Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 4 of 343
Found at i:1358332 original size:28 final size:28
Alignment explanation
Indices: 1358292--1358348 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1358282 GCAACGGACC
1358292 AATATTCAATACAGATAGAGAAAATTAA
1 AATATTCAATACAGATAGAGAAAATTAA
1358320 AATATTCAATACAGATAGAGAAAATTAA
1 AATATTCAATACAGATAGAGAAAATTAA
1358348 A
1 A
1358349 CCACTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (28 bp):
AATATTCAATACAGATAGAGAAAATTAA
Found at i:1362413 original size:16 final size:16
Alignment explanation
Indices: 1362392--1362427 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1362382 ATTTACGTTA
1362392 ATTTTGAG-TTTAATTT
1 ATTTTGAGTTTTAA-TT
1362408 ATTTTGAGTTTTAATT
1 ATTTTGAGTTTTAATT
1362424 ATTT
1 ATTT
1362428 AAGTTTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (16 bp):
ATTTTGAGTTTTAATT
Found at i:1365468 original size:23 final size:23
Alignment explanation
Indices: 1365441--1365485 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1365431 AGAAATAAAA
1365441 ATATAATTTTAT-TTCATATTAAC
1 ATATAATTTTATGTTCA-ATTAAC
1365464 ATATAATTTTATGTTCAATTAA
1 ATATAATTTTATGTTCAATTAA
1365486 GGTATGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATAATTTTATGTTCAATTAAC
Found at i:1366618 original size:17 final size:17
Alignment explanation
Indices: 1366598--1366633 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1366588 TTTTAATTCG
*
1366598 TTATAATTTTTACAAAT
1 TTATAATTTTAACAAAT
1366615 TTATAATTTTAACAAAT
1 TTATAATTTTAACAAAT
1366632 TT
1 TT
1366634 TAAATAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATTTTAACAAAT
Found at i:1366750 original size:27 final size:28
Alignment explanation
Indices: 1366710--1366768 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1366700 ATACTGGTTA
* * *
1366710 AAAAATTTTAAATTTTATAAAA-AAATAT
1 AAAAATTGTAAA-TTTAAAAAAGAAACAT
1366738 AAAAATTGT-AATTTAAAAAAGAAACAT
1 AAAAATTGTAAATTTAAAAAAGAAACAT
1366765 AAAA
1 AAAA
1366769 TAATGTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.30
27 11 0.41
28 8 0.30
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATTGTAAATTTAAAAAAGAAACAT
Found at i:1374204 original size:31 final size:31
Alignment explanation
Indices: 1374157--1374233 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1374147 TATAAAATTT
*
1374157 AAATTTAG-T-ATATATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTATTTTTAG
1374186 AAATTTAGTTAATTTATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTATTTTTAG
*
1374217 AAATTTAGTTACTTTAT
1 AAATTTAGTTAATTTAT
1374234 TTTTTAGGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 8 0.18
30 1 0.02
31 35 0.80
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (31 bp):
AAATTTAGTTAATTTATACTTTTATTTTTAG
Found at i:1374251 original size:30 final size:31
Alignment explanation
Indices: 1374157--1374253 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
1374147 TATAAAATTT
* * *
1374157 AAATTTAG-T-ATATATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTAGTTTCAG
* *
1374186 AAATTTAGTTAATTTATACTTTTATTTTTAG
1 AAATTTAGTTAATTTATACTTTTAGTTTCAG
* *
1374217 AAATTTAGTTACTTTAT-TTTTTAGGTTTCA-
1 AAATTTAGTTAATTTATACTTTTA-GTTTCAG
1374247 AAATTTA
1 AAATTTA
1374254 TATCTAATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.13
30 13 0.22
31 39 0.65
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (31 bp):
AAATTTAGTTAATTTATACTTTTAGTTTCAG
Found at i:1380140 original size:27 final size:26
Alignment explanation
Indices: 1380110--1380171 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1380100 AGATAATTAA
1380110 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
1380137 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
1380164 AATAAAAT
1 AATAAAAT
1380172 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:1386648 original size:5 final size:5
Alignment explanation
Indices: 1386638--1386666 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1386628 ACTATTTGTG
1386638 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1386667 AACACACGGA
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:1389892 original size:18 final size:18
Alignment explanation
Indices: 1389864--1389904 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1389854 AATGTAAGAG
* *
1389864 AATAA-TAAAATATTAAT
1 AATAATTAAAATAGTAAA
1389881 AATAATTAAAATAGTAAA
1 AATAATTAAAATAGTAAA
1389899 AATAAT
1 AATAAT
1389905 AATAGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AATAATTAAAATAGTAAA
Found at i:1390117 original size:16 final size:17
Alignment explanation
Indices: 1390098--1390135 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1390088 AAAAGGAAAT
1390098 AATAATATGGTAA-AAA
1 AATAATATGGTAATAAA
*
1390114 AATAATATGTTAATAAA
1 AATAATATGGTAATAAA
1390131 AATAA
1 AATAA
1390136 CAGTAGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (17 bp):
AATAATATGGTAATAAA
Found at i:1390151 original size:3 final size:3
Alignment explanation
Indices: 1390145--1390217 Score: 69
Period size: 3 Copynumber: 24.3 Consensus size: 3
1390135 ACAGTAGTAG
* * * * *
1390145 TAA TAA TAA TAG TAA GAA TAA TAA TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1390192 T-A TAA CTAAA TAA TAA TAA TAA TAA T
1 TAA TAA -T-AA TAA TAA TAA TAA TAA T
1390218 GTTAATGGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
2 4 0.07
3 48 0.86
4 2 0.04
5 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1390186 original size:17 final size:17
Alignment explanation
Indices: 1390164--1390212 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 17
1390154 TAGTAAGAAT
1390164 AATAATGATAATATAAC-
1 AATAAT-ATAATATAACA
1390181 AATAATAGTAATATAACTA
1 AATAATA-TAATATAAC-A
1390200 AATAATAATAATA
1 AATAAT-ATAATA
1390213 ATAATGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 15 0.54
19 11 0.39
20 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (17 bp):
AATAATATAATATAACA
Found at i:1390205 original size:19 final size:17
Alignment explanation
Indices: 1390145--1390212 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 17
1390135 ACAGTAGTAG
*
1390145 TAATAATAATAGTAAGAA
1 TAATAATAATA-TAACAA
1390163 TAATAATGATAATATAACAA
1 TAAT-A--ATAATATAACAA
*
1390183 TAATAGTAATATAACTAAA
1 TAATAATAATATAAC--AA
1390202 TAATAATAATA
1 TAATAATAATA
1390213 ATAATGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.21
18 4 0.10
19 14 0.33
20 9 0.21
21 6 0.14
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TAATAATAATATAACAA
Found at i:1396008 original size:16 final size:15
Alignment explanation
Indices: 1395966--1396015 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1395956 AGATGATTTT
1395966 ATAAA-AAAAT-ATA
1 ATAAATAAAATAATA
1395979 ATAAATAAAA-AATA
1 ATAAATAAAATAATA
*
1395993 TTAAATTAAAATAATA
1 ATAAA-TAAAATAATA
1396009 A-AAATAA
1 ATAAATAA
1396016 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 8 0.26
16 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:1398869 original size:30 final size:30
Alignment explanation
Indices: 1398810--1398898 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 30
1398800 TTGGTTACTA
* *
1398810 TTTTTTTTAATTTGGTACTAAAAAACTTGACAC
1 TTTTTCTTAATTTGGTACT---AATCTTGACAC
1398843 TTTTTCTTAATTTGGTACTAATCTTGACAC
1 TTTTTCTTAATTTGGTACTAATCTTGACAC
* * *
1398873 TTTCTCTTAAATTAGTACTTAATCTT
1 TTTTTCTTAATTTGGTAC-TAATCTT
1398899 TTTGGGGTCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 25 0.50
31 7 0.14
33 18 0.36
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTTTCTTAATTTGGTACTAATCTTGACAC
Found at i:1399420 original size:59 final size:59
Alignment explanation
Indices: 1399339--1399483 Score: 175
Period size: 59 Copynumber: 2.5 Consensus size: 59
1399329 CTAAATTAGT
* * * * * * *
1399339 AAAAAATGCCAAGTTCATGTACCAAATTGGG-TCCACAAAGAGTTTAGGTACCCAATTAG
1 AAAAAATGCCAAGTTCAAGTACCAAATTGGGCT-AAAAAAAAGTTTAGATACCAAATTAA
* * *
1399398 GAAAAGTGTCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTAGATACCAAATTAA
