Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 4 of 202
Found at i:1160120 original size:22 final size:22
Alignment explanation
Indices: 1160095--1160165 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1160085 ATTATTAAGC
1160095 TAGAATACAAACAATAACAAAT
1 TAGAATACAAACAATAACAAAT
** *
1160117 TAGAA-A-AATTACCCT-TCTAAAT
1 TAGAATACAA--ACAATAAC-AAAT
*
1160139 TAGAATACAAATAATAACAAAT
1 TAGAATACAAACAATAACAAAT
1160161 TAGAA
1 TAGAA
1160166 GACCAAGTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 28 0.78
23 2 0.06
24 2 0.06
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.24
Consensus pattern (22 bp):
TAGAATACAAACAATAACAAAT
Found at i:1168997 original size:2 final size:2
Alignment explanation
Indices: 1168990--1169045 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1168980 ATGTATATCA
*
1168990 AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1169032 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
1169046 CTATTTTCTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1174979 original size:16 final size:18
Alignment explanation
Indices: 1174944--1174981 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1174934 ATCCTTATTT
1174944 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
1174962 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
1174978 AAAT
1 AAAT
1174982 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:1181010 original size:18 final size:19
Alignment explanation
Indices: 1180981--1181024 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1180971 CTTAGTAGAC
*
1180981 TGAAAAAGAAATTGAAAAGA
1 TGAAAAAGAAATAG-AAAGA
1181001 T-AAAAA-AAATAGAAAGA
1 TGAAAAAGAAATAGAAAGA
1181018 TGAAAAA
1 TGAAAAA
1181025 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 5 0.23
20 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
TGAAAAAGAAATAGAAAGA
Found at i:1187345 original size:3 final size:3
Alignment explanation
Indices: 1187337--1187369 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1187327 TGGCTGATAT
*
1187337 TGA TGA TGA TGA TGC TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1187370 ACCATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1190231 original size:17 final size:19
Alignment explanation
Indices: 1190204--1190241 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1190194 AGTTTTAATT
1190204 TTTTTTAATC-ATTTCAAG
1 TTTTTTAATCAATTTCAAG
1190222 TTTTTT-ATCAATTTCAAG
1 TTTTTTAATCAATTTCAAG
1190240 TT
1 TT
1190242 CGAATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTTAATCAATTTCAAG
Found at i:1194547 original size:2 final size:2
Alignment explanation
Indices: 1194540--1194580 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1194530 AATTTAAATG
1194540 AT AT AT AT AT 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 AT AT AT AT AT A
1194581 AATGTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1194700 original size:3 final size:3
Alignment explanation
Indices: 1194692--1194725 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1194682 CCACAACACA
*
1194692 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1194726 TTCAATGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1194939 original size:21 final size:21
Alignment explanation
Indices: 1194915--1194956 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1194905 ACAAAATAAC
* *
1194915 AAATCAGTCCTTATATGTTAG
1 AAATCAGTCCCTATACGTTAG
1194936 AAATCAGTCCCTATACGTTAG
1 AAATCAGTCCCTATACGTTAG
1194957 CATGAGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
AAATCAGTCCCTATACGTTAG
Found at i:1197875 original size:31 final size:32
Alignment explanation
Indices: 1197837--1197912 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1197827 TTAATATAAC
*
1197837 ATTTGGTACCTGAACTTGAC-AATTTTTCCTA
1 ATTTGGTACCTAAACTTGACTAATTTTTCCTA
**
1197868 ATTTGGTACCTAAACTTGACTCTTTTTTCCTA
1 ATTTGGTACCTAAACTTGACTAATTTTTCCTA
**
1197900 ATTTTATACCTAA
1 ATTTGGTACCTAA
1197913 TCTTTTTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 19 0.49
32 20 0.51
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (32 bp):
ATTTGGTACCTAAACTTGACTAATTTTTCCTA
Found at i:1204282 original size:58 final size:58
Alignment explanation
Indices: 1204217--1204340 Score: 248
Period size: 58 Copynumber: 2.1 Consensus size: 58
1204207 GTCATCTTAC
1204217 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1204275 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1 TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
1204333 TTGAAAAT
1 TTGAAAAT
1204341 GTGGCAATGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (58 bp):
TTGAAAATAATGTGAATCTTTGAAATTTGGTCTTACTAGTAGATGAATGAACTTATAT
Found at i:1219346 original size:20 final size:20
Alignment explanation
Indices: 1219297--1219346 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1219287 AACTTAGCTC
*
1219297 TTAACATTTATATTTTTTTAA
1 TTAA-ATTTTTATTTTTTTAA
* *
1219318 TTTAGTTTTTATTTTTTTAA
1 TTAAATTTTTATTTTTTTAA
1219338 TTAAATTTT
1 TTAAATTTT
1219347 ACCTCCATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTAAATTTTTATTTTTTTAA
Found at i:1226843 original size:8 final size:8
Alignment explanation
Indices: 1226830--1226862 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1226820 GGATTTAGGT
1226830 TTATTTTA
1 TTATTTTA
1226838 TTATTTTA
1 TTATTTTA
1226846 TTATTTTA
1 TTATTTTA
1226854 TTATTTTA
1 TTATTTTA
1226862 T
1 T
1226863 CAATTACGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTA
Found at i:1232330 original size:22 final size:21
Alignment explanation
Indices: 1232305--1232348 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1232295 TTCGATTTTT
1232305 AGTTCAAAGTAATTTTATGTTG
1 AGTTCAAAGTAATTTTA-GTTG
* **
1232327 AGTTGAATTTAATTTTAGTTG
1 AGTTCAAAGTAATTTTAGTTG
1232348 A
1 A
1232349 TCAGATATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (21 bp):
AGTTCAAAGTAATTTTAGTTG
Found at i:1232419 original size:17 final size:18
Alignment explanation
Indices: 1232399--1232434 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1232389 TATAAATTCT
1232399 TTAAAAATATA-TATTAA
1 TTAAAAATATATTATTAA
*
1232416 TTAAAATTATATTATTAA
1 TTAAAAATATATTATTAA
1232434 T
1 T
1232435 ATGTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAATATATTATTAA
Found at i:1232543 original size:22 final size:22
Alignment explanation
Indices: 1232515--1232560 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1232505 ACCAAATATT
*
1232515 TAAAATTATTTTTTTTAAATCA
1 TAAAATTATTTTTCTTAAATCA
1232537 TAAAATTATTTTTCTTAAATCA
1 TAAAATTATTTTTCTTAAATCA
1232559 TA
1 TA
1232561 TTAACAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAATTATTTTTCTTAAATCA
Found at i:1235465 original size:28 final size:28
Alignment explanation
Indices: 1235425--1235486 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
1235415 TCAATCTGTG
1235425 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1235453 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1235481 TTAAAT
1 TTAAAT
1235487 GTGCTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (28 bp):
TTAAATTTTTCTCTCTTAAAGCTTAAGC
