Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 4 of 210
Found at i:1332766 original size:16 final size:16
Alignment explanation
Indices: 1332745--1332780 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1332735 AATATAATTT
1332745 ATAATATTTTAATTAA
1 ATAATATTTTAATTAA
* *
1332761 ATAATATTTTTATTAT
1 ATAATATTTTAATTAA
1332777 ATAA
1 ATAA
1332781 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATATTTTAATTAA
Found at i:1334829 original size:20 final size:21
Alignment explanation
Indices: 1334775--1334820 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1334765 TTGATATGTT
1334775 AGTGAAGAAAAATAAGAGAAA
1 AGTGAAGAAAAATAAGAGAAA
1334796 AGTGAAGAAAAATAAGAG-AA
1 AGTGAAGAAAAATAAGAGAAA
1334816 AGTGA
1 AGTGA
1334821 TGGGAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (21 bp):
AGTGAAGAAAAATAAGAGAAA
Found at i:1345266 original size:15 final size:17
Alignment explanation
Indices: 1345234--1345266 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1345224 CATACCAGCT
1345234 TCAGCTTCTTCATACTA
1 TCAGCTTCTTCATACTA
1345251 TCAGCTT-TTC-TACTA
1 TCAGCTTCTTCATACTA
1345266 T
1 T
1345267 TCTTTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.21, C:0.27, G:0.06, T:0.45
Consensus pattern (17 bp):
TCAGCTTCTTCATACTA
Found at i:1349610 original size:28 final size:28
Alignment explanation
Indices: 1349578--1349633 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1349568 AGAGAGACAG
1349578 GCTGAGTCTTTGGAGATGCATATAAGAA
1 GCTGAGTCTTTGGAGATGCATATAAGAA
1349606 GCTGAGTCTTTGGAGATGCATATAAGAA
1 GCTGAGTCTTTGGAGATGCATATAAGAA
1349634 AGAATGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (28 bp):
GCTGAGTCTTTGGAGATGCATATAAGAA
Found at i:1355159 original size:19 final size:16
Alignment explanation
Indices: 1355111--1355159 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
1355101 ATTTACTTTC
1355111 CCTC-AAACTTTTATT
1 CCTCAAAACTTTTATT
1355126 CCTCAAAACTTTTTATTTT
1 CCTCAAAAC-TTTTA--TT
1355145 CCTCCAAAACTTTTA
1 CCT-CAAAACTTTTA
1355160 CTTCTCACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 5 0.17
19 10 0.34
20 6 0.21
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.45
Consensus pattern (16 bp):
CCTCAAAACTTTTATT
Found at i:1358294 original size:62 final size:60
Alignment explanation
Indices: 1358139--1358325 Score: 202
Period size: 58 Copynumber: 3.1 Consensus size: 60
1358129 GAGCTCGAAC
* * *
1358139 TTTTTTTTGTTCAAGTTAGGC-CATAAACTTGGAAATTGTTCCCACATTAGGGTCTAAAC--
1 TTTTTTTTGTTCAAGTTA-GCTC-TGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
* * *
1358198 -TTTTTTTATTCAAGTTAGGTCCTGAACTTGGCAATTGTTCCCACATTGGGGCCTAAACCTT
1 TTTTTTTTGTTCAAGTTAGCT-CTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAA-CTT
* * * * *
1358259 TTTTTTTTGTTTAAGTTAGACTCTGAATTTGGCAATTGTTCTCACATTAGGGCTTGAACTT
1 TTTTTTTTGTTCAAGTTAG-CTCTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
1358320 TTTTTT
1 TTTTTT
1358326 AGTCCAAGTT
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.01
58 47 0.44
59 2 0.02
61 9 0.08
62 47 0.44
63 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (60 bp):
TTTTTTTTGTTCAAGTTAGCTCTGAACTTGGCAATTGTTCCCACATTAGGGCCTAAACTT
Found at i:1372363 original size:31 final size:30
Alignment explanation
Indices: 1372300--1372367 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1372290 TGACTCCACC
*
1372300 AAATAAAATATTATTTTTTATATTTAATTT
1 AAATAAAATATTATTTTATATATTTAATTT
1372330 AAATAAAATATT-TTTTATAGT-TTTAAAATTT
1 AAATAAAATATTATTTTATA-TATTT--AATTT
1372361 AAATAAA
1 AAATAAA
1372368 CGAAAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.26
30 13 0.38
31 12 0.35
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATAAAATATTATTTTATATATTTAATTT
Found at i:1373981 original size:13 final size:13
Alignment explanation
Indices: 1373955--1373989 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
1373945 ATCCATTTTC
1373955 TCTAAGTGCATCAT
1 TCTAAGT-CATCAT
1373969 TCTAAGTCATCAT
1 TCTAAGTCATCAT
1373982 TCTAAGTC
1 TCTAAGTC
1373990 CCTATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (13 bp):
TCTAAGTCATCAT
Found at i:1385091 original size:2 final size:2
Alignment explanation
Indices: 1385084--1385114 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1385074 TCTAAACCAA
1385084 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
1385115 ATAAATAGGT
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:1388252 original size:2 final size:2
Alignment explanation
Indices: 1388247--1388271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1388237 ATTTTGTGTG
1388247 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1388272 TAAGTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1389956 original size:16 final size:16
Alignment explanation
Indices: 1389935--1389975 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1389925 TTTGATTCGT
1389935 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1389951 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
1389967 TGTAATGGA
1 TGTATTGGA
1389976 AAAGCTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1390242 original size:18 final size:17
Alignment explanation
Indices: 1390221--1390255 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1390211 TTATTATTAA
*
1390221 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1390239 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1390256 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1390385 original size:16 final size:16
Alignment explanation
Indices: 1390348--1390389 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1390338 TTAATCATAT
*
1390348 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1390364 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1390379 TTAAAATATAT
1 TTAAAATATAT
1390390 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1390396 original size:14 final size:15
Alignment explanation
Indices: 1390357--1390398 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1390347 TTTAAACATA
*
1390357 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1390372 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1390386 A-TATAATTTAATA
1 ATTATAATTAAATA
1390399 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1390507 original size:16 final size:16
Alignment explanation
Indices: 1390467--1390509 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1390457 GTAAAATATA
*
1390467 AATTAACATA-ATTAT
1 AATTAAAATATATTAT
*
1390482 TATT-AAATATATTAT
1 AATTAAAATATATTAT
1390497 AATTAAAATATAT
1 AATTAAAATATAT
1390510 AATNNNNNNN
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:1393463 original size:15 final size:15
Alignment explanation
Indices: 1393443--1393473 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1393433 ATATTATGTA
1393443 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
1393458 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
1393473 T
1 T
1393474 TGAAGGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (15 bp):
TAATTGAGGTAAAAT
Found at i:1406161 original size:31 final size:32
Alignment explanation
Indices: 1406123--1406196 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 32
1406113 TCTGAATACC
* *
1406123 ATACATGAA-TTATGGTTTAA-TGTGCAATTGT
1 ATACATGAACTT-TGATTTAATTGTGCAATTAT
1406154 ATACATGAACTTTGATTTAATTTTGTGCAATTAT
1 ATACATGAACTTTGATTTAA--TTGTGCAATTAT
1406188 ATACATGAA
1 ATACATGAA
1406197 ATTTTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 16 0.43
32 2 0.05
34 19 0.51
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (32 bp):
ATACATGAACTTTGATTTAATTGTGCAATTAT
Found at i:1410231 original size:18 final size:19
Alignment explanation
Indices: 1410204--1410244 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1410194 TGGGTAGATG
* *
1410204 AAGAAGAGAAAAA-AGTGC
1 AAGAAAAGAAAAACAGAGC
1410222 AAGAAAAGAAAAACAGAGC
1 AAGAAAAGAAAAACAGAGC
1410241 AAGA
1 AAGA
1410245 CCAGAACCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.66, C:0.07, G:0.24, T:0.02
Consensus pattern (19 bp):
AAGAAAAGAAAAACAGAGC
Found at i:1410561 original size:2 final size:2
Alignment explanation
Indices: 1410554--1410583 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1410544 GGTTAACATA
1410554 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
1410584 TGAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1412637 original size:2 final size:2
Alignment explanation
