Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 14 of 19
Found at i:1620267 original size:22 final size:21
Alignment explanation
Indices: 1620227--1620271 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1620217 AAATAATTAA
*
1620227 AATATAATATTATAAAAATAT
1 AATATAATATAATAAAAATAT
*
1620248 AATATAAATATAATACAAATAT
1 AATAT-AATATAATAAAAATAT
1620270 AA
1 AA
1620272 AAATATCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAATATAATAAAAATAT
Found at i:1623023 original size:13 final size:14
Alignment explanation
Indices: 1622989--1623023 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1622979 TAAAAAAATT
1622989 AAATTTAATCATAA
1 AAATTTAATCATAA
1623003 AAATTTTAAT-ATAA
1 AAA-TTTAATCATAA
1623017 AAATTTA
1 AAATTTA
1623024 TTTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 10 0.50
15 6 0.30
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTTAATCATAA
Found at i:1628064 original size:18 final size:17
Alignment explanation
Indices: 1628041--1628095 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 17
1628031 ATTTACTGAT
1628041 AAATTATATATATTTTTA
1 AAATTA-ATATATTTTTA
1628059 AAATTAATTATTATTTTTA
1 AAATTAA-TA-TATTTTTA
*
1628078 AAATTAATATAATTTTA
1 AAATTAATATATTTTTA
1628095 A
1 A
1628096 TACGACAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.26
18 10 0.29
19 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTAATATATTTTTA
Found at i:1629025 original size:2 final size:2
Alignment explanation
Indices: 1629018--1629053 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1629008 CAGATAAAAT
1629018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1629054 GAGGTTTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1629500 original size:22 final size:21
Alignment explanation
Indices: 1629472--1629537 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1629462 TAATAAATAT
1629472 AAAATTAAAAATAATTTCATAA
1 AAAATTAAAAATAATTT-ATAA
*
1629494 AAAATTAAAATTAATTTATAA
1 AAAATTAAAAATAATTTATAA
*
1629515 TAATAA-TAATAATATATTTATAA
1 -AA-AATTAAAAATA-ATTTATAA
1629538 TTAATATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 4 0.11
22 24 0.63
23 10 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTAAAAATAATTTATAA
Found at i:1629533 original size:23 final size:25
Alignment explanation
Indices: 1629507--1629552 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1629497 ATTAAAATTA
*
1629507 ATTTATAA-TAATA-ATAATAATAT
1 ATTTATAATTAATATACAATAATAT
1629530 ATTTATAATTAATATACAATAAT
1 ATTTATAATTAATATACAATAAT
1629553 TTTGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTATAATTAATATACAATAATAT
Found at i:1629682 original size:4 final size:4
Alignment explanation
Indices: 1629673--1629705 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1629663 GAGAGACAGG
*
1629673 GCGA GCGA GCGA GCGA GCGA GCGA GAGA GCGA G
1 GCGA GCGA GCGA GCGA GCGA GCGA GCGA GCGA G
1629706 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.52, T:0.00
Consensus pattern (4 bp):
GCGA
Found at i:1629706 original size:8 final size:8
Alignment explanation
Indices: 1629675--1629715 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1629665 GAGACAGGGC
*
1629675 GAGCGAGC
1 GAGCGAGA
*
1629683 GAGCGAGC
1 GAGCGAGA
1629691 GAGCGAGA
1 GAGCGAGA
1629699 GAGCGAGA
1 GAGCGAGA
*
1629707 GAGAGAGA
1 GAGCGAGA
1629715 G
1 G
1629716 GTTGTCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.51, T:0.00
Consensus pattern (8 bp):
GAGCGAGA
Found at i:1629710 original size:12 final size:12
Alignment explanation
Indices: 1629675--1629713 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1629665 GAGACAGGGC
*
1629675 GAGCGAGCGAGC
1 GAGCGAGCGAGA
1629687 GAGCGAGCGAGA
1 GAGCGAGCGAGA
*
1629699 GAGCGAGAGAGA
1 GAGCGAGCGAGA
1629711 GAG
1 GAG
1629714 AGGTTGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.51, T:0.00
Consensus pattern (12 bp):
GAGCGAGCGAGA
Found at i:1629864 original size:2 final size:2
Alignment explanation
Indices: 1629851--1629886 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1629841 CATGCAATTC
*
1629851 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1629887 TTCATTCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1629945 original size:20 final size:20
Alignment explanation
Indices: 1629902--1629953 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1629892 TCGAATGCCC
*
1629902 AAATAAATATTTTTTTAAAA
1 AAATAAATATATTTTTAAAA
*
1629922 AAATAAATA-ATTTTTAATAT
1 AAATAAATATATTTTTAA-AA
1629942 AAATATAATATA
1 AAATA-AATATA
1629954 ATTAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 4 0.15
22 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAAATATATTTTTAAAA
Found at i:1630053 original size:20 final size:20
Alignment explanation
Indices: 1630020--1630077 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1630010 ATTAATAATA
1630020 TATATTTA-AT-ATTTATAT
1 TATATTTATATAATTTATAT
*
1630038 TATATTTATATAATTTACAT
1 TATATTTATATAATTTATAT
* * * *
1630058 AATTTTTATAAAATATATAT
1 TATATTTATATAATTTATAT
1630078 AATGTAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 8 0.25
19 2 0.06
20 22 0.69
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTTATATAATTTATAT
Found at i:1630079 original size:20 final size:19
Alignment explanation
Indices: 1630042--1630097 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
1630032 TTATATTATA
* * *
1630042 TTTATATAATTTACATAATT
1 TTTATAAAATATATATAA-T
1630062 TTTATAAAATATATATAAT
1 TTTATAAAATATATATAAT
* *
1630081 GTAAT-AAATATATATAA
1 TTTATAAAATATATATAA
1630098 ATTAAGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 15 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTATAAAATATATATAAT
Found at i:1630188 original size:18 final size:16
Alignment explanation
Indices: 1630152--1630190 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1630142 TATAATTTTA
1630152 ATTTTATTAATATAAT
1 ATTTTATTAATATAAT
*
1630168 ATTTTATATAATTTAAAT
1 ATTTTAT-TAATAT-AAT
1630186 ATTTT
1 ATTTT
1630191 TAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATTAATATAAT
Found at i:1630203 original size:30 final size:29
Alignment explanation
Indices: 1630119--1630222 Score: 86
Period size: 32 Copynumber: 3.3 Consensus size: 29
1630109 CACGATATTA
1630119 AAATTTTTTAAAATTATTTATTT-TATAATTT
1 AAATTTTTT-AAA-TATTT-TTTATATAATTT
* *
1630150 TAATTTTATTAATATAATATTTTATATAATTT
1 AAATTTT-TTAA-AT-ATTTTTTATATAATTT
*
1630182 AAATATTTTTAAATATTTTTTA-AAAATTT
1 AAAT-TTTTTAAATATTTTTTATATAATTT
1630211 AATATATTTTTA
1 AA-AT-TTTTTA
1630223 TTAAATAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
29 8 0.13
30 16 0.26
31 14 0.23
32 21 0.34
33 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
AAATTTTTTAAATATTTTTTATATAATTT
Found at i:1630503 original size:3 final size:3
Alignment explanation
Indices: 1630495--1630533 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1630485 TAGGCCTAAC