1 AAAAAATGCCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTAGATACCAAATTAA
*
1399457 AAAAAATGCCAAGTTCAAATACCAAAT
1 AAAAAATGCCAAGTTCAAGTACCAAAT
1399484 GCTATTTTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 70 0.99
60 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (59 bp):
AAAAAATGCCAAGTTCAAGTACCAAATTGGGCTAAAAAAAAGTTTAGATACCAAATTAA
Found at i:1399826 original size:47 final size:47
Alignment explanation
Indices: 1399757--1399850 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1399747 AATTCGTGCC
*
1399757 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGGTTGATTAGTAT
1 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1399804 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1 TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
1399851 AAATTTGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (47 bp):
TTTAAAATTTTGAGATATTTTGGATTCGACATTTGATTGATTAGTAT
Found at i:1399837 original size:24 final size:24
Alignment explanation
Indices: 1399763--1399837 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
1399753 TGCCTTTAAA
1399763 ATTTTGAGATATTTTGGATTCGAC
1 ATTTTGAGATATTTTGGATTCGAC
* * * ** *
1399787 A-TTTG-GTTGA-TTAGTATTTTAAA
1 ATTTTGAGAT-ATTTTGGA-TTCGAC
1399810 ATTTTGAGATATTTTGGATTCGAC
1 ATTTTGAGATATTTTGGATTCGAC
1399834 ATTT
1 ATTT
1399838 GATTGATTAG
Statistics
Matches: 34, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
22 6 0.18
23 9 0.26
24 13 0.38
25 6 0.18
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (24 bp):
ATTTTGAGATATTTTGGATTCGAC
Found at i:1402241 original size:25 final size:26
Alignment explanation
Indices: 1402213--1402263 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1402203 CTTATTTCAT
*
1402213 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
1402238 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
1402264 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:1402256 original size:26 final size:24
Alignment explanation
Indices: 1402225--1402273 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1402215 AATAAAAAAT
*
1402225 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
1402251 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
1402274 TAAGACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:1403494 original size:14 final size:14
Alignment explanation
Indices: 1403475--1403511 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1403465 TACACTGGAA
*
1403475 GAAAAGTTTCTAAC
1 GAAAAGTCTCTAAC
1403489 GAAAAGTCTCTAAC
1 GAAAAGTCTCTAAC
1403503 GAAAAGTCT
1 GAAAAGTCT
1403512 TGAAAATAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (14 bp):
GAAAAGTCTCTAAC
Found at i:1406333 original size:16 final size:16
Alignment explanation
Indices: 1406300--1406333 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1406290 TGTTCTTGTT
* *
1406300 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
1406316 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
1406332 AA
1 AA
1406334 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:1409068 original size:17 final size:17
Alignment explanation
Indices: 1409046--1409080 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1409036 ATCATATGGC
1409046 TTTTAAAACATTCATAT
1 TTTTAAAACATTCATAT
1409063 TTTTAAAACATTCATAT
1 TTTTAAAACATTCATAT
1409080 T
1 T
1409081 ATAAACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAAACATTCATAT
Found at i:1409088 original size:15 final size:17
Alignment explanation
Indices: 1409049--1409085 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1409039 ATATGGCTTT
*
1409049 TAAAACATTCATATTTT
1 TAAAACATTCATATTTA
1409066 TAAAACATTCATA-TTA
1 TAAAACATTCATATTTA
1409082 TAAA
1 TAAA
1409086 CATGTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAACATTCATATTTA
Found at i:1411715 original size:31 final size:31
Alignment explanation
Indices: 1411647--1411708 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1411637 ATAACCTTTA
1411647 TAATAAAACATAAAACCATTATATTTAATGG
1 TAATAAAACATAAAACCATTATATTTAATGG
*
1411678 TAATAAAATATAAAACCATTATATTTAATGG
1 TAATAAAACATAAAACCATTATATTTAATGG
1411709 CTATAAACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (31 bp):
TAATAAAACATAAAACCATTATATTTAATGG
Found at i:1411898 original size:14 final size:15
Alignment explanation
Indices: 1411881--1411909 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1411871 ATACGAGAAT
1411881 TTCACACA-TATAAA
1 TTCACACATTATAAA
1411895 TTCACACATTATAAA
1 TTCACACATTATAAA
1411910 AACATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TTCACACATTATAAA
Found at i:1417241 original size:17 final size:18
Alignment explanation
Indices: 1417219--1417259 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1417209 CGTTTCTTTT
1417219 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
1417236 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
1417254 T-TTTTG
1 TCTTTTG
1417260 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:1417243 original size:24 final size:25
Alignment explanation
Indices: 1417190--1417243 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1417180 AACAAATTCT
* *
1417190 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
1417215 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
1417238 TTTTTT
1 TTTTTT
1417244 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:1419513 original size:15 final size:15
Alignment explanation
Indices: 1419495--1419524 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1419485 CTAGACCGTA
1419495 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
1419510 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
1419525 CCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:1419520 original size:13 final size:12
Alignment explanation
Indices: 1419502--1419562 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
1419492 GTATGCAATT
1419502 TTTTTTTTTGCAA
1 TTTTTTTTT-CAA
*
1419515 TTTTTTTTTTC-C
1 -TTTTTTTTTCAA
*
1419527 TTTTTTTTTCGGA
1 TTTTTTTTTC-AA
*
1419540 TTTTTTTTTTAA
1 TTTTTTTTTCAA
1419552 CTTTTTTTTTC
1 -TTTTTTTTTC
1419563 GAAGCTACGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 10 0.26
12 1 0.03
13 19 0.49
14 9 0.23
ACGTcount: A:0.08, C:0.10, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:1419530 original size:26 final size:26
Alignment explanation
Indices: 1419501--1419565 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
1419491 CGTATGCAAT
* *
1419501 TTTTTTTTTTGCAATTTTTTTTTT-CC
1 TTTTTTTTTCG-AATTTTTTTTTTAAC
*
1419527 TTTTTTTTTCGGATTTTTTTTTTAAC
1 TTTTTTTTTCGAATTTTTTTTTTAAC
1419553 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
1419566 GCTACGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 11 0.32
26 23 0.68
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (26 bp):
TTTTTTTTTCGAATTTTTTTTTTAAC
Found at i:1420811 original size:23 final size:23
Alignment explanation
Indices: 1420785--1420837 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1420775 ATAAGTGCCA
1420785 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1420808 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1420831 CACTGAT
1 CACTGAT
1420838 CAATAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1420937 original size:8 final size:8
Alignment explanation
Indices: 1420924--1420952 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1420914 ACCCGGGACT
1420924 CACTGTAA
1 CACTGTAA
1420932 CACTGTAA
1 CACTGTAA
1420940 CACTGTAA
1 CACTGTAA
1420948 CACTG
1 CACTG
1420953 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:1421083 original size:18 final size:17
Alignment explanation
Indices: 1421057--1421095 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1421047 ATTTTCCTTC
1421057 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
1421074 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
1421092 CACA
1 CACA
1421096 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:1428120 original size:23 final size:23
Alignment explanation