Indices: 1412630--1412654 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1412620 CTTTTACCTA
1412630 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1412655 AGAGTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1423703 original size:21 final size:22
Alignment explanation
Indices: 1423660--1423704 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1423650 AAAAGTAAAT
**
1423660 AATCCAAATATGAATTGACCTA
1 AATCCAAATATGAAACGACCTA
*
1423682 AATCCAAAT-TGAAACGAGCTA
1 AATCCAAATATGAAACGACCTA
1423703 AA
1 AA
1423705 ATAATCGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (22 bp):
AATCCAAATATGAAACGACCTA
Found at i:1431021 original size:7 final size:7
Alignment explanation
Indices: 1431009--1431039 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1430999 TAATGCTATG
1431009 TTTGGAT
1 TTTGGAT
1431016 TTTGGAT
1 TTTGGAT
1431023 TTTGGAT
1 TTTGGAT
1431030 TTTGGAT
1 TTTGGAT
1431037 TTT
1 TTT
1431040 AACTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (7 bp):
TTTGGAT
Found at i:1433123 original size:64 final size:64
Alignment explanation
Indices: 1432996--1433123 Score: 148
Period size: 64 Copynumber: 2.0 Consensus size: 64
1432986 CGAGCATCCC
* * * ** **
1432996 GATCGGTATTAATCCTGCATGTATTGCGGACATACCACAACTTTTTGTGAGTGTCCTGTTATAT
1 GATCGGTATTAATCCTGCATGTATTGCGGACATACCACAACTCTTTATAAGCATCCTAATATAT
* * * * *
1433060 GATCGGTATTGATCTTGCATGTATTGCTGACATACCGCAGCTCTTTATAAGCATCCTAATATAT
1 GATCGGTATTAATCCTGCATGTATTGCGGACATACCACAACTCTTTATAAGCATCCTAATATAT
1433124 ATCTCTTCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (64 bp):
GATCGGTATTAATCCTGCATGTATTGCGGACATACCACAACTCTTTATAAGCATCCTAATATAT
Found at i:1444458 original size:10 final size:11
Alignment explanation
Indices: 1444431--1444458 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1444421 TGCAATTAAC
1444431 TGAAAAATTTA
1 TGAAAAATTTA
1444442 TGAAAAATTTA
1 TGAAAAATTTA
1444453 TGAAAA
1 TGAAAA
1444459 GAGATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (11 bp):
TGAAAAATTTA
Found at i:1447875 original size:43 final size:43
Alignment explanation
Indices: 1447806--1447906 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
1447796 ATGTTCCAAT
*
1447806 ATCGATTTGAGA-TTCGTGTAAGACCATAGCTCGGCTATTGCC
1 ATCGATTTGAGATTTCGTATAAGACCATAGCTCGGCTATTGCC
* *
1447848 ATCGATTTGAGATTTCGTATAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTATAAGACCATAGCTCGGCTATTGCC
**
1447891 ATCGATACGAGATTTC
1 ATCGATTTGAGATTTC
1447907 CATGTAAGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 12 0.23
43 41 0.77
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTATAAGACCATAGCTCGGCTATTGCC
Found at i:1457209 original size:26 final size:26
Alignment explanation
Indices: 1457180--1457235 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1457170 AATGGTTGAG
1457180 AATGGCAGTTGGAATTTGGTATTACT
1 AATGGCAGTTGGAATTTGGTATTACT
* * *
1457206 AATGGCGGTTGGAATTTTGTATTAGT
1 AATGGCAGTTGGAATTTGGTATTACT
1457232 AATG
1 AATG
1457236 CTCCCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (26 bp):
AATGGCAGTTGGAATTTGGTATTACT
Found at i:1459860 original size:13 final size:13
Alignment explanation
Indices: 1459842--1459866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1459832 TAATTTATGT
1459842 GTGTGAAAATTTC
1 GTGTGAAAATTTC
1459855 GTGTGAAAATTT
1 GTGTGAAAATTT
1459867 TATCGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:1461612 original size:41 final size:41
Alignment explanation
Indices: 1461567--1461834 Score: 493
Period size: 41 Copynumber: 6.5 Consensus size: 41
1461557 GACTTTAAGT
1461567 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1461608 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
1461649 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
1461690 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1461731 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
1461772 CTAGCAGGCTAAGTGCCGGTGAT-TAGAATCAGGTTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
1461813 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
1461835 ATATGTTAAA
Statistics
Matches: 221, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
40 1 0.00
41 220 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:1461963 original size:103 final size:103
Alignment explanation
Indices: 1461832--1462039 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
1461822 TAAGTGCCGG
1461832 TGAATATGTTAAATTAAGTGATTATATGCATTTGATATATATATATATATAAAAATGATTATGGG
1 TGAATATGTTAAATTAAGTGATTATATGCATTTGATATATATATATATATAAAAATGATTATGGG
1461897 ATATATATAATGGATAATTACATGAGCATTTGTCTATA
66 ATATATATAATGGATAATTACATGAGCATTTGTCTATA
*
1461935 TGAATATGTTAAATTAAGTGATTATATGCATTTGATATATATATATATATATAAATGATTATGGG
1 TGAATATGTTAAATTAAGTGATTATATGCATTTGATATATATATATATATAAAAATGATTATGGG
1462000 ATATATATAATGGATAATTACATGAGCATTTGTCTATA
66 ATATATATAATGGATAATTACATGAGCATTTGTCTATA
1462038 TG
1 TG
1462040 TATTTGATGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (103 bp):
TGAATATGTTAAATTAAGTGATTATATGCATTTGATATATATATATATATAAAAATGATTATGGG
ATATATATAATGGATAATTACATGAGCATTTGTCTATA
Found at i:1463867 original size:18 final size:18
Alignment explanation
Indices: 1463843--1463885 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1463833 TTCGTTTCCA
1463843 AAACATTATTC-ATTTAC
1 AAACATTATTCAATTTAC
*
1463860 AAATCATTATTCAATTTCC
1 AAA-CATTATTCAATTTAC
1463879 AAACATT
1 AAACATT
1463886 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (18 bp):
AAACATTATTCAATTTAC
Found at i:1467670 original size:17 final size:17
Alignment explanation
Indices: 1467627--1467677 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1467617 TTAGCCATTT
*
1467627 ATTTTTATTTC-ATTTTA
1 ATTTTT-TTTCAATTTAA
*
1467644 TTTTTCTTTTCAATTTAA
1 ATTTT-TTTTCAATTTAA
1467662 ATTTTTTTTCTAATTT
1 ATTTTTTTTC-AATTT
1467678 TTTCTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTTCAATTTAA
Found at i:1473907 original size:119 final size:119
Alignment explanation
Indices: 1473696--1473934 Score: 433
Period size: 119 Copynumber: 2.0 Consensus size: 119
1473686 TGTATGGCAT
*
1473696 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATATCATTAGTAATGATATAAAATGA
1 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
* *
1473761 AATTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACGTTCACCAAACCTAA
66 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
*
1473815 TACACATTAGATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
1 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
*
1473880 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTACCATTCACCAAACCTAA
66 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
1473934 T
1 T
1473935 TTTCAATAAT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 115 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (119 bp):
TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
Found at i:1474194 original size:12 final size:12
Alignment explanation
Indices: 1474177--1474201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1474167 CGCCAACTTG
1474177 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1474189 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1474201 T
1 T
1474202 GGTTTTGATT
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:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTTCTTGCTT
Found at i:1483392 original size:111 final size:111
Alignment explanation
Indices: 1483266--1483490 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
1483256 CATTTTATCA
1483266 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1483331 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
66 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
*
1483377 AATCCAGTGCTGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1483442 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
66 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
1483488 AAT
1 AAT
1483491 AAAAATTTGA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (111 bp):
AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
Found at i:1507384 original size:2 final size:2
Alignment explanation
Indices: 1507377--1507403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1507367 ACAAAATCAT
1507377 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1507404 TATTATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1509253 original size:18 final size:17