Found at i:1236565 original size:15 final size:15
Alignment explanation
Indices: 1236545--1236574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1236535 TGATTTTGAT
1236545 ATTTTAAAATTTAAA
1 ATTTTAAAATTTAAA
*
1236560 ATTTTAATATTTAAA
1 ATTTTAAAATTTAAA
1236575 TAAAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAATTTAAA
Found at i:1246045 original size:3 final size:3
Alignment explanation
Indices: 1246037--1246075 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1246027 ATTTTTCCAA
1246037 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1246076 GTGATCTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1249512 original size:83 final size:84
Alignment explanation
Indices: 1249425--1249581 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 84
1249415 AGGGGGGCTA
* * *
1249425 AAGTGCAATTTTACTATATGTTAGTTTATAATTTCT-T-TATTTATAAGAGGACTGAATTGAAAA
1 AAGTGCAATTTCACTATATATTAATTTATAATTT-TATCTATTTATAAGAGGACTGAATTGAAAA
1249488 TTTTTCATTTGGGGTGGTCG
65 TTTTTCATTTGGGGTGGTCG
* *
1249508 AAGTGCAATTTCACTATATATTAATTTATAGTTTTATCTATTTATAAGAGGACTGAATTGAAATT
1 AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTATAAGAGGACTGAATTGAAAAT
1249573 TTTTCATTT
66 TTTTCATTT
1249582 TCCCCTGCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 1 0.01
83 31 0.46
84 35 0.52
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (84 bp):
AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTATAAGAGGACTGAATTGAAAAT
TTTTCATTTGGGGTGGTCG
Found at i:1253465 original size:2 final size:2
Alignment explanation
Indices: 1253458--1253489 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1253448 TATTATTGTA
1253458 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
1253490 GCTTTGACTC
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):
AT
Found at i:1255757 original size:16 final size:16
Alignment explanation
Indices: 1255738--1255782 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1255728 ACACAAAATT
1255738 AAAATAATCCAAACCC
1 AAAATAATCCAAACCC
* ***
1255754 AAAATAATCTAAATTT
1 AAAATAATCCAAACCC
1255770 AAAATAATCCAAA
1 AAAATAATCCAAA
1255783 ACTTTGAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAATCCAAACCC
Found at i:1256445 original size:8 final size:8
Alignment explanation
Indices: 1256432--1256461 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1256422 TTTTATGCCC
*
1256432 TTTAAATT
1 TTTAAAAT
1256440 TTTAAAAT
1 TTTAAAAT
1256448 TTTAAAAT
1 TTTAAAAT
1256456 TTTAAA
1 TTTAAA
1256462 TTAGTAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1263050 original size:2 final size:2
Alignment explanation
Indices: 1263043--1263090 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1263033 TGCATGTCTT
1263043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1263085 TA TA TA
1 TA TA TA
1263091 AGGTTTTAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1273804 original size:31 final size:31
Alignment explanation
Indices: 1273763--1273831 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1273753 GTAACAAAAT
* *
1273763 AGTCATTGAACTACTT-GAAA-ATTTTCATTTA
1 AGTCACTGAACTA-TTCGAAATATCTT-ATTTA
1273794 AGTCACTGAACTATTCGAAATATCTTATTTA
1 AGTCACTGAACTATTCGAAATATCTTATTTA
*
1273825 AGGCACT
1 AGTCACT
1273832 AGCCTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.06
31 27 0.82
32 4 0.12
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (31 bp):
AGTCACTGAACTATTCGAAATATCTTATTTA
Found at i:1277070 original size:14 final size:15
Alignment explanation
Indices: 1277046--1277075 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1277036 GTATCTAGAT
1277046 AATTAATTAATATTA
1 AATTAATTAATATTA
1277061 AATT-ATTAATATTA
1 AATTAATTAATATTA
1277075 A
1 A
1277076 TTAGTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATTAATATTA
Found at i:1277087 original size:14 final size:13
Alignment explanation
Indices: 1277045--1277078 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1277035 AGTATCTAGA
1277045 TAATTAATTAATAT
1 TAATT-ATTAATAT
1277059 TAAATTATTAATAT
1 T-AATTATTAATAT
1277073 TAATTA
1 TAATTA
1277079 GTTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 10 0.53
15 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTATTAATAT
Found at i:1277301 original size:17 final size:19
Alignment explanation
Indices: 1277263--1277301 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1277253 AATTATAACG
1277263 AATATAAATACAATATTTA
1 AATATAAATACAATATTTA
*
1277282 AATATAATTA-AATA-TTA
1 AATATAAATACAATATTTA
1277299 AAT
1 AAT
1277302 TTGTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAATACAATATTTA
Found at i:1289476 original size:9 final size:9
Alignment explanation
Indices: 1289462--1289547 Score: 93
Period size: 9 Copynumber: 9.4 Consensus size: 9
1289452 TTTGATTAAA
1289462 AATTACCCG
1 AATTACCCG
1289471 AATTACCCG
1 AATTACCCG
1289480 AATTACCCG
1 AATTACCCG
*
1289489 AATTAACCG
1 AATTACCCG
* *
1289498 AATTAACAG
1 AATTACCCG
*
1289507 AATTAACCG
1 AATTACCCG
1289516 AATTA-CCG
1 AATTACCCG
*
1289524 AAAAATACCCG
1 --AATTACCCG
*
1289535 AATTACCTG
1 AATTACCCG
1289544 AATT
1 AATT
1289548 TTTTTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:1289822 original size:22 final size:22
Alignment explanation
Indices: 1289794--1289946 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
1289784 TTTATTGTTC
*
1289794 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
1289816 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
1289838 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
1289860 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
1289882 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
1289904 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
1289926 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
1289947 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:1290093 original size:4 final size:4
Alignment explanation
Indices: 1290084--1290112 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1290074 NGTAACCGTA
1290084 ACGT ACGT ACGT ACGT ACGT ACGT ACGT A
1 ACGT ACGT ACGT ACGT ACGT ACGT ACGT A
1290113 TTTTTCGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (4 bp):
ACGT
Found at i:1294665 original size:2 final size:2
Alignment explanation
Indices: 1294658--1294682 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1294648 ATACTTTAAT
1294658 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
1294683 TACTTTTATA
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:1295915 original size:2 final size:2
Alignment explanation
Indices: 1295908--1295938 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1295898 GCTGCCATCT
1295908 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 T
1295939 TATCATAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1298846 original size:25 final size:25
Alignment explanation
Indices: 1298818--1298891 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 25
1298808 AGGCTCCAAC
1298818 CTGAACTTAACTAAAAGAATATAAT
1 CTGAACTTAACTAAAAGAATATAAT
* * ** *
1298843 CTGAACCTAA--AAAAG-CTCCAAC