Indices: 1428094--1428169 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
1428084 ATAAGTGCCA
1428094 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1428117 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1428140 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1428163 CACTGAT
1 CACTGAT
1428170 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1428269 original size:8 final size:8
Alignment explanation
Indices: 1428256--1428284 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1428246 ACCCGGGACT
1428256 CACTGTAA
1 CACTGTAA
1428264 CACTGTAA
1 CACTGTAA
1428272 CACTGTAA
1 CACTGTAA
1428280 CACTG
1 CACTG
1428285 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:1428415 original size:18 final size:17
Alignment explanation
Indices: 1428389--1428427 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1428379 ATTTTCCTTC
1428389 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
1428406 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
1428424 CACA
1 CACA
1428428 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:1437042 original size:21 final size:21
Alignment explanation
Indices: 1437016--1437056 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1437006 ATCTGCTCAA
* *
1437016 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1437037 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1437057 TCGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1438692 original size:3 final size:3
Alignment explanation
Indices: 1438674--1438816 Score: 85
Period size: 3 Copynumber: 47.3 Consensus size: 3
1438664 TTTTGTTGCT
* * *
1438674 TTA TCA TTA TTTA TTA TTA TTA TTTA TTA TTA TTA TCTA TTA TCA ATA
1 TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA
* * * * * *
1438722 TTA TTA TTA CTA TTA TT- TTT TTA CTA TTA TTA TT- TCA CATA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * * * *
1438766 TTA TTT TTT TTG TTA TTA TTA TTA TTA CTA TT- GTA TTA TTA CTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1438813 TTA T
1 TTA T
1438817 ATTCTCATCT
Statistics
Matches: 106, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
2 4 0.04
3 92 0.87
4 10 0.09
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1438747 original size:14 final size:14
Alignment explanation
Indices: 1438728--1438775 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
1438718 AATATTATTA
1438728 TTACTATTATTTTT
1 TTACTATTATTTTT
1438742 TTACTATTATTATTT
1 TTACTATTATT-TTT
*
1438757 CACATACTATTATTTTT
1 ---TTACTATTATTTTT
1438774 TT
1 TT
1438776 TGTTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 12 0.43
15 3 0.11
17 3 0.11
18 10 0.36
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTACTATTATTTTT
Found at i:1438749 original size:35 final size:35
Alignment explanation
Indices: 1438685--1438751 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1438675 TATCATTATT
1438685 TATTATTATTATTTATTATTATTATCTATTATCAA
1 TATTATTATTATTTATTATTATTATCTATTATCAA
*
1438720 TATTATTATTACTATTATT-TTTTTA-CTATTAT
1 TATTATTATTA-T-TTATTATTATTATCTATTAT
1438752 TATTTCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
35 18 0.62
36 6 0.21
37 5 0.17
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (35 bp):
TATTATTATTATTTATTATTATTATCTATTATCAA
Found at i:1438866 original size:14 final size:15
Alignment explanation
Indices: 1438835--1438872 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1438825 CTGTGTTTAT
1438835 TTTTTATTTATCTAA
1 TTTTTATTTATCTAA
1438850 TTTTTATTTATCT-A
1 TTTTTATTTATCTAA
*
1438864 TTTATATTT
1 TTTTTATTT
1438873 CTGTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATTTATCTAA
Found at i:1439112 original size:19 final size:19
Alignment explanation
Indices: 1439084--1439132 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1439074 TGTTTTTGCC
* *
1439084 TATTTCATTTCTTATTTTT
1 TATTTTATTTATTATTTTT
1439103 TATTTTATTTTATTATTTTT
1 TATTTTA-TTTATTATTTTT
1439123 TA-TTTATTTA
1 TATTTTATTTA
1439133 AACTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 13 0.48
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTATTTATTATTTTT
Found at i:1439120 original size:8 final size:7
Alignment explanation
Indices: 1439090--1439176 Score: 52
Period size: 7 Copynumber: 11.4 Consensus size: 7
1439080 TGCCTATTTC
*
1439090 ATTTCTT
1 ATTTTTT
1439097 ATTTTTT
1 ATTTTTT
1439104 A--TTTT
1 ATTTTTT
1439109 ATTTTATT
1 ATTTT-TT
1439117 ATTTTTT
1 ATTTTTT
1439124 ATTTATTT
1 ATTT-TTT
1439132 AAACTTTTTAAT
1 --A-TTTTT--T
*
1439144 AGTTTTT
1 ATTTTTT
1439151 ATTTATTT
1 ATTT-TTT
*
1439159 ATTTACTT
1 ATTT-TTT
1439167 ATTTTTT
1 ATTTTTT
1439174 ATT
1 ATT
1439177 CTTGCCCATA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
5 5 0.08
7 24 0.37
8 24 0.37
9 4 0.06
10 4 0.06
11 3 0.05
12 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (7 bp):
ATTTTTT
Found at i:1441433 original size:7 final size:7
Alignment explanation
Indices: 1441421--1441450 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1441411 AAATCAAAGT
1441421 CAAAATG
1 CAAAATG
1441428 CAAAATG
1 CAAAATG
1441435 CAAAATG
1 CAAAATG
1441442 CAAAATG
1 CAAAATG
1441449 CA
1 CA
1441451 GTGCTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (7 bp):
CAAAATG
Found at i:1443897 original size:14 final size:14
Alignment explanation
Indices: 1443878--1443904 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1443868 GAACTAAAAG
1443878 AACTCCTAAATAAA
1 AACTCCTAAATAAA
1443892 AACTCCTAAATAA
1 AACTCCTAAATAA
1443905 GTAATTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (14 bp):
AACTCCTAAATAAA
Found at i:1455292 original size:43 final size:43
Alignment explanation
Indices: 1455211--1455292 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
1455201 AAATTAAATT
* *
1455211 TTTATAATTTTAAGAGTTCAAAGTATAATTTTACTTTTATTAA
1 TTTAAAATTTTAAAAGTTCAAAGTATAATTTTACTTTTATTAA
1455254 TTTAAAATTTTAAAAGTT-AAA-TAATAATTTTACATTTTA
1 TTTAAAATTTTAAAAGTTCAAAGT-ATAATTTTAC-TTTTA
1455293 AATGTCTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 13 0.37
43 21 0.60
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (43 bp):
TTTAAAATTTTAAAAGTTCAAAGTATAATTTTACTTTTATTAA
Found at i:1466061 original size:18 final size:18
Alignment explanation
Indices: 1466034--1466068 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1466024 GATAAATCCT
1466034 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
1466052 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
1466069 TATATTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:1476875 original size:17 final size:17
Alignment explanation
Indices: 1476821--1476876 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1476811 TTTAAAAGAT
1476821 ATTTTA-TAAT-TTTTA
1 ATTTTATTAATATTTTA
*
1476836 ATATTTGTT-ATATGTTTA
1 AT-TTTATTAATAT-TTTA
1476854 GATTTTATTAATATTTTA
1 -ATTTTATTAATATTTTA
1476872 ATTTT
1 ATTTT
1476877 TCAAGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 2 0.06
16 5 0.15
17 7 0.21
18 13 0.39
19 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTTTATTAATATTTTA
Found at i:1478305 original size:107 final size:106
Alignment explanation
Indices: 1478086--1478821 Score: 631
Period size: 107 Copynumber: 7.0 Consensus size: 106
1478076 AAAATTCAAA
* * * *
1478086 TTTTTTTTAAAACTCGTATTTTCGGAGAGTAAAAAAATTTTTTCAAAAAAAATTTTGAATTTTTT
1 TTTTTTTTAAAACTCGTATTTTC-GATAG-CAAAAATTTTTTTTAAAAAAAATTTTGAATTTTTT
* *
1478151 TTTGTACTGGGTGCCAGCCATTGACAGACCAGCACCCAAAATTTT
64 TTTGTACTGGGTGCCGGCCA-TGACAGGCCAGCA-CCAAAATTTT
*
1478196 TTTTTTTTAAAACTCGTATTTTCGAATAGCAAAAATTTTTTTTTAAAAAAAATTTCGAA-TTTTT
1 TTTTTTTTAAAACTCGTATTTTCG-ATAGCAAAAA-TTTTTTTTAAAAAAAATTTTGAATTTTTT
* *
1478260 TTTGTACTGGGTGCTGGCC-TGTCAGGCCAGCATCC-AAATTTT
64 TTTGTACTGGGTGCCGGCCATGACAGGCCAGCA-CCAAAATTTT
*** *
1478302 TTTTTAAAAAAAAACTCGTATTTTCTGATAGC-AAAATTTTTTTTTAAAAAAA--TTGAA--TTT
1 TTTTT--TTTAAAACTCGTATTTTC-GATAGCAAAAATTTTTTTTAAAAAAAATTTTGAATTTTT
* *
1478362 TTTT-TATTGGGTGCCGGCCATTGACAGGCCAACACTCAAAATTTT
63 TTTTGTACTGGGTGCCGGCCA-TGACAGGCCAGCAC-CAAAATTTT