Alignment explanation
Indices: 1509230--1509264 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
1509220 ATATATCATT
1509230 AAAAATTAATTAAAAATA
1 AAAAATT-ATTAAAAATA
1509248 AAAAATTATTAAAAATA
1 AAAAATTATTAAAAATA
1509265 GATTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATTAAAAATA
Found at i:1511115 original size:3 final size:3
Alignment explanation
Indices: 1511107--1511138 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1511097 TGTGAGCTGC
1511107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1511139 TTGGGTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1514532 original size:32 final size:34
Alignment explanation
Indices: 1514493--1514582 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 34
1514483 CCTATATAAA
1514493 AAATAGTTTGATACCCTGTGCATTTGGATATA-T
1 AAATAGTTTGATACCCTGTGCATTTGGATATATT
* *
1514526 -AATAGTTTGATACCTTGTGCAATTTGGTTATATT
1 AAATAGTTTGATACCCTGTGC-ATTTGGATATATT
*
1514560 AAACTAGTTCGATACCCTGTGCA
1 AAA-TAGTTTGATACCCTGTGCA
1514583 CTGCTCAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 19 0.39
33 10 0.20
34 1 0.02
35 3 0.06
36 16 0.33
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (34 bp):
AAATAGTTTGATACCCTGTGCATTTGGATATATT
Found at i:1514800 original size:112 final size:108
Alignment explanation
Indices: 1514622--1514842 Score: 320
Period size: 112 Copynumber: 2.0 Consensus size: 108
1514612 GTATTTTATA
* * *
1514622 AAAATACTGAAATCACATGACAAGAATATTTAAAACCTATATAAAAATTGAATTTTCATAATCAC
1 AAAATACTGAAATCACATGACAAGAATAATAAAAACCCATATAAAAATTGAATTTTCATAATCAC
1514687 ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
66 ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
*
1514730 AAAATATTGAAATCACATGACAA-AATAAAAATAAAAACCACATATAAAAAATT-AATTTTTCAT
1 AAAATACTGAAATCACATGACAAGAAT---AATAAAAACC-CATAT-AAAAATTGAA-TTTTCAT
**
1514793 AATCACATGTTAATAACAATTAATAAAATTTTATTTATAATTTTAAATT
60 AATCACATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
1514842 A
1 A
1514843 TTTTTTATTC
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
107 3 0.03
108 22 0.22
110 8 0.08
111 6 0.06
112 62 0.61
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (108 bp):
AAAATACTGAAATCACATGACAAGAATAATAAAAACCCATATAAAAATTGAATTTTCATAATCAC
ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
Found at i:1519736 original size:520 final size:520
Alignment explanation
Indices: 1518861--1519904 Score: 1935
Period size: 520 Copynumber: 2.0 Consensus size: 520
1518851 TGGACAAAAA
* *
1518861 GAGCTATTTTCAAGATCCACACGGCCTGGGGCCTGGGCATTTCCACATGGGCTGGCCACACGCAT
1 GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
1518926 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
1518991 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
*
1519056 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAATATTG
196 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
1519121 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
261 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
1519186 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
326 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
1519251 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
*
1519316 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTACTTCATGTTTAATGTGCTTATTTCAGTG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
* * *
1519381 GAGCTGTTTTCAGGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCCC
1 GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
* *
1519446 ATGTGCCAGTCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCATAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
* **
1519511 TTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCGGAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
*
1519576 GAACGAAGAAAATACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
196 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
* *
1519641 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTTTTGTTGTTATCCTAAT
261 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
*
1519706 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
326 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
*
1519771 AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
1519836 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
1519901 GAGC
1 GAGC
1519905 AAAAGTCCCT
Statistics
Matches: 507, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
520 507 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (520 bp):
GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
Found at i:1524589 original size:28 final size:29
Alignment explanation
Indices: 1524540--1524604 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
1524530 TTCGTAAATT
* *
1524540 TAAAATTTAATCATTATCCTTTT-ATTTC
1 TAAAATTTAATCACTATACTTTTAATTTC
* * *
1524568 TAAAATTTAGTCCCTATACTTTTCAATTTT
1 TAAAATTTAATCACTATACTTTT-AATTTC
1524598 TAAAATT
1 TAAAATT
1524605 CAGGTCTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 19 0.63
30 11 0.37
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAAATTTAATCACTATACTTTTAATTTC
Found at i:1530704 original size:31 final size:31
Alignment explanation
Indices: 1530666--1530728 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1530656 GTACTATGGA
1530666 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1530697 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1530728 G
1 G
1530729 CTTTCTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (31 bp):
GGTTACTGCACTAAGAGTCAGATTGTATTTT
Found at i:1538424 original size:13 final size:13
Alignment explanation
Indices: 1538403--1538433 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1538393 TATAAACGCG
*
1538403 TGTACTTTTTGCA
1 TGTATTTTTTGCA
1538416 TGTATTTTTTGCA
1 TGTATTTTTTGCA
1538429 TGTAT
1 TGTAT
1538434 ACTTAAACCT
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:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (13 bp):
TGTATTTTTTGCA
Found at i:1539810 original size:32 final size:32
Alignment explanation
Indices: 1539747--1539806 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1539737 TCCGAAATCA
*
1539747 AAATTGAACCAAACCTTAAATAACTTGAATTT
1 AAATTGAACCAAACCTAAAATAACTTGAATTT
*
1539779 AAATTG-ACCATAACC-AAAATGACTTGAA
1 AAATTGAACCA-AACCTAAAATAACTTGAA
1539807 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (32 bp):
AAATTGAACCAAACCTAAAATAACTTGAATTT
Found at i:1541517 original size:31 final size:31
Alignment explanation
Indices: 1541481--1541539 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1541471 ATCAACTCAG
*
1541481 TGACTTAAATAAAAACTTTTAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
** *
1541512 TGACTTAAATGGAAACTTTCGAATAGTT
1 TGACTTAAATAAAAACTTTCAAATAGTT
1541540 TAGTGACCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAA
Found at i:1542308 original size:151 final size:151
Alignment explanation
Indices: 1542121--1542577 Score: 896
Period size: 151 Copynumber: 3.0 Consensus size: 151
1542111 TCCCTCTTTC
1542121 TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1 TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1542186 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
66 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
1542251 TTTTTTGGATATCCTTTTGTG
131 TTTTTTGGATATCCTTTTGTG
* *
1542272 TTTGCTAATTTTCATTTCTTTGATTTTTTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1 TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1542337 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
66 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
1542402 TTTTTTGGATATCCTTTTGTG
131 TTTTTTGGATATCCTTTTGTG
1542423 TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1 TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
1542488 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
66 TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
1542553 TTTTTTGGATATCCTTTTGTG
131 TTTTTTGGATATCCTTTTGTG
1542574 TTTG
1 TTTG
1542578 ATGAACTCTT
Statistics
Matches: 302, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 302 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (151 bp):
TTTGCTAATTTTCATTTCTTTGATATATTTTTTTATTTTGTTTACTACCCATTTAAGCTTTAGTG
TTTTTCTTGGTGGTAAAGTATGAATTTTGAAATGTTTGATGAAAATAAATGGTTGCAGCTTTACT
TTTTTTGGATATCCTTTTGTG
Found at i:1547499 original size:26 final size:24
Alignment explanation