1 CTGAACTTAACTAAAAGAATATAAT
*
1298865 CTGAACTTAGCTAAAAGAATATAAT
1 CTGAACTTAACTAAAAGAATATAAT
1298890 CT
1 CT
1298892 TCAAAATTAG
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
22 11 0.31
23 5 0.14
24 5 0.14
25 14 0.40
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.24
Consensus pattern (25 bp):
CTGAACTTAACTAAAAGAATATAAT
Found at i:1298861 original size:47 final size:47
Alignment explanation
Indices: 1298792--1298891 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
1298782 CAAACCTAGG
*
1298792 TAATCTGAACCTAAAAAGGCTCCAACCTGAACTTAACTAAAAGAATA
1 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
*
1298839 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAGCTAAAAGAATA
1 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
1298886 TAATCT
1 TAATCT
1298892 TCAAAATTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (47 bp):
TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
Found at i:1298868 original size:22 final size:22
Alignment explanation
Indices: 1298796--1298870 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1298786 CCTAGGTAAT
*
1298796 CTGAACCTAAAAAGGCTCCAAC
1 CTGAACCTAAAAAAGCTCCAAC
* * ** *
1298818 CTGAACTTAACTAAAAGAATATAAT
1 CTGAACCTAA--AAAAG-CTCCAAC
1298843 CTGAACCTAAAAAAGCTCCAAC
1 CTGAACCTAAAAAAGCTCCAAC
1298865 CTGAAC
1 CTGAAC
1298871 TTAGCTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 4 0.10
25 12 0.31
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (22 bp):
CTGAACCTAAAAAAGCTCCAAC
Found at i:1301620 original size:39 final size:41
Alignment explanation
Indices: 1301558--1301646 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
1301548 TGAAAAGTAT
*
1301558 TTATATT-AAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1301598 TTATATTAAAAAACAC-A-AATAAATATAATAATTATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1301637 TTACATTAAA
1 TTATATTAAA
1301647 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 29 0.64
40 8 0.18
41 8 0.18
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:1302894 original size:52 final size:52
Alignment explanation
Indices: 1302797--1302895 Score: 117
Period size: 52 Copynumber: 1.9 Consensus size: 52
1302787 AAAATAAAAA
* *
1302797 ACTCAAGCCTTAAACCTACCCTGACCCCAATTGACTCAATCCAAAAAGGAAT
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAAGGAAT
* * * * * * *
1302849 ACTCAAGCGTTAGACCTGCCCTGATCTCAATTAACCCGATTCAAAAA
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAA
1302896 ATAAAAATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 38 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.21
Consensus pattern (52 bp):
ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAAGGAAT
Found at i:1306284 original size:3 final size:3
Alignment explanation
Indices: 1306278--1306303 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1306268 ATTAAAAACC
1306278 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1306304 ATAAACATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1307563 original size:29 final size:30
Alignment explanation
Indices: 1307496--1307563 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1307486 ATTTGCAATT
* * *
1307496 ATTTGATTCTTTTTAATAGTATAGAGACTAC
1 ATTTGA-TCTATTTAATAATAAAGAGACTAC
*
1307527 A-TTAATCTATTTAATAATAAAGAGACTA-
1 ATTTGATCTATTTAATAATAAAGAGACTAC
1307555 ATTTGATCT
1 ATTTGATCT
1307564 GGTCCCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 3 0.10
31 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
ATTTGATCTATTTAATAATAAAGAGACTAC
Found at i:1312534 original size:29 final size:28
Alignment explanation
Indices: 1312471--1312526 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1312461 TATACATGCT
*
1312471 AAACATTTAATAATTTTTTATTATATAAA
1 AAACATTTAAT-ATTTTTTATTATAAAAA
1312500 AAACATTTAATATTTTTT-TTA-AAAAA
1 AAACATTTAATATTTTTTATTATAAAAA
1312526 A
1 A
1312527 TCCAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 3 0.12
28 7 0.27
29 11 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
AAACATTTAATATTTTTTATTATAAAAA
Found at i:1318355 original size:15 final size:17
Alignment explanation
Indices: 1318318--1318355 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1318308 TAGAAATTAA
1318318 AATATTCAAATCTGTAT
1 AATATTCAAATCTGTAT
*
1318335 ATTATTCAAAT-T-TAT
1 AATATTCAAATCTGTAT
1318350 AATATT
1 AATATT
1318356 TAAAATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (17 bp):
AATATTCAAATCTGTAT
Found at i:1320483 original size:19 final size:21
Alignment explanation
Indices: 1320442--1320483 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
1320432 AAATTATGTG
*
1320442 AAAATAGTTTAATTTTAATAT
1 AAAATAGTTTAATTTTAACAT
*
1320463 AAAATA-TTT-ATTTTTACAT
1 AAAATAGTTTAATTTTAACAT
1320482 AA
1 AA
1320484 GAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATAGTTTAATTTTAACAT
Found at i:1320888 original size:5 final size:6
Alignment explanation
Indices: 1320871--1320903 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
1320861 TAAAGTATGT
1320871 TAAAAA TAAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA TA
1320904 TTTATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:1332384 original size:30 final size:31
Alignment explanation
Indices: 1332326--1332384 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1332316 CTCTATTAAA
*
1332326 AAAGAGTAAATTAGTCTTTGTATGTTAAATC
1 AAAGAGTAAATTAATCTTTGTATGTTAAATC
* *
1332357 AAAGAGTAAATTAAT-TTTTTCTGTTAAA
1 AAAGAGTAAATTAATCTTTGTATGTTAAA
1332385 AATTCTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (31 bp):
AAAGAGTAAATTAATCTTTGTATGTTAAATC
Found at i:1332916 original size:6 final size:6
Alignment explanation
Indices: 1332905--1332929 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1332895 TCAGGTTCCC
1332905 ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
1332930 TGTATGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:1333190 original size:66 final size:66
Alignment explanation
Indices: 1333084--1333270 Score: 331
Period size: 66 Copynumber: 2.8 Consensus size: 66
1333074 GAAAGGAAAA
*
1333084 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACA-AAGA
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATC-AAAGAAGA
1333148 GG
65 GG
*
1333150 AAAGAGAAAATAACCTCATTCATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
1333215 G
66 G
*
1333216 AAAGAGAATATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1333271 TCTCAAAATG
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
65 2 0.02
66 114 0.98
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (66 bp):
AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
G
Found at i:1335909 original size:29 final size:28
Alignment explanation
Indices: 1335856--1335913 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1335846 GTAAATTTTA
1335856 CATTTTAGTCTCTAAAAATAGAATAAAAT
1 CATTTTAGTCTCTAAAAATA-AATAAAAT
*
1335885 CATTTTAGTCCTTTTAAAAAT-AATAAAAT
1 CATTTTAGT-C-TCTAAAAATAAATAAAAT
1335914 TATAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (28 bp):
CATTTTAGTCTCTAAAAATAAATAAAAT
Found at i:1335946 original size:23 final size:22