1630495 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1630534 TTTCTCTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1630761 original size:25 final size:25
Alignment explanation
Indices: 1630720--1630771 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1630710 GTTTATTAAA
* *
1630720 AATATATGAATATATATAATTTTTT
1 AATATATGAATAAATATAATATTTT
1630745 AATATAT-ATATAAATATAATATTTT
1 AATATATGA-ATAAATATAATATTTT
1630770 AA
1 AA
1630772 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATATATGAATAAATATAATATTTT
Found at i:1633310 original size:21 final size:21
Alignment explanation
Indices: 1633286--1633326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1633276 ATTTATTATT
*
1633286 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1633307 TAAATATTAATAAAAAATAT
1 TAAATATTAATAAAAAATAT
1633327 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1634650 original size:14 final size:14
Alignment explanation
Indices: 1634617--1634650 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1634607 TTAAAGTATG
1634617 TATTTAATTTTTAA
1 TATTTAATTTTTAA
* *
1634631 TTTTTAATTTTTTA
1 TATTTAATTTTTAA
1634645 TATTTA
1 TATTTA
1634651 GGAGATCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTAATTTTTAA
Found at i:1637294 original size:26 final size:25
Alignment explanation
Indices: 1637265--1637314 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1637255 TGATTGATTA
*
1637265 TTTTATAAATTAACAAATATTTTATT
1 TTTTATAAATTAAAAAAT-TTTTATT
*
1637291 TTTTATATATTAAAAAATTTTTAT
1 TTTTATAAATTAAAAAATTTTTAT
1637315 AATTAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTATAAATTAAAAAATTTTTATT
Found at i:1638479 original size:17 final size:18
Alignment explanation
Indices: 1638440--1638478 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1638430 TTGAAAGTAA
*
1638440 AAAATGATTGGGAAAGGC
1 AAAATGATTGGGAAAAGC
1638458 AAAAT-ATTGGTGAAAAGC
1 AAAATGATTGG-GAAAAGC
1638476 AAA
1 AAA
1638479 TGGGAGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (18 bp):
AAAATGATTGGGAAAAGC
Found at i:1639136 original size:26 final size:25
Alignment explanation
Indices: 1639083--1639148 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
1639073 ATAAATATAT
* * **
1639083 ATATATATCTATAAAATAATAATCAA
1 ATAT-TATATATAATATAATAAAAAA
*
1639109 ATTTTGATATATAATATAATAAAAAA
1 ATATT-ATATATAATATAATAAAAAA
1639135 ATATTATATA-AATA
1 ATATTATATATAATA
1639149 GATTAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.12
25 6 0.18
26 23 0.70
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATATTATATATAATATAATAAAAAA
Found at i:1639247 original size:15 final size:14
Alignment explanation
Indices: 1639227--1639264 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1639217 AATAAGATAG
1639227 ATTTATCAATTTTTT
1 ATTTAT-AATTTTTT
*
1639242 ATTTATATTTTTTT
1 ATTTATAATTTTTT
1639256 A-TTATAATT
1 ATTTATAATT
1639265 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTATAATTTTTT
Found at i:1639285 original size:27 final size:27
Alignment explanation
Indices: 1639257--1639323 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1639247 TATTTTTTTA
1639257 TTATAATTATATTTAAAATATTATATAT
1 TTATAATTATATTTAAAATATTA-ATAT
*
1639285 TTATAATAAT-TTTAAAATATTAATAAT
1 TTATAATTATATTTAAAATATTAAT-AT
1639312 TTATAA-TATATT
1 TTATAATTATATT
1639324 AATTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.11
27 22 0.63
28 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATAATTATATTTAAAATATTAATAT
Found at i:1639310 original size:17 final size:18
Alignment explanation
Indices: 1639288--1639326 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1639278 TATATATTTA
1639288 TAATAATTT-TAAAATAT
1 TAATAATTTATAAAATAT
*
1639305 TAATAATTTATAATATAT
1 TAATAATTTATAAAATAT
1639323 TAAT
1 TAAT
1639327 TTTAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATTTATAAAATAT
Found at i:1639362 original size:17 final size:17
Alignment explanation
Indices: 1639241--1639363 Score: 51
Period size: 17 Copynumber: 7.3 Consensus size: 17
1639231 ATCAATTTTT
* *
1639241 TATTTATATTTTTTTAT
1 TATTTATATATTTTTAA
* *
1639258 TA-TAAT-TATATTTAA
1 TATTTATATATTTTTAA
* *
1639273 AATATTATATATTTATAA
1 TAT-TTATATATTTTTAA
* * *
1639291 TAATTT-TAAAATATTAA
1 T-ATTTATATATTTTTAA
*
1639308 TAATTTATA-ATATATTAA
1 T-ATTTATATAT-TTTTAA
* *
1639326 T-TTTAATAAATTTTT-T
1 TATTT-ATATATTTTTAA
1639342 TATTTATATATTTTTAA
1 TATTTATATATTTTTAA
1639359 TATTT
1 TATTT
1639364 TAATTATTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
15 7 0.09
16 16 0.21
17 33 0.42
18 20 0.26
19 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTATATATTTTTAA
Found at i:1640965 original size:27 final size:28
Alignment explanation
Indices: 1640928--1640998 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
1640918 CATTAATTAA
*
1640928 TTAAAAT--AATTTAATATTT-ATTTTT
1 TTAAAATAAAATTTAATATTTAAATTTT
1640953 TTAAAATAAAATTTTAA-ATTTAAATTTT
1 TTAAAATAAAA-TTTAATATTTAAATTTT
* *
1640981 ATAAAAAAAAATATTAAT
1 TTAAAATAAAAT-TTAAT
1640999 GTTACGAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 7 0.19
27 7 0.19
28 23 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAAAATAAAATTTAATATTTAAATTTT
Found at i:1641471 original size:31 final size:29
Alignment explanation
Indices: 1641429--1641494 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
1641419 GATTAAATTT
* *
1641429 AATTAATTTAAATTAATTTATTTAATTTTAA
1 AATTAAATTAAATTAA-TT-GTTAATTTTAA
*
1641460 AATTAAATTAAATTAATTGTTAATTTTTA
1 AATTAAATTAAATTAATTGTTAATTTTAA
1641489 AATTAA
1 AATTAA
1641495 TAATAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 15 0.47
30 2 0.06
31 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AATTAAATTAAATTAATTGTTAATTTTAA
Found at i:1641602 original size:32 final size:32
Alignment explanation
Indices: 1641559--1641619 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1641549 ATTTTTATAT
1641559 AATAATATAAATAATTA-TTTTAA-AAAATTTAA
1 AATAATATAAAT--TTACTTTTAATAAAATTTAA
*
1641591 AATAATGTAAATTTACTTTTAATAAAATT
1 AATAATATAAATTTACTTTTAATAAAATT
1641620 AATTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 3 0.12
31 6 0.23
32 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (32 bp):
AATAATATAAATTTACTTTTAATAAAATTTAA
Found at i:1649259 original size:18 final size:18
Alignment explanation
Indices: 1649238--1649293 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
1649228 TATGTATAAA
1649238 TTTTTATATTTATATTAT
1 TTTTTATATTTATATTAT
*
1649256 TTTTTAAATTTAT-TATAT
1 TTTTTATATTTATAT-TAT
*
1649274 TTTAATTATTTTTATATTAT
1 TTT--TTATATTTATATTAT
1649294 ATAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.03
18 18 0.58
20 11 0.35
21 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATATTTATATTAT
Found at i:1649275 original size:27 final size:26
Alignment explanation
Indices: 1649234--1649286 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1649224 AATTTATGTA