*** * ** *** *
1478407 TTTTTAAAAAAACTCGTATTTTTTGATAATAAAAA-AAATTTTGAAAAAAATTTTG-ATTTTTTT
1 TTTTTTTTAAAACTCGTA-TTTTCGATAGCAAAAATTTTTTTTAAAAAAAATTTTGAATTTTTTT
*
1478470 TTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAATTTT
65 TTGTACTGGGTGCCGGCCA-TGACAGGCCAGCA-CCAAAATTTT
* * * *** * *
1478514 TTTTTTTTAAAACTCGTACTTTCGGAGAGTAAAAA-AAATTTTGAAAAAAGTTTTGAATTTTTTT
1 TTTTTTTTAAAACTCGTATTTTC-GATAGCAAAAATTTTTTTTAAAAAAAATTTTGAATTTTTTT
*
1478578 TTGTACTTGGTGCCGGCCATTGACAGGCCAGCACCAAAA--TT
65 TTGTACTGGGTGCCGGCCA-TGACAGGCCAGCACCAAAATTTT
* **
1478619 TTTTTTTT-AAACTCGTATTTTC-AGTGAGCAAAAAATTTTTTTAAAAAAAAACTTGAATTTTTT
1 TTTTTTTTAAAACTCGTATTTTCGA-T-AGCAAAAATTTTTTTTAAAAAAAATTTTGAATTTTTT
****
1478682 TTTGTACTGGGTGCCGGCCATTGACAGG-CAGCACTCAAAAAAAA
64 TTTGTACTGGGTGCCGGCCA-TGACAGGCCAGCAC-CAAAATTTT
*** *
1478726 AAATTTTT--AACTCGTATTTTCGA-AG-AGAAAATTTTTTTT-TAAAAAA--TTGAA-TTTTTT
1 TTTTTTTTAAAACTCGTATTTTCGATAGCA-AAAATTTTTTTTAAAAAAAATTTTGAATTTTTTT
* * ** *
1478783 TTATACTTGGTGCCAACAATTGACAGGCCAGCACCAAAA
65 TTGTACTGGGTGCCGGCCA-TGACAGGCCAGCACCAAAA
1478822 AAAAATTTTT
Statistics
Matches: 536, Mismatches: 62, Indels: 66
0.81 0.09 0.10
Matches are distributed among these distances:
100 33 0.06
101 11 0.02
102 14 0.03
103 43 0.08
104 64 0.12
105 78 0.15
106 50 0.09
107 108 0.20
108 60 0.11
109 29 0.05
110 46 0.09
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (106 bp):
TTTTTTTTAAAACTCGTATTTTCGATAGCAAAAATTTTTTTTAAAAAAAATTTTGAATTTTTTTT
TGTACTGGGTGCCGGCCATGACAGGCCAGCACCAAAATTTT
Found at i:1478404 original size:211 final size:211
Alignment explanation
Indices: 1478094--1478721 Score: 623
Period size: 211 Copynumber: 2.9 Consensus size: 211
1478084 AATTTTTTTT
* * * * * *
1478094 AAAACTCGTATTTTCGGAGAGTAAAAAAATTTTTTCAAAAAAAATTTTGAATTTTTTTTTGTACT
1 AAAACTCGTACTTTCGGAGAGCAAAAAAA-ATTTTGAAAAAAGA--TTGAA-TTTTTTTTGTATT
* *
1478159 GGGTGCCAGCCATTGACAGACCAGCACCCAAAATTTTTTTTTTTTAAAACTCGTATTTTCGAATA
62 GGGTGCCGGCCATTGACAGGCCAGCA-CCAAAATTTTTTTTTTTTAAAACTCGTATTTTCGAATA
* *
1478224 GCAAAAATTTTTTTTTAAAAAAAATTTCGAATTTTTTTTGTACTGGGTGCTGGCC-TGTCAGGCC
126 GCAAAAA-TTTTTTTTAAAAAAAATTT-GAATTTTTTTTGTACTGGGTGCCGGCCATGACAGGCC
*
1478288 AGCATCC-AAATTTTTTTTTAAAAA
189 AGCACCCAAAATTTTTTTTT--AAA
* * * **** *
1478312 AAAACTCGTATTTTCTGATAGCAAAATTTTTTTTTAAAAAA-ATTGAA-TTTTTTT-TATTGGGT
1 AAAACTCGTACTTTCGGAGAGCAAAAAAAATTTTGAAAAAAGATTGAATTTTTTTTGTATTGGGT
* *** * **
1478374 GCCGGCCATTGACAGGCCAACACTCAAAATTTTTTTTTAAAAAAACTCGTATTTTTTG-ATAATA
66 GCCGGCCATTGACAGGCCAGCAC-CAAAATTTTTTTTTTTTAAAACTCGTA-TTTTCGAATAGCA
*** * * * *
1478438 AAAAAAATTTTGAAAAAAATTTTGATTTTTTTTTGTACTGGGTGCCAGCCATTGACAGGCCAGCA
129 AAAATTTTTTTTAAAAAAAATTTGAATTTTTTTTGTACTGGGTGCCGGCCA-TGACAGGCCAGCA
***
1478503 CCCAAAATTTTTTTTTTTT
193 CCCAAAATTTTTTTTTAAA
* *
1478522 AAAACTCGTACTTTCGGAGAGTAAAAAAAATTTTGAAAAAAGTTTTGAATTTTTTTTTGTACTT-
1 AAAACTCGTACTTTCGGAGAGCAAAAAAAATTTTGAAAAAAG-ATTGAA-TTTTTTTTGTA-TTG
*
1478586 GGTGCCGGCCATTGACAGGCCAGCACCAAAA--TTTTTTTTTT-AAACTCGTATTTTC-AGTGAG
63 GGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTTTAAAACTCGTATTTTCGAAT-AG
* *
1478647 CAAAAAATTTTTTTAAAAAAAAACTTGAATTTTTTTTTGTACTGGGTGCCGGCCATTGACAGG-C
127 C-AAAAATTTTTTTTAAAAAAAATTTGAA-TTTTTTTTGTACTGGGTGCCGGCCA-TGACAGGCC
*
1478711 AGCACTCAAAA
189 AGCACCCAAAA
1478722 AAAAAAATTT
Statistics
Matches: 338, Mismatches: 57, Indels: 36
0.78 0.13 0.08
Matches are distributed among these distances:
209 24 0.07
210 52 0.15
211 82 0.24
212 67 0.20
213 32 0.09
214 17 0.05
215 27 0.08
216 3 0.01
217 11 0.03
218 23 0.07
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (211 bp):
AAAACTCGTACTTTCGGAGAGCAAAAAAAATTTTGAAAAAAGATTGAATTTTTTTTGTATTGGGT
GCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTTTTTTAAAACTCGTATTTTCGAATAGCAAA
AATTTTTTTTAAAAAAAATTTGAATTTTTTTTGTACTGGGTGCCGGCCATGACAGGCCAGCACCC
AAAATTTTTTTTTAAA
Found at i:1478455 original size:12 final size:12
Alignment explanation
Indices: 1478438--1478462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1478428 TTTGATAATA
1478438 AAAAAAATTTTG
1 AAAAAAATTTTG
1478450 AAAAAAATTTTG
1 AAAAAAATTTTG
1478462 A
1 A
1478463 TTTTTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAAAAATTTTG
Found at i:1480035 original size:29 final size:28
Alignment explanation
Indices: 1479977--1480037 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
1479967 CTATAATTTT
*
1479977 TTTAATAAAATAACTAATTTATTTTTAAA
1 TTTAATAAAATAACTAATTTA-TTTAAAA
1480006 TTTAATAAACATATACTAATTTA-TTAAAA
1 TTTAATAAA-ATA-ACTAATTTATTTAAAA
1480035 TTT
1 TTT
1480038 TTTACACCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 17 0.59
30 3 0.10
31 9 0.31
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATAAAATAACTAATTTATTTAAAA
Found at i:1482470 original size:22 final size:23
Alignment explanation
Indices: 1482415--1482467 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1482405 AACAGCCAAC
*
1482415 AACTTAAATAAAAACTTTTAAAT
1 AACTTAAATAAAAACTTTCAAAT
1482438 AACTTAAATAAAAACTTTCAAAT
1 AACTTAAATAAAAACTTTCAAAT
*
1482461 AATTTAA
1 AACTTAA
1482468 TAACTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (23 bp):
AACTTAAATAAAAACTTTCAAAT
Found at i:1515270 original size:89 final size:89
Alignment explanation
Indices: 1515119--1515296 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
1515109 TCTTGACAGA
* *
1515119 GGAGAGAAACAAAATCCTGACATAGGGACAATACTTTAAAGTTGTTGGGGGTTCGACTGTCTACC
1 GGAGAGAAACAAAATCCCGACATAGGGACAATACTTTAAAGTTGTTGGGGGATCGACTGTCTACC
1515184 TATCAGACAACACTTTGAAAACTT
66 TATCAGACAACACTTTGAAAACTT
1515208 GGAGAGAAACAAAATCCCGACATAGGGACAATACTTTAAAGTTGTTGGGGGATCGACTGTCTACC
1 GGAGAGAAACAAAATCCCGACATAGGGACAATACTTTAAAGTTGTTGGGGGATCGACTGTCTACC
1515273 TATCAGACAACACTTTGAAAACTT
66 TATCAGACAACACTTTGAAAACTT
1515297 CTCCTAAAAG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (89 bp):
GGAGAGAAACAAAATCCCGACATAGGGACAATACTTTAAAGTTGTTGGGGGATCGACTGTCTACC
TATCAGACAACACTTTGAAAACTT
Found at i:1516856 original size:20 final size:20
Alignment explanation
Indices: 1516819--1516857 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1516809 TTTTTGATTT
* *
1516819 TTTTGACTTTTTTTTTTATG
1 TTTTGACTTTTATGTTTATG
*
1516839 TTTTGTCTTTTATGTTTAT
1 TTTTGACTTTTATGTTTAT
1516858 TTATGTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.74
Consensus pattern (20 bp):
TTTTGACTTTTATGTTTATG
Found at i:1516860 original size:10 final size:10
Alignment explanation
Indices: 1516847--1516871 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1516837 TGTTTTGTCT
1516847 TTTATGTTTA
1 TTTATGTTTA
1516857 TTTATGTTTA
1 TTTATGTTTA
1516867 TTTAT
1 TTTAT
1516872 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
TTTATGTTTA
Found at i:1516980 original size:21 final size:19
Alignment explanation
Indices: 1516956--1517017 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 19
1516946 TTAAATATAT
1516956 ATTTTGAAATTACTTTTTTAA
1 ATTTT-AAATTA-TTTTTTAA
1516977 ATTTTAAATATTATTTTTTAA
1 ATTTT-AA-ATTATTTTTTAA
*
1516998 ATATTAAATATATTTTTTAA
1 ATTTTAAAT-TATTTTTTAA
1517018 TAATATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 19 0.51
22 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAATTATTTTTTAA
Found at i:1517028 original size:22 final size:20
Alignment explanation
Indices: 1516969--1517030 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
1516959 TTGAAATTAC
* *
1516969 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATAAAATA-TA
*
1516990 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATAAAATATA
1517010 TTTTTTAATAATATAAAATAT
1 TTTTTT-A-AATATAAAATAT
1517031 TTAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 8 0.22
21 18 0.49
22 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTAAATATAAAATATA
Found at i:1517032 original size:20 final size:20
Alignment explanation
Indices: 1516969--1517017 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
1516959 TTGAAATTAC
*
1516969 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATTAAATA-TA