Indices: 1547450--1547496 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1547440 TTGCTAATTT
1547450 TTATATTTTTTAATTTTCTCTTAA
1 TTATATTTTTTAATTTTCTCTTAA
*
1547474 TTATAATTATTTT-ATTTTATCTT
1 TTAT-ATT-TTTTAATTTTCTCTT
1547497 TAAAAATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 12 0.60
26 4 0.20
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATATTTTTTAATTTTCTCTTAA
Found at i:1554654 original size:16 final size:16
Alignment explanation
Indices: 1554604--1554677 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
1554594 AATCGAATTA
*
1554604 ATTTTAATTTTG-ATC
1 ATTTTAAATTTGAATC
** * *
1554619 ATTTTAAAGATAAATT
1 ATTTTAAATTTGAATC
*
1554635 ATTTTAAATTTGACTC
1 ATTTTAAATTTGAATC
* *
1554651 ATTTCAAAATTCGAATC
1 ATTT-TAAATTTGAATC
1554668 GATTTTAAAT
1 -ATTTTAAAT
1554678 ATCAATCCGA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
15 8 0.19
16 17 0.40
17 13 0.31
18 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (16 bp):
ATTTTAAATTTGAATC
Found at i:1558233 original size:29 final size:28
Alignment explanation
Indices: 1558178--1558233 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1558168 AAAATTTAAG
*
1558178 ATTTAATCCTTTATTTTAATTATATATA
1 ATTTAATCCTTTATTTTAATAATATATA
* *
1558206 ATTTGATCCTTTATTTTTATAATGATAT
1 ATTTAATCCTTTATTTTAATAAT-ATAT
1558234 TAGTTAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (28 bp):
ATTTAATCCTTTATTTTAATAATATATA
Found at i:1572540 original size:3 final size:3
Alignment explanation
Indices: 1572534--1572562 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1572524 AAAAAAAAAA
1572534 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1572563 AGGAAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1575476 original size:13 final size:13
Alignment explanation
Indices: 1575458--1575523 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1575448 TAGATTTTTC
1575458 CTAAATATTATCA
1 CTAAATATTATCA
1575471 CTAAATAATT-T--
1 CTAAAT-ATTATCA
1575482 -TAAATATTATCA
1 CTAAATATTATCA
*
1575494 CTAAATAGT-T--
1 CTAAATATTATCA
1575504 CTAAATATTATCA
1 CTAAATATTATCA
1575517 CTAAATA
1 CTAAATA
1575524 ACTAAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
9 3 0.07
10 14 0.33
11 1 0.02
12 1 0.02
13 21 0.49
14 3 0.07
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1575486 original size:23 final size:23
Alignment explanation
Indices: 1575458--1575524 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
1575448 TAGATTTTTC
1575458 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
* *
1575481 TTAAATATTATCACTAAATAGTT
1 CTAAATATTATCACTAAATAATT
1575504 CTAAATATTATCACTAAATAA
1 CTAAATATTATCACTAAATAA
1575525 CTAAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:1578425 original size:31 final size:32
Alignment explanation
Indices: 1578390--1578459 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 32
1578380 GTCACAAAAT
* *
1578390 AATCACTGAATC-ATTCAAAAG-TTTTCATTTA
1 AATCACTGAAACTATGCAAAAGCTTTT-ATTTA
* *
1578421 AATCA-TTAAACTATGCAAACGCTTTTATTTA
1 AATCACTGAAACTATGCAAAAGCTTTTATTTA
1578452 AATCACTG
1 AATCACTG
1578460 GACTATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.13
31 22 0.71
32 5 0.16
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (32 bp):
AATCACTGAAACTATGCAAAAGCTTTTATTTA
Found at i:1582504 original size:18 final size:19
Alignment explanation
Indices: 1582481--1582516 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1582471 TTTTGATATT
1582481 TGAACAAGAAA-AAAATTA
1 TGAACAAGAAATAAAATTA
*
1582499 TGAACAATAAATAAAATT
1 TGAACAAGAAATAAAATT
1582517 TTACAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
TGAACAAGAAATAAAATTA
Found at i:1586698 original size:50 final size:50
Alignment explanation
Indices: 1586560--1586699 Score: 199
Period size: 50 Copynumber: 2.8 Consensus size: 50
1586550 GATAATAACA
**
1586560 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * ** *
1586611 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
1586661 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACC
1586700 ATGTCCCAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 45 0.58
51 33 0.42
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:1586711 original size:29 final size:29
Alignment explanation
Indices: 1586669--1586728 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1586659 GGTGCCAACG
1586669 CCATGTCCCAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
1586698 CCATGTCCCAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
1586727 CC
1 CC
1586729 TCTCATCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (29 bp):
CCATGTCCCAGACATGGTCTTACATGGGA
Found at i:1586751 original size:79 final size:79
Alignment explanation
Indices: 1586619--1586778 Score: 293
Period size: 79 Copynumber: 2.0 Consensus size: 79
1586609 GGTGCCCATG
*
1586619 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
1586684 GGTCTTACATGGGA
66 GGTCTTACATGGGA
* *
1586698 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACAT
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
1586763 GGTCTTACATGGGA
66 GGTCTTACATGGGA
1586777 CC
1 CC
1586779 TCTCATCTCG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (79 bp):
CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
GGTCTTACATGGGA
Found at i:1586773 original size:50 final size:50
Alignment explanation
Indices: 1586698--1586831 Score: 268
Period size: 50 Copynumber: 2.7 Consensus size: 50
1586688 TTACATGGGA
1586698 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1586748 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
1586798 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
1586832 TTACCCAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.20, C:0.32, G:0.22, T:0.26
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATG
Found at i:1586801 original size:129 final size:130
Alignment explanation
Indices: 1586568--1586828 Score: 452
Period size: 129 Copynumber: 2.0 Consensus size: 130
1586558 CATGCCAAAG
** *
1586568 CCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCCCAGACA
1 CCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGTCCCAGACA
*
1586633 TGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
66 TGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
*
1586698 CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAATGCCATGTCCCAGACA
1 CCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGTCCCAGACA
* *
1586762 TGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
66 TGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1586827 CC
1 CC
1586829 TCTTTACCCA
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 95 0.77
130 29 0.23
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (130 bp):
CCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATCGGTGCCAATGCCATGTCCCAGACA
TGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
Found at i:1587191 original size:30 final size:30
Alignment explanation
Indices: 1587156--1587213 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1587146 CCTCGACTCT
*
1587156 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1587186 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1587214 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1595215 original size:31 final size:31
Alignment explanation
Indices: 1595172--1595230 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1595162 AAATGGTTAT
1595172 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
1 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
* * *
1595203 TGAATTATTCGAAAGTTTTTATTTAAGT
1 TGAACTATTCGAAAGCTTTCATTTAAGT
1595231 AATTGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (31 bp):
TGAACTATTCGAAAGCTTTCATTTAAGTCAC
Found at i:1607669 original size:22 final size:22
Alignment explanation
Indices: 1607632--1607681 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1607622 TGAAGTTTAC
*
1607632 AATTATTTTTATATTAAGATTTT
1 AATT-TTTTTAAATTAAGATTTT
*
1607655 AATTTTTTTAAATTAAGTTTTT
1 AATTTTTTTAAATTAAGATTTT
1607677 AATTT
1 AATTT
1607682 GATAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
AATTTTTTTAAATTAAGATTTT
Found at i:1617295 original size:13 final size:13
Alignment explanation
Indices: 1617277--1617301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1617267 TTTTAAAAAT
1617277 ATTTTCTATTTTA
1 ATTTTCTATTTTA
1617290 ATTTTCTATTTT
1 ATTTTCTATTTT