1649234 TAAATTTTTATA-TTTATATTATTTTT
1 TAAATTTTTATATTTTA-ATTATTTTT
1649260 TAAATTTATTATATTTTAATTATTTTT
1 TAAATTT-TTATATTTTAATTATTTTT
1649287 ATATTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.28
27 14 0.56
28 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TAAATTTTTATATTTTAATTATTTTT
Found at i:1652359 original size:11 final size:11
Alignment explanation
Indices: 1652343--1652373 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1652333 AAACATATTC
1652343 AATTATATTTT
1 AATTATATTTT
1652354 AATTATATTTT
1 AATTATATTTT
*
1652365 AACTATATT
1 AATTATATT
1652374 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATATTTT
Found at i:1652373 original size:32 final size:30
Alignment explanation
Indices: 1652337--1652397 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
1652327 ATATTCAAAC
1652337 ATATTCAATTATATTTTAATTATATTTTAACT
1 ATATTCAATTATATTTTAATT-T-TTTTAACT
* *
1652369 ATATTCAATTTTATTTTTATTTTTTTAAC
1 ATATTCAATTATATTTTAATTTTTTTAAC
1652398 GTATCAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
31 1 0.04
32 19 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATTCAATTATATTTTAATTTTTTTAACT
Found at i:1653387 original size:14 final size:14
Alignment explanation
Indices: 1653355--1653389 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
1653345 ATAGAAATGT
1653355 ATTTAAAAAATATA
1 ATTTAAAAAATATA
1653369 A--TAAAAAATATA
1 ATTTAAAAAATATA
1653381 ATTTAAAAA
1 ATTTAAAAA
1653390 TTTTTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.63
14 7 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTTAAAAAATATA
Found at i:1653569 original size:13 final size:14
Alignment explanation
Indices: 1653546--1653574 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1653536 AATTTATTTA
1653546 AATTATTAAATTAT
1 AATTATTAAATTAT
1653560 AATT-TTAAATTAT
1 AATTATTAAATTAT
1653573 AA
1 AA
1653575 AAATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTATTAAATTAT
Found at i:1654770 original size:21 final size:22
Alignment explanation
Indices: 1654745--1654791 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1654735 AATTTAAAAA
*
1654745 TTAAAAGTTTATT-AT-ATTTAT
1 TTAAAAATTTATTGATAATTT-T
1654766 TTAAAAATTTATTGATAATTTT
1 TTAAAAATTTATTGATAATTTT
1654788 TTAA
1 TTAA
1654792 GTATTCACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
22 7 0.30
23 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTAAAAATTTATTGATAATTTT
Found at i:1655323 original size:18 final size:18
Alignment explanation
Indices: 1655292--1655335 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1655282 ATTTTAAATT
*
1655292 TAAAAAAT-ATATTTATA
1 TAAAAAATAAAATTTATA
*
1655309 TAAAAAATAAAATTTATT
1 TAAAAAATAAAATTTATA
*
1655327 TAGAAAATA
1 TAAAAAATA
1655336 GATTGAACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAAATAAAATTTATA
Found at i:1655506 original size:40 final size:40
Alignment explanation
Indices: 1655462--1655539 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
1655452 GATTTAATAT
1655462 TTTTTAA-GATAAATCT-ATTATTTAAAAAAAAAATTGATTC
1 TTTTTAAGGA-AAAT-TAATTATTTAAAAAAAAAATTGATTC
* * *
1655502 TTTTTAAGGAAGATTAATTTTTTTAAAAAAAAATTGAT
1 TTTTTAAGGAAAATTAATTATTTAAAAAAAAAATTGAT
1655540 AATTTTGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.03
40 30 0.91
41 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (40 bp):
TTTTTAAGGAAAATTAATTATTTAAAAAAAAAATTGATTC
Found at i:1655814 original size:17 final size:15
Alignment explanation
Indices: 1655792--1655826 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
1655782 GTGTGATTGG
1655792 TAAAAAAGATAGAAAAA
1 TAAAAAAGA-A-AAAAA
1655809 TAAAAAAGAAAAAAA
1 TAAAAAAGAAAAAAA
1655824 TAA
1 TAA
1655827 TTTATATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 1 0.06
17 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
TAAAAAAGAAAAAAA
Found at i:1656550 original size:21 final size:21
Alignment explanation
Indices: 1656524--1656567 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1656514 GACACTCAAA
1656524 TAATTTAAATATATTAA-TATT
1 TAATTTAAATA-ATTAATTATT
*
1656545 TAATTTAATTAATTAATTATT
1 TAATTTAAATAATTAATTATT
1656566 TA
1 TA
1656568 TTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTTAAATAATTAATTATT
Found at i:1656603 original size:20 final size:20
Alignment explanation
Indices: 1656580--1656629 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1656570 TTTTAATTAA
1656580 AAAATTTAAATA-TAAATAAT
1 AAAATTTAAATATTAAAT-AT
1656600 AAAATTTAAA-ATTAAATAT
1 AAAATTTAAATATTAAATAT
*
1656619 AAAAATTAAAT
1 AAAATTTAAAT
1656630 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTTAAATATTAAATAT
Found at i:1656618 original size:26 final size:26
Alignment explanation
Indices: 1656580--1656632 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1656570 TTTTAATTAA
1656580 AAAATTTAAATATAAATAATAAAATTT
1 AAAATTTAAATATAAA-AATAAAATTT
*
1656607 AAAA-TTAAATATAAAAATTAAATTT
1 AAAATTTAAATATAAAAATAAAATTT
1656632 A
1 A
1656633 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.40
26 11 0.44
27 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAATTTAAATATAAAAATAAAATTT
Found at i:1656650 original size:45 final size:45
Alignment explanation
Indices: 1656596--1656681 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
1656586 TAAATATAAA
1656596 TAATAAAATTTAAAATTAAATATAA-AAA-TT-AAATTTATTTTTTAT
1 TAATAAAA-TT-AAATTAAATA-AATAAATTTAAAATTTATTTTTTAT
* *
1656641 TAATTAAATTAAATTAATTAAATAAATTTAAAATTTATTTT
1 TAATAAAATTAAATTAAATAAATAAATTTAAAATTTATTTT
1656682 AAATTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 2 0.06
43 12 0.33
44 4 0.11
45 18 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (45 bp):
TAATAAAATTAAATTAAATAAATAAATTTAAAATTTATTTTTTAT
Found at i:1656667 original size:38 final size:35
Alignment explanation
Indices: 1656603--1656695 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 35
1656593 AAATAATAAA
* ***
1656603 ATTTAAAATTAAATATAAAAATTAAATTTATTTTTT
1 ATTTTAAATTAAAT-TAAAAATTAAATTTAAAATTT
1656639 ATTAATTAAATTAAATTAATTAAA-TAAATTTAAAATTT
1 ATT--TTAAATTAAATTAA--AAATTAAATTTAAAATTT
1656677 ATTTTAAATTAAATTAAAA
1 ATTTTAAATTAAATTAAAA
1656696 TTTTTAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
34 2 0.04
36 17 0.35
37 3 0.06
38 24 0.49
39 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
ATTTTAAATTAAATTAAAAATTAAATTTAAAATTT
Found at i:1656671 original size:14 final size:14
Alignment explanation
Indices: 1656639--1656668 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1656629 TTTATTTTTT
1656639 ATTAATTAAATTAA
1 ATTAATTAAATTAA
1656653 ATTAATTAAA-TAA
1 ATTAATTAAATTAA
1656666 ATT
1 ATT
1656669 TAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAATTAAATTAA
Found at i:1656684 original size:22 final size:20
Alignment explanation
Indices: 1656658--1656715 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 20
1656648 ATTAAATTAA
1656658 TTAAATAAATTTAAAATTTATT
