Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 4 of 109
Found at i:1136595 original size:32 final size:32
Alignment explanation
Indices: 1136559--1136638 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
1136549 AAATATTTTT
* **
1136559 CAGATCTATATCATGAAA-ATTATATCCATTAA
1 CAGATCTATAACATGAAAGA-TATATCCACAAA
* *
1136591 CAGATCTAAAACAT-AAAGATATATTCACAAA
1 CAGATCTATAACATGAAAGATATATCCACAAA
1136622 CAGATCTATAACATGAA
1 CAGATCTATAACATGAA
1136639 GTTATATACC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (32 bp):
CAGATCTATAACATGAAAGATATATCCACAAA
Found at i:1143600 original size:47 final size:47
Alignment explanation
Indices: 1143531--1143624 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1143521 GATCGAACTA
1143531 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
1 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
*
1143578 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTGAATCC
1 AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
1143625 GACATATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (47 bp):
AATTTGGTTAAGCCGGATTCAAATCTTAAATATTTAAATTTAAATCC
Found at i:1147534 original size:246 final size:246
Alignment explanation
Indices: 1147100--1147581 Score: 964
Period size: 246 Copynumber: 2.0 Consensus size: 246
1147090 TGCATATTAA
1147100 CACTTTGGTCTTTTACCCAGAACTACCAGCAACCTCTGCAGCTCTCTGTCTCATCATCTCCATCA
1 CACTTTGGTCTTTTACCCAGAACTACCAGCAACCTCTGCAGCTCTCTGTCTCATCATCTCCATCA
1147165 CAGCAGCCCTACGTCGTGAATCAGATTGTTGTTGAAGCCTCCTCAAATGTTCCTTTAGGTCTCTG
66 CAGCAGCCCTACGTCGTGAATCAGATTGTTGTTGAAGCCTCCTCAAATGTTCCTTTAGGTCTCTG
1147230 TATTAGCAAGTTTTAACTTTATTAGCTTTAAATTGCACCAAGGAGTACATAACATATGGCTGTTA
131 TATTAGCAAGTTTTAACTTTATTAGCTTTAAATTGCACCAAGGAGTACATAACATATGGCTGTTA
1147295 AGGAGGGAGAAAGGCAAATGTACCTGCAACGTGGTACGTGGAAATGCATAT
196 AGGAGGGAGAAAGGCAAATGTACCTGCAACGTGGTACGTGGAAATGCATAT
1147346 CACTTTGGTCTTTTACCCAGAACTACCAGCAACCTCTGCAGCTCTCTGTCTCATCATCTCCATCA
1 CACTTTGGTCTTTTACCCAGAACTACCAGCAACCTCTGCAGCTCTCTGTCTCATCATCTCCATCA
1147411 CAGCAGCCCTACGTCGTGAATCAGATTGTTGTTGAAGCCTCCTCAAATGTTCCTTTAGGTCTCTG
66 CAGCAGCCCTACGTCGTGAATCAGATTGTTGTTGAAGCCTCCTCAAATGTTCCTTTAGGTCTCTG
1147476 TATTAGCAAGTTTTAACTTTATTAGCTTTAAATTGCACCAAGGAGTACATAACATATGGCTGTTA
131 TATTAGCAAGTTTTAACTTTATTAGCTTTAAATTGCACCAAGGAGTACATAACATATGGCTGTTA
1147541 AGGAGGGAGAAAGGCAAATGTACCTGCAACGTGGTACGTGG
196 AGGAGGGAGAAAGGCAAATGTACCTGCAACGTGGTACGTGG
1147582 CATTGAGATT
Statistics
Matches: 236, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 236 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (246 bp):
CACTTTGGTCTTTTACCCAGAACTACCAGCAACCTCTGCAGCTCTCTGTCTCATCATCTCCATCA
CAGCAGCCCTACGTCGTGAATCAGATTGTTGTTGAAGCCTCCTCAAATGTTCCTTTAGGTCTCTG
TATTAGCAAGTTTTAACTTTATTAGCTTTAAATTGCACCAAGGAGTACATAACATATGGCTGTTA
AGGAGGGAGAAAGGCAAATGTACCTGCAACGTGGTACGTGGAAATGCATAT
Found at i:1150114 original size:18 final size:18
Alignment explanation
Indices: 1150091--1150127 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1150081 TACAATGATA
1150091 AAAAACCTTGCCTGCTAG
1 AAAAACCTTGCCTGCTAG
1150109 AAAAACCTTGCCTGCTAG
1 AAAAACCTTGCCTGCTAG
1150127 A
1 A
1150128 GTATCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (18 bp):
AAAAACCTTGCCTGCTAG
Found at i:1158532 original size:6 final size:6
Alignment explanation
Indices: 1158521--1158547 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1158511 AGGTAGTTCC
1158521 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1158548 TAATCTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:1158634 original size:19 final size:20
Alignment explanation
Indices: 1158600--1158677 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 20
1158590 TTCTGTGTTT
*
1158600 ATATTTGTATTATTTAATAA
1 ATATTTGTATTTTTTAATAA
*
1158620 ATATTT-TATTTTTTAATTATT
1 ATATTTGTATTTTTTAA-TA-A
*
1158641 ATAATTTGTA-TTATTAATAA
1 AT-ATTTGTATTTTTTAATAA
1158661 ATATTT-TATTTTTTAAT
1 ATATTTGTATTTTTTAAT
1158678 TATTATAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.04
19 20 0.42
20 10 0.21
21 4 0.08
22 10 0.21
23 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATATTTGTATTTTTTAATAA
Found at i:1158658 original size:41 final size:42
Alignment explanation
Indices: 1158598--1158685 Score: 162
Period size: 41 Copynumber: 2.1 Consensus size: 42
1158588 ATTTCTGTGT
1158598 TTAT-ATTTGTATTATTTAATAAATATTTTATTTTTTAATTA
1 TTATAATTTGTATTATTTAATAAATATTTTATTTTTTAATTA
1158639 TTATAATTTGTATTA-TTAATAAATATTTTATTTTTTAATTA
1 TTATAATTTGTATTATTTAATAAATATTTTATTTTTTAATTA
1158680 TTATAA
1 TTATAA
1158686 AAATTAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 36 0.78
42 10 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (42 bp):
TTATAATTTGTATTATTTAATAAATATTTTATTTTTTAATTA
Found at i:1158665 original size:25 final size:25
Alignment explanation
Indices: 1158637--1158691 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
1158627 ATTTTTTAAT
1158637 TATTATAATTTGT-ATTATTAATAAA
1 TATTATAATTTGTAATTATT-ATAAA
* * *
1158662 TATTTTATTTTTTAATTATTATAAA
1 TATTATAATTTGTAATTATTATAAA
*
1158687 AATTA
1 TATTA
1158692 ATATATAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATTATAATTTGTAATTATTATAAA
Found at i:1178366 original size:26 final size:26
Alignment explanation
Indices: 1178331--1178398 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1178321 GGTCCAACAA
1178331 TTAAGGCTTCAATTGGTAGGATTTAAG
1 TTAA-GCTTCAATTGGTAGGATTTAAG
1178358 TTAAGCTTCAATTGGTAGGATTTAAG
1 TTAAGCTTCAATTGGTAGGATTTAAG
1178384 TTAAGCTTCAATTGG
1 TTAAGCTTCAATTGG
1178399 GAGGTCATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (26 bp):
TTAAGCTTCAATTGGTAGGATTTAAG
Found at i:1180421 original size:28 final size:28
Alignment explanation
Indices: 1180390--1180446 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1180380 TCTTGACTAG
*
1180390 AGCTTATTCAATTTTATGCTTTGGTTGA
1 AGCTTATTCAATTTTATGCTTCGGTTGA
1180418 AGCTTATTCAATTTTATGCTTCGGTTGA
1 AGCTTATTCAATTTTATGCTTCGGTTGA
1180446 A
1 A
1180447 AGCCAATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (28 bp):
AGCTTATTCAATTTTATGCTTCGGTTGA
Found at i:1187201 original size:10 final size:10
Alignment explanation
Indices: 1187186--1187213 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1187176 TGAACACCAT
1187186 AAACAAAAGA
1 AAACAAAAGA
1187196 AAACAAAAGA