1617302 TTAAAATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTATTTTA
Found at i:1618448 original size:3 final size:3
Alignment explanation
Indices: 1618435--1618467 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1618425 GATCATTAAA
1618435 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1618468 AATTCGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1634169 original size:19 final size:21
Alignment explanation
Indices: 1634123--1634178 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
1634113 GAAAAATTAT
1634123 AATTTTTATAATTTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1634144 AAATTTTAT-A-TTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1634163 -ATTTTTTTAATTTTCT
1 AATTTTTATAATTTTCT
1634179 CACAACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 6 0.20
21 8 0.27
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTTTATAATTTTCTTTAC
Found at i:1636394 original size:15 final size:16
Alignment explanation
Indices: 1636369--1636401 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1636359 TCGATTCCCA
*
1636369 AAGATTTTATTGGTTT
1 AAGATTTTATTAGTTT
1636385 AAGA-TTTATTAGTTT
1 AAGATTTTATTAGTTT
1636400 AA
1 AA
1636402 TATACGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
AAGATTTTATTAGTTT
Found at i:1646020 original size:16 final size:17
Alignment explanation
Indices: 1645988--1646019 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1645978 CATTTCACGA
1645988 ATAATGGGATTCTTTTT
1 ATAATGGGATTCTTTTT
1646005 ATAA-GGGATT-TTTTT
1 ATAATGGGATTCTTTTT
1646020 TTAACGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (17 bp):
ATAATGGGATTCTTTTT
Found at i:1646373 original size:21 final size:21
Alignment explanation
Indices: 1646313--1646378 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
1646303 GATTTTTATT
*
1646313 ATTAT-TATATTTTATTAATTTA
1 ATTATATAT-TTTTATT-ATTCA
* * *
1646335 ATTTTATATTGTGATTATTCA
1 ATTATATATTTTTATTATTCA
1646356 ATTATATATTTTTATTATCTCA
1 ATTATATATTTTTATTAT-TCA
1646378 A
1 A
1646379 GTTTTTATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 19 0.54
22 13 0.37
23 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTATATATTTTTATTATTCA
Found at i:1649175 original size:2 final size:2
Alignment explanation
Indices: 1649129--1649158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1649119 AATAAAATTA
1649129 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
1649159 TTGAATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1652154 original size:31 final size:31
Alignment explanation
Indices: 1652118--1652199 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
1652108 TAAATTAGGC
* *
1652118 CTTGAACTTTGTAATTGA-TCCCACATTGGGG
1 CTTGAACTTTATAATT-ATTCCCACATTGGGA
* *
1652149 CTTGAA-TTAAATAATTATTCCCATATTGGGA
1 CTTGAACTT-TATAATTATTCCCACATTGGGA
*
1652180 CTTGAACTTTTATTATTATT
1 CTTGAAC-TTTATAATTATT
1652200 ATAAAAGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 3 0.07
31 28 0.68
32 8 0.20
33 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (31 bp):
CTTGAACTTTATAATTATTCCCACATTGGGA
Found at i:1659868 original size:2 final size:2
Alignment explanation
Indices: 1659855--1659904 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1659845 ATTAACAATA
*
1659855 AT AT AT AA 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
1659897 AT AT AT AT
1 AT AT AT AT
1659905 TTAGGTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1672232 original size:23 final size:23
Alignment explanation
Indices: 1672205--1672254 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1672195 CACTCAAATT
* * *
1672205 TTAAAAATTATAAAATATAAAAA
1 TTAAAAACTACAAAATAAAAAAA
*
1672228 TTAAAAACTACCAAATAAAAAAA
1 TTAAAAACTACAAAATAAAAAAA
1672251 TTAA
1 TTAA
1672255 TCCATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAAAACTACAAAATAAAAAAA
Found at i:1672744 original size:22 final size:22
Alignment explanation
Indices: 1672719--1672761 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1672709 ATTGGAAGGA
*
1672719 AAAACTC-AGCTATCAAATTGAC
1 AAAACTCAAG-TACCAAATTGAC
1672741 AAAACTCAAGTACCAAATTGA
1 AAAACTCAAGTACCAAATTGA
1672762 GAATTGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAACTCAAGTACCAAATTGAC
Found at i:1678114 original size:5 final size:5
Alignment explanation
Indices: 1678106--1678130 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1678096 CAAAGCAACC
1678106 GGCAA GGCAA GGCAA GGCAA GGCAA
1 GGCAA GGCAA GGCAA GGCAA GGCAA
1678131 TGGCTATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GGCAA
Found at i:1685647 original size:23 final size:23
Alignment explanation
Indices: 1685617--1685662 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1685607 GGCCAGTTCG
1685617 AATTCAACTCATTTTTGGGTTGT
1 AATTCAACTCATTTTTGGGTTGT
1685640 AATTCAACTCATTTTTGGGTTGT
1 AATTCAACTCATTTTTGGGTTGT
1685663 TTTAGGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (23 bp):
AATTCAACTCATTTTTGGGTTGT
Found at i:1688821 original size:2 final size:2
Alignment explanation
Indices: 1688814--1688839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1688804 TCAGCTCACT
1688814 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
1688840 ATAATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1689658 original size:23 final size:23
Alignment explanation
Indices: 1689631--1689676 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1689621 TGAACAAGAG
1689631 GTTCTCGTCCCATCAGGTATCAA
1 GTTCTCGTCCCATCAGGTATCAA
*
1689654 GTTCTCGTCCTATCAGGTATCAA
1 GTTCTCGTCCCATCAGGTATCAA
1689677 AATCCAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (23 bp):
GTTCTCGTCCCATCAGGTATCAA
Found at i:1693408 original size:3 final size:3
Alignment explanation
Indices: 1693400--1693429 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1693390 TTGCTTAGAT
1693400 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1693430 TCTTTGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1697698 original size:19 final size:19
Alignment explanation
Indices: 1697674--1697730 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1697664 CTTTTTTTCC
1697674 TTAAATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
* *
1697693 TTAAATTTCACATT-TTGTA
1 TTAAATTT-ATATTATTGAA
*
1697712 CT--ATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
1697729 TT
1 TT
1697731 GTTTAATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
19 13 0.43
20 4 0.13
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAAATTTATATTATTGAA
Found at i:1704830 original size:13 final size:13
Alignment explanation
Indices: 1704812--1704836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1704802 TTAATGTTTA
1704812 ATATTTTAAATAT
1 ATATTTTAAATAT
1704825 ATATTTTAAATA
1 ATATTTTAAATA
1704837 AGTTGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:1727143 original size:18 final size:18
Alignment explanation
Indices: 1727120--1727161 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1727110 CATTAATACA
*
1727120 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
1727138 AGAACCGGAAGCCGAACC
1 AGAACCGGAAACAGAACC
1727156 AGAACC
1 AGAACC
1727162 AGAGCATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.31, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:1727258 original size:3 final size:3
Alignment explanation
Indices: 1727250--1727282 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1727240 GTCACCCTTT
1727250 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1727283 AAATCACTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1733032 original size:26 final size:28
Alignment explanation
Indices: 1732996--1733048 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1732986 TCACAAGTTC
1732996 AGTTCTAATGTATATTTT-TC-TCGAAG
1 AGTTCTAATGTATATTTTCTCTTCGAAG
*
1733022 AGTTTTAATGTATATTTTCTCTTCGAA
1 AGTTCTAATGTATATTTTCTCTTCGAA
1733049 TTTGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 2 0.08
28 5 0.21
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (28 bp):
AGTTCTAATGTATATTTTCTCTTCGAAG
Found at i:1734267 original size:213 final size:214
Alignment explanation
Indices: 1733936--1734344 Score: 633
Period size: 213 Copynumber: 1.9 Consensus size: 214
1733926 TTTTTGTTGG
* * * ** *
1733936 TTATGGTTTCTTATTGTATATATATTGGGGATGTTTAGTTCTTCTAGGACCTAGGTTAATGCTTA
1 TTATGGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTA
*