1 TTAAATAAA-TTAAAATTT-TT
1656680 TTAAATTAAATTAAAATTTTT
1 TTAAA-TAAATTAAAATTTTT
**
1656701 AAAAATAAAATTAAA
1 TTAAAT-AAATTAAA
1656716 TCAAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 14 0.44
23 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAATAAATTAAAATTTTT
Found at i:1659828 original size:2 final size:2
Alignment explanation
Indices: 1659821--1659857 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1659811 AGCCTAGTAT
1659821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1659858 AGTAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1660035 original size:13 final size:14
Alignment explanation
Indices: 1660003--1660033 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1659993 TTTTTTCCCC
*
1660003 AAAATGATATTAAA
1 AAAATGATAATAAA
1660017 AAAATGATAATAAA
1 AAAATGATAATAAA
1660031 AAA
1 AAA
1660034 TGTAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAATGATAATAAA
Found at i:1661724 original size:24 final size:24
Alignment explanation
Indices: 1661697--1661770 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
1661687 AAATATAAAT
1661697 TAAATATATAAATATTTTAATATA
1 TAAATATATAAATATTTTAATATA
* * *
1661721 TAAAT-TAATAATAAATTTAAAT-TT
1 TAAATAT-ATAA-ATATTTTAATATA
**
1661745 TTTATATATAAATATTTTAA-ATA
1 TAAATATATAAATATTTTAATATA
1661768 TAA
1 TAA
1661771 TTAATACTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
23 10 0.28
24 17 0.47
25 9 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATATATAAATATTTTAATATA
Found at i:1661735 original size:46 final size:45
Alignment explanation
Indices: 1661681--1661776 Score: 124
Period size: 48 Copynumber: 2.1 Consensus size: 45
1661671 CGATAAAAAA
1661681 TAAT-ATAAATATAAA-TTAAATATATAAATATTTTAATATATAAAT
1 TAATAATAAATATAAATTTAAATATATAAATATTTTAA-ATAT-AAT
* **
1661726 TAATAATAAATTTAAATTTTTTATATATAAATATTTTAAATATAAT
1 TAATAATAAATATAAA-TTTAAATATATAAATATTTTAAATATAAT
1661772 TAATA
1 TAATA
1661777 CTTTATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
45 4 0.09
46 18 0.40
47 4 0.09
48 19 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (45 bp):
TAATAATAAATATAAATTTAAATATATAAATATTTTAAATATAAT
Found at i:1661740 original size:12 final size:13
Alignment explanation
Indices: 1661689--1661740 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 13
1661679 AATAATATAA
*
1661689 ATATAAATTAAAT
1 ATATAAATTTAAT
1661702 ATATAAATATTTTAAT
1 ATAT-AA-A-TTTAAT
1661718 ATATAAA-TTAAT
1 ATATAAATTTAAT
1661730 A-ATAAATTTAA
1 ATATAAATTTAA
1661741 ATTTTTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 5 0.15
12 10 0.29
13 4 0.12
14 3 0.09
15 3 0.09
16 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAATTTAAT
Found at i:1661762 original size:15 final size:15
Alignment explanation
Indices: 1661700--1661770 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
1661690 TATAAATTAA
1661700 ATATATAAATATTTT
1 ATATATAAATATTTT
**
1661715 AATATATAAATTAATAAT
1 -ATATATAAA-T-ATTTT
* * *
1661733 AAATTTAAATTTTTT
1 ATATATAAATATTTT
1661748 ATATATAAATATTTT
1 ATATATAAATATTTT
*
1661763 AAATATAA
1 ATATATAA
1661771 TTAATACTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
15 21 0.50
16 10 0.24
17 8 0.19
18 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATAAATATTTT
Found at i:1662047 original size:23 final size:21
Alignment explanation
Indices: 1662008--1662070 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
1661998 TTTTTTTATC
*
1662008 ATAAT-TATGTTAA-AAATTA
1 ATAATATATATTAATAAATTA
*
1662027 TATACATATATTTTAATAAATTA
1 -ATA-ATATATATTAATAAATTA
*
1662050 ATAATTTATATTATATAAATT
1 ATAATATATATTA-ATAAATT
1662071 TTAAAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.08
21 10 0.28
22 17 0.47
23 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATATATATTAATAAATTA
Found at i:1668432 original size:18 final size:18
Alignment explanation
Indices: 1668394--1668432 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1668384 TGACATAATG
* * *
1668394 ATATATTTAAAATTTTTT
1 ATATACTTAAAAATTTAT
1668412 ATATACTTAAAAATTTAT
1 ATATACTTAAAAATTTAT
1668430 ATA
1 ATA
1668433 AACATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATACTTAAAAATTTAT
Found at i:1669171 original size:13 final size:13
Alignment explanation
Indices: 1669153--1669183 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1669143 ATTAGTTGAT
1669153 TTTTTTTTCTTTC
1 TTTTTTTTCTTTC
*
1669166 TTTTTTTTTTTTC
1 TTTTTTTTCTTTC
1669179 TTTTT
1 TTTTT
1669184 GATGTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:1669358 original size:14 final size:13
Alignment explanation
Indices: 1669320--1669363 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1669310 AAATTAATTA
*
1669320 TTTGATTTTTAAAT
1 TTTGATTTTT-TAT
*
1669334 TTTTATTTTTTAT
1 TTTGATTTTTTAT
1669347 TTTGATTATTTTAT
1 TTTGATT-TTTTAT
1669361 TTT
1 TTT
1669364 TTATAATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTGATTTTTTAT
Found at i:1670408 original size:2 final size:2
Alignment explanation
Indices: 1670398--1670428 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1670388 TTTATGTGTG
*
1670398 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1670429 GTATGTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1671618 original size:11 final size:11
Alignment explanation
Indices: 1671598--1671720 Score: 60
Period size: 11 Copynumber: 11.1 Consensus size: 11
1671588 GATATAAAAA
1671598 ATAATATAAAT
1 ATAATATAAAT
*
1671609 ATAATTTAAAT
1 ATAATATAAAT
*
1671620 ACATAA-ATAATT
1 --ATAATATAAAT
* *
1671632 ATAGTATGAATT
1 ATAATAT-AAAT
*
1671644 ATAA-ATATAT
1 ATAATATAAAT
* **
1671654 -TAAAATTTAT
1 ATAATATAAAT
1671664 ATAAATATAAA-
1 AT-AATATAAAT
1671675 AT-ATATTAAAT
1 ATAATA-TAAAT
1671686 ATAAT-TATAAT
1 ATAATATA-AAT
1671697 ATAATTATAAAT
1 ATAA-TATAAAT
*
1671709 ATAACATAAAT
1 ATAATATAAAT
1671720 A
1 A
1671721 CATGAATTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
9 6 0.07
10 16 0.18
11 33 0.38
12 26 0.30
13 6 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1671669 original size:50 final size:50
Alignment explanation
Indices: 1671598--1671737 Score: 137
Period size: 50 Copynumber: 2.8 Consensus size: 50
1671588 GATATAAAAA
**
1671598 ATAA-TATAAATATAATTTAAATACATAAATAATTATAGTATGAATTATAA-
1 ATAATTATAAATATAACATAAATACATAAATAATTA-AGTAT-AATTATAAT
* * * *
1671648 ATATATTA-AAAT-TTATATAAATATA-AAATATATTAAATATAATTATAAT
1 ATA-ATTATAAATATAACATAAATACATAAATA-ATTAAGTATAATTATAAT
* *
1671697 ATAATTATAAATATAACATAAATACATGAATTATTAAGTAT
1 ATAATTATAAATATAACATAAATACATAAATAATTAAGTAT
1671738 TTAAAAGTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
48 12 0.16
49 16 0.22
50 35 0.48
51 8 0.11
52 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (50 bp):
ATAATTATAAATATAACATAAATACATAAATAATTAAGTATAATTATAAT
Found at i:1671671 original size:6 final size:6
Alignment explanation
Indices: 1671662--1671712 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
