
Indices: 3519496--3519702 Score: 337
Period size: 106 Copynumber: 2.0 Consensus size: 106
3519486 TTTCTTGACA
* *
3519496 AAATGAATTTAAAGAAGTTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTCAAATG-AATTTGA
1 AAATGAATTTAAAAAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTCAAATGAAATTTGA
3519560 AAGCAA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
66 AAG-AAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
* *
3519601 AAATGAATTTGAAAAAAGCTAAGCTTGATTTTCAGGAGTTTCTTGATGTTTTCAAATGAAATTTT
1 AAATGAATTT-AAAAAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTCAAATGAAATTTG
*
3519666 AAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATG
65 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
3519703 ATAATTGTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
105 10 0.11
106 46 0.49
107 38 0.40
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (106 bp):
AAATGAATTTAAAAAAGCTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTCAAATGAAATTTGA
AAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
Found at i:3519696 original size:54 final size:53
Alignment explanation
Indices: 3519496--3519760 Score: 293
Period size: 53 Copynumber: 4.9 Consensus size: 53
3519486 TTTCTTGACA
* *
3519496 AAATGAA-TTTAAAGAAGTTAAGCCTGATTTTCAGGAGTTTCTTGATGTTTTC
1 AAATGAATTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTC
* * *
3519548 AAATGAATTTGAAAGCAA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
1 AAATGAATTTTAAAG-AAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTC
* * * *
3519601 AAATGAATTTGAAAAAAGCTAAGCTTGATTTTCAGGAGTTTCTTGATGTTTTC
1 AAATGAATTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTC
*
3519654 AAATGAAATTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGATAATTGT-
1 AAATG-AATTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATG-T--TT-TC
* * * * *
3519711 AAACGAAAGTTTTTAAAGAAACTAAGCTTGATTCTCAAGGGTTTCTTGAT
1 AAATG-AA--TTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGAT
3519761 TAGTAAGTCT
Statistics
Matches: 182, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
52 9 0.05
53 87 0.48
54 40 0.22
55 1 0.01
57 9 0.05
58 1 0.01
59 35 0.19
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (53 bp):
AAATGAATTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTC
Found at i:3519870 original size:41 final size:42
Alignment explanation
Indices: 3519764--3519870 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
3519754 TCTTGATTAG
* * * * *
3519764 TAAGTCTTTCAGGCCA-TCAGTAAGTCTTTCGAGTATGATTCT
1 TAAGTCTTTCGGGTCATTCA-TAAGTCTTTCGAGCAAGATTCA
* * *
3519806 TAAATCCTTCGGGTCATAT-ATAAGTCTTTCGAGCAAGA-TGA
1 TAAGTCTTTCGGGTCAT-TCATAAGTCTTTCGAGCAAGATTCA
3519847 TAAGTCTTTCGGGTCATTCATAAG
1 TAAGTCTTTCGGGTCATTCATAAG
3519871 ACCTTTGGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
40 1 0.02
41 21 0.40
42 28 0.54
43 1 0.02
44 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (42 bp):
TAAGTCTTTCGGGTCATTCATAAGTCTTTCGAGCAAGATTCA
Found at i:3520111 original size:145 final size:145
Alignment explanation
Indices: 3519848--3520211 Score: 507
Period size: 145 Copynumber: 2.5 Consensus size: 145
3519838 GCAAGATGAT
* * * * * * *
3519848 AAGTCTTTCGGGTCATTCATAAGACCTTTGGGAAGGATGTTTTCAACATTTTCTTTGCTCGATTC
1 AAGTCCTTCGGGACATCCATAAGACCTTTGGGCAGGATGTTTTCAATATTTCCTTTGTTCGATTC
* * *
3519913 ACAGCACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAAC
66 ACAACATTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATACACAAC
3519978 ACTTCGAATCAGCTA
131 ACTTCGAATCAGCTA
*
3519993 AAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCAATATTTCCTTTGTTCGATTC
1 AAGTCCTTCGGGACATCCATAAGACCTTTGGGCAGGATGTTTTCAATATTTCCTTTGTTCGATTC
** * * *
3520058 ACAACATTTCGAATCAGCAACGCCCCATTAGAGGGGTTAACATTTTATGTTGCTTGATACACAAC