1516990 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATTAAATATA
1517010 TTTTTTAA
1 TTTTTTAA
1517018 TAATATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAATATTAAATATA
Found at i:1517057 original size:22 final size:21
Alignment explanation
Indices: 1517029--1517090 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
1517019 AATATAAAAT
1517029 ATTTAAATATTTTAAAATCATA
1 ATTTAAATATTTTAAAATCA-A
*
1517051 ATTTAAAATATTATAAAA-CAA
1 ATTT-AAATATTTTAAAATCAA
1517072 A-TTAAATAATATTTAAAAT
1 ATTTAAAT-AT-TTTAAAAT
1517091 ATTATAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 8 0.24
22 6 0.18
23 12 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTAAATATTTTAAAATCAA
Found at i:1517067 original size:23 final size:21
Alignment explanation
Indices: 1517029--1517090 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1517019 AATATAAAAT
1517029 ATTT-AAATATTTTAAAATCATA
1 ATTTAAAATA-TTTAAAATCA-A
1517051 ATTTAAAATATTATAAAA-CAA
1 ATTTAAAATATT-TAAAATCAA
*
1517072 ATTAAATAATATTTAAAAT
1 ATTTAA-AATATTTAAAAT
1517091 ATTATAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.31
22 14 0.40
23 10 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTAAAATATTTAAAATCAA
Found at i:1517088 original size:21 final size:23
Alignment explanation
Indices: 1517031--1517090 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
1517021 TATAAAATAT
1517031 TTAAAT-AT-TTTAAAATCATAA
1 TTAAATAATATTTAAAATCATAA
*
1517052 TTTAA-AATATTATAAAA-CA-AA
1 TTAAATAATATT-TAAAATCATAA
1517073 TTAAATAATATTTAAAAT
1 TTAAATAATATTTAAAAT
1517091 ATTATAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 17 0.53
22 10 0.31
23 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAATAATATTTAAAATCATAA
Found at i:1517260 original size:23 final size:22
Alignment explanation
Indices: 1517184--1517260 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
1517174 AAGTAATTTC
**
1517184 AAAATATATATTTAAAATTTAGAA
1 AAAATATATATTTAAAATTT--TT
*
1517208 AAATATATATATTAATAAAATATTT
1 AAA-ATATATATT--TAAAATTTTT
*
1517233 CAAATATATATTTCAAAATTTTT
1 AAAATATATATTT-AAAATTTTT
1517256 AAAAT
1 AAAAT
1517261 TAATAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 12 0.28
24 12 0.28
25 11 0.26
27 7 0.16
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (22 bp):
AAAATATATATTTAAAATTTTT
Found at i:1517260 original size:49 final size:48
Alignment explanation
Indices: 1517179--1517273 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
1517169 TAACAAAGTA
*
1517179 ATTTCAAAATATATATTTAAAATTTAGAAAAATATATATATTAATAAAAT
1 ATTTCAAAATATATATTTAAAATTTAGAAAAAT-TA-ATAATAATAAAAT
**
1517229 ATTTC-AAATATATATTTCAAAATTT-TTAAAATTAATAATAATAAA
1 ATTTCAAAATATATATTT-AAAATTTAGAAAAATTAATAATAATAAA
1517274 TAAAATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 10 0.24
48 2 0.05
49 17 0.41
50 12 0.29
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (48 bp):
ATTTCAAAATATATATTTAAAATTTAGAAAAATTAATAATAATAAAAT
Found at i:1517277 original size:4 final size:4
Alignment explanation
Indices: 1517268--1517311 Score: 70
Period size: 4 Copynumber: 10.5 Consensus size: 4
1517258 AATTAATAAT
1517268 AATA AATAA AATA AATAA AATA AATA AATA AATA AATA AATA AA
1 AATA AAT-A AATA AAT-A AATA AATA AATA AATA AATA AATA AA
1517312 CATAAAAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 30 0.79
5 8 0.21
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1517280 original size:9 final size:9
Alignment explanation
Indices: 1517255--1517317 Score: 85
Period size: 9 Copynumber: 7.0 Consensus size: 9
1517245 TCAAAATTTT
*
1517255 TAAAATTAA
1 TAAAATAAA
1517264 TAATAATAAA
1 TAA-AATAAA
1517274 TAAAATAAA
1 TAAAATAAA
1517283 TAAAATAAA
1 TAAAATAAA
1517292 T-AAATAAA
1 TAAAATAAA
1517300 T-AAATAAA
1 TAAAATAAA
1517308 TAAACATAAA
1 TAAA-ATAAA
1517318 AGACAAAAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
8 16 0.32
9 21 0.42
10 13 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1517280 original size:51 final size:50
Alignment explanation
Indices: 1517179--1517280 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 50
1517169 TAACAAAGTA
*
1517179 ATTTCAAAATATATATTTAAAATTTAGAAAAATATATATATTAATAAAAT
1 ATTTCAAAATATATATTTAAAATTTAGAAAAATATATATATAAATAAAAT
** *
1517229 ATTTC-AAATATATATTTCAAAATTTTTAAAATTA-ATAATAATAAATAAAAT
1 ATTTCAAAATATATATTT-AAAATTTAGAAAAATATAT-AT-ATAAATAAAAT
1517280 A
1 A
1517281 AATAAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
49 14 0.31
50 20 0.44
51 11 0.24
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (50 bp):
ATTTCAAAATATATATTTAAAATTTAGAAAAATATATATATAAATAAAAT
Found at i:1517289 original size:51 final size:49
Alignment explanation
Indices: 1517184--1517289 Score: 115
Period size: 51 Copynumber: 2.1 Consensus size: 49
1517174 AAGTAATTTC
* **
1517184 AAAATATATATTTAAAATTTAGAAAAATATATATATTAATAAAATATTT
1 AAAATATATATTTAAAATTTAGAAAAATATATATATAAATAAAATAAAT
* ** *
1517233 CAAATATATATTTCAAAATTTTTAAAATTA-ATAATAATAAATAAAATAAAT
1 AAAATATATATTT-AAAATTTAGAAAAATATAT-AT-ATAAATAAAATAAAT
1517284 AAAATA
1 AAAATA
1517290 AATAAATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
49 14 0.30
50 15 0.33
51 17 0.37
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (49 bp):
AAAATATATATTTAAAATTTAGAAAAATATATATATAAATAAAATAAAT
Found at i:1517345 original size:9 final size:9
Alignment explanation
Indices: 1517333--1517366 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1517323 AAAACATAAA
1517333 AAAAAAGTC
1 AAAAAAGTC
1517342 AAAAAAGTC
1 AAAAAAGTC
*
1517351 AAAAAAGTA
1 AAAAAAGTC
1517360 AAAAAAG
1 AAAAAAG
1517367 AAAAGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:1517375 original size:9 final size:9
Alignment explanation
Indices: 1517332--1517376 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
1517322 AAAAACATAA
1517332 AAAAAAAGT
1 AAAAAAAGT
*
1517341 CAAAAAAGT
1 AAAAAAAGT
*
1517350 CAAAAAAGT
1 AAAAAAAGT
1517359 AAAAAAAG-
1 AAAAAAAGT
1517367 AAAAGAAAGT
1 AAAA-AAAGT
1517377 GACATGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 4 0.12
9 28 0.88
ACGTcount: A:0.73, C:0.04, G:0.13, T:0.09
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:1531530 original size:58 final size:56
Alignment explanation
Indices: 1531451--1531596 Score: 141
Period size: 58 Copynumber: 2.5 Consensus size: 56
1531441 CAACATTTCT
* * * *
1531451 CACATTGGGGCTCGAACTTTTTTTTTTTCAACTTAGGTCTTAG-CTTGGAAATTGTTCC
1 CACATTGGGGCT-AAAATTTTTTTTTTT-AACTTAAGTC-CAGACTTGGAAATTGTTCC
* *
1531509 CACATTGGGGTCTAAAATTTTTTTTATTTAAGTTAAGTCCAGAACTTGGCAATTGTTCC
1 CACATTGGGG-CTAAAATTTTTTTT-TTTAACTTAAGTCCAG-ACTTGGAAATTGTTCC
* * * *
1531568 CATATTGGGGCCAGAATCTTTTTTTTTAA
1 CACATTGGGGCTAAAATTTTTTTTTTTAA
1531597 TCTAAGTTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
57 7 0.09
58 39 0.53
59 28 0.38
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (56 bp):
CACATTGGGGCTAAAATTTTTTTTTTTAACTTAAGTCCAGACTTGGAAATTGTTCC
Found at i:1534072 original size:24 final size:25
Alignment explanation
Indices: 1534045--1534133 Score: 128
Period size: 26 Copynumber: 3.6 Consensus size: 25
1534035 TTGGGGGTTT
1534045 TTTTTTTTTGTTTTTTGGAGG-GTG
1 TTTTTTTTTGTTTTTTGGAGGAGTG
1534069 TTTTTTTTTGTTTTTTGGAGGAG-G
1 TTTTTTTTTGTTTTTTGGAGGAGTG
*
1534093 TTTGTTTTTTTGTTTTTTGGAGGAGGG
1 -TT-TTTTTTTGTTTTTTGGAGGAGTG
*
1534120 TTGTTTTTTGTTTT
1 TTTTTTTTTGTTTT
1534134 GGAAAGGCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
24 22 0.37
25 14 0.23
26 23 0.38
27 1 0.02
ACGTcount: A:0.06, C:0.00, G:0.28, T:0.66
Consensus pattern (25 bp):
TTTTTTTTTGTTTTTTGGAGGAGTG
Found at i:1534084 original size:26 final size:26
Alignment explanation
Indices: 1534032--1534133 Score: 99
Period size: 26 Copynumber: 4.1 Consensus size: 26
1534022 CAAGACTTTG
1534032 TTTTTGG-GG-GT-TTTTTTTTTTTGT
1 TTTTTGGAGGAGTGTTTTTTTTTTT-T
*
1534056 TTTTTGGAGG-GTG-TTTTTTTTTGT
1 TTTTTGGAGGAGTGTTTTTTTTTTTT
*
1534080 TTTTTGGAGGAG-GTTTGTTTTTTTGT
1 TTTTTGGAGGAGTGTTT-TTTTTTTTT
* * *
1534106 TTTTTGGAGGAGGGTTGTTTTTTGTT
1 TTTTTGGAGGAGTGTTTTTTTTTTTT