1671652 ATTAAAATTT
* * *
1671662 ATATAA ATATAA A-ATAT AT-TAA ATATAA TTAT-A ATATAA TTATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1671707 ATATAA
1 ATATAA
1671713 CATAAATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 12 0.33
6 24 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:1671686 original size:16 final size:17
Alignment explanation
Indices: 1671654--1671711 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1671644 ATAAATATAT
*
1671654 TAAAATTTATATAAATA
1 TAAAATATATATAAATA
1671671 TAAAATATAT-TAAATA
1 TAAAATATATATAAATA
* *
1671687 T-AATTATAATATAATTA
1 TAAAATAT-ATATAAATA
1671704 T-AAATATA
1 TAAAATATA
1671712 ACATAAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 5 0.14
16 10 0.29
17 20 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATATATATAAATA
Found at i:1674988 original size:19 final size:19
Alignment explanation
Indices: 1674960--1674996 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1674950 TTTTTAAATA
*
1674960 AATATCAAAATTAAATTAT
1 AATATCAAAATAAAATTAT
*
1674979 AATATTAAAATAAAATTA
1 AATATCAAAATAAAATTA
1674997 AAAATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATCAAAATAAAATTAT
Found at i:1675704 original size:2 final size:2
Alignment explanation
Indices: 1675697--1675744 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
1675687 ATGCCCCTAA
* *
1675697 AT AT AT AT AT AT AT AT AT AT AT AT GT GAT -T AT -T TT 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
1675738 AT AT AT A
1 AT AT AT A
1675745 ATTATTATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.93
3 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1675736 original size:21 final size:21
Alignment explanation
Indices: 1675710--1675750 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1675700 TATATATATA
* *
1675710 TATATATATATGTGATTATTT
1 TATATATATATATAATTATTT
1675731 TATATATATATATAATTATT
1 TATATATATATATAATTATT
1675751 ATCAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TATATATATATATAATTATTT
Found at i:1679067 original size:28 final size:28
Alignment explanation
Indices: 1679036--1679090 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1679026 AGTAATACTA
*
1679036 ATTAAGATAA-TATTTTAAAAAAATTATG
1 ATTAAGA-AATTATTTGAAAAAAATTATG
* *
1679064 ATTAATAAATTATTTGAAAATAATTAT
1 ATTAAGAAATTATTTGAAAAAAATTAT
1679091 ATATTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
ATTAAGAAATTATTTGAAAAAAATTATG
Found at i:1688671 original size:2 final size:2
Alignment explanation
Indices: 1688664--1688694 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1688654 TATTGAAGAA
1688664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1688695 AAAGGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1689071 original size:2 final size:2
Alignment explanation
Indices: 1689064--1689105 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1689054 TTAATTTTCC
1689064 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
1689106 TTGGAAGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1689185 original size:16 final size:17
Alignment explanation
Indices: 1689164--1689206 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1689154 AGATCATTCG
1689164 AATATTATATTTAT-AA
1 AATATTATATTTATAAA
*
1689180 AATATTAT-TTTTTAAA
1 AATATTATATTTATAAA
1689196 AATAATTATAT
1 AAT-ATTATAT
1689207 AAATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 13 0.57
17 5 0.22
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTATATTTATAAA
Found at i:1689361 original size:12 final size:12
Alignment explanation
Indices: 1689344--1689378 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1689334 ATTAATTATC
1689344 AAGATTAAAATT
1 AAGATTAAAATT
1689356 AAGATTAAAATT
1 AAGATTAAAATT
*
1689368 AAAATTAAAAT
1 AAGATTAAAAT
1689379 CAGCAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
AAGATTAAAATT
Found at i:1689362 original size:6 final size:6
Alignment explanation
Indices: 1689347--1689378 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1689337 AATTATCAAG
*
1689347 ATTAAA ATTAAG ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT
1689379 CAGCAAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:1690468 original size:175 final size:175
Alignment explanation
Indices: 1690164--1690555 Score: 739
Period size: 175 Copynumber: 2.2 Consensus size: 175
1690154 AAAATTTGTC
* *
1690164 TATCTTGTTTTAGCCATTAATGTTGGATCCAAGTAAACGATAAATTTCCATTGAAGGAACCCTAG
1 TATCTTG-TTTATCCATTAATGTTGGATCCAAGTAAACGATAAATATCCATTGAAGGAACCCTAG
1690229 GACTACGATGGGGAGTTGAGGGGAGGGGGGGACCATTTCATTACGTGGGATAACCCTTGTTCCCT
65 GACTACGATGGGGAGTTGAGGGGAGGGGGGGACCATTTCATTACGTGGGATAACCCTTGTTCCCT
1690294 CACTCTTTTTTCTTTTAATTTCTAATTTTAACATAAACAAGTTAAT
130 CACTCTTTTTTCTTTTAATTTCTAATTTTAACATAAACAAGTTAAT
1690340 TATCTTGTTTATCCATTAATGTTGGATCCAAGTAAACGATAAATATCCATTGAAGGAACCCTAGG
1 TATCTTGTTTATCCATTAATGTTGGATCCAAGTAAACGATAAATATCCATTGAAGGAACCCTAGG
1690405 ACTACGATGGGGAGTTGAGGGGAGGGGGGGACCATTTCATTACGTGGGATAACCCTTGTTCCCTC
66 ACTACGATGGGGAGTTGAGGGGAGGGGGGGACCATTTCATTACGTGGGATAACCCTTGTTCCCTC
*
1690470 GCTCTTTTTTCTTTTAATTTCTAATTTTAACATAAACAAGTTAAT
131 ACTCTTTTTTCTTTTAATTTCTAATTTTAACATAAACAAGTTAAT
1690515 TATCTTGTTTATCCATTAATGTTGGATCCAAGTAAAACGAT
1 TATCTTGTTTATCCATTAATGTTGGATCCAAGT-AAACGAT
1690556 TTAAACTGTG
Statistics
Matches: 212, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
175 198 0.93
176 14 0.07
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (175 bp):
TATCTTGTTTATCCATTAATGTTGGATCCAAGTAAACGATAAATATCCATTGAAGGAACCCTAGG
ACTACGATGGGGAGTTGAGGGGAGGGGGGGACCATTTCATTACGTGGGATAACCCTTGTTCCCTC
ACTCTTTTTTCTTTTAATTTCTAATTTTAACATAAACAAGTTAAT
Found at i:1690996 original size:2 final size:2
Alignment explanation
Indices: 1690991--1691030 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1690981 AATCTCTCAT
1690991 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1691031 ACAAAATCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1692159 original size:13 final size:13
Alignment explanation
Indices: 1692098--1692207 Score: 63
Period size: 13 Copynumber: 8.8 Consensus size: 13
1692088 TAAATAATAA
*
1692098 TTATAA-TATAAT
1 TTATAATTATTAT
1692110 ATTATAATTATTAT
1 -TTATAATTATTAT
* *
1692124 TTAAAAATTTTTAT
1 TT-ATAATTATTAT
* *
1692138 TTTTTATTATTAT
1 TTATAATTATTAT
*
1692151 TTATAATTAATAT
1 TTATAATTATTAT
* *
1692164 TTAT-TTTAATTAA
1 TTATAATT-ATTAT
*
1692177 TTATAA-TAATA-
1 TTATAATTATTAT
1692188 TT-T-ATTA-TAT
1 TTATAATTATTAT
1692198 TTATAATTAT
1 TTATAATTAT
1692208 AATAATTAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
9 3 0.04
10 5 0.07
11 3 0.04
12 9 0.12
13 37 0.51
14 16 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATAATTATTAT
Found at i:1692229 original size:42 final size:40
Alignment explanation
Indices: 1692170--1692252 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 40