1734001 TTTCATGTTTATCCTGCATATTTGATGGTTCGTTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
66 TTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
* *
1734066 TATGACCAGTCCAATTTGTGCTGGTTTTTACTCC-ATTTTTGTGAATT-GGGTTCTTGAGATAAT
131 TATGACCAATCCAATTTGTGCTGGTTTTTAATCCTATTTTTGTGAATTGGGGTTCTTGAGATAAT
1734129 GGTGTTTTTTCATTTGTTT
196 GGTGTTTTTTCATTTGTTT
* * *
1734148 TTATCGGTTTCTTATTATATATTTGTTGGGTATATTTAGTTCCTCTAGGACCTAGCCTAACGCTT
1 TTAT-GGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTT
* * * *
1734213 CTTTCATGTTTATTCTGCATATTTGGTGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGGAG
65 ATTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAG
*
1734278 CTATGACCAATCCAATTTGTGCTGGTTTTTAATCCTTTTTTTTGTGAATTGGGGTTCTTGAGATA
130 CTATGACCAATCCAATTTGTGCTGGTTTTTAATCC-TATTTTTGTGAATTGGGGTTCTTGAGATA
1734343 AT
194 AT
1734345 TCTGCTTTTC
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
212 4 0.02
213 144 0.82
215 12 0.07
216 16 0.09
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (214 bp):
TTATGGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTA
TTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
TATGACCAATCCAATTTGTGCTGGTTTTTAATCCTATTTTTGTGAATTGGGGTTCTTGAGATAAT
GGTGTTTTTTCATTTGTTT
Found at i:1742602 original size:26 final size:27
Alignment explanation
Indices: 1742554--1742605 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1742544 TCATATAAAT
*
1742554 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
*
1742581 AAAATAAATTATT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
1742606 TACGGTGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:1742787 original size:25 final size:25
Alignment explanation
Indices: 1742724--1742787 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1742714 AAATATTTTA
*
1742724 ATATATAATTTATACACATACAAGT
1 ATATATAATATATACACATACAAGT
* * *
1742749 ATATCTTAATTATATACATATA-AATT
1 ATAT-ATAA-TATATACACATACAAGT
1742775 ATATATGAATATA
1 ATATAT-AATATA
1742788 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 12 0.39
27 10 0.32
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATATAATATATACACATACAAGT
Found at i:1746442 original size:20 final size:20
Alignment explanation
Indices: 1746417--1746456 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1746407 AATATTTTCC
* *
1746417 AGTAAATCATTTTGCAGAAA
1 AGTAAAACATTTTCCAGAAA
1746437 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTCCAGAAA
1746457 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTCCAGAAA
Found at i:1746471 original size:34 final size:35
Alignment explanation
Indices: 1746405--1746471 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1746395 CAAACACTGG
* *
1746405 AAAATATTTTCCAGTAAATCATTTTGCAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1746440 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1746472 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1752735 original size:186 final size:183
Alignment explanation
Indices: 1752408--1752753 Score: 453
Period size: 186 Copynumber: 1.9 Consensus size: 183
1752398 ATCACATAAA
* * * *
1752408 CCAACCAACATTATGTAACTAGTTCAAATGGCAAACCCTTTGCGGGTACGAACATTGGGTCATTC
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
* * * *
1752473 TTATCAAACATTAGGACAAGTTTATGCTCTAACAACGATTGAAGTTGCAAAACATCATTCACAGT
66 TTATCAAACATTAGGACAAGCTTATACTCTAACAACGATTGAAATTG-AAAACATCATTCACAGC
*
1752538 GACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
130 AACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
* ** * * * **
1752592 CCAACCTACATTACGTGGCTAGTGCAAAAGGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTT
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGG-TACGAACATTGGATCATT
*
1752657 CTTATCAAACGTTAGGACAAGCTTATACATCTAACAATC-ATTGAAATCATG-AAACATCATTCA
65 CTTATCAAACATTAGGACAAGCTTATAC-TCTAACAA-CGATTGAAAT--TGAAAACATCATTCA
*
1752720 CAGCAACATCAAGAATTGTCGGAATACTAATAAA
126 CAGCAACATCAAGAATTGTCGAAATACTAATAAA
1752754 CACTGTACAG
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
184 39 0.28
185 38 0.28
186 58 0.42
187 1 0.01
188 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (183 bp):
CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
TTATCAAACATTAGGACAAGCTTATACTCTAACAACGATTGAAATTGAAAACATCATTCACAGCA
ACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
Found at i:1752903 original size:155 final size:155
Alignment explanation
Indices: 1752621--1752908 Score: 418
Period size: 155 Copynumber: 1.9 Consensus size: 155
1752611 TAGTGCAAAA
** * * *
1752621 GGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTTCTTATCAAACGTTAGGACAAGCTTATACA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACATTAGGACAAGCTTATACA
* *
1752686 TCTAACAATCATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
66 TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
1752751 AAACACTGTACAGAAACGCCGCAAC
131 AAACACTGTACAGAAACGCCGCAAC
1752776 GGCAAACCCTTTGCAGGATTCGAAC-TT-CATCTCGATCTTATCAAACATTAGGACAAGCTTATA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCAT-T-GATCTTATCAAACATTAGGACAAGCTTATA
* * ** * **
1752839 CGTCCAACAATAATTGAAGTTGTGAAACATCATTCACAGCGATGTCAAGAATTGTCGGAATACTA
64 CATCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTA
1752904 ATAAA
129 ATAAA
1752909 GACCGTACGT
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
153 2 0.02
154 3 0.03
155 112 0.96
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (155 bp):
GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACATTAGGACAAGCTTATACA
TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
AAACACTGTACAGAAACGCCGCAAC
Found at i:1755497 original size:25 final size:27
Alignment explanation
Indices: 1755469--1755519 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1755459 GGTACTACTA
*
1755469 CTTGTT-ATA-AACATTTTTATAAAGG
1 CTTGTTAATAGAACATATTTATAAAGG
*
1755494 CTTGTTAATAGAATATATTTATAAAG
1 CTTGTTAATAGAACATATTTATAAAG
1755520 TTTATGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTGTTAATAGAACATATTTATAAAGG
Found at i:1758374 original size:54 final size:53
Alignment explanation
Indices: 1758262--1758545 Score: 145
Period size: 54 Copynumber: 5.3 Consensus size: 53
1758252 GCAGAGTTTG
* * * * * * *
1758262 ATTCTCTTCTAGAAATTCGGTTTCCAGTAATGATCC-TCTCAGGGGTTATG-GTTG
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGA-CCTTATCA-GGATT-GGAGTTA
* *
1758316 ATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGA-GTTA
* ** * * * * *
1758370 ATTCCGC-TCTAGGAAG-TTGATCCCCAGTAACGATCC-CA-CCGGAAGTGGGAGTTG
1 ATTCC-CTTCTA-GAAGTTTGGTTTCCAGTAATGA-CCTTATCAGG-A-TTGGAGTTA
* *
1758424 ATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGATGTTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGA-GTTA
* ** * * * *
1758478 ATTCCGC-TCTAGGAAG-TTGATCGCCAGTAATGAGCC-CATCAGAAGTGGGAGTTG
1 ATTCC-CTTCTA-GAAGTTTGGTTTCCAGTAATGA-CCTTATCAGGA-TTGGAGTTA
1758532 ATTCCCTTCTAGAA
1 ATTCCCTTCTAGAA
1758546 ATCTGAATTC
Statistics
Matches: 174, Mismatches: 38, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
52 1 0.01
53 23 0.13
54 127 0.73
55 23 0.13
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (53 bp):
ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGAGTTA
Found at i:1758381 original size:108 final size:107
Alignment explanation
Indices: 1758312--1758545 Score: 317
Period size: 108 Copynumber: 2.2 Consensus size: 107
1758302 AGGGGTTATG
* * *
1758312 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
* * *
1758377 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
**
1758420 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGATGTTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
* * * * *
1758485 TCTAGGAAGTTGATCGCCAGTAATGAGCCCATCA-GAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCA-CAGGAAGTAGGA
1758528 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
1758546 ATCTGAATTC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 115 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (107 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
TCTAGAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
Found at i:1763597 original size:21 final size:21
Alignment explanation
Indices: 1763573--1763621 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1763563 TTTTGAGAAC
*
1763573 ATTATTTTTTTTTAAAAATTT
1 ATTATTTATTTTTAAAAATTT
* ***
1763594 ATTAATTATTTTTATTTATTT
1 ATTATTTATTTTTAAAAATTT
1763615 ATTATTT
1 ATTATTT