1 AAACAAAAGA
1187206 AAACAAAA
1 AAACAAAA
1187214 AAACAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (10 bp):
AAACAAAAGA
Found at i:1187669 original size:4 final size:4
Alignment explanation
Indices: 1187660--1187706 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1187650 TCATCAAAGT
* * * *
1187660 TACA TACA TACA TACA CACA TACA TGCA TGCA TACA TATA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
1187707 GTATACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1191379 original size:94 final size:95
Alignment explanation
Indices: 1191218--1191406 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 95
1191208 GGTCTAGGTT
1191218 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
1191283 CCAC-AAAACTAGGTAGGTTTATGACAACA
66 CCACAAAAACTAGGTAGGTTTATGACAACA
* *
1191312 TCTTCACTACTGGTGAAGAATCTAAGGGAAGACTAAGAACAATAATGTTGAAACTACATATAAAC
1 TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
1191377 CCACAAAAACTAGGTAGGTTTATGACAACA
66 CCACAAAAACTAGGTAGGTTTATGACAACA
1191407 CAACAATACC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 67 0.73
95 25 0.27
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.23
Consensus pattern (95 bp):
TCTTCACTACTGGTGAAGAATCTAAGAGAAGACTAAGAACAACAATGTTGAAACTACATATAAAC
CCACAAAAACTAGGTAGGTTTATGACAACA
Found at i:1191649 original size:2 final size:2
Alignment explanation
Indices: 1191642--1191671 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1191632 CATTGTATGT
1191642 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
1191672 CACACTTGGT
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):
TA
Found at i:1207741 original size:13 final size:13
Alignment explanation
Indices: 1207723--1207752 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1207713 GGCACTATTG
*
1207723 ACAAAATTGGGTC
1 ACAAAATTAGGTC
1207736 ACAAAATTAGGTC
1 ACAAAATTAGGTC
1207749 ACAA
1 ACAA
1207753 CATGGGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (13 bp):
ACAAAATTAGGTC
Found at i:1209316 original size:17 final size:17
Alignment explanation
Indices: 1209294--1209326 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1209284 TATTTAATTT
1209294 TTATTT-ATAAATATATA
1 TTATTTAAT-AATATATA
1209311 TTATTTAATAATATAT
1 TTATTTAATAATATAT
1209327 TTGTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTAATAATATATA
Found at i:1214828 original size:9 final size:9
Alignment explanation
Indices: 1214814--1214850 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1214804 TATAGTTTGA
1214814 TATTCGAAT
1 TATTCGAAT
1214823 TATTCGAAT
1 TATTCGAAT
* *
1214832 TATTTGAGT
1 TATTCGAAT
1214841 TATTCGAAT
1 TATTCGAAT
1214850 T
1 T
1214851 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1214921 original size:9 final size:9
Alignment explanation
Indices: 1214904--1214934 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1214894 TCGAGTTGAT
1214904 TCGAATAAC
1 TCGAATAAC
*
1214913 TCGATTAAC
1 TCGAATAAC
1214922 TCGAATAAC
1 TCGAATAAC
1214931 TCGA
1 TCGA
1214935 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1216946 original size:10 final size:10
Alignment explanation
Indices: 1216931--1216955 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1216921 AGGCTTAATT
1216931 AAAAGAAATA
1 AAAAGAAATA
1216941 AAAAGAAATA
1 AAAAGAAATA
1216951 AAAAG
1 AAAAG
1216956 GATCTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAAGAAATA
Found at i:1223830 original size:32 final size:32
Alignment explanation
Indices: 1223789--1223853 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1223779 AAATCCTTAA
1223789 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
1 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
*
1223821 TGTTTTTGTTTTTCTAGAGCACTATTGTAGGT
1 TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
1223853 T
1 T
1223854 TGAAGGCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (32 bp):
TGTTTTTGTTTTACTAGAGCACTATTGTAGGT
Found at i:1224768 original size:2 final size:2
Alignment explanation
Indices: 1224761--1224788 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1224751 ATATTCAATG
1224761 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
1224789 ATTATGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1224890 original size:67 final size:68
Alignment explanation
Indices: 1224791--1224928 Score: 269
Period size: 67 Copynumber: 2.0 Consensus size: 68
1224781 TATATATAAT
1224791 TATGTCAAACGCCGCGTGGGCATGGTTGGTCTATATCCTTCTATTGACTTCTTTTCTTTATATGT
1 TATGTCAAACGCCGCGTGGGCATGGTTGGTCTATATCCTTCTATTGACTTCTTTTCTTTATATGT
1224856 ATA
66 ATA
1224859 TATGTCAAACG-CGCGTGGGCATGGTTGGTCTATATCCTTCTATTGACTTCTTTTCTTTATATGT
1 TATGTCAAACGCCGCGTGGGCATGGTTGGTCTATATCCTTCTATTGACTTCTTTTCTTTATATGT
1224923 ATA
66 ATA
1224926 TAT
1 TAT
1224929 ATATTTATTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 59 0.84
68 11 0.16
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (68 bp):
TATGTCAAACGCCGCGTGGGCATGGTTGGTCTATATCCTTCTATTGACTTCTTTTCTTTATATGT
ATA
Found at i:1226873 original size:21 final size:20
Alignment explanation
Indices: 1226847--1226901 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1226837 TATAGAGATA
*
1226847 AAAAATGATATTAAATTTAT
1 AAAAATGATATTAAAGTTAT
1226867 AATAAAT-A-ATGTACAAGTT-T
1 AA-AAATGATAT-TA-AAGTTAT
1226887 AAAAATGATATTAAA
1 AAAAATGATATTAAA
1226902 AAATTACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
19 8 0.28
20 11 0.38
21 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAAATGATATTAAAGTTAT
Found at i:1230654 original size:18 final size:19
Alignment explanation
Indices: 1230631--1230672 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1230621 AGTACAGGGA
1230631 CTAATAGAAAAT-TTT-AAC
1 CTAATA-AAAATCTTTGAAC
*
1230649 CTAATATAAATCTTTGAAC
1 CTAATAAAAATCTTTGAAC
1230668 CTAAT
1 CTAAT
1230673 TGCCGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (19 bp):
CTAATAAAAATCTTTGAAC
Found at i:1238289 original size:27 final size:27
Alignment explanation
Indices: 1238259--1238318 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1238249 ATAGGTGGTG
*
1238259 CCTATCC-AGTAGGCGCCACTGGTGACT
1 CCTATCCGA-TAGGCGCCACGGGTGACT
* * *
1238286 CCTATTCGATAGGTGCCTCGGGTGACT
1 CCTATCCGATAGGCGCCACGGGTGACT
1238313 CCTATC
1 CCTATC
1238319 AATAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.27