1692160 ATATTTATTT
* *** *
1692170 TAATTAATTATAATAATATTTATTATATTTATAATTATAA
1 TAATTAAATATAATAATACAAAATATATTTATAATTATAA
*
1692210 TAATTAAATATAATATAATACAAAATATATTTATATTTATAA
1 TAATTAAATAT-A-ATAATACAAAATATATTTATAATTATAA
1692252 T
1 T
1692253 TTAAATCCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 10 0.29
41 1 0.03
42 24 0.69
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
TAATTAAATATAATAATACAAAATATATTTATAATTATAA
Found at i:1692959 original size:2 final size:2
Alignment explanation
Indices: 1692943--1692996 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1692933 GCAAAGCGTG
* *
1692943 TA TA TA TT TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1692985 GA TA TA GA TA TA
1 TA TA TA TA TA TA
1692997 GGGGAGAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1693506 original size:14 final size:14
Alignment explanation
Indices: 1693482--1693515 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1693472 CATATAAAAT
1693482 ATTTAAAATTTTAAA
1 ATTT-AAATTTTAAA
*
1693497 ATTTAAATTTTAAT
1 ATTTAAATTTTAAA
1693511 ATTTA
1 ATTTA
1693516 TAATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTAAATTTTAAA
Found at i:1693961 original size:9 final size:8
Alignment explanation
Indices: 1693950--1693974 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1693940 TTATTATTTA
1693950 AAAATATT
1 AAAATATT
1693958 AAAATATT
1 AAAATATT
1693966 AAAATATT
1 AAAATATT
1693974 A
1 A
1693975 CTTGTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATATT
Found at i:1695353 original size:2 final size:2
Alignment explanation
Indices: 1695340--1695370 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1695330 TTTAGGTAAC
*
1695340 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1695371 AGAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1699345 original size:27 final size:28
Alignment explanation
Indices: 1699293--1699347 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1699283 AATTTTCTTC
* *
1699293 TAAAAGTAACAAAATTAGAAGTAAAAAA
1 TAAAAGTAAAAAAATTAGAAGGAAAAAA
1699321 TAAAA-TAAAAAAATTTA-AAGGAAAAAA
1 TAAAAGTAAAAAAA-TTAGAAGGAAAAAA
1699348 GATAGATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (28 bp):
TAAAAGTAAAAAAATTAGAAGGAAAAAA
Found at i:1700048 original size:19 final size:21
Alignment explanation
Indices: 1700024--1700073 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
1700014 CTAATTAATT
*
1700024 TAAATTTTTA-TTTAA-AAAA
1 TAAATTTTAATTTTAATAAAA
*
1700043 TAAATTTAAATTTTAATAAAA
1 TAAATTTTAATTTTAATAAAA
1700064 TATAATTTTA
1 TA-AATTTTA
1700074 TGTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 5 0.20
21 6 0.24
22 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTTAATTTTAATAAAA
Found at i:1702130 original size:6 final size:6
Alignment explanation
Indices: 1702121--1702176 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
1702111 TTTGATAATA
* *
1702121 ATAAAT ATAATAAT ATAAAT AT-AAT ATAAAA ATAATT A-AAAT AT-AAT
1 ATAAAT AT-A-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1702168 ATAAAT ATA
1 ATAAAT ATA
1702177 TAATTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 14 0.34
6 20 0.49
7 2 0.05
8 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:1702146 original size:11 final size:11
Alignment explanation
Indices: 1702130--1702176 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
1702120 AATAAATATA
1702130 ATAATATAAAT
1 ATAATATAAAT
*
1702141 ATAATATAAAA
1 ATAATATAAAT
1702152 ATAAT-TAAAAT
1 ATAATAT-AAAT
1702163 ATAATATAAAT
1 ATAATATAAAT
1702174 ATA
1 ATA
1702177 TAATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 1 0.03
11 30 0.94
12 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1702162 original size:22 final size:24
Alignment explanation
Indices: 1702118--1702183 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 24
1702108 ATATTTGATA
1702118 ATAATA-AATATAATAA-TATAAAT
1 ATAATATAA-ATAATAATTATAAAT
1702141 ATAATATAAA-AATAATTA-AAAT
1 ATAATATAAATAATAATTATAAAT
1702163 ATAATATAAATATATAATTAT
1 ATAATATAAATA-ATAATTAT
1702184 TTTAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
22 19 0.50
23 10 0.26
24 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAAATAATAATTATAAAT
Found at i:1702406 original size:17 final size:17
Alignment explanation
Indices: 1702386--1702430 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1702376 AAAGTTCGGA
*
1702386 TATTTATTAAAATTTTT
1 TATTTATAAAAATTTTT
1702403 TATTTATAAAAATTTTAT
1 TATTTATAAAAATTTT-T
1702421 T-TTTA-AAAAA
1 TATTTATAAAAA
1702431 AATTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.19
17 19 0.73
18 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATAAAAATTTTT
Found at i:1702420 original size:15 final size:15
Alignment explanation
Indices: 1702386--1702429 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1702376 AAAGTTCGGA
*
1702386 TATTTATTAAAATTTTT
1 TATTTA-TAAAA-ATTT
1702403 TATTTATAAAAATTT
1 TATTTATAAAAATTT
*
1702418 TATTTTTAAAAA
1 TATTTATAAAAA
1702430 AAATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 5 0.20
17 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATAAAAATTT
Found at i:1702882 original size:2 final size:2
Alignment explanation
Indices: 1702875--1702906 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1702865 TAAAATTAAA
*
1702875 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1702907 CTAAAGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1703057 original size:7 final size:7
Alignment explanation
Indices: 1703047--1703076 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1703037 AAAAAATAAA
1703047 AATTTTT
1 AATTTTT
1703054 AATTTTT
1 AATTTTT
1703061 AATTTTT
1 AATTTTT
*
1703068 AAATTTT
1 AATTTTT
1703075 AA
1 AA
1703077 ATTTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
AATTTTT
Found at i:1703072 original size:15 final size:15
Alignment explanation
Indices: 1703046--1703080 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1703036 TAAAAAATAA
1703046 AAATTTTT-AATTTT
1 AAATTTTTAAATTTT
*
1703060 TAATTTTTAAATTTT
1 AAATTTTTAAATTTT
1703075 AAATTT
1 AAATTT
1703081 ATATTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AAATTTTTAAATTTT
Found at i:1704286 original size:24 final size:23
Alignment explanation
Indices: 1704259--1704310 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1704249 AAAAAACGAT
*
1704259 AAAA-GAAGAGAGAAAAAATTAAA
1 AAAATGAA-AGAGAAAAAATGAAA
*
1704282 GAAAATGAAAGAGTAAAAATGAAA
1 -AAAATGAAAGAGAAAAAATGAAA
1704306 AAAAT
1 AAAAT
1704311 TAATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.20
24 17 0.68
25 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (23 bp):
AAAATGAAAGAGAAAAAATGAAA
Found at i:1704875 original size:22 final size:22
Alignment explanation
Indices: 1704843--1704884 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1704833 GACTAAAGTT
*
1704843 TTCATATATACACATACATACC