Alignment explanation
Indices: 1335896--1335946 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
1335886 ATTTTAGTCC
*
1335896 TTTTAAAAATAATAAAATTATA
1 TTTTAAAAATAATAAAATTACA
** *
1335918 AATTAATAAATGATAAAATTACA
1 TTTTAA-AAATAATAAAATTACA
1335941 TTTTAA
1 TTTTAA
1335947 CATCTCAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTAAAAATAATAAAATTACA
Found at i:1337239 original size:27 final size:27
Alignment explanation
Indices: 1337207--1337260 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1337197 AGAAATTTTA
1337207 AATTTAACCAAGTTCAAGTTATTAATT
1 AATTTAACCAAGTTCAAGTTATTAATT
** *
1337234 AATTTAATGAAGTTGAAGTTATTAATT
1 AATTTAACCAAGTTCAAGTTATTAATT
1337261 TTTAATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (27 bp):
AATTTAACCAAGTTCAAGTTATTAATT
Found at i:1337776 original size:2 final size:2
Alignment explanation
Indices: 1337769--1337794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1337759 CCTTAGGTAG
1337769 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
1337795 TAGTTTTTAG
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):
AT
Found at i:1340487 original size:2 final size:2
Alignment explanation
Indices: 1340480--1340518 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1340470 NNNNNNNNNN
1340480 AT AT AT AT 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 AT AT AT AT A
1340519 GATAGATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1340594 original size:4 final size:4
Alignment explanation
Indices: 1340585--1340612 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1340575 ACATATATAG
1340585 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1340613 GTATGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:1346619 original size:27 final size:27
Alignment explanation
Indices: 1346565--1346627 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
1346555 TAAATTTCAA
*
1346565 AATTATATATAAACTTTAATTTAATGT
1 AATTATACATAAACTTTAATTTAATGT
**
1346592 ACA-TATACATAAACTTTAATTTGGTGT
1 A-ATTATACATAAACTTTAATTTAATGT
1346619 AATTATACA
1 AATTATACA
1346628 CGTAAAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
AATTATACATAAACTTTAATTTAATGT
Found at i:1352370 original size:43 final size:42
Alignment explanation
Indices: 1352322--1352406 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1352312 TGATTACCCA
* *
1352322 TTTCTCGTTTTTTTAAATTATATTGGAAATCGCTGAGTTTATC
1 TTTCTCCTTTTTCT-AATTATATTGGAAATCGCTGAGTTTATC
* *
1352365 TTTCTCCTTTTTCTGATTATATTGGGAATCGCTGAGTTTATC
1 TTTCTCCTTTTTCTAATTATATTGGAAATCGCTGAGTTTATC
1352407 GACTTAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 26 0.68
43 12 0.32
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTCTCCTTTTTCTAATTATATTGGAAATCGCTGAGTTTATC
Found at i:1354967 original size:13 final size:13
Alignment explanation
Indices: 1354928--1354971 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1354918 CTGAAAATTT
1354928 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1354941 TTTTGCAT-GGAAAA
1 TTTT--ATGGGAAAA
1354955 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1354968 TTTT
1 TTTT
1354972 TCTCCAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (13 bp):
TTTTATGGGAAAA
Found at i:1354972 original size:14 final size:14
Alignment explanation
Indices: 1354927--1354972 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1354917 TCTGAAAATT
1354927 TTTTTATGGGAAAA
1 TTTTTATGGGAAAA
*
1354941 TTTTGCAT-GGAAAA
1 TTTT-TATGGGAAAA
1354955 -TTTTATGGGAAAA
1 TTTTTATGGGAAAA
1354968 TTTTT
1 TTTTT
1354973 CTCCAGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.33
14 14 0.52
15 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (14 bp):
TTTTTATGGGAAAA
Found at i:1360044 original size:177 final size:177
Alignment explanation
Indices: 1359713--1360044 Score: 486
Period size: 177 Copynumber: 1.9 Consensus size: 177
1359703 TTTAGTATGC
* * *
1359713 AATCCCTAATAAACCTCGAAACAGTCTTTTGTATGGTATTGACGCAATGTATAGTTTACAGTTCT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* * * * *
1359778 TTGACTCGATCATACGATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGTAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
* * *
1359843 ATGACAGAAGTTGTATTGAAAAAGTTCAACTCGACCGCCAGTATCCA
131 ACGACAGAAGTCGTATTCAAAAAGTTCAACTCGACCGCCAGTATCCA
** * * *
1359890 AATCCCGAATAAACCTCGAGGCGGTCTTTTGAATGGTATTGACACAATGTATGGTTTACAGTTTT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* *
1359955 TTGACTCGAAGAAACAATGAGGCTATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
1360020 ACGACAGAAAGTCGTA-TCAAAAAGT
131 ACGACAG-AAGTCGTATTCAAAAAGT
1360045 CTAAAAAACT
Statistics
Matches: 136, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 129 0.95
178 7 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (177 bp):
AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
ACGACAGAAGTCGTATTCAAAAAGTTCAACTCGACCGCCAGTATCCA
Found at i:1361187 original size:19 final size:20
Alignment explanation
Indices: 1361163--1361218 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
1361153 TCGTTTTTAA
1361163 GTATTTTCCGTCAAAATC-C
1 GTATTTTCCGTCAAAATCAC
*
1361182 GTATTTTCCATCAAAATTCAC
1 GTATTTTCCGTCAAAA-TCAC
*
1361203 -CATTTTCCGTCAAAAT
1 GTATTTTCCGTCAAAAT
1361219 TCGCCATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 15 0.47
21 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (20 bp):
GTATTTTCCGTCAAAATCAC
Found at i:1361209 original size:20 final size:20
Alignment explanation
Indices: 1361184--1361225 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1361174 CAAAATCCGT
1361184 ATTTTCCATCAAAATTCACC
1 ATTTTCCATCAAAATTCACC
* *
1361204 ATTTTCCGTCAAAATTCGCC
1 ATTTTCCATCAAAATTCACC
1361224 AT
1 AT
1361226 CAATATGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTCCATCAAAATTCACC
Found at i:1361994 original size:57 final size:56
Alignment explanation
Indices: 1361912--1362021 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 56
1361902 CTGGTCAAAC
* * *
1361912 TTTATAATTAGTATCTTTATTTTACTCAACTTATAAATTTAGTCCCTTATTTTAAAT
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTT-TTTTAAAT
*
1361969 TTTATAATTAGTCCCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1362022 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (56 bp):
TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTAAAT
Found at i:1362012 original size:31 final size:29
Alignment explanation
Indices: 1361932--1362021 Score: 98
Period size: 26 Copynumber: 3.1 Consensus size: 29
1361922 GTATCTTTAT
1361932 TTTACTCAACTTATAAATTTAGTCCCTTA
1 TTTACTCAACTTATAAATTTAGTCCCTTA
* *
1361961 TTT--T-AAATTTTATAA-TTAGTCCCTGTA
1 TTTACTCAACTTATA-AATTTAGTCCCT-TA
*
1361988 TCTTACTCAACTTATAAATTTAGTCCCTTT
1 T-TTACTCAACTTATAAATTTAGTCCCTTA
1362018 TTTA
1 TTTA
1362022 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 15 0.31
27 6 0.12
28 2 0.04
29 6 0.12
30 5 0.10
31 15 0.31
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTACTCAACTTATAAATTTAGTCCCTTA
Found at i:1366173 original size:33 final size:33
Alignment explanation