1763622 GGAGAATGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTTATTTTTAAAAATTT
Found at i:1766033 original size:24 final size:23
Alignment explanation
Indices: 1765988--1766033 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1765978 ATATAGGTAG
*
1765988 AAAAAATATAAAAGTAATTTTTA
1 AAAAAATATAAAAGAAATTTTTA
1766011 AAAAAATTATAAAA-AAATATTTT
1 AAAAAA-TATAAAAGAAAT-TTTT
1766034 CATAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAATATAAAAGAAATTTTTA
Found at i:1767896 original size:17 final size:17
Alignment explanation
Indices: 1767876--1767922 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
1767866 CAATAATTAC
*
1767876 ATAAATAATAAAATTTT
1 ATAAAAAATAAAATTTT
1767893 ATAAAAAATAAAATTTT
1 ATAAAAAATAAAATTTT
1767910 ATAAAAAATAAAA
1 ATAAAAAATAAAA
1767923 AAAAGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATAAAATTTT
Found at i:1775367 original size:275 final size:275
Alignment explanation
Indices: 1774874--1775394 Score: 864
Period size: 275 Copynumber: 1.9 Consensus size: 275
1774864 AAAAAAACCA
* *
1774874 AAGAAACAATCACTAAAAGTTTCATATGACTTTGCTTAAATTAAATTTCTTCAAAAAAAATTTTA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTC--AAAAAATTTTA
* * * *
1774939 AATTGAAATAAAACTTATGCTTCTCATTACATTTGGTTGAATACAATGAGTGTTACAAGCTCAAC
64 AAATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
*
1775004 CTTGCAAATCATGTAAGCTAAAAAAGTTAATAAACTCCATTTTTCTTGTATTTTCTATAACTTTC
129 CTTGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTC
* *
1775069 CTCGAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAATAACTAAATTTCCAAAAAAAG
194 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAG
1775134 TGACGCAAACATGAGCT
259 TGACGCAAACATGAGCT
* * *
1775151 AAGAAACAATTACTACAGGTTTAATACGACTTTGCTTAAATTAAATTTCTTC-AAAAATTTTAAA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
*
1775215 ATGAAATAAAACTTATGCTTCTCACTGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAGCC
66 ATGAAATAAAACTTATGCTTCTCA-TGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACC
* *
1775280 TTGCAAATCATGTAAGCTAAAAAAGTTAACGAACTCCATTTTTCTTGTATTTTCTATCACTTTCC
130 TTGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTCC
*
1775345 TCAAACTTTCTCGACACCCAAACAGAGCTTCATCATTCAACAAGAACTAA
195 TCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAA
1775395 GTCCCCCCCC
Statistics
Matches: 227, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
274 35 0.15
275 145 0.64
277 47 0.21
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (275 bp):
AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
ATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACCT
TGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTCCT
CAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAGTG
ACGCAAACATGAGCT
Found at i:1780435 original size:11 final size:12
Alignment explanation
Indices: 1780412--1780440 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1780402 TATTTGATTG
1780412 TAATATCAATAA
1 TAATATCAATAA
1780424 TAATAT-AATAA
1 TAATATCAATAA
1780435 TAATAT
1 TAATAT
1780441 TATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATATCAATAA
Found at i:1780447 original size:23 final size:23
Alignment explanation
Indices: 1780412--1780460 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1780402 TATTTGATTG
*
1780412 TAATATCAATAA-TAATATAATAA
1 TAATATCAATAATTAAT-TAAAAA
* *
1780435 TAATATTATTAATTAATTAAAAA
1 TAATATCAATAATTAATTAAAAA
1780458 TAA
1 TAA
1780461 AATAGCAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATCAATAATTAATTAAAAA
Found at i:1781884 original size:50 final size:50
Alignment explanation
Indices: 1781799--1782074 Score: 200
Period size: 50 Copynumber: 5.6 Consensus size: 50
1781789 CAGGGAAGTG
* *
1781799 AGATTCGCTGTTGTAGCTTCAATTTTTTAAATTGCAATGTCGGGGGAGCA
1 AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAATGTCGGGGGAGCA
*** * * ** *
1781849 AGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTGC-ATCGCCTGAAG-GTA
1 AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAAT-GTCGGGGGAGCA
* * * * * *
1781898 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCA
1 AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAATGTCGGGGGAGCA
*** * * * ** *
1781948 AGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTAC-ATCGCCTGAAG-GTA
1 AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAAT-GTCGGGGGAGCA
* * * * * * * *
1781997 AGATTCACCGTTGTGGCTTCGATCTTTTAAACTGTAATGTCGGGGAAGCA
1 AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAATGTCGGGGGAGCA
*
1782047 AGATTTGCTGTTGTAGCTTCAATCTGTT
1 AGATTCGCTGTTGTAGCTTCAATCTGTT
1782075 CCGTTGCATC
Statistics
Matches: 158, Mismatches: 62, Indels: 12
0.68 0.27 0.05
Matches are distributed among these distances:
49 65 0.41
50 93 0.59
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (50 bp):
AGATTCGCTGTTGTAGCTTCAATCTGTTAAATTGCAATGTCGGGGGAGCA
Found at i:1781970 original size:99 final size:99
Alignment explanation
Indices: 1781799--1782135 Score: 575
Period size: 99 Copynumber: 3.4 Consensus size: 99
1781789 CAGGGAAGTG
* * * * * *
1781799 AGATTCGCTGTTGTAGCTTCAATTTTTTAAATTGCAATGTCGGGGGAGCAAGATTCGCTGTTGTA
1 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTA
1781864 GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
66 GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
1781898 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTA
1 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTA
*
1781963 GCTTCAATCTGTTCCGTTACATCGCCTGAAGGTA
66 GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
* * *
1781997 AGATTCACCGTTGTGGCTTCGATCTTTTAAACTGTAATGTCGGGGAAGCAAGATTTGCTGTTGTA
1 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTA
1782062 GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
66 GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
*
1782096 AGATTCGCCGCTGTGGCTTCGATCTTTTAAACTGCAATGT
1 AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGT
1782136 ATGGTTACTT
Statistics
Matches: 224, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 224 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (99 bp):
AGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTA
GCTTCAATCTGTTCCGTTGCATCGCCTGAAGGTA
Found at i:1782010 original size:49 final size:49
Alignment explanation
Indices: 1781848--1782120 Score: 198
Period size: 49 Copynumber: 5.5 Consensus size: 49
1781838 TCGGGGGAGC
*
1781848 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
* * * **** ** *
1781897 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAACTGCAAT-GTCGGGGAA-GC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGC-ATCG-C-CTGAAGGT
* *
1781947 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTACATCGCCTGAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
* * * * * ** *
1781996 AAGATTCACCGTTGTGGCTTCGATCTTTTAAACTGTAATG--TCG-GGGAA-GC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTT---CCGT--TGCATCGCCTGAAGGT
* *
1782046 AAGATTTGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
* * *
1782095 AAGATTCGCCGCTGTGGCTTCGATCT
1 AAGATTCGCCGTTGTAGCTTCAATCT
1782121 TTTAAACTGC
Statistics
Matches: 162, Mismatches: 48, Indels: 28
0.68 0.20 0.12
Matches are distributed among these distances:
45 2 0.01
47 6 0.04
48 6 0.04
49 79 0.49
50 56 0.35
51 6 0.04
52 6 0.04
54 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (49 bp):
AAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGAAGGT
Found at i:1800337 original size:6 final size:6
Alignment explanation
Indices: 1800322--1800389 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
1800312 AGGTAGCCAA
1800322 TATT-G TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG
1 TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG
1800369 TATTGG TATTGG TATTGG TAT
1 TATTGG TATTGG TATTGG TAT
1800390 CAGTACTGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 4 0.06
6 58 0.94
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (6 bp):
TATTGG
Found at i:1817009 original size:30 final size:29
Alignment explanation
Indices: 1816973--1817040 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1816963 ATAGTTGGAC
* *
1816973 CTAAATT-TTGAAAATTGAAAAGTAGAGGGA
1 CTAAATTCCTGAAAA-T-AAAAGTACAGGGA
*
1817003 CTAAATTCCTGGAAATAAAAGTACAGGGA
1 CTAAATTCCTGAAAATAAAAGTACAGGGA
1817032 CTAAATTCC
1 CTAAATTCC
1817041 AAATTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.62
30 8 0.24