Consensus pattern (27 bp):
CCTATCCGATAGGCGCCACGGGTGACT
Found at i:1238363 original size:16 final size:16
Alignment explanation
Indices: 1238342--1238378 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1238332 AAATAAAAAT
1238342 AAAATTACATTACA-AA
1 AAAATTACATTA-ATAA
1238358 AAAATTACATTAATAA
1 AAAATTACATTAATAA
1238374 AAAAT
1 AAAAT
1238379 CACAAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:1238537 original size:99 final size:102
Alignment explanation
Indices: 1238355--1238606 Score: 314
Period size: 99 Copynumber: 2.5 Consensus size: 102
1238345 ATTACATTAC
* *
1238355 AAAAAAA-TTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACTT
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACAC---A--AAACACTAACAATTTATATAACTT
* * *
1238419 AATCATAAATTATTAACAAAATAACTATAAAATTATTTTTAA
61 AATCATAAATAACTAACAAAATAACTATAAAAATATTTTTAA
* *
1238461 AAAAAAATTT-CATTACTAAAAAATCACAAATCACAAAACACTAACAATTTATA-AAC-TAATCA
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCA
* **
1238523 TAAATAACTGACAAAATAACTATAAAAATATTTTTTT
66 TAAATAACTAACAAAATAACTATAAAAATATTTTTAA
* * *
1238560 AAAATATTTTACAGTACTAAAAAATCACAAAACACAAAAAACTAACA
1 AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACA
1238607 TAAATTACTA
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
99 45 0.34
100 36 0.27
101 18 0.14
103 1 0.01
106 29 0.22
107 2 0.02
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.28
Consensus pattern (102 bp):
AAAAAAATTTACAGTACTAAAAAATCACAAAACACAAAACACTAACAATTTATATAACTTAATCA
TAAATAACTAACAAAATAACTATAAAAATATTTTTAA
Found at i:1238630 original size:12 final size:12
Alignment explanation
Indices: 1238593--1238636 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1238583 ATCACAAAAC
1238593 ACAAAA-AACTA
1 ACAAAATAACTA
*
1238604 ACATAAATTACTA
1 ACA-AAATAACTA
*
1238617 ACAAAATAATTA
1 ACAAAATAACTA
1238629 ACAAAATA
1 ACAAAATA
1238637 GTTTTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 3 0.11
12 18 0.64
13 7 0.25
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (12 bp):
ACAAAATAACTA
Found at i:1247017 original size:173 final size:174
Alignment explanation
Indices: 1246692--1247040 Score: 673
Period size: 173 Copynumber: 2.0 Consensus size: 174
1246682 GTTTAATCCA
1246692 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
1 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
1246757 CTATTGAAAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAAT
66 CTATTG-AAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAAT
1246822 GCTTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
130 GCTTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
1246867 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
1 AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
*
1246932 CTATTG-AAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAATTAAAATG
66 CTATTGAAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATG
1246996 CTTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
131 CTTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
1247040 A
1 A
1247041 CGAATATAAT
Statistics
Matches: 173, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
173 102 0.59
175 71 0.41
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (174 bp):
AACTGTATAAACAATTCTGGTATCTCATTATTCTTTTACTCCATTGTTTAACTTGCAAAACAACT
CTATTGAAAAAAAAATGTTACAACATCTATTTCAACACTAACTTTAACAAAAGCAAACTAAAATG
CTTTTTCAATAACATAAATTTATTGTTGTATCAAATTTTCTAGC
Found at i:1248245 original size:54 final size:54
Alignment explanation
Indices: 1248171--1248280 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
1248161 AAACCAAAAA
* *
1248171 TCCCAATATGAACAGTCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
1 TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
*
1248225 TCCCAAAATGAATAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
1 TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
1248279 TC
1 TC
1248281 GAAAACCAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.22
Consensus pattern (54 bp):
TCCCAAAATGAACAGCCCCAAAAGTCCGGAGAGTTCAAAAATTACAAAACTCTT
Found at i:1249843 original size:68 final size:68
Alignment explanation
Indices: 1249734--1249870 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
1249724 TCATTTTTCG
*
1249734 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTGTAGGGGCAAAATGGTAATTGTGCCTAAGATG
1 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
1249799 TGA
66 TGA
1249802 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
1 AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
1249867 TGA
66 TGA
1249870 A
1 A
1249871 TTGGATTGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (68 bp):
AGCCTAGGGAGTAAATCAGAATTAATTAAAAGTATAGGGGCAAAATGGTAATTGTGCCTAAGATG
TGA
Found at i:1250442 original size:25 final size:24
Alignment explanation
Indices: 1250371--1250450 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 24
1250361 CCGTTATATA
* *
1250371 GCTCTTCGGAGCTTCCCGACTAAAG
1 GCTCTTCGGAGCTTCCC-AATAATG
**
1250396 GCTCTTTTATGAGCTTCCCAATTAATG
1 GCTC--TTCGGAGCTTCCCAA-TAATG
*
1250423 GCTCTTCGGAGCTTCCCAATATTG
1 GCTCTTCGGAGCTTCCCAATAATG
1250447 GCTC
1 GCTC
1250451 GCTTGAACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.18
25 17 0.38
26 1 0.02
27 19 0.42
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (24 bp):
GCTCTTCGGAGCTTCCCAATAATG
Found at i:1250532 original size:25 final size:24
Alignment explanation
Indices: 1250478--1250549 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1250468 ATGTGCTCGT
* *
1250478 ATGAGGTTCCCATTAATGGCTCTC
1 ATGAGCTTCCCATTAATGGCTCAC
*
1250502 -TGGAGCTTCCCGTTACATGGCTCAC
1 AT-GAGCTTCCCATTA-ATGGCTCAC
1250527 ATGAGCTT-CCATTATATGGCTCA
1 ATGAGCTTCCCATTA-ATGGCTCA
1250550 AGAGATAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 24 0.60
25 14 0.35
26 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (24 bp):
ATGAGCTTCCCATTAATGGCTCAC
Found at i:1256215 original size:17 final size:17
Alignment explanation
Indices: 1256193--1256226 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1256183 TTAATATAAA
1256193 TAAATAAATTTCCCAAT
1 TAAATAAATTTCCCAAT
* *
1256210 TAAATAATTTTCTCAAT
1 TAAATAAATTTCCCAAT
1256227 GCAATTCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAAATTTCCCAAT
Found at i:1259081 original size:31 final size:28
Alignment explanation
Indices: 1259038--1259094 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
1259028 TCTCAAATGT
*
1259038 ACACAGCCATGTGAACCGCCCGTGTGGGG
1 ACACAGCCATGTG-ACCACCCGTGTGGGG
*
1259067 ACACACGCCAATGTGGCCACCCGTGTGG
1 ACACA-GCC-ATGTGACCACCCGTGTGG
1259095 TTACGAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 14 0.58
31 5 0.21
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (28 bp):
ACACAGCCATGTGACCACCCGTGTGGGG
Found at i:1259659 original size:11 final size:11
Alignment explanation
Indices: 1259643--1259682 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1259633 CTCCCACAAC
1259643 TAAAATAAAAA
1 TAAAATAAAAA
*
1259654 TAAAATAGAAA
1 TAAAATAAAAA
1259665 TAAAATAATAAA
1 TAAAATAA-AAA
*
1259677 CAAAAT
1 TAAAAT
1259683 CTTCTATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:1262826 original size:19 final size:21
Alignment explanation
Indices: 1262790--1262830 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1262780 TTCTTTGCTC
1262790 TTTTGCTTCGAGTTTGCTTTTG
1 TTTTGCTTCGAG-TTGCTTTTG
1262812 TTTTGCTTCG-G-TGCTTTTG
1 TTTTGCTTCGAGTTGCTTTTG
1262831 AGAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.02, C:0.15, G:0.24, T:0.59
Consensus pattern (21 bp):
TTTTGCTTCGAGTTGCTTTTG
Found at i:1269167 original size:22 final size:22
Alignment explanation
Indices: 1269134--1269189 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1269124 ATTTTGTATT
*
1269134 AATTTATCAAATTGAAC-TAAA
1 AATTTATTAAATTGAACTTAAA
* *
1269155 AATATTATTAAATTTATCTTAAA
1 AAT-TTATTAAATTGAACTTAAA
1269178 AATTTA-TAAATT
1 AATTTATTAAATT
1269190 TTATAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.30
22 14 0.47
23 7 0.23
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTATTAAATTGAACTTAAA
Found at i:1269692 original size:22 final size:23
Alignment explanation
Indices: 1269667--1269712 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1269657 TTTAAACATC
1269667 AATTACAAAA-TTAAAATAAAAA
1 AATTACAAAAGTTAAAATAAAAA
* *
1269689 AATTTCAAAAGGTTAAAATGAAAA
1 AATTACAAAA-GTTAAAATAAAAA
1269713 TTTACTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (23 bp):
AATTACAAAAGTTAAAATAAAAA
Found at i:1270944 original size:2 final size:2
Alignment explanation
Indices: 1270937--1270962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1270927 ATGTAGGTTC
1270937 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
1270963 TCCCCTCATT
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:1278797 original size:50 final size:50
Alignment explanation
Indices: 1278735--1279525 Score: 633
Period size: 50 Copynumber: 15.8 Consensus size: 50
1278725 TAATTAACTA
* * **
1278735 CAATGTCGGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
1278785 CAATATCGGGGAAGCCAGATTCACCGTTGTAGCTTCAAT-TCGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT-TTTTAATTG
* * * *
1278835 CACCT-CCAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 CA-ATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
1278885 CAATGCCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * **
1278935 CACCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * *
1278985 CAATGTC-GGGAAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTCACTG
1 CAATGTCAGGG-AAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * **
1279035 CACTG-CTAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * *
1279085 CAATGTC-GGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTG
1 CAATGTCAGGG-AAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * **
1279135 CACTG-CTAGGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTG
1 CAATGTC-AGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** *
1279185 CAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * ** *
1279235 CACCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
* * * * ** ** *
1279285 CAATGTCGGGGAAGCAATATTCACCATTGTAGCTTCAATATGCTCCACTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * ** * * *
1279335 CACCGCCAGGGAAGTAAGATTTGCCATTGT-GAATTCAACCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAG-CTTCAATCTTTTTAATTG
* * * ** * *
1279385 CAATGTCAGGGAAGCAAGATTCACTGGTGTAGCTTCAATCTGTTCCACTA
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
** * * * *
1279435 CACCGCCAAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
*
1279485 CAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT
1 CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCT
1279526 GTTCCACTAC
Statistics
Matches: 567, Mismatches: 160, Indels: 28
0.75 0.21 0.04
Matches are distributed among these distances:
49 11 0.02
50 545 0.96
51 11 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
CAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTTTTTAATTG
Found at i:1278869 original size:100 final size:100
Alignment explanation
Indices: 1278743--1279589 Score: 1246
Period size: 100 Copynumber: 8.5 Consensus size: 100
1278733 TACAATGTCG
* * *
1278743 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCCAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
1278808 CCGTTGTAGCTTCAAT-TCGTTCCACTGCACCTCCA
66 CCGTTGTAGCTTCAATCT-GTTCCACTGCACCGCCA
* * * *
1278843 GGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGCCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
1278908 CCGTTGTAGCTTCAATCTATTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
*
1278943 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGAAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
1279008 CCGTTGTAGCTTCAATCTGTTTCACTGCACTGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
1279043 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGAAAGTAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
1279108 CCGTTGTAGCTTCAATCTGTTTCACTGCACTGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
** *
1279143 GGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
1279208 CCATTGTAGCTTCAATCTGTTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* *
1279243 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCGGGGAAGCAATATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
1279308 CCATTGTAGCTTCAATATGCTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * ** * *
1279343 GGGAAGTAAGATTTGCCATTGTGAATTCAACCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