1534132 TT
1 TT
1534134 GGAAAGGCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
24 19 0.28
25 16 0.24
26 30 0.44
27 3 0.04
ACGTcount: A:0.05, C:0.00, G:0.29, T:0.66
Consensus pattern (26 bp):
TTTTTGGAGGAGTGTTTTTTTTTTTT
Found at i:1538719 original size:22 final size:21
Alignment explanation
Indices: 1538676--1538721 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1538666 TCCATATATA
**
1538676 AAATATTTATTTGTTACATTT
1 AAATATTTATTTAATACATTT
*
1538697 AAATATCTTATTTAATACCTTT
1 AAATAT-TTATTTAATACATTT
1538719 AAA
1 AAA
1538722 ACTTTAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATATTTATTTAATACATTT
Found at i:1541474 original size:32 final size:32
Alignment explanation
Indices: 1541408--1541472 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1541398 AATTAAATTG
* *
1541408 AATTTAACAAAACAATTAAATCTGAATTTTAA
1 AATTTAACAAAACAAATAAATCTAAATTTTAA
*
1541440 AATTTAA-AAAGCAAATAAAT-TAAATTCTTAA
1 AATTTAACAAAACAAATAAATCTAAATT-TTAA
1541471 AA
1 AA
1541473 ATACAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 5 0.17
31 17 0.59
32 7 0.24
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (32 bp):
AATTTAACAAAACAAATAAATCTAAATTTTAA
Found at i:1546174 original size:30 final size:30
Alignment explanation
Indices: 1546124--1546181 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
1546114 AAGAGTTGTG
1546124 GAAATTTATATTGAAAAGGTTGGAAATGTA
1 GAAATTTATATTGAAAAGGTTGGAAATGTA
1546154 GAAACTTTATATTG-AAAGGTTGGAAATG
1 GAAA-TTTATATTGAAAAGGTTGGAAATG
1546182 ATTTGTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (30 bp):
GAAATTTATATTGAAAAGGTTGGAAATGTA
Found at i:1546970 original size:31 final size:30
Alignment explanation
Indices: 1546918--1546993 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
1546908 TTATTTGATC
*
1546918 AATTTTAGTCCCTAGAATTTTTGAATTG-GTA
1 AATTTTAGT-CCTAGAATTTTTAAATTGTG-A
* * *
1546949 AATTTTAGTCCTTGTACTTTTTAAATTTTGA
1 AATTTTAGTCCTAG-AATTTTTAAATTGTGA
1546980 AATTTTAGTCCTAG
1 AATTTTAGTCCTAG
1546994 CCCAAACAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 4 0.11
31 33 0.87
32 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (30 bp):
AATTTTAGTCCTAGAATTTTTAAATTGTGA
Found at i:1548277 original size:51 final size:51
Alignment explanation
Indices: 1548217--1548442 Score: 278
Period size: 51 Copynumber: 4.7 Consensus size: 51
1548207 TACAAATCAA
* *
1548217 ATCTCTAAGAATATAAAATCATATCTTCTAAGATTACATATCATATCTAAG
1 ATCTCTAAGAATATAAAATAATATCTTATAAGATTACATATCATATCTAAG
*
1548268 ATCTCTAAGAATATAAAATAATATCTTATAAGATTTCATATCATATCTAAG
1 ATCTCTAAGAATATAAAATAATATCTTATAAGATTACATATCATATCTAAG
*
1548319 ATCTCTAA-AAT-T---AT-A-A---TATAATA-T-CATATCATATCTAAG
1 ATCTCTAAGAATATAAAATAATATCTTATAAGATTACATATCATATCTAAG
* * *
1548358 ATCTCTAAGATTATAATATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGAATATAAAATAATATCTTATAAGATTACATATCATATCTAAG
* * *
1548409 ATCTCTAAGATTATAAAATCATATCTTTTAAGAT
1 ATCTCTAAGAATATAAAATAATATCTTATAAGAT
1548443 CATGTTTCCA
Statistics
Matches: 154, Mismatches: 9, Indels: 24
0.82 0.05 0.13
Matches are distributed among these distances:
39 23 0.15
40 3 0.02
41 7 0.05
44 3 0.02
45 2 0.01
46 3 0.02
49 7 0.05
50 4 0.03
51 102 0.66
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.38
Consensus pattern (51 bp):
ATCTCTAAGAATATAAAATAATATCTTATAAGATTACATATCATATCTAAG
Found at i:1548293 original size:22 final size:22
Alignment explanation
Indices: 1548217--1548293 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
1548207 TACAAATCAA
*
1548217 ATCTCTAAGAATATAAAATCAT
1 ATCTCTAAGAATATAAAATAAT
** *
1548239 ATCTTCTAAGATTACATATCATATCTAAG
1 ATC-TCTAAG---A-ATAT-A-AAATAAT
1548268 ATCTCTAAGAATATAAAATAAT
1 ATCTCTAAGAATATAAAATAAT
1548290 ATCT
1 ATCT
1548294 TATAAGATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
22 11 0.27
23 7 0.17
24 4 0.10
25 1 0.02
26 1 0.02
27 4 0.10
28 7 0.17
29 6 0.15
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGAATATAAAATAAT
Found at i:1548348 original size:39 final size:39
Alignment explanation
Indices: 1548303--1548382 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
1548293 TTATAAGATT
1548303 TCATATCATATCTAAGATCTCTAAAATTATAATATAATA
1 TCATATCATATCTAAGATCTCTAAAATTATAATATAATA
*
1548342 TCATATCATATCTAAGATCTCTAAGATTATAATATAATA
1 TCATATCATATCTAAGATCTCTAAAATTATAATATAATA
1548381 TC
1 TC
1548383 TTATAAGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (39 bp):
TCATATCATATCTAAGATCTCTAAAATTATAATATAATA
Found at i:1548402 original size:90 final size:90
Alignment explanation
Indices: 1548253--1548433 Score: 308
Period size: 90 Copynumber: 2.0 Consensus size: 90
1548243 TCTAAGATTA
*
1548253 CATATCATATCTAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTTCATATCATATCTAA
1 CATATCATATCTAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
*
1548318 GATCTCTAAAATTATAATATAATAT
66 GATCTCTAAAATTATAAAATAATAT
* *
1548343 CATATCATATCTAAGATCTCTAAGATTATAATATAATATCTTATAAGATTCCATATCATATCTAA
1 CATATCATATCTAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
* *
1548408 GATCTCTAAGATTATAAAATCATAT
66 GATCTCTAAAATTATAAAATAATAT
1548433 C
1 C
1548434 TTTTAAGATC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.38
Consensus pattern (90 bp):
CATATCATATCTAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
GATCTCTAAAATTATAAAATAATAT
Found at i:1551222 original size:22 final size:22
Alignment explanation
Indices: 1551190--1551273 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 22
1551180 AGGTATCTAC
*
1551190 AAATCAAATCTCTAAGAATATA
1 AAATCATATCTCTAAGAATATA
*
1551212 AAATCATATCTTCTAAGATTACATATC
1 AAATCATATC-TCTAAG---A-ATATA
*
1551239 ATATCTAATATCTCTAAGAATATA
1 AAATC--ATATCTCTAAGAATATA
*
1551263 AAATAATATCT
1 AAATCATATCT
1551274 TTTAAGATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 15 0.31
23 6 0.12
24 7 0.14
25 1 0.02
26 1 0.02
27 8 0.16
28 6 0.12
29 5 0.10
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATCATATCTCTAAGAATATA
Found at i:1551257 original size:51 final size:51
Alignment explanation
Indices: 1551197--1551381 Score: 280
Period size: 51 Copynumber: 3.6 Consensus size: 51
1551187 TACAAATCAA
* *
1551197 ATCTCTAAGAATATAAAATCATATCTTCTAAGATTACATATCATATCTAAT
1 ATCTCTAAGAATATAAAATAATATCTTTTAAGATTACATATCATATCTAAT
* *
1551248 ATCTCTAAGAATATAAAATAATATCTTTTAAGATTTCATATCATATCTAAG
1 ATCTCTAAGAATATAAAATAATATCTTTTAAGATTACATATCATATCTAAT
* * * *
1551299 ATCTCTAAGATTATAATATAATATCTTATAAGATTGCATATCATATCTAAT
1 ATCTCTAAGAATATAAAATAATATCTTTTAAGATTACATATCATATCTAAT
* *
1551350 ATCTCTAAGATTATAAAATCATATCTTTTAAG
1 ATCTCTAAGAATATAAAATAATATCTTTTAAG
1551382 CTCATGTTTC
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 122 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (51 bp):
ATCTCTAAGAATATAAAATAATATCTTTTAAGATTACATATCATATCTAAT
Found at i:1551293 original size:22 final size:22
Alignment explanation
Indices: 1551268--1551346 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
1551258 ATATAAAATA
1551268 ATATCTTTTAAGATTTCATATC
1 ATATCTTTTAAGATTTCATATC
* *
1551290 ATATCTAAGATCTCTAAGATTATAATATA
1 ATATCT----T-T-TAAGATT-TCATATC
* *
1551319 ATATCTTATAAGATTGCATATC
1 ATATCTTTTAAGATTTCATATC
1551341 ATATCT
1 ATATCT
1551347 AATATCTCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
22 16 0.36
23 7 0.16
25 1 0.02
26 1 0.02
27 1 0.02
28 7 0.16
29 11 0.25
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (22 bp):
ATATCTTTTAAGATTTCATATC
Found at i:1556899 original size:12 final size:12
Alignment explanation
Indices: 1556884--1556908 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1556874 TAATCCTGAT
1556884 TCTAAAAAATTA
1 TCTAAAAAATTA
1556896 TCTAAAAAATTA
1 TCTAAAAAATTA
1556908 T
1 T
1556909 AAAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTAAAAAATTA
Found at i:1561246 original size:31 final size:29
Alignment explanation
Indices: 1561161--1561252 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 29
1561151 ATGTAATTTA
*
1561161 ATATATGAACTTTAA-TTTGATGCAATCAT
1 ATATATGAACTTTAATTTTGATTCAA-CAT