31 5 0.15
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
CTAAATTCCTGAAAATAAAAGTACAGGGA
Found at i:1819724 original size:31 final size:30
Alignment explanation
Indices: 1819669--1819733 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
1819659 TAATCAATTT
1819669 AAAAGTTGGAACTTCTGTACAATTAACCAA
1 AAAAGTTGGAACTTCTGTACAATTAACCAA
* *
1819699 AAAAGTTGAGAACTTTTTGTA-AATTAACCCA
1 AAAAGTTG-GAAC-TTCTGTACAATTAACCAA
1819730 AAAA
1 AAAA
1819734 TAACATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 17 0.55
32 6 0.19
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAAGTTGGAACTTCTGTACAATTAACCAA
Found at i:1828323 original size:13 final size:13
Alignment explanation
Indices: 1828307--1828355 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
1828297 TAAACCAAAT
*
1828307 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
*
1828320 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
1828333 -TTT-AAAAGCAC
1 TTTTCAAAAGCAC
1828344 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1828356 TTGAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
11 9 0.31
12 3 0.10
13 12 0.41
14 5 0.17
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1836575 original size:29 final size:29
Alignment explanation
Indices: 1836533--1836590 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1836523 GCAACCCATT
*
1836533 TTTATTATCATATCGAAACGATATTCCTA
1 TTTATTATCATATCAAAACGATATTCCTA
*
1836562 TTTATTATCATATCAAAACGCTATTCCTA
1 TTTATTATCATATCAAAACGATATTCCTA
1836591 ATAGAAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTATTATCATATCAAAACGATATTCCTA
Found at i:1838186 original size:15 final size:16
Alignment explanation
Indices: 1838166--1838197 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1838156 ATTATTTAAA
1838166 TTTTAAAA-TTATTAT
1 TTTTAAAATTTATTAT
1838181 TTTTAAAATTTATTAT
1 TTTTAAAATTTATTAT
1838197 T
1 T
1838198 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAAATTTATTAT
Found at i:1838214 original size:18 final size:18
Alignment explanation
Indices: 1838193--1838254 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1838183 TTAAAATTTA
1838193 TTATTAAAATAAAATAAT
1 TTATTAAAATAAAATAAT
* *
1838211 TTATTACAATAATA-AAT
1 TTATTAAAATAAAATAAT
* *
1838228 TATATTAATTATATTAATAAT
1 T-TATTAA-AATA-AAATAAT
1838249 TTATTA
1 TTATTA
1838255 TATTATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.12
18 17 0.50
19 3 0.09
20 6 0.18
21 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTAAAATAAAATAAT
Found at i:1838224 original size:21 final size:21
Alignment explanation
Indices: 1838187--1838226 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1838177 TTATTTTTAA
*
1838187 AATTTATTATTAAAATAAAAT
1 AATTTATTATCAAAATAAAAT
1838208 AATTTATTA-CAATAATAAA
1 AATTTATTATCAA-AATAAA
1838227 TTATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTATTATCAAAATAAAAT
Found at i:1839448 original size:2 final size:2
Alignment explanation
Indices: 1839441--1839475 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1839431 ATCAAGAAAT
1839441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1839476 CTTTGAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1842162 original size:197 final size:196
Alignment explanation
Indices: 1841750--1842332 Score: 672
Period size: 197 Copynumber: 2.9 Consensus size: 196
1841740 ATGTTGTTCG
** * *
1841750 GACTCTTCATTTTTCTTGAAGCAC-CAGTGTTTGACAGATGGATATTACATGGAAAACCTTTGAA
1 GACTCTTCATTTTTCTTGAAGCACTC-GTGTCGGACACATGGATATTACATAGAAAACCTTTG-A
* * * * * * *
1841814 AAATGAAAATTCTTACGATACTCGTGTCAAATGCACACCCGTATTTGACACTCACACCCAAGTCC
64 AAA-G-----CCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCC
* * *
1841879 GAATAACATAGGGCAAAATTCACTATGCCAACTAACAATTGACAGCTAGGGATCACACAATGATA
123 GAGTAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATA
1841944 AGTTGCTCA
188 AGTTGCTCA
*
1841953 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACGCATGGATATTACATAGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
* * * *
1842018 AGCCTAATGATACTC-TCATTAAATACAAACCCATATTTGACACTTACA-TCAGAGTCTGAGTAA
66 AGCCTAACGATACTCGT-ATTAAATACAAACCCATATTTGACACTCACACCCA-AGTCCGAGTAA
* * * * * *
1842081 CGTAAGGGCAAAATTAACTGTGTCAACTGACAATTGACAGCAAGCGG-TCACACAATGCTATGTT
129 CAT-AGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAG-GGATCACACAATGATAAGTT
1842145 GCTCA
192 GCTCA
** * * * *
1842150 TG-CTCTTCATTTTTCTTGAAGCACTCGTGTTTGATATATGTATATTACATGGAAAACCTTTGAA
1 -GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAA
* * * *
1842214 AAGTCTAACGATACTCGTGTTAAATACATACCCATTTTTGACACTCACACCCAAGTCCGAGTAAC
65 AAGCCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAAC
*
1842279 ATAGGGCAAAATTCACTATGTCAACTAACAAATCGACAGCAAGGGATCATCACA
130 ATAGGGCAAAATTCACTATGTCAACTAAC-AATTGACAGCAAGGGATCA-CACA
1842333 CAAGATTTTT
Statistics
Matches: 324, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
195 3 0.01
196 72 0.22
197 178 0.55
198 10 0.03
201 1 0.00
202 4 0.01
203 55 0.17
204 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (196 bp):
GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
AGCCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAACA
TAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATAAGTTGCTC
A
Found at i:1848043 original size:2 final size:2
Alignment explanation
Indices: 1848036--1848067 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1848026 CTTTGCATGT
1848036 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
1848068 CACTATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1849149 original size:20 final size:20
Alignment explanation
Indices: 1849124--1849165 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1849114 AGTTTGACGT
1849124 AATCTAATATTAAATAAATA
1 AATCTAATATTAAATAAATA
1849144 AATCTAATATTAAATAAATA
1 AATCTAATATTAAATAAATA
1849164 AA
1 AA
1849166 GGGTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AATCTAATATTAAATAAATA
Found at i:1853458 original size:15 final size:15
Alignment explanation
Indices: 1853435--1853471 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1853425 TTGCCTCATA
*
1853435 TTACATTTTAGTCAC
1 TTACGTTTTAGTCAC
*
1853450 TTACGTTTTAGTGAC
1 TTACGTTTTAGTCAC
1853465 TTACGTT
1 TTACGTT
1853472 ATCGTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:1857553 original size:23 final size:23
Alignment explanation
Indices: 1857527--1857624 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
1857517 ATAAGTGCCA
1857527 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1857550 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1857573 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1857595 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1857618 CACTGAT
1 CACTGAT
1857625 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1857592 original size:45 final size:46
Alignment explanation
Indices: 1857527--1857624 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
1857517 ATAAGTGCCA
* *
1857527 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1857573 CACTGA-ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1857618 CACTGAT
1 CACTGAT
1857625 CAATAACACT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:1857884 original size:17 final size:17
Alignment explanation
Indices: 1857850--1857887 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1857840 ATTTTCCTTC
*
1857850 CACATTCAATATTGATT
1 CACATTCAATATTAATT
1857867 CACATATCAATA-TAATT
1 CACAT-TCAATATTAATT
1857884 CACA
1 CACA
1857888 ATTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (17 bp):
CACATTCAATATTAATT
Found at i:1859210 original size:16 final size:17
Alignment explanation
Indices: 1859177--1859215 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1859167 ACCTGACACC
1859177 TTATTTTATTTTTATTT
1 TTATTTTATTTTTATTT
*
1859194 TTATTTT-TTTTTCTTT
1 TTATTTTATTTTTATTT
1859210 TTATTT
1 TTATTT
1859216 ATTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
TTATTTTATTTTTATTT
Found at i:1859260 original size:16 final size:16
Alignment explanation
Indices: 1859235--1859268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1859225 TGTCTTTCTC
*
1859235 TTTAAATTTTTTCTTT
1 TTTAAATTTTTTATTT
*
1859251 TTTAAGTTTTTTATTT
1 TTTAAATTTTTTATTT
1859267 TT
1 TT
1859269 CTTATTTTAT
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:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTAAATTTTTTATTT
Done.