1279408 CTGGTGTAGCTTCAATCTGTTCCACTACACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * *
1279443 AGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
1279508 CCGTTGTAGCTTCAATCTGTTCCACTACACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
1279543 GAGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTTAATTGCAAT
1 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTTAATTGCAAT
1279590 CTCAGGGGTA
Statistics
Matches: 680, Mismatches: 65, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
100 665 0.98
101 15 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
Found at i:1279762 original size:15 final size:15
Alignment explanation
Indices: 1279722--1279762 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
1279712 TAACTAGATG
1279722 TGTATGAATGATATT
1 TGTATGAATGATATT
*
1279737 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
1279753 TGTATGAATG
1 TGTATGAATG
1279763 CAAAATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:1280540 original size:13 final size:13
Alignment explanation
Indices: 1280506--1280532 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1280496 TTCGTTCTTC
1280506 TTTTCTTTTTATT
1 TTTTCTTTTTATT
1280519 TTTTCTTTTTATT
1 TTTTCTTTTTATT
1280532 T
1 T
1280533 CTTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTATT
Found at i:1280998 original size:5 final size:5
Alignment explanation
Indices: 1280972--1281017 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
1280962 CCCGGTAGAG
*
1280972 GTTTT -TTTT CTTTT -TTTCT GTTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTT-T GTTTT GTTTT GTTTT GTTTT GTTTT GT
1281018 GCCTCCACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 7 0.18
5 28 0.74
6 3 0.08
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:1283757 original size:24 final size:25
Alignment explanation
Indices: 1283730--1283782 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
1283720 AGCCTTTTCG
*
1283730 TGAAATTTAATACAAATG-ATGCAA
1 TGAAATGTAATACAAATGCATGCAA
* *
1283754 TGAAATGTAATACAGATGCATGGAA
1 TGAAATGTAATACAAATGCATGCAA
1283779 TGAA
1 TGAA
1283783 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATACAAATGCATGCAA
Found at i:1291099 original size:25 final size:25
Alignment explanation
Indices: 1291039--1291199 Score: 177
Period size: 25 Copynumber: 6.6 Consensus size: 25
1291029 ATGTAACAGA
*
1291039 AAGCTCATAAGAGCC-ATAAT-GGG
1 AAGCTCATAAGAGCCAATTATCGGG
1291062 AAGCTCATAAGAGCCAATTATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
*
1291087 AAGCTC-TAGAGAGCCAATTATTGGG
1 AAGCTCATA-AGAGCCAATTATCGGG
* * *
1291112 AAGCTCATACGAGCC-ATAAACGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* * *
1291136 AAGCTCATAAGAGCTAAATAACGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* *
1291161 AAGCTCATGAGAGCCTATTATCGGG
1 AAGCTCATAAGAGCCAATTATCGGG
* *
1291186 ACGCTCGTAAGAGC
1 AAGCTCATAAGAGC
1291200 TATGGTGTGT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
23 15 0.13
24 25 0.22
25 73 0.63
26 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
AAGCTCATAAGAGCCAATTATCGGG
Found at i:1291165 original size:74 final size:73
Alignment explanation
Indices: 1291039--1291199 Score: 216
Period size: 74 Copynumber: 2.2 Consensus size: 73
1291029 ATGTAACAGA
* * *
1291039 AAGCTCATAAGAGCCATAATGGGAAGCTCATAAGAGCCAATTATCGGGAAGCTC-TAGAGAGCCA
1 AAGCTCATAAGAGCCATAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCAT-GAGAGCCA
*
1291103 ATTATTGGG
65 ATTATCGGG
* * *
1291112 AAGCTCATACGAGCCATAAACGGGAAGCTCATAAGAGCTAAATAACGGGAAGCTCATGAGAGCCT
1 AAGCTCATAAGAGCCAT-AACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCA
1291177 ATTATCGGG
65 ATTATCGGG
* *
1291186 ACGCTCGTAAGAGC
1 AAGCTCATAAGAGC
1291200 TATGGTGTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
73 16 0.21
74 59 0.78
75 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (73 bp):
AAGCTCATAAGAGCCATAACGGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCAA
TTATCGGG
Found at i:1302011 original size:19 final size:19
Alignment explanation
Indices: 1301987--1302026 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1301977 GGTACTTAAA
*
1301987 AACTTTGAATCAAAGATAT
1 AACTTTGAAGCAAAGATAT
1302006 AACTTTGAAGCAAAGATAT
1 AACTTTGAAGCAAAGATAT
1302025 AA
1 AA
1302027 TAACATGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (19 bp):
AACTTTGAAGCAAAGATAT
Found at i:1302364 original size:15 final size:15
Alignment explanation
Indices: 1302339--1302373 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1302329 GACTCTATTT
*
1302339 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
1302353 TAATTAATATTAAGA
1 TAATTAATATTAAGA
1302368 TAATTA
1 TAATTA
1302374 TTAAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:1302389 original size:18 final size:18
Alignment explanation
Indices: 1302368--1302411 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1302358 AATATTAAGA
1302368 TAATTATTAAG-TATTATT
1 TAATT-TTAAGATATTATT
* *
1302386 TAATTTTAGGATTTTATT
1 TAATTTTAAGATATTATT
1302404 TAATTTTA
1 TAATTTTA
1302412 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TAATTTTAAGATATTATT
Found at i:1302411 original size:10 final size:10
Alignment explanation
Indices: 1302396--1302425 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1302386 TAATTTTAGG
1302396 ATTTTATTTA
1 ATTTTATTTA
1302406 ATTTTATTTA
1 ATTTTATTTA
1302416 ATTTTATTTA
1 ATTTTATTTA
1302426 TCTTCAATTA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTATTTA
Found at i:1305173 original size:3 final size:3
Alignment explanation
Indices: 1305167--1305197 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1305157 TCTCCAACTC
1305167 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1305198 GCTTTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1311412 original size:69 final size:69
Alignment explanation
Indices: 1311330--1311469 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
1311320 GATCTACATG
1311330 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1311395 TGTA
66 TGTA
1311399 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1 AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
1311464 TGTA
66 TGTA
1311468 AA
1 AA
1311470 ATTACTTAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (69 bp):