1 TTCATACATACACATACATACC
*
1704865 TTCATACATACATATACATA
1 TTCATACATACACATACATA
1704885 TACATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (22 bp):
TTCATACATACACATACATACC
Found at i:1708063 original size:24 final size:24
Alignment explanation
Indices: 1708031--1708076 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1708021 GTATGTTGTT
1708031 ATTTATTTATTTT-TTAATATTTTA
1 ATTTATTTATTTTATTAA-ATTTTA
*
1708055 ATTTTTTTATTTTATTAAATTT
1 ATTTATTTATTTTATTAAATTT
1708077 AATAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTATTTATTTTATTAAATTTTA
Found at i:1710480 original size:2 final size:2
Alignment explanation
Indices: 1710473--1710506 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1710463 ATAACTATAG
1710473 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1710507 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1718490 original size:15 final size:16
Alignment explanation
Indices: 1718470--1718499 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1718460 TTTAAATCTA
1718470 AATATAAATA-ATTTT
1 AATATAAATATATTTT
1718485 AATATAAATATATTT
1 AATATAAATATATTT
1718500 AATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATAAATATATTTT
Found at i:1718502 original size:21 final size:21
Alignment explanation
Indices: 1718459--1718505 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1718449 ATTTTATATT
* *
1718459 ATTTAAATCTAAATATAAATA
1 ATTTTAATATAAATATAAATA
**
1718480 ATTTTAATATAAATATATTTA
1 ATTTTAATATAAATATAAATA
1718501 ATTTT
1 ATTTT
1718506 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTAATATAAATATAAATA
Found at i:1719865 original size:21 final size:20
Alignment explanation
Indices: 1719841--1719898 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
1719831 AATTTAATAA
1719841 TTTATATATTTATATTATAT
1 TTTATATATTTATATTATAT
1719861 TTT-TACGTA-TTATAATTATAT
1 TTTATA--TATTTAT-ATTATAT
*
1719882 TTAATATATTATATATT
1 TTTATATATT-TATATT
1719899 TATAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
19 2 0.06
20 9 0.29
21 15 0.48
22 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTATATATTTATATTATAT
Found at i:1720028 original size:27 final size:26
Alignment explanation
Indices: 1719959--1720033 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
1719949 TTCATATATT
* * * *
1719959 TTTATTATATTTATATCATTTTTAGA
1 TTTATTATATTTATTTTATATTTAAA
1719985 TTATATTATATTTTATTTTATATTTAAA
1 TT-TATTATA-TTTATTTTATATTTAAA
1720013 TTTATTATA-TTATATTTATAT
1 TTTATTATATTTAT-TTTATAT
1720034 CATATCTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 4 0.10
26 9 0.21
27 14 0.33
28 15 0.36
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTATTATATTTATTTTATATTTAAA
Found at i:1720033 original size:11 final size:11
Alignment explanation
Indices: 1719953--1720038 Score: 60
Period size: 11 Copynumber: 8.5 Consensus size: 11
1719943 AATGCATTCA
*
1719953 TATATTTTTAT
1 TATATTTATAT
1719964 TATATTTATAT
1 TATATTTATAT
* * *
1719975 CATTTTTAGAT
1 TATATTTATAT
1719986 TATA--T-TA-
1 TATATTTATAT
*
1719993 TAT-TTTATTT
1 TATATTTATAT
*
1720003 TATATTTAAAT
1 TATATTTATAT
1720014 T-TA-TTATAT
1 TATATTTATAT
1720023 TATATTTATAT
1 TATATTTATAT
*
1720034 CATAT
1 TATAT
1720039 CTTTTAAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 8 0.14
10 7 0.12
11 36 0.64
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1720488 original size:10 final size:10
Alignment explanation
Indices: 1720445--1720495 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
1720435 GTATATTATA
1720445 TTAATATATT
1 TTAATATATT
1720455 TT-ATCATATT
1 TTAAT-ATATT
1720465 TTAAT-TATAT
1 TTAATATAT-T
1720475 TTAATATATT
1 TTAATATATT
1720485 TTAATA-ATT
1 TTAATATATT
1720494 TT
1 TT
1720496 TAATTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 10 0.27
10 22 0.59
11 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TTAATATATT
Found at i:1720507 original size:20 final size:20
Alignment explanation
Indices: 1720445--1720507 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1720435 GTATATTATA
* *
1720445 TTAAT-ATATTTTATCATATT
1 TTAATAATATTTAAT-ATAAT
* *
1720465 TTAATTATATTTAATATATT
1 TTAATAATATTTAATATAAT
* *
1720485 TTAATAATTTTTAATTTAAT
1 TTAATAATATTTAATATAAT
1720505 TTA
1 TTA
1720508 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATAATATTTAATATAAT
Found at i:1720507 original size:30 final size:30
Alignment explanation
Indices: 1720439--1720500 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1720429 ATGTATGTAT
*
1720439 ATTATA-TTAATATATTTTATCATATTTTA
1 ATTATATTTAATATATTTTATAATATTTTA
1720468 ATTATATTTAATATATTTTAATAAT-TTTTA
1 ATTATATTTAATATATTTT-ATAATATTTTA
1720498 ATT
1 ATT
1720501 TAATTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.20
30 20 0.67
31 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTATATTTAATATATTTTATAATATTTTA
Found at i:1721250 original size:17 final size:17
Alignment explanation
Indices: 1721204--1721253 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
1721194 TATTATATAT
*
1721204 TTATATAAATTTTAATA
1 TTATATAATTTTTAATA
**
1721221 -TAT-TAATAATTAATA
1 TTATATAATTTTTAATA
1721236 TTATATAATTTTTAATA
1 TTATATAATTTTTAATA
1721253 T
1 T
1721254 ATTTATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 9 0.35
16 6 0.23
17 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATAATTTTTAATA
Found at i:1721294 original size:16 final size:16
Alignment explanation
Indices: 1721233--1721294 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
1721223 TTAATAATTA
1721233 ATATTATATAATTTTTAAT
1 ATATTATAT-ATTTTT--T
*
1721252 ATATTTATTTTATTTTTT
1 ATA-TTA-TATATTTTTT
* *
1721270 ATGTAATATATTTTTT
1 ATATTATATATTTTTT
1721286 ATATTATAT
1 ATATTATAT
1721295 TTTAATTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 16 0.46
17 2 0.06
18 3 0.09
19 3 0.09
20 9 0.26
21 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATATTATATATTTTTT
Found at i:1721326 original size:23 final size:23
Alignment explanation
Indices: 1721273--1721320 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1721263 ATTTTTTATG
* *
1721273 TAATATATTTTTTATATTATATTT
1 TAAT-TATTTTTAATATTATATTA
1721297 TAATTATTTTTAATATTAT-TTA
1 TAATTATTTTTAATATTATATTA
1721319 TA
1 TA
1721321 TTTTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 14 0.64
24 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TAATTATTTTTAATATTATATTA
Found at i:1721327 original size:39 final size:39
Alignment explanation
Indices: 1721230--1721328 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
1721220 ATATTAATAA
* *
1721230 TTAATATTATATA-ATTTT-TAATATATTTATTTTATTT
1 TTAATATTATATATATTTTATATTATATTTATATTATTT
* * * *
1721267 TTTATGTAATATATTTTTTATATTATATTT-TAATTATTT
1 TTAATATTATATATATTTTATATTATATTTAT-ATTATTT
*
1721306 TTAATATTATTTATATTTTATAT
1 TTAATATTATATATATTTTATAT
1721329 AATCATATCA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
37 10 0.21
38 5 0.10