Indices: 1366131--1366197 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1366121 TAAAACAGCG
1366131 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
1366164 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
1366197 C
1 C
1366198 TTACCAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (33 bp):
CAACTTTAATATAACACCACAAGAAACCTAATA
Found at i:1367177 original size:16 final size:16
Alignment explanation
Indices: 1367142--1367186 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1367132 ATCTTTATTT
*
1367142 GAATAAATGTAGAGCGAA
1 GAATAAA-G-AGAACGAA
1367160 GAATAAAGAGAACGAA
1 GAATAAAGAGAACGAA
*
1367176 GAACAAAGAGA
1 GAATAAAGAGA
1367187 GCAATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 1 0.04
18 7 0.28
ACGTcount: A:0.58, C:0.07, G:0.27, T:0.09
Consensus pattern (16 bp):
GAATAAAGAGAACGAA
Found at i:1369448 original size:16 final size:18
Alignment explanation
Indices: 1369427--1369460 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1369417 AAATTTTTTT
1369427 TAAAAAA-AT-TATAATA
1 TAAAAAATATATATAATA
1369443 TAAAAAATATATATAATA
1 TAAAAAATATATATAATA
1369461 CTTCAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATATATATAATA
Found at i:1374897 original size:22 final size:22
Alignment explanation
Indices: 1374872--1374917 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1374862 AGCTTTAAAA
*
1374872 TTCACTTTGATACCTGAGCTTT
1 TTCAATTTGATACCTGAGCTTT
* *
1374894 TTCAATTTGATACTTGAGTTTT
1 TTCAATTTGATACCTGAGCTTT
1374916 TT
1 TT
1374918 TTCTCCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (22 bp):
TTCAATTTGATACCTGAGCTTT
Found at i:1400135 original size:12 final size:12
Alignment explanation
Indices: 1400120--1400149 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1400110 AATTGAGAGG
*
1400120 TTAATTTTTTAA
1 TTAATTTGTTAA
1400132 TTAATTTGTTAA
1 TTAATTTGTTAA
1400144 TTAATT
1 TTAATT
1400150 GATGCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TTAATTTGTTAA
Found at i:1405880 original size:19 final size:21
Alignment explanation
Indices: 1405843--1405886 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
1405833 TTTCTTAGAT
1405843 TTACTGGCATTTAATTTATTC
1 TTACTGGCATTTAATTTATTC
1405864 TTACTGGCA-TT-ATTTATTC
1 TTACTGGCATTTAATTTATTC
1405883 TTAC
1 TTAC
1405887 ATGCAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (21 bp):
TTACTGGCATTTAATTTATTC
Found at i:1411734 original size:34 final size:34
Alignment explanation
Indices: 1411691--1411771 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
1411681 TTGTATCAAA
1411691 TAAATAATTTTTAATTTTTATTATCTTATACTAT
1 TAAATAATTTTTAATTTTTATTATCTTATACTAT
1411725 TAAATAATTTTTAATTTTTATTATCTTATACTAT
1 TAAATAATTTTTAATTTTTATTATCTTATACTAT
*
1411759 T-AATTATTTTTAA
1 TAAATAATTTTTAA
1411772 ATATAATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 11 0.24
34 35 0.76
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (34 bp):
TAAATAATTTTTAATTTTTATTATCTTATACTAT
Found at i:1411781 original size:33 final size:34
Alignment explanation
Indices: 1411691--1411781 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
1411681 TTGTATCAAA
* * *
1411691 TAAATAATTTTTAATTTTTATTATCTTATACTAT
1 TAAATAATTTTTAAATATAATTATCTTATACTAT
* * *
1411725 TAAATAATTTTTAATTTTTATTATCTTATACTAT
1 TAAATAATTTTTAAATATAATTATCTTATACTAT
*
1411759 T-AATTATTTTTAAATATAATTAT
1 TAAATAATTTTTAAATATAATTAT
1411782 GTTGGAGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 18 0.34
34 35 0.66
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (34 bp):
TAAATAATTTTTAAATATAATTATCTTATACTAT
Found at i:1413026 original size:23 final size:23
Alignment explanation
Indices: 1412935--1413029 Score: 136
Period size: 23 Copynumber: 4.1 Consensus size: 23
1412925 TGTGTATCCT
* * *
1412935 TTCATATTCAAGCCTCTTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* *
1412958 TTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTC
*
1412981 TTCATATTCAAGTCTTTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
1413004 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
1413027 TTC
1 TTC
1413030 TAACTTTTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.22, C:0.28, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:1416078 original size:19 final size:21
Alignment explanation
Indices: 1416041--1416084 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
1416031 TTTCTTAGAT
1416041 TTACTGGCATTTAATTTATTC
1 TTACTGGCATTTAATTTATTC
1416062 TTACTGGCA-TT-ATTTATTC
1 TTACTGGCATTTAATTTATTC
1416081 TTAC
1 TTAC
1416085 ATGCAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (21 bp):
TTACTGGCATTTAATTTATTC
Found at i:1417594 original size:16 final size:15
Alignment explanation
Indices: 1417573--1417606 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1417563 GAACATTTTA
1417573 ATTTTTTA-ATATAT
1 ATTTTTTATATATAT
1417587 ATATTTTTATATATAT
1 AT-TTTTTATATATAT
1417603 ATTT
1 ATTT
1417607 GATTTACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 8 0.44
16 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTTATATATAT
Found at i:1417598 original size:14 final size:15
Alignment explanation
Indices: 1417575--1417606 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1417565 ACATTTTAAT
1417575 TTTTTAATATATATA
1 TTTTTAATATATATA
1417590 TTTTT-ATATATATA
1 TTTTTAATATATATA
1417604 TTT
1 TTT
1417607 GATTTACAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATATATATA
Found at i:1428896 original size:26 final size:26
Alignment explanation
Indices: 1428843--1428898 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1428833 CGATATATGA
1428843 CTCTTTGTGAGCTTTTCGATTAAAGG
1 CTCTTTGTGAGCTTTTCGATTAAAGG
*
1428869 CTCTTTGTGAGC-TTTCTGATTAATGG
1 CTCTTTGTGAGCTTTTC-GATTAAAGG
1428895 CTCT
1 CTCT
1428899 CCGGAGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (26 bp):
CTCTTTGTGAGCTTTTCGATTAAAGG
Found at i:1428905 original size:25 final size:25
Alignment explanation
Indices: 1428851--1428971 Score: 63
Period size: 25 Copynumber: 4.9 Consensus size: 25
1428841 GACTCTTTGT
* **
1428851 GAGCTTT-TCGATTAAAGGCTCTTTG
1 GAGCTTTCT-GATTAATGGCTCTCCG
1428876 TGAGCTTTCTGATTAATGGCTCTCCG
1 -GAGCTTTCTGATTAATGGCTCTCCG
* * * * **
1428902 GAGCTTCCCGA-T-ATAGCTCGCTT
1 GAGCTTTCTGATTAATGGCTCTCCG
* *
1428925 GAAC-TTCTCGA-TATATGGCTATCCG
1 GAGCTTTCT-GATTA-ATGGCTCTCCG
*
1428950 GAGCTTCCTGATTAATGGCTCT
1 GAGCTTTCTGATTAATGGCTCT
1428972 TCAGAGCTAC
Statistics
Matches: 69, Mismatches: 20, Indels: 13
0.68 0.20 0.13
Matches are distributed among these distances:
22 2 0.03
23 13 0.19
24 1 0.01
25 27 0.39
26 25 0.36
27 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
GAGCTTTCTGATTAATGGCTCTCCG
Found at i:1431347 original size:23 final size:23
Alignment explanation
Indices: 1431316--1431360 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1431306 CAAAATTAAT
* *
1431316 AAAATAAATAATAAAATAATGAG
1 AAAAGAAATAAAAAAATAATGAG
1431339 AAAAGAAATAAAAAAATAATGA
1 AAAAGAAATAAAAAAATAATGA
1431361 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAGAAATAAAAAAATAATGAG
Found at i:1441513 original size:2 final size:2
Alignment explanation