AATGGAGCATGAACCATGACAGTTAGATTGTTAAAATATTATGCGTAAAAGAAGTGATAAAAGAG
TGTA
Found at i:1331147 original size:24 final size:24
Alignment explanation
Indices: 1331118--1331179 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1331108 TCAAAGAAGT
*
1331118 TGATAGTAATAGTGCAAGCTATGA
1 TGATAGTAATAGTGCAAACTATGA
1331142 TGATAGTAATAGTGCAAACTATGA
1 TGATAGTAATAGTGCAAACTATGA
*
1331166 TGATAGTGATAGTG
1 TGATAGTAATAGTG
1331180 AACTTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (24 bp):
TGATAGTAATAGTGCAAACTATGA
Found at i:1336486 original size:26 final size:26
Alignment explanation
Indices: 1336450--1336503 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1336440 TTCATCTCTC
1336450 CTAGGTATTTAGAAAATTAGTTAATG
1 CTAGGTATTTAGAAAATTAGTTAATG
*
1336476 CTAGGTATTTAGAAAATTAGTTCATG
1 CTAGGTATTTAGAAAATTAGTTAATG
1336502 CT
1 CT
1336504 TGAAAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (26 bp):
CTAGGTATTTAGAAAATTAGTTAATG
Found at i:1349569 original size:13 final size:13
Alignment explanation
Indices: 1349551--1349576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349541 GAATTTTTAA
1349551 GAATCGTTAACAC
1 GAATCGTTAACAC
1349564 GAATCGTTAACAC
1 GAATCGTTAACAC
1349577 TTTTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
GAATCGTTAACAC
Found at i:1350697 original size:11 final size:12
Alignment explanation
Indices: 1350680--1350724 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
1350670 GATTGTTTGA
1350680 ATATTTTATTAT
1 ATATTTTATTAT
1350692 -TATTTTATTAT
1 ATATTTTATTAT
*
1350703 AGATATTTATT-T
1 ATAT-TTTATTAT
1350715 ATATTTTATT
1 ATATTTTATT
1350725 TAATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 17 0.59
12 6 0.21
13 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:1355343 original size:17 final size:19
Alignment explanation
Indices: 1355315--1355363 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
1355305 TAAAAAGGAA
*
1355315 ATAATAAGTAAATAAATA-
1 ATAATAAATAAATAAATAC
1355333 A-AATAAATAAAT-AATAC
1 ATAATAAATAAATAAATAC
1355350 ATAA-AAATAAATAA
1 ATAATAAATAAATAA
1355364 CCTAGACAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 19 0.70
18 4 0.15
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAATAAATAAATAAATAC
Found at i:1356849 original size:51 final size:49
Alignment explanation
Indices: 1356794--1357050 Score: 236
Period size: 51 Copynumber: 5.3 Consensus size: 49
1356784 CCACTACAAT
*
1356794 TTCAGGGAGATAAGACTTGTAACTTGTAGCTTCT-ATCTGTTCCACTGAAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTT-TAATCTGTTCCACTGAAAC
*
1356845 TTCAGGGAAATAAGA---T--TTGTAGCTTTAATCTGTTCCA-TTACAAC
1 TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGA-AAC
* * *
1356889 TTCAGGGAGATAAGATTTGTGACTTGTAGCTTTAATCTGTTCTACTGCAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTTTAATCTGTTCCACTGAAAC
* * * *
1356940 TTCAGGGAAATAAGATT-TGC--ATA--TTCAATCTG-TCCACTGTAAC
1 TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGAAAC
* *
1356983 TTCAAGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACT-ACAAC
1 TTCAGGGAAATAAGA-TTGT-ACTTGTAGCTTTAATCTGTTCCACTGA-AAC
1357034 TTCAGGGAAATAAGATT
1 TTCAGGGAAATAAGATT
1357051 TTCTATCTTC
Statistics
Matches: 167, Mismatches: 20, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
43 25 0.15
44 46 0.28
45 1 0.01
46 3 0.02
47 1 0.01
48 4 0.02
49 1 0.01
50 12 0.07
51 73 0.44
52 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (49 bp):
TTCAGGGAAATAAGATTGTACTTGTAGCTTTAATCTGTTCCACTGAAAC
Found at i:1357092 original size:45 final size:45
Alignment explanation
Indices: 1356823--1357220 Score: 301
Period size: 45 Copynumber: 8.6 Consensus size: 45
1356813 TAACTTGTAG
* * * *
1356823 CTTCTATCTGTTCCACTGAAACTTCAGGGAA-ATAAGATTTG-TAG
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* * * * * *
1356867 CTTTAATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGTGACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA-TT-TG-C---TAT
* * *
1356918 CTTTAATCTGTTCTACTGCAACTTCAGGGAA-ATAAGATTTGC-AT
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* * *
1356962 ATTCAATCTG-TCCACTGTAACTTCAAGG-AGATAAGATTTGTAACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAGATTTG---C---TAT
* * * *
1357012 CTTTAATCTGTTCCACTACAACTTCAGGGAA-ATAAGATTTTCTAT
1 CTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTGCTAT
* **
1357057 CTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGATTCACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
* * * *
1357102 CTTCAATTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAC
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
* *
1357147 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
*
1357192 CTTCAATC--CATCCCACTGCAACTTTAGGA
1 CTTCAATCTGC-T-CCACTGCAACTTCAGGA
1357221 GTATGAGTAA
Statistics
Matches: 290, Mismatches: 40, Indels: 47
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.00
43 28 0.10
44 42 0.14
45 141 0.49
46 3 0.01
48 2 0.01
49 2 0.01
50 12 0.04
51 55 0.19
52 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCTAT
Found at i:1357159 original size:90 final size:92
Alignment explanation
Indices: 1356763--1357185 Score: 435
Period size: 95 Copynumber: 4.5 Consensus size: 92
1356753 ATAGGTATAG
* * * * * *
1356763 GATTTGTTGCTTCAATCTTCTCCACTACAATTTCAGGGAGATAAGACTTGTAACTTGTAGCTTCT
1 GATTTGCTACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTCA
* *
1356828 ATCTGTTCCACTGAAACTTCAGGGAAATAA
63 ATCTGTTCTACTGCAACTTCAGGGAAATAA
* * * * * *
1356858 GATTTG-TAGCTTTAATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGTGACTTGTAGCTTT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTC
1356922 AATCTGTTCTACTGCAACTTCAGGGAAATAA
62 AATCTGTTCTACTGCAACTTCAGGGAAATAA
* * *
1356953 GATTTGCATA-TTCAATCTG-TCCACTGTAACTTCAAGGAGATAAGATTTGTAACTTGTAGCTTT
1 GATTTGC-TACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAAC-T-TAGCTTC
* *
1357016 AATCTGTTCCACTACAACTTCAGGGAAATAA
62 AATCTGTTCTACTGCAACTTCAGGGAAATAA
* * * * *
1357047 GATTTTCTATCTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGA-T-TCAC-TATCTTCAAT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTAGCTTCAAT
* * *
1357109 TTGCTCTACTGCAACTTCAGGGAGATAA
65 CTGTTCTACTGCAACTTCAGGGAAATAA
*
1357137 GATTTGCTACCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 GATTTGCTA-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1357186 TGCTATCTTC