39 33 0.69
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (39 bp):
TTAATATTATATATATTTTATATTATATTTATATTATTT
Found at i:1721328 original size:16 final size:16
Alignment explanation
Indices: 1721276--1721328 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1721266 TTTTATGTAA
* *
1721276 TATATTTTTTATATTA
1 TATATTATTTATATTT
* *
1721292 TATTTTAATTAT-TTT
1 TATATTATTTATATTT
1721307 TAATATTATTTATATTT
1 T-ATATTATTTATATTT
1721324 TATAT
1 TATAT
1721329 AATCATATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 22 0.76
17 4 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTATTTATATTT
Found at i:1721503 original size:5 final size:5
Alignment explanation
Indices: 1721493--1721521 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1721483 CAAAGAATAA
1721493 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1721522 ATGCATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1723431 original size:12 final size:12
Alignment explanation
Indices: 1723416--1723457 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1723406 TAGTATTATA
1723416 TTTATATTATTT
1 TTTATATTATTT
*
1723428 TTTATATTATAT
1 TTTATATTATTT
*
1723440 TTTA-ATAATTT
1 TTTATATTATTT
1723451 TTTATAT
1 TTTATAT
1723458 CGTATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1723435 original size:23 final size:23
Alignment explanation
Indices: 1723409--1723457 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1723399 TTAACAATAG
*
1723409 TATTATA-TTTATATTATTTTTTA
1 TATTATATTTTA-ATAATTTTTTA
1723432 TATTATATTTTAATAATTTTTTA
1 TATTATATTTTAATAATTTTTTA
1723455 TAT
1 TAT
1723458 CGTATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTATATTTTAATAATTTTTTA
Found at i:1723530 original size:18 final size:19
Alignment explanation
Indices: 1723498--1723536 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1723488 ATTTTACATC
1723498 AAAATCTAATTCTGAAAAAA
1 AAAATCTAA-TCTGAAAAAA
1723518 AAAATCTAA-CTGAAAAAA
1 AAAATCTAATCTGAAAAAA
1723536 A
1 A
1723537 CTATTACATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAATCTAATCTGAAAAAA
Found at i:1723721 original size:14 final size:14
Alignment explanation
Indices: 1723702--1723729 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1723692 ATAATATTAG
1723702 AAAATATTTAAATT
1 AAAATATTTAAATT
1723716 AAAATATTTAAATT
1 AAAATATTTAAATT
1723730 TGAGTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATATTTAAATT
Found at i:1724236 original size:11 final size:11
Alignment explanation
Indices: 1724220--1724244 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1724210 TATATACTTT
1724220 TTTATTTTTTA
1 TTTATTTTTTA
1724231 TTTATTTTTTA
1 TTTATTTTTTA
1724242 TTT
1 TTT
1724245 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:1724316 original size:21 final size:21
Alignment explanation
Indices: 1724286--1724348 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1724276 TAATTTAATA
*
1724286 AATA-AAAATATTTAGAT-TT
1 AATATAAAATATTTAAATATT
* *
1724305 AATTCTAAAATATATAAATATT
1 AA-TATAAAATATTTAAATATT
*
1724327 AATATAAAATATTATTAATATT
1 AATATAAAATATT-TAAATATT
1724349 TTATTATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 20 0.59
22 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATAAAATATTTAAATATT
Found at i:1730263 original size:27 final size:28
Alignment explanation
Indices: 1730230--1730290 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
1730220 TAAAAAATTT
*
1730230 TTAAAATTTAAATTTTGATATTTGTATC
1 TTAAAATTTAAATTTCGATATTTGTATC
*
1730258 -TAAAATTTTAATTTCGATATTTGTATC
1 TTAAAATTTAAATTTCGATATTTGTATC
1730285 TTAAAA
1 TTAAAA
1730291 GATGATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (28 bp):
TTAAAATTTAAATTTCGATATTTGTATC
Found at i:1735099 original size:36 final size:37
Alignment explanation
Indices: 1735045--1735115 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
1735035 TAAAATTAAC
1735045 ATATATAACGTATGTATATATTTAA-ACA-TAAATATTT
1 ATATATAACGTA-GT-TATATTTAATACATTAAATATTT
*
1735082 ATATAT-ACGTATTTATATTTAATACATTAAATAT
1 ATATATAACGTAGTTATATTTAATACATTAAATAT
1735116 CATTGAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 9 0.29
35 4 0.13
36 12 0.39
37 6 0.19
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATAACGTAGTTATATTTAATACATTAAATATTT
Found at i:1738203 original size:28 final size:28
Alignment explanation
Indices: 1738171--1738226 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1738161 GGTAATTTAG
1738171 TCACTCATCATACATAAAATTAAAGTGA
1 TCACTCATCATACATAAAATTAAAGTGA
*
1738199 TCACTCATGATACATAAAATTAAAGTGA
1 TCACTCATCATACATAAAATTAAAGTGA
1738227 GGCACCAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (28 bp):
TCACTCATCATACATAAAATTAAAGTGA
Found at i:1740846 original size:18 final size:17
Alignment explanation
Indices: 1740825--1740893 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 17
1740815 ATTTAATATT
1740825 TAATTTAAAATTAATTAA
1 TAATTTAAAATT-ATTAA
1740843 TAATAAATTAAAAATT-TTAAA
1 TAAT---TT-AAAATTATT-AA
* *
1740864 TAAATATAAAATTATAAA
1 T-AATTTAAAATTATTAA
1740882 TAATTTAAAATT
1 TAATTTAAAATT
1740894 TAATCTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
17 10 0.24
18 13 0.32
19 2 0.05
20 2 0.05
21 5 0.12
22 9 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTTAAAATTATTAA
Found at i:1740856 original size:22 final size:22
Alignment explanation
Indices: 1740817--1740858 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1740807 AATAAAATAT
* * *
1740817 TTAATATTTAATTTAAAATTAA
1 TTAATAATAAATTAAAAATTAA
1740839 TTAATAATAAATTAAAAATT
1 TTAATAATAAATTAAAAATT
1740859 TTAAATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATAATAAATTAAAAATTAA
Found at i:1741393 original size:3 final size:3
Alignment explanation
Indices: 1741385--1741440 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1741375 CTATGCAAGG
1741385 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1741433 ATT ATT AT
1 ATT ATT AT
1741441 GGTCATGGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1741728 original size:22 final size:22
Alignment explanation
Indices: 1741686--1741729 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1741676 AATACATATA
*
1741686 TTTATATATTAGATTTATATTT
1 TTTATATATTAGAATTATATTT
*
1741708 TTTATAATATTATAATT-TATTT
1 TTTAT-ATATTAGAATTATATTT
1741730 AAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATATATTAGAATTATATTT
Found at i:1741751 original size:21 final size:20
Alignment explanation
Indices: 1741699--1741758 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
1741689 ATATATTAGA
*
1741699 TTTATATT-TTTTATAATAT
1 TTTATATTATTTTAAAATAT
*
1741718 TATA-ATT-TATTTAAAATAT
1 TTTATATTAT-TTTAAAATAT
*
1741737 TTTATATTAATTTTAATATAT
1 TTTATATT-ATTTTAAAATAT
1741758 T
1 T
1741759 AATAATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 15 0.45
20 3 0.09
21 10 0.30
22 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATTATTTTAAAATAT
Done.