Indices: 1441508--1441532 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1441498 ACACACATAC
1441508 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
1441533 GCTAATTCCC
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:1442080 original size:2 final size:2
Alignment explanation
Indices: 1442073--1442106 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1442063 TATAGGGATC
1442073 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
1442107 TACTCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1444129 original size:2 final size:2
Alignment explanation
Indices: 1444118--1444153 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1444108 TTCTTAATTA
1444118 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1444154 TTGGACCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1444220 original size:2 final size:2
Alignment explanation
Indices: 1444213--1444242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1444203 GGGATTATGC
1444213 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
1444243 TATTCCAATA
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:1444759 original size:2 final size:2
Alignment explanation
Indices: 1444752--1444790 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1444742 ACATACCAGG
1444752 AT AT AT AT 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 AT AT AT AT A
1444791 AAATTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1446636 original size:45 final size:45
Alignment explanation
Indices: 1446586--1446671 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1446576 TCCTTGCTGC
*
1446586 GTATAAATAATTAATAATAAATGCTATATAATTTAGTTAAAATTA
1 GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAAATTA
* * *
1446631 GTATAAGTAATTTATAATAAATATTATATAATTTAGTTAAA
1 GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAA
1446672 TATATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (45 bp):
GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAAATTA
Found at i:1446673 original size:20 final size:20
Alignment explanation
Indices: 1446610--1446674 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 20
1446600 TAATAAATGC
*
1446610 TATATAATTTAGTTAAAATTAG
1 TATATAATTTAGTT-AAA-TAT
1446632 TATAAGTAATTTA-TAATAAATAT
1 TAT-A-TAATTTAGT--TAAATAT
1446655 TATATAATTTAGTTAAATAT
1 TATATAATTTAGTTAAATAT
1446675 ATAATAAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 5 0.14
23 7 0.19
24 10 0.27
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATAATTTAGTTAAATAT
Found at i:1446681 original size:20 final size:20
Alignment explanation
Indices: 1446613--1446681 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 20
1446603 TAAATGCTAT
1446613 ATAATTTAGTTAAAATTAGTATA
1 ATAATTTAGTT-AAA-TA-TATA
1446636 AGTAATTTA-TAATAAATAT-TA
1 A-TAATTTAGT--TAAATATATA
1446657 TATAATTTAGTTAAATATATA
1 -ATAATTTAGTTAAATATATA
1446678 ATAA
1 ATAA
1446682 GTCAAAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
20 11 0.28
21 11 0.28
22 3 0.08
23 4 0.10
24 10 0.25
25 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
ATAATTTAGTTAAATATATA
Found at i:1450645 original size:24 final size:24
Alignment explanation
Indices: 1450582--1450633 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1450572 TTTCTAGAAG
* * *
1450582 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1450606 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1450630 ATTT
1 ATTT
1450634 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:1452295 original size:26 final size:26
Alignment explanation
Indices: 1452239--1452288 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1452229 AACAGAATAA
* *
1452239 ACAAAACACAAACCATGATAGTGTAG
1 ACAAAACAAAAACCACGATAGTGTAG
*
1452265 ACAAAACAAAAACTACGATAGTGT
1 ACAAAACAAAAACCACGATAGTGT
1452289 GGTCAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (26 bp):
ACAAAACAAAAACCACGATAGTGTAG
Found at i:1457692 original size:21 final size:24
Alignment explanation
Indices: 1457667--1457720 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
1457657 TGATGATTTA
1457667 AAATTAAAAT-TA-AATT-ATATC
1 AAATTAAAATATATAATTAATATC
1457688 AAATTAAAATATATTAATTAAATATC
1 AAATTAAAATATA-TAATT-AATATC
1457714 AAATTAA
1 AAATTAA
1457721 TTATAGTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.36
22 2 0.07
24 4 0.14
26 12 0.43
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATTAAAATATATAATTAATATC
Found at i:1459215 original size:14 final size:15
Alignment explanation
Indices: 1459196--1459228 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1459186 TGTATAAAAT
*
1459196 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
1459210 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
1459225 AAAT
1 AAAT
1459229 GCTAGATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:1464967 original size:2 final size:2
Alignment explanation
Indices: 1464960--1465003 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1464950 ATCTTATTCT
1464960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1465002 TA
1 TA
1465004 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1465395 original size:2 final size:2
Alignment explanation
Indices: 1465390--1465450 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1465380 TAATTATTAC
1465390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1465432 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1465451 GAATTGTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1466617 original size:19 final size:21
Alignment explanation
Indices: 1466588--1466634 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1466578 ATTTAACCTC
*
1466588 AAACTCAAACCCT-GAA-CCT
1 AAACCCAAACCCTCGAATCCT
*
1466607 GAACCCAAACCCTCGAATCCT
1 AAACCCAAACCCTCGAATCCT
1466628 AAACCCA
1 AAACCCA
1466635 TCAGGGTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.40, C:0.40, G:0.06, T:0.13
Consensus pattern (21 bp):
AAACCCAAACCCTCGAATCCT
Found at i:1466659 original size:21 final size:21
Alignment explanation
Indices: 1466635--1466697 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
1466625 CCTAAACCCA
*
1466635 TCAGGGTTCGAGGTTTAAGAT
1 TCAGGGTTCAAGGTTTAAGAT
* *
1466656 TCA-GGTTTAAGGTTTACGAT
1 TCAGGGTTCAAGGTTTAAGAT
* *
1466676 TCAGAGTTCAAGGTTTTAGAT
1 TCAGGGTTCAAGGTTTAAGAT
1466697 T
1 T
1466698 TGAGGTTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
TCAGGGTTCAAGGTTTAAGAT
Found at i:1466668 original size:20 final size:21
Alignment explanation
Indices: 1466635--1466697 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1466625 CCTAAACCCA
* *
1466635 TCAGGGTTCGAGGTTTAAGAT
1 TCAGAGTTCAAGGTTTAAGAT
* *
1466656 TCAG-GTTTAAGGTTTACGAT
1 TCAGAGTTCAAGGTTTAAGAT
*
1466676 TCAGAGTTCAAGGTTTTAGAT
1 TCAGAGTTCAAGGTTTAAGAT
1466697 T
1 T
1466698 TGAGGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
TCAGAGTTCAAGGTTTAAGAT
Found at i:1466705 original size:21 final size:20
Alignment explanation
Indices: 1466639--1466711 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
1466629 AACCCATCAG
* *
1466639 GGTTCGAGGTTTAAGATTCA