Statistics
Matches: 283, Mismatches: 38, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
90 73 0.26
91 1 0.00
93 5 0.02
94 76 0.27
95 103 0.36
96 23 0.08
97 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (92 bp):
GATTTGCTACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAACTTAGCTTCAATC
TGTTCTACTGCAACTTCAGGGAAATAA
Found at i:1357210 original size:90 final size:91
Alignment explanation
Indices: 1356725--1357215 Score: 406
Period size: 95 Copynumber: 5.3 Consensus size: 91
1356715 CTTCTTTAAG
* ** * * * * * *
1356725 TAGCTTCATTCTAACCCACTGCAACTTCATAGG-TATAGGATTTGTTGCTTCAATCTTCTCCACT
1 TAGCTTCAATCTGTCCCACTGCAACTTCA-GGGAAATAAGATTTGCTACTTCAATCTGCTCCACT
* * *
1356789 ACAATTTCAGGGAGATAAGACTTGTAACTT
65 GCAACTTCAGGGAGATAAGA-TT-TGAC-T
* * * * * *
1356819 GTAGCTTCTATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTG-TAGCTTTAATCTGTTCCAT
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
*
1356883 TACAACTTCAGGGAGATAAGATTTGTGACTT
64 TGCAACTTCAGGGAGATAAGA-TT-TGAC-T
* * *
1356914 GTAGCTTTAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCATA-TTCAATCTG-TCCAC
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGC-TACTTCAATCTGCTCCAC
* *
1356977 TGTAACTTCAAGGAGATAAGATTTGTAACTT
64 TGCAACTTCAGGGAGATAAGATTTG--AC-T
* * * * *
1357008 GTAGCTTTAATCTGTTCCACTACAACTTCAGGGAAATAAGATTTTCTATCTTCAATTTGCTCCAC
1 -TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
* *
1357073 TGCAACTTCAGGAAGATAAGA-TTCAC-
64 TGCAACTTCAGGGAGATAAGATTTGACT
* * * * *
1357099 TATCTTCAATTTG-CTCTACTGCAACTTCAGGGAGATAAGATTTGCTACCTTTAATCTGCTCCAC
1 TAGCTTCAATCTGTC-CCACTGCAACTTCAGGGAAATAAGATTTGCTA-CTTCAATCTGCTCCAC
1357163 TGCAACTTCAGGGAGATAAGATTTG-C-
64 TGCAACTTCAGGGAGATAAGATTTGACT
* **
1357189 TATCTTCAATCCATCCCACTGCAACTT
1 TAGCTTCAATCTGTCCCACTGCAACTT
1357216 TAGGAGTATG
Statistics
Matches: 333, Mismatches: 51, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
90 94 0.28
91 3 0.01
92 2 0.01
93 6 0.02
94 72 0.22
95 131 0.39
96 23 0.07
97 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (91 bp):
TAGCTTCAATCTGTCCCACTGCAACTTCAGGGAAATAAGATTTGCTACTTCAATCTGCTCCACTG
CAACTTCAGGGAGATAAGATTTGACT
Found at i:1364983 original size:256 final size:253
Alignment explanation
Indices: 1364576--1365063 Score: 824
Period size: 256 Copynumber: 1.9 Consensus size: 253
1364566 GAATAAAATA
1364576 AATAAAATAAAACAAAATAAAAGCATCATTAAATACAAAAAAATCAAAATAAAAAAATGGTAAGC
1 AATAAAATAAAACAAAATAAAAGCATCATTAAATACAAAAAAATCAAAATAAAAAAATGGTAAGC
*
1364641 AAATAAATAAAATAAATAAGACACAACACAAAAAAAAAAACTAAACAGAGATAAAGGTGATTAAA
66 AAATAAATAAAATAAATAAGACACAACACAAAAAAAAAAACTAAACAGAGATAAAGGGGATTAAA
1364706 TTGACATTGAGATAAAATTAAGAGTCCAAATCCTAATAAAATAAGTTTATGAATACAAAAGGGGC
131 TTGACATTGAGATAAAATTAAGAGTCCAAATCCTAATAAAATAAGTTTATGAATACAAAAGGGGC
1364771 TAAAATTATAATAAAATAAACGCAAAAGGACTAAATTATAATAATAAGGAAGTTCAAG
196 TAAAATTATAATAAAATAAACGCAAAAGGACTAAATTATAATAATAAGGAAGTTCAAG
* *
1364829 AATAAAAT-AAATAAAATAAAAGCAT-AGTTAAATAC-AAAATATCAAAATAAAAAAATGGTAAG
1 AATAAAATAAAACAAAATAAAAGCATCA-TTAAATACAAAAAAATCAAAATAAAAAAATGGTAAG
1364891 -AAATAAATAAAATAAATAAGACACAACAACAACAAAAAAAAAAAACCT-AACAGAGATAAAAGG
65 CAAATAAATAAAATAAATAAG--AC-ACAAC-AC-AAAAAAAAAAA-CTAAACAGAGAT-AAAGG
*
1364954 GGATTAAATTGACATTGAGATAAAATTAAGAGTCCAAATCCTAATAAATTAAGTTTATGAATACA
123 GGATTAAATTGACATTGAGATAAAATTAAGAGTCCAAATCCTAATAAAATAAGTTTATGAATACA
*
1365019 AGAGGGGCTAAAATTATAATAAAATAAACGCAAAAGGACTAAATT
188 AAAGGGGCTAAAATTATAATAAAATAAACGCAAAAGGACTAAATT
1365064 GAAGTTTAAT
Statistics
Matches: 222, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
250 20 0.09
251 27 0.12
252 26 0.12
253 13 0.06
254 2 0.01
255 20 0.09
256 114 0.51
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.20
Consensus pattern (253 bp):
AATAAAATAAAACAAAATAAAAGCATCATTAAATACAAAAAAATCAAAATAAAAAAATGGTAAGC
AAATAAATAAAATAAATAAGACACAACACAAAAAAAAAAACTAAACAGAGATAAAGGGGATTAAA
TTGACATTGAGATAAAATTAAGAGTCCAAATCCTAATAAAATAAGTTTATGAATACAAAAGGGGC
TAAAATTATAATAAAATAAACGCAAAAGGACTAAATTATAATAATAAGGAAGTTCAAG
Found at i:1370056 original size:2 final size:2
Alignment explanation
Indices: 1370044--1370073 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1370034 AATAAAGGGT
1370044 TA TA GTA 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 T
1370074 GGATTTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1384632 original size:17 final size:17
Alignment explanation
Indices: 1384610--1384642 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1384600 AAAGGAAGAA
1384610 AACATACTGAAAGCCAC
1 AACATACTGAAAGCCAC
1384627 AACATACTGAAAGCCA
1 AACATACTGAAAGCCA
1384643 AGTCTTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.27, G:0.12, T:0.12
Consensus pattern (17 bp):
AACATACTGAAAGCCAC
Found at i:1391693 original size:2 final size:2
Alignment explanation
Indices: 1391681--1391711 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1391671 ACATTGAAAA
1391681 AT AT CAT 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
1391712 TAGAAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1392706 original size:2 final size:2
Alignment explanation
Indices: 1392694--1392726 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1392684 ACATAGAAAA
1392694 AT AT CAT 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
1392727 TAGAAAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1393257 original size:13 final size:13
Alignment explanation
Indices: 1393239--1393265 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1393229 ACTAATTGTC
1393239 ATTATTAAATATG
1 ATTATTAAATATG
1393252 ATTATTAAATATG
1 ATTATTAAATATG
1393265 A
1 A
1393266 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTATTAAATATG
Found at i:1398033 original size:2 final size:2
Alignment explanation
Indices: 1398021--1398053 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1398011 ACATAGAAAA
1398021 AT AT CAT 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
1398054 TAGAAAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1398181 original size:17 final size:18
Alignment explanation
Indices: 1398156--1398190 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1398146 AAAGTATAGC
1398156 TATAAATATATA-TAGAA
1 TATAAATATATATTAGAA
*
1398173 TATATATATATATTAGAA