* * * *
1561190 ATACATGGAACTTTACTTGTAATTCAA-AT
1 ATATAT-GAACTTTAATTTTGATTCAACAT
1561219 GGATATATGAAACTTTAATTTTGATTCAAC-T
1 --ATATATG-AACTTTAATTTTGATTCAACAT
1561250 ATA
1 ATA
1561253 CATATTTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
29 10 0.21
30 9 0.19
31 29 0.60
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (29 bp):
ATATATGAACTTTAATTTTGATTCAACAT
Found at i:1571248 original size:7 final size:7
Alignment explanation
Indices: 1571216--1571251 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1571206 ATTGTAGAAC
*
1571216 ATAGAAT
1 ATAGTAT
*
1571223 ATAGAAT
1 ATAGTAT
1571230 ATAGTAT
1 ATAGTAT
1571237 ATAGTAT
1 ATAGTAT
1571244 ATAGTAT
1 ATAGTAT
1571251 A
1 A
1571252 GTGGATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (7 bp):
ATAGTAT
Found at i:1571248 original size:14 final size:14
Alignment explanation
Indices: 1571210--1571251 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1571200 TAAAATATTG
* *
1571210 TAGAACATAGAATA
1 TAGAATATAGTATA
1571224 TAGAATATAGTATA
1 TAGAATATAGTATA
*
1571238 TAGTATATAGTATA
1 TAGAATATAGTATA
1571252 GTGGATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33
Consensus pattern (14 bp):
TAGAATATAGTATA
Found at i:1582355 original size:27 final size:27
Alignment explanation
Indices: 1582317--1582370 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1582307 TTCTAAATCA
1582317 GTCTTAAGTTTCAAAACGTTATAATTG
1 GTCTTAAGTTTCAAAACGTTATAATTG
1582344 GTCTTAAGTTTCAAAACGTTATAATTG
1 GTCTTAAGTTTCAAAACGTTATAATTG
1582371 AACTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (27 bp):
GTCTTAAGTTTCAAAACGTTATAATTG
Found at i:1585179 original size:19 final size:19
Alignment explanation
Indices: 1585132--1585173 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1585122 TGGGTAGATG
* *
1585132 AAGAAGAGAAAAAAAGTGC
1 AAGAAAAGAAAAAAAGAGC
*
1585151 AAGAAAAGAAAAACAGAGC
1 AAGAAAAGAAAAAAAGAGC
1585170 AAGA
1 AAGA
1585174 CCAGAACTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.07, G:0.24, T:0.02
Consensus pattern (19 bp):
AAGAAAAGAAAAAAAGAGC
Found at i:1586737 original size:15 final size:15
Alignment explanation
Indices: 1586713--1586747 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1586703 GAGTTAATTT
*
1586713 AAATTTAAATTAAAC
1 AAATTCAAATTAAAC
*
1586728 AAATTCAAATTAATC
1 AAATTCAAATTAAAC
1586743 AAATT
1 AAATT
1586748 ATTATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTCAAATTAAAC
Found at i:1595283 original size:16 final size:16
Alignment explanation
Indices: 1595251--1595281 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1595241 CAAGTTTGAG
1595251 TCATTTTAAGTTTAAA
1 TCATTTTAAGTTTAAA
1595267 TCATTTTAA-TTTAAA
1 TCATTTTAAGTTTAAA
1595282 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
TCATTTTAAGTTTAAA
Found at i:1602358 original size:14 final size:14
Alignment explanation
Indices: 1602335--1602365 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1602325 TTGAAAATAT
1602335 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
1602349 GTTGATTTGGATTG
1 GTTGAATTGGATTG
1602363 GTT
1 GTT
1602366 TCGATATAAT
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:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:1610081 original size:31 final size:31
Alignment explanation
Indices: 1610046--1610107 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1610036 TTATGGTAGT
*
1610046 AGAGGGGCTACAGTCAAAATTTGACCAAATA
1 AGAGGGGCTAAAGTCAAAATTTGACCAAATA
1610077 AGAGGGGCTAAAGTCAAAATTTGACCAAATA
1 AGAGGGGCTAAAGTCAAAATTTGACCAAATA
1610108 TATTTACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (31 bp):
AGAGGGGCTAAAGTCAAAATTTGACCAAATA
Found at i:1618684 original size:27 final size:26
Alignment explanation
Indices: 1618615--1618709 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 26
1618605 TTAATTATTT
* *
1618615 TTTAAAATTTTAAAA-TATTAAAA-A
1 TTTAATATTTTAAAATTTTTAAAATA
* * *
1618639 TAT-ATATATTAATACATTTTTAATAGT-
1 TTTAATATTTTAA-A-ATTTTTAA-AATA
1618666 TTTAATGATTTTAAAATTTTTAAAATA
1 TTTAAT-ATTTTAAAATTTTTAAAATA
*
1618693 TTTAATTTTTTAAAATT
1 TTTAATATTTTAAAATT
1618710 AATTAAATGC
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
23 7 0.13
24 3 0.06
25 1 0.02
26 17 0.31
27 17 0.31
28 3 0.06
29 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAATATTTTAAAATTTTTAAAATA
Found at i:1618715 original size:18 final size:17
Alignment explanation
Indices: 1618682--1618715 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1618672 GATTTTAAAA
*
1618682 TTTTTAAAATATTTAAT
1 TTTTTAAAATAATTAAT
1618699 TTTTTAAAATTAATTAA
1 TTTTTAAAA-TAATTAA
1618716 ATGCTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAAAATAATTAAT
Found at i:1628069 original size:52 final size:52
Alignment explanation
Indices: 1628007--1628111 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
1627997 TTAAATATCA
*
1628007 AGCTAACAAACTTAATTCGGTGAATTGTGTTTTAAGTATTAATTATGATAAT
1 AGCTAACAAACTTAATTCGGTGAACTGTGTTTTAAGTATTAATTATGATAAT
1628059 AGCTAACAAACTTAATTCGGTGAACTGTGTTTTAAGTATTAATTATGATAAT
1 AGCTAACAAACTTAATTCGGTGAACTGTGTTTTAAGTATTAATTATGATAAT
1628111 A
1 A
1628112 TTTCAAGCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (52 bp):
AGCTAACAAACTTAATTCGGTGAACTGTGTTTTAAGTATTAATTATGATAAT
Found at i:1630440 original size:30 final size:30
Alignment explanation
Indices: 1630404--1630464 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1630394 CACGGGCTGG
*
1630404 CACATGGGCATGTGGCCTGCCCGTGTGGAT
1 CACATGGCCATGTGGCCTGCCCGTGTGGAT
*
1630434 CACATGGCCATGTGGCCTTCCCGTGTGGAT
1 CACATGGCCATGTGGCCTGCCCGTGTGGAT
1630464 C
1 C
1630465 CTGAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.13, C:0.30, G:0.33, T:0.25
Consensus pattern (30 bp):
CACATGGCCATGTGGCCTGCCCGTGTGGAT
Found at i:1635218 original size:29 final size:29
Alignment explanation
Indices: 1635146--1635257 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
1635136 ACCCCTACAT
* *
1635146 ACATGCATATGGCCCACTAGGCCCAA-TC
1 ACATTCATATGACCCACTAGGCCCAATTC
* * *
1635174 TCATTCATATGGCCCATCT-GGCCCAGTTC
1 ACATTCATATGACCCA-CTAGGCCCAATTC
* *
1635203 ATATTCTTATGACCCACTAGGCCCAATTC
1 ACATTCATATGACCCACTAGGCCCAATTC
* * *
1635232 ACATTCATATGGCACATTAGGCCCAA
1 ACATTCATATGACCCACTAGGCCCAA
1635258 ATCATATTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 22 0.32
29 46 0.68
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (29 bp):
ACATTCATATGACCCACTAGGCCCAATTC
Found at i:1635255 original size:58 final size:57
Alignment explanation
Indices: 1635153--1635265 Score: 156
Period size: 58 Copynumber: 2.0 Consensus size: 57
1635143 CATACATGCA
* * * **
1635153 TATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATCTGGCCCAGTTCATATTCT
1 TATGACCCACTAGGCCCAATCACATTCATATGGCACATCTGGCCCAAATCATATTCT
1635210 TATGACCCACTAGGCCCAATTCACATTCATATGGCACAT-TAGGCCCAAATCATATT
1 TATGACCCACTAGGCCCAA-TCACATTCATATGGCACATCT-GGCCCAAATCATATT
1635266 ATACTCATGC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 19 0.39
58 30 0.61
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (57 bp):
TATGACCCACTAGGCCCAATCACATTCATATGGCACATCTGGCCCAAATCATATTCT
Found at i:1635509 original size:24 final size:24
Alignment explanation
Indices: 1635453--1635511 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1635443 GTAGCCCAAC
*
1635453 TTTTGG-TATTTCGGTATTTCGGCA
1 TTTTGGCT-TTTCAGTATTTCGGCA
**
1635477 TTTCAGCTTTTCAGTATTTCGGCA
1 TTTTGGCTTTTCAGTATTTCGGCA
1635501 TTTTGGCTTTT
1 TTTTGGCTTTT
1635512 GCTGATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (24 bp):
TTTTGGCTTTTCAGTATTTCGGCA
Found at i:1641289 original size:30 final size:30
Alignment explanation
Indices: 1641253--1641310 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1641243 ACATGCCATT
*
1641253 TATTAGTTAAATTAACTGTTTCCATAACAG
1 TATTAGTTAAATTAACGGTTTCCATAACAG
1641283 TATTAGTTAAATTAACGGTTTCCATAAC
1 TATTAGTTAAATTAACGGTTTCCATAAC
1641311 GGTAATGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (30 bp):
TATTAGTTAAATTAACGGTTTCCATAACAG