1 GGTTCAAGGTTTTAGATTCA
*
1466659 GGTTTAAGG-TTTACGATTCA
1 GGTTCAAGGTTTTA-GATTCA
*
1466679 GAGTTCAAGGTTTTAGATTTGA
1 G-GTTCAAGGTTTTAGA-TTCA
*
1466701 GGTTCATGGTT
1 GGTTCAAGGTT
1466712 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 18 0.42
22 8 0.19
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40
Consensus pattern (20 bp):
GGTTCAAGGTTTTAGATTCA
Found at i:1467757 original size:16 final size:17
Alignment explanation
Indices: 1467728--1467765 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1467718 AATGCTAATG
1467728 ACAATCGAACTAAAACT
1 ACAATCGAACTAAAACT
1467745 -CAATC-AACATAAAACT
1 ACAATCGAAC-TAAAACT
1467761 ACAAT
1 ACAAT
1467766 TTTTAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (17 bp):
ACAATCGAACTAAAACT
Found at i:1468460 original size:4 final size:4
Alignment explanation
Indices: 1468451--1468502 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
1468441 CGAGCCTTTG
*
1468451 TTTA TTTA TTTA TTT- TATTA TTT- TTTA -TTA -TTA TTT- TTTA TTCA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1468495 TTTA TTTA
1 TTTA TTTA
1468503 GTACTCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 13 0.32
4 27 0.66
5 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1468469 original size:13 final size:12
Alignment explanation
Indices: 1468451--1468501 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
1468441 CGAGCCTTTG
1468451 TTTATTTATTTAT
1 TTTA-TTATTTAT
1468464 TTTATTA-TT-T
1 TTTATTATTTAT
*
1468474 TTTATTATTATTT
1 TTTATTATT-TAT
1468487 TTTATTCATTTAT
1 TTTATT-ATTTAT
1468500 TT
1 TT
1468502 AGTACTCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 8 0.24
11 3 0.09
12 4 0.12
13 15 0.45
14 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:1468478 original size:10 final size:11
Alignment explanation
Indices: 1468460--1468497 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
1468450 GTTTATTTAT
1468460 TTATTTTATTA
1 TTATTTTATTA
1468471 TT-TTTTATTA
1 TTATTTTATTA
1468481 TTATTTT-TTA
1 TTATTTTATTA
1468491 TTCATTT
1 TT-ATTT
1468498 ATTTAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:1484463 original size:26 final size:26
Alignment explanation
Indices: 1484411--1484463 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1484401 TAAATCCTAA
* *
1484411 ATTATAAAAATAATATTTTATAAATG
1 ATTATAAAAATAATATCTGATAAATG
* * *
1484437 ATTATTAAAATTATATCTGATATATG
1 ATTATAAAAATAATATCTGATAAATG
1484463 A
1 A
1484464 AATTATTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
ATTATAAAAATAATATCTGATAAATG
Found at i:1485070 original size:10 final size:10
Alignment explanation
Indices: 1485057--1485086 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1485047 ATACTTGCAG
1485057 ATACATATAT
1 ATACATATAT
1485067 ATACATATAT
1 ATACATATAT
1485077 ATACATATAT
1 ATACATATAT
1485087 GTCTATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATATAT
Found at i:1485360 original size:2 final size:2
Alignment explanation
Indices: 1485353--1485393 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1485343 ACTCAATAAC
1485353 AT AT AT AT AT 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 AT AT AT AT AT A
1485394 ATCTTGTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1487375 original size:16 final size:16
Alignment explanation
Indices: 1487354--1487398 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1487344 TTTATATTCA
1487354 AGTTTAGATCATTTCAG
1 AGTTTAGATCATTT-AG
1487371 A-TTTAGATCGA-TTAG
1 AGTTTAGATC-ATTTAG
1487386 AGTTTAGATCATT
1 AGTTTAGATCATT
1487399 CAAGTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.16
16 19 0.76
17 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (16 bp):
AGTTTAGATCATTTAG
Found at i:1502646 original size:4 final size:4
Alignment explanation
Indices: 1502637--1502666 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1502627 TATTAAAAGT
1502637 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
1502667 TGATTTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1503721 original size:3 final size:3
Alignment explanation
Indices: 1503713--1503738 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1503703 TTATCAGACA
1503713 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1503739 ATTCAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1504547 original size:17 final size:18
Alignment explanation
Indices: 1504527--1504563 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1504517 TTCTCATTTT
1504527 TTAAAAAATTA-ATAAAA
1 TTAAAAAATTATATAAAA
1504544 TT-AAAAATTATATAAAA
1 TTAAAAAATTATATAAAA
1504561 TTA
1 TTA
1504564 TTAGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAAAATTATATAAAA
Found at i:1516114 original size:15 final size:15
Alignment explanation
Indices: 1516094--1516126 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1516084 TGGTAACTAA
1516094 TCTGTGAAGATGCAT
1 TCTGTGAAGATGCAT
1516109 TCTGTGAAGATGCAT
1 TCTGTGAAGATGCAT
1516124 TCT
1 TCT
1516127 TTGGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (15 bp):
TCTGTGAAGATGCAT
Found at i:1530474 original size:19 final size:20
Alignment explanation
Indices: 1530439--1530482 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1530429 ATTTAAACTA
*
1530439 AATTTTATAACTATTTT-AT
1 AATTTTATAAATATTTTAAT
1530458 AATTTTATAAA-ATTTTTAAT
1 AATTTTATAAATA-TTTTAAT
1530478 AATTT
1 AATTT
1530483 ATTTCATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTATAAATATTTTAAT
Found at i:1531988 original size:199 final size:197
Alignment explanation
Indices: 1531630--1532235 Score: 864
Period size: 198 Copynumber: 3.1 Consensus size: 197
1531620 AAGCCCCCCT
* * **
1531630 GGTACTTCCTTTTTTGA-TGATTTTCTAAATTACCTGTAAACCTGAACTAATTAAATTTGATGAT
1 GGTACTT-CTTTTTTGACAG-TTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGAT
* * *
1531694 ATTATGTACTTAA-TCGTGCTAGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
64 ATTACGCACTTAAGT-GTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
*
1531758 ATTTGAAATTTGGGTTATTGG-TTTCCTGTGTAAACATTAGAGGAACCCTCT-TTTTGAAGTAGA
128 ATTTGAAA-TTGGGTTATTGGTTTTGCTGTGT-AACATTAGAGGAA-CCT-TATTTTGAAGTAGA
1531821 ACGATGGTC
189 ACGATGGTC
* * *
1531830 AGTACTTCTTTTTTGACAGTTTTCTAAACTACCCGTAAACCCAAACTAATTAAATTTGATGATAC
1 GGTACTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGATAT
* * *
1531895 TACACACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCTATGCTTGAATAATT
66 TACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATAATT
*
1531960 TGAAATTGGGTTTTTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
131 TGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
1532025 TC
196 TC
* * *
1532027 GGTAATTCTTTTTTTTTGACA--ATTCTAAACTACCTGTAAACCCAAGCTAATTAAATTTGATGA
1 GGT-A--CTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGA
* * **
1532090 TATTACGCAGTTAAGCGTGCTCGAATCCACAATCTCTGAGTTGCTGCAATAGCAATGCTTGAATA
63 TATTACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
1532155 ATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGA
128 ATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGA
**
1532220 CAGTC
193 TGGTC