66 ACAACATTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATACACAAC
*
3520123 ACTTCGAATCAGCTT
131 ACTTCGAATCAGCTA
** * *
3520138 AAGTCCTTCGGGACATCCATAAGACCTTCAGCCAGGATGTTTTCAATA-TTCCTTCGCTT-GATT
1 AAGTCCTTCGGGACATCCATAAGACCTTTGGGCAGGATGTTTTCAATATTTCCTTTG-TTCGATT
*
3520201 CACGACATTTC
65 CACAACATTTC
3520212 AAATTAGTGA
Statistics
Matches: 196, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
144 21 0.11
145 175 0.89
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (145 bp):
AAGTCCTTCGGGACATCCATAAGACCTTTGGGCAGGATGTTTTCAATATTTCCTTTGTTCGATTC
ACAACATTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATACACAAC
ACTTCGAATCAGCTA
Found at i:3520522 original size:36 final size:36
Alignment explanation
Indices: 3520476--3520559 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
3520466 TATATTTTTT
* *
3520476 TCTTAAAACAAACTTTGCCTCA-CTAGAGACAGTTTC
1 TCTTCAAACAAACTTTACCTCACCT-GAGACAGTTTC
* * *
3520512 TC-TCGAAACAAATTTTATCTCACCTGAGATAGTTTC
1 TCTTC-AAACAAACTTTACCTCACCTGAGACAGTTTC
3520548 TCTTCAAACAAA
1 TCTTCAAACAAA
3520560 TTTCTTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 1 0.03
36 35 0.88
37 4 0.10
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.32
Consensus pattern (36 bp):
TCTTCAAACAAACTTTACCTCACCTGAGACAGTTTC
Found at i:3521123 original size:139 final size:139
Alignment explanation
Indices: 3520832--3521616 Score: 973
Period size: 139 Copynumber: 5.7 Consensus size: 139
3520822 GGGTAAACCA
* * *
3520832 ATCAACATTTTCAAT-TACGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
1 ATCAACATTTTCAGTGGA-GAGTTCATAATGAGAAGAACTCATCTGAT-GAGGGAGAAGAAGTTC
** * * * *
3520896 ATAATGAGAAGAGTTTGTTCGACCTATCA-CTCAATTAAT-GTCAT-T----TTGAATCAGCGAC
64 ATAATGAGAAGAACTTGTTCAACCT-T-AGCTCGATTCATCG-CATATGGAGTTGAATCAGCAAC
* *
3520954 GCCTCACTCAAGGG
126 ACCTCACTCGAGGG
* *
3520968 ATCAACA-TTTCTAGTGGAGAGTTCATAATGAAAAGAACTCATATGATGAGGGAGAAGAAGTTCA
1 ATCAACATTTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCA
* * *
3521032 TAATGAGATGAACTTATTCAACTTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
3521097 CACTCGAGGG
130 CACTCGAGGG
* * * *
3521107 ATCAATATTTTCAGTGGAGAGTTCTTAATGAGAAGAACGCATCTGATGAGGGAGAAGAATTTCAT
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
* * * * *
3521172 AATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCGTATATGGAGTTTAATCTGAAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
*
3521237 ACTCAAGGG
131 ACTCGAGGG
* * *
3521246 ATCAATA-ATTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 ATCAACATTTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCA
* * *
3521310 TAATAAGAAGAACTTGTTCAACTTTAGCTCGATTCATTGCATATGGAGTTGAATCAGCAACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCT
3521375 CACTCGAGGG
130 CACTCGAGGG
* * * * * * *
3521385 ATCAACATTTCCAATGGAGAGTTCATAAAGAAAACAACTCATCCGATGAGGGAGAATAAGTTCAT
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
* * * * *
3521450 AATGAGAAGAATTTATTCAACCTTAGCTCGATTCTTCACATATGGAGTTGAATCATCAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
3521515 AC-CTGAGGG
131 ACTC-GAGGG
* * * *
3521524 ATCAACATGTCCA-TGTGAGAGTTCAAAATGAGAAGAACTCATCTGATAAGGGAGAAGAAGTTCA
1 ATCAACATTTTCAGTG-GAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCA
3521588 TAATGAGAAGAACTTGTTCAACCTTAGCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCT
3521617 TGTTTCCATT
Statistics
Matches: 564, Mismatches: 71, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
133 1 0.00
134 12 0.02
135 41 0.07
136 35 0.06
137 1 0.00
138 6 0.01
139 462 0.82
140 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (139 bp):
ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:3522221 original size:19 final size:19
Alignment explanation
Indices: 3522193--3522231 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3522183 ATGTAAGGCA