Found at i:1646488 original size:39 final size:39
Alignment explanation
Indices: 1646428--1646516 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
1646418 GCTCTGATGA
* *
1646428 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGG
*
1646467 GCTTTAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGG
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGG
1646506 GCTTCAGTTAG
1 GCTTCAGTTAG
1646517 ATTTCGGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGG
Found at i:1646509 original size:21 final size:21
Alignment explanation
Indices: 1646444--1646510 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1646434 GTTAGCCTTC
1646444 GGGCTTCCGTTTAGCACTTAT
1 GGGCTTCCGTTTAGCACTTAT
* **
1646465 GTGCTTTAG-TTAGC-CTTCA-
1 GGGCTTCCGTTTAGCACTT-AT
1646484 -GGCTTCCGTTTAGCACTTAT
1 GGGCTTCCGTTTAGCACTTAT
1646504 GGGCTTC
1 GGGCTTC
1646511 AGTTAGATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 5 0.14
19 9 0.26
20 9 0.26
21 12 0.34
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (21 bp):
GGGCTTCCGTTTAGCACTTAT
Found at i:1652824 original size:18 final size:18
Alignment explanation
Indices: 1652801--1652857 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1652791 CCCAACTACT
* *
1652801 GTATACGTGAACAGTACC
1 GTATACATGAATAGTACC
*
1652819 GTATACATGAATAGTGCC
1 GTATACATGAATAGTACC
1652837 GTATACATGAATAGTACC
1 GTATACATGAATAGTACC
1652855 GTA
1 GTA
1652858 AACGGTCGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (18 bp):
GTATACATGAATAGTACC
Found at i:1664704 original size:18 final size:18
Alignment explanation
Indices: 1664653--1664714 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
1664643 TATCGGTATC
*
1664653 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAGTT
* * *
1664671 TTTCAATAGCAATCAGTT
1 ATTCAGTAACAATCAGTT
* *
1664689 ATTCAGTAACAGTCAGTC
1 ATTCAGTAACAATCAGTT
1664707 ATTCAGTA
1 ATTCAGTA
1664715 CCTTTATCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (18 bp):
ATTCAGTAACAATCAGTT
Found at i:1664921 original size:44 final size:44
Alignment explanation
Indices: 1664867--1664958 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
1664857 CCGATGTAAT
* * *
1664867 AGTAATAGTACGACACACATGGTGCCTCATCGACTTGAA-GTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGAC-TCAAGGTCGA
** *
1664911 AGTAACAGTACGACACTTATAGTGCCTCATTGACTCAAGGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
1664955 AGTA
1 AGTA
1664959 TCTCTGAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
Found at i:1670672 original size:27 final size:27
Alignment explanation
Indices: 1670624--1670782 Score: 157
Period size: 27 Copynumber: 5.9 Consensus size: 27
1670614 GCAAGGCTGC
* *
1670624 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
1670651 CAGATATTATGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
1670677 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
1670704 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
* *
1670731 TAGATATATGTGGCAAAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
1670758 CAGAAAATTGTGGCATAGCCACCAG
1 CAG-ATATTGTGGCAGAGCCACCAG
1670783 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.09
27 96 0.86
28 6 0.05
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:1670718 original size:54 final size:54
Alignment explanation
Indices: 1670624--1670782 Score: 214
Period size: 54 Copynumber: 3.0 Consensus size: 54
1670614 GCAAGGCTGC
* * * * *
1670624 CAGATAT-TGTGACGAAGTCACCAGATACAGAT-ATTATGGCAGAGCCACCAGAA
1 CAGATATATGTGGCAAAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGAA
* *
1670677 CAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCACCAGAA
1 CAGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
* *
1670731 TAGATATATGTGGCAAAGCCACCAGATCAGAAAATTGTGGCATAGCCACCAG
1 CAGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
1670783 GACGCTTCCT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 12 0.13
54 81 0.87
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CAGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
Found at i:1672365 original size:26 final size:26
Alignment explanation
Indices: 1672334--1672441 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1672324 TGAAATGCCC
*
1672334 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1672360 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1672386 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
1672412 ACCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1672438 ATCA
1 ATCA
1672442 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1674852 original size:5 final size:5
Alignment explanation
Indices: 1674842--1674875 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
1674832 AACTATGTGT
1674842 AAATA AAATA AAATA AAATA AAATA AAGATA AAA
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAA
1674876 AATAAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1679288 original size:5 final size:5
Alignment explanation
Indices: 1679278--1679310 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1679268 CCAATTTGTA
1679278 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1679311 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1682736 original size:32 final size:32
Alignment explanation
Indices: 1682695--1682759 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1682685 ATACAATAAA
1682695 AAAGATTGGAATTATGCACAATAAACTTTGTT
1 AAAGATTGGAATTATGCACAATAAACTTTGTT
1682727 AAAGATTGGAATTATGCACAATAAACTTTGTT
1 AAAGATTGGAATTATGCACAATAAACTTTGTT
1682759 A
1 A
1682760 CCTTGTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (32 bp):
AAAGATTGGAATTATGCACAATAAACTTTGTT
Found at i:1700649 original size:26 final size:26
Alignment explanation
Indices: 1700620--1700727 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1700610 TGGTACAAAT
1700620 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1700646 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1700672 TAATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1700698 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1700724 TGAT
1 TGAT
1700728 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1710252 original size:17 final size:17
Alignment explanation
Indices: 1710230--1710269 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1710220 CTCTTTAAAA
1710230 GCCCGATAAATGAAAGT
1 GCCCGATAAATGAAAGT
* * *
1710247 GCCCGATTAATTAGAGT
1 GCCCGATAAATGAAAGT
1710264 GCCCGA
1 GCCCGA
1710270 CAAACGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (17 bp):
GCCCGATAAATGAAAGT
Found at i:1711364 original size:26 final size:26
Alignment explanation
Indices: 1711335--1711390 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1711325 TGATACAAAT
1711335 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1711361 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1711387 TGAT
1 TGAT
1711391 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1718357 original size:26 final size:26
Alignment explanation
Indices: 1718328--1718434 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
1718318 TGATACAAAT
1718328 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1718354 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1718379 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1718405 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1718431 TGAT
1 TGAT
1718435 GGGAATTTCA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 24 0.31
26 54 0.69
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1718383 original size:51 final size:52
Alignment explanation
Indices: 1718328--1718434 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 52
1718318 TGATACAAAT
*
1718328 TGATAATGGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
1718379 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
1718431 TGAT
1 TGAT
1718435 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 33 0.61
52 21 0.39
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCA
Done.