1532225 GGTACTTCTTT
1 GGTACTTCTTT
1532236 ATAGAGGCTT
Statistics
Matches: 367, Mismatches: 32, Indels: 19
0.88 0.08 0.05
Matches are distributed among these distances:
195 6 0.02
196 1 0.00
197 27 0.07
198 191 0.52
199 121 0.33
200 21 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (197 bp):
GGTACTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGATAT
TACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATAATT
TGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
TC
Found at i:1536533 original size:29 final size:29
Alignment explanation
Indices: 1536486--1536544 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1536476 ATAAAAAGAT
* * *
1536486 TTCATTAAATAGTATAGGGGTTAAATTGA
1 TTCATTAAATAATAGAGGGGCTAAATTGA
* *
1536515 TTCATTTAATAATAGAGGGGCTAATTTGA
1 TTCATTAAATAATAGAGGGGCTAAATTGA
1536544 T
1 T
1536545 ACGGTCCCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (29 bp):
TTCATTAAATAATAGAGGGGCTAAATTGA
Found at i:1537163 original size:16 final size:17
Alignment explanation
Indices: 1537142--1537179 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1537132 TAAGATCTAT
*
1537142 TAAAAT-AATTTAAACC
1 TAAAATAAATCTAAACC
1537158 TAAAATAAATCTAAACC
1 TAAAATAAATCTAAACC
1537175 -AAAAT
1 TAAAAT
1537180 TTTCAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAAATCTAAACC
Found at i:1539157 original size:98 final size:98
Alignment explanation
Indices: 1538988--1539184 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
1538978 GTACAATAAA
* *
1538988 ACTTTAAAAGAATATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1539053 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
1539086 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
* *
1539151 CCTCTAGAATCCCAAACTTGTAATATTTCCTTT
66 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
1539184 A
1 A
1539185 TGATTTTTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:1540549 original size:23 final size:22
Alignment explanation
Indices: 1540506--1540563 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1540496 AAAGGGTATC
* *
1540506 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1540527 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1540550 TACATATCATATCT
1 TACAAATCATATCT
1540564 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1540579 original size:21 final size:21
Alignment explanation
Indices: 1540553--1540614 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1540543 CTAAGATTAC
1540553 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
1540574 ATATCATATCTAGGATTGC--
1 ATATCATATCTAAGATTGCAT
1540593 ATATC-TATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1540613 AT
1 AT
1540615 CCTCAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.32
19 5 0.14
20 2 0.05
21 18 0.49
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:1542297 original size:16 final size:15
Alignment explanation
Indices: 1542279--1542320 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
1542269 TAAATTCTCA
1542279 AAAAATAAAAAATTC
1 AAAAATAAAAAATTC
*
1542294 AAAAATATATAAATTC
1 AAAAATA-AAAAATTC
1542310 AAAAATAAAAA
1 AAAAATAAAAA
1542321 TAATTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAAATTC
Found at i:1542551 original size:17 final size:19
Alignment explanation
Indices: 1542529--1542567 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1542519 TAAAACTCTT
*
1542529 AAAAATT-T-TATTTTAAA
1 AAAAATTATATATATTAAA
1542546 AAAAATTATATATATTAAA
1 AAAAATTATATATATTAAA
1542565 AAA
1 AAA
1542568 TACTTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATATATATTAAA
Found at i:1543934 original size:19 final size:17
Alignment explanation
Indices: 1543898--1543936 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1543888 TACAGCGACT
*
1543898 AAATGACATTGTAATAA
1 AAATGACATTGAAATAA
1543915 AAATGACATTTTGAAATAA
1 AAATGACA--TTGAAATAA
1543934 AAA
1 AAA
1543937 AAATATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (17 bp):
AAATGACATTGAAATAA
Found at i:1546135 original size:181 final size:177
Alignment explanation
Indices: 1545833--1546396 Score: 599
Period size: 180 Copynumber: 3.1 Consensus size: 177
1545823 GTTTCTTTCA
* * *
1545833 AATTT-TCATTGCAATGCATAAGTAGAGCAAGCTGT-TAACTAACAATGTGCATCGTGATCGATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
* ** * *
1545896 ATTGTTGATCAATTTGCGTGCTATTTTTTAAATCTGATTTAAG-TATTTTT-TCAATTTTTTAAG
66 ATTGTTGATCAATTTGCATGCTA-TTTTT-AAT-TTTTTTAAGTTTTTTTTGTTAATTTTTTAAG
**
1545959 AGAAAAGG-GAGAAAAAAGAGGAATAGTGTTTTTTTTTTTTGCTTCTTTATTCC
128 -GAAAAGGAG-GAAAAAAGAGGAATAGTGTTGATTTTTTTT-CTTCTTTATT-C
* *
1546012 AATTTCTCAGTGCAATGCATGAGTAGAGGAAGCTGTGTAACTAACAGTGTACATCGTGATCGATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
*
1546077 ATTGTTTATCAATTTGCATGCTATTTTTAATTTTTTTAAAGTTTTTTTTGTTAA-TTTTTAATGG
66 ATTGTTGATCAATTTGCATGCTATTTTTAATTTTTTT-AAGTTTTTTTTGTTAATTTTTTAA-GG
* *
1546141 AAAAAGAGGAAAAAAGAGGAATAGTGTTGATTTTTCTTCTTCTTTATTTC
129 AAAAGGAGGAAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTTA-TTC
* * * * *
1546191 AATTTCTAAGTGCAATGCATAAGCAGAGGAAGCCGTG--AGTAACAATGTACATCGTGATCTATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
* * ***
1546254 ATTGTCGATCAAGTTGCATGCTA-TTTT-ATTTTATTCTCTCTTTTTTATCTGTTTTTAAAATTT
66 ATTGTTGATCAATTTGCATGCTATTTTTAATTTT-TT-TAAGTTTTTT-T-TG---TT--AA-TT
* *
1546317 TTTTAAGGGAAAAGGAGGAAAAAAAGAGGAATAGTGTTGATTCTTTTTCCTCTTTAATTC
121 TTTTAA-GGAAAAGGAGG-AAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTT-ATTC
*
1546377 AATTTCTCAGTGTAATGCAT
1 AATTTCTCAGTGCAATGCAT
1546397 GAGTGCATTG
Statistics
Matches: 329, Mismatches: 35, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
175 5 0.02
176 12 0.04
177 45 0.14
178 6 0.02
179 53 0.16
180 80 0.24
181 54 0.16
183 2 0.01
185 17 0.05
186 54 0.16
187 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.41
Consensus pattern (177 bp):
AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
ATTGTTGATCAATTTGCATGCTATTTTTAATTTTTTTAAGTTTTTTTTGTTAATTTTTTAAGGAA
AAGGAGGAAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTTATTC
Found at i:1549586 original size:13 final size:14
Alignment explanation
Indices: 1549563--1549599 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1549553 TGCATGTATG
1549563 TATGCATGTATATA
1 TATGCATGTATATA
*
1549577 TATG-ATGTATATG
1 TATGCATGTATATA
1549590 TATGCATGTA
1 TATGCATGTA
1549600 ATCAACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (14 bp):
TATGCATGTATATA
Found at i:1556692 original size:25 final size:25
Alignment explanation
Indices: 1556664--1556753 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
1556654 CCAAATATCG
1556664 GGAAGCTCAAGAGAGATGTTAACTA
1 GGAAGCTCAAGAGAGATGTTAACTA
* * * *
1556689 GGAATCTCATGAGAGTCAAG-TATC-A
1 GGAAGCTCAAGAGAG--ATGTTAACTA
* *
1556714 AGAAGCTCAAGAGAGCTGTTAACTA
1 GGAAGCTCAAGAGAGATGTTAACTA
* *
1556739 GGAATCTCATGAGAG
1 GGAAGCTCAAGAGAG
1556754 TCAAGTATCA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 39 0.81
26 3 0.06
27 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (25 bp):
GGAAGCTCAAGAGAGATGTTAACTA
Done.