3522193 TTTTTCAGCAATA-AAATT
1 TTTTTCAGCAATAGAAATT
*
3522211 TTTTCTCAGCACTAGAAATT
1 TTTT-TCAGCAATAGAAATT
3522231 T
1 T
3522232 ACGAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (19 bp):
TTTTTCAGCAATAGAAATT
Found at i:3523365 original size:14 final size:15
Alignment explanation
Indices: 3523348--3523386 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
3523338 CATTTTAGTA
*
3523348 TTTATTATTTA-AGC
1 TTTATTATTTAGAAC
3523362 TTTATTATTTAGAAC
1 TTTATTATTTAGAAC
*
3523377 TTTAATATTT
1 TTTATTATTT
3523387 GTAATGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTATTATTTAGAAC
Found at i:3525206 original size:18 final size:19
Alignment explanation
Indices: 3525156--3525208 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3525146 GAAAAATTAG
3525156 TTGAGTATCGATACCCTCACC
1 TTGAGTATCGATA--CTCACC
* *
3525177 ATG-GTATTGATACTC-CC
1 TTGAGTATCGATACTCACC
3525194 TTGAGTATCGATACT
1 TTGAGTATCGATACT
3525209 AAAATTGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 4 0.15
18 13 0.48
20 8 0.30
21 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (19 bp):
TTGAGTATCGATACTCACC
Found at i:3526481 original size:22 final size:23
Alignment explanation
Indices: 3526456--3526501 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3526446 ATTTTGTAAC
3526456 TCGACTCAAATTTG-AAAATTTT
1 TCGACTCAAATTTGTAAAATTTT
* **
3526478 TCGAGTTGAATTTGTAAAATTTT
1 TCGACTCAAATTTGTAAAATTTT
3526501 T
1 T
3526502 GAGTTTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (23 bp):
TCGACTCAAATTTGTAAAATTTT
Found at i:3526509 original size:23 final size:22
Alignment explanation
Indices: 3526464--3526506 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3526454 ACTCGACTCA
3526464 AATTTGAAAATTTTTCGAGTTG
1 AATTTGAAAATTTTTCGAGTTG
3526486 AATTTGTAAAATTTTT-GAGTT
1 AATTTG-AAAATTTTTCGAGTT
3526507 TGAGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
AATTTGAAAATTTTTCGAGTTG
Found at i:3526562 original size:37 final size:37
Alignment explanation
Indices: 3526512--3526583 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
3526502 GAGTTTGAGT
3526512 AAAAAAGGTCAATTTTTTATAAAGTCGAGTTGAGTAA
1 AAAAAAGGTCAATTTTTTATAAAGTCGAGTTGAGTAA
3526549 AAAAAAGGTCAATTTTTTATAAAGTCGAGTTGAGT
1 AAAAAAGGTCAATTTTTTATAAAGTCGAGTTGAGT
3526584 TTTTCATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (37 bp):
AAAAAAGGTCAATTTTTTATAAAGTCGAGTTGAGTAA
Found at i:3528122 original size:33 final size:33
Alignment explanation
Indices: 3528072--3528139 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
3528062 CAAATAAGAC
* *
3528072 TATAAACTTATTTTAATATCAATTGGCTTAATA
1 TATAAACTTATTCTAATATAAATTGGCTTAATA
* *
3528105 TATAAACTTGTTCTAATATAAATTTGCTTAATA
1 TATAAACTTATTCTAATATAAATTGGCTTAATA
3528138 TA
1 TA
3528140 AAAAAATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (33 bp):
TATAAACTTATTCTAATATAAATTGGCTTAATA
Found at i:3528138 original size:15 final size:15
Alignment explanation
Indices: 3528084--3528141 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
3528074 TAAACTTATT
* *
3528084 TTAATATCAATTGGC
1 TTAATATAAATTTGC
* *
3528099 TTAATATATAAACTTGT
1 TT-A-ATATAAATTTGC
3528116 TCTAATATAAATTTGC
1 T-TAATATAAATTTGC
3528132 TTAATATAAA
1 TTAATATAAA
3528142 AAAATGTCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.32
16 12 0.35
17 10 0.29
18 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (15 bp):
TTAATATAAATTTGC
Found at i:3543661 original size:24 final size:24
Alignment explanation
Indices: 3543620--3543665 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3543610 AATATGTTCG
*
3543620 TTTATGTTCATTCATTTATATTTA
1 TTTATGTTCACTCATTTATATTTA
* *
3543644 TTTATGTTCGCTCGTTTATATT
1 TTTATGTTCACTCATTTATATT
3543666 CAACCCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.61
Consensus pattern (24 bp):
TTTATGTTCACTCATTTATATTTA
Done.