1 TATAAATATATATTAGAA
1398191 AGCTATTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TATAAATATATATTAGAA
Found at i:1398264 original size:132 final size:134
Alignment explanation
Indices: 1398028--1398306 Score: 517
Period size: 132 Copynumber: 2.1 Consensus size: 134
1398018 AAAATATCAT
* *
1398028 ATATATATATATATATATATATATATTAGAAAGCTATTAGAAATTATACACTAAAACCATGATGA
1 ATATATATAGATATATATATATATATTAGAAAGCTATTAGAAATTATAAACTAAAACCATGATGA
1398093 GTTTTAGAAAGAAAAAAGAAGAAGAAGGTGTTTTTTGATAATTTGAGGTTCGTAAAGTATAGCTA
66 GTTTTAGAAAGAAAAAAGAAGAAGAAGGTGTTTTTTGATAATTTGAGGTTCGTAAAGTATAGCTA
1398158 T-AA
131 TAAA
1398161 ATATATATAGA-ATATATATATATATTAGAAAGCTATTAGAAATTATAAACTAAAACCATGATGA
1 ATATATATAGATATATATATATATATTAGAAAGCTATTAGAAATTATAAACTAAAACCATGATGA
1398225 GTTTTAGAAAGAAAAAAGAAGAAGAAGGTGTTTTTTGATAATTTGAGGTTCGTAAAGTATAGCTA
66 GTTTTAGAAAGAAAAAAGAAGAAGAAGGTGTTTTTTGATAATTTGAGGTTCGTAAAGTATAGCTA
1398290 TAAA
131 TAAA
1398294 ATTATATATAGAT
1 A-TATATATAGAT
1398307 TTGAGCGGGA
Statistics
Matches: 141, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
132 118 0.84
133 13 0.09
134 10 0.07
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.34
Consensus pattern (134 bp):
ATATATATAGATATATATATATATATTAGAAAGCTATTAGAAATTATAAACTAAAACCATGATGA
GTTTTAGAAAGAAAAAAGAAGAAGAAGGTGTTTTTTGATAATTTGAGGTTCGTAAAGTATAGCTA
TAAA
Found at i:1398716 original size:13 final size:13
Alignment explanation
Indices: 1398698--1398724 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1398688 ACTAATTGTC
1398698 ATTATTAAATATG
1 ATTATTAAATATG
1398711 ATTATTAAATATG
1 ATTATTAAATATG
1398724 A
1 A
1398725 AAGATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTATTAAATATG
Found at i:1399683 original size:59 final size:60
Alignment explanation
Indices: 1399582--1399705 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 60
1399572 ATTAAGCATT
1399582 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
* *
1399642 AAAA-ATGCATTTAAGTGATTATGAGTATAAAATTCACAATTAACATCAAATAATCACTC
1 AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
1399701 AAAAC
1 AAAAC
1399706 GCATTAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 57 0.93
60 4 0.07
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (60 bp):
AAAACATGAATTTAAGTGATTATAAGTATAAAATTCACAATTAACATCAAATAATCACTC
Found at i:1403952 original size:2 final size:2
Alignment explanation
Indices: 1403908--1403936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1403898 GTTATGTGTG
1403908 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 T
1403937 GAAAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1405549 original size:3 final size:3
Alignment explanation
Indices: 1405541--1405567 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1405531 CCTTGGGCTT
1405541 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1405568 AGAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1405783 original size:13 final size:14
Alignment explanation
Indices: 1405765--1405844 Score: 85
Period size: 14 Copynumber: 5.8 Consensus size: 14
1405755 GGCCCACTTT
1405765 GCGCA-GCCCAGTA
1 GCGCAGGCCCAGTA
* *
1405778 GCGCAGGCCCACTTT
1 GCGCAGGCCCA-GTA
1405793 GCGCA-GCCCAGTA
1 GCGCAGGCCCAGTA
* *
1405806 GCGCAGGCCCACTTT
1 GCGCAGGCCCA-GTA
1405821 GCGCA-GCCCAGTA
1 GCGCAGGCCCAGTA
1405834 GCGCAGGCCCA
1 GCGCAGGCCCA
1405845 ACGCAGGCAG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
13 17 0.31
14 25 0.46
15 12 0.22
ACGTcount: A:0.19, C:0.40, G:0.30, T:0.11
Consensus pattern (14 bp):
GCGCAGGCCCAGTA
Found at i:1405855 original size:56 final size:58
Alignment explanation
Indices: 1405749--1405877 Score: 183
Period size: 56 Copynumber: 2.2 Consensus size: 58
1405739 TAGCAGGTCT
***
1405749 GCAGCAGGCCCACTTTGCGCAGCCCAGTAGCGCAGGCCCACTTTGCGCAGCCCAG-TA
1 GCAGCAGGCCCACTTTGCGCAGCCCAGTAGCGCAGGCCCACGCAGCGCAGCCCAGCTA
1405806 GC-GCAGGCCCACTTTGCGCAGCCCAGTAGCGCAGGCCCAACGCAG-GCAGCCCAGCACTA
1 GCAGCAGGCCCACTTTGCGCAGCCCAGTAGCGCAGGCCC-ACGCAGCGCAGCCCAG--CTA
1405865 GCAGCAGGCCCAC
1 GCAGCAGGCCCAC
1405878 CAGCATAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
56 45 0.70
57 5 0.08
59 4 0.06
60 10 0.16
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (58 bp):
GCAGCAGGCCCACTTTGCGCAGCCCAGTAGCGCAGGCCCACGCAGCGCAGCCCAGCTA
Found at i:1405859 original size:28 final size:28
Alignment explanation
Indices: 1405752--1405844 Score: 186
Period size: 28 Copynumber: 3.3 Consensus size: 28
1405742 CAGGTCTGCA
1405752 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1405780 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1405808 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1 GCAGGCCCACTTTGCGCAGCCCAGTAGC
1405836 GCAGGCCCA
1 GCAGGCCCA
1405845 ACGCAGGCAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.13
Consensus pattern (28 bp):
GCAGGCCCACTTTGCGCAGCCCAGTAGC
Found at i:1405944 original size:14 final size:14
Alignment explanation
Indices: 1405925--1405976 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
1405915 GAAACAGGCC
1405925 AGAAAAAAGAGAGA
1 AGAAAAAAGAGAGA
* *
1405939 AGAAAAAAGAAAAA
1 AGAAAAAAGAGAGA
1405953 AGAAAAAA-A-AGA
1 AGAAAAAAGAGAGA
*
1405965 AAAAAAAAGAGA
1 AGAAAAAAGAGA
1405977 AAAAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.28
13 2 0.06
14 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGAGAGA
Found at i:1405958 original size:28 final size:28
Alignment explanation
Indices: 1405926--1406037 Score: 122
Period size: 28 Copynumber: 3.9 Consensus size: 28
1405916 AAACAGGCCA
1405926 GAAAAAAGAGAGAAGAAAAAAGAAAAAA-
1 GAAAAAAGAGAGAA-AAAAAAGAAAAAAG
* *
1405954 GAAAAAAAAGAAAAAAAAAGAGAAAAAAAG
1 GAAAAAAGAGAGAAAAAAA-AG-AAAAAAG
*
1405984 GAAAAAAGAG-GAAAAAAGAGGAAAAAAG
1 GAAAAAAGAGAGAAAAAA-AAGAAAAAAG
1406012 GAAAAAA-AGAGAAAAATGAAAGAAAA
1 GAAAAAAGAGAGAAAAA--AAAGAAAA
1406038 GTTAAATTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
27 7 0.10
28 34 0.48
29 19 0.27
30 11 0.15
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (28 bp):
GAAAAAAGAGAGAAAAAAAAGAAAAAAG
Found at i:1405961 original size:10 final size:10
Alignment explanation
Indices: 1405948--1406037 Score: 76
Period size: 10 Copynumber: 9.1 Consensus size: 10
1405938 AAGAAAAAAG
1405948 AAAAAAG-AA
1 AAAAAAGAAA
1405957 AAAAAAGAAA
1 AAAAAAGAAA
*
1405967 AAAAAAGAGA
1 AAAAAAGAAA
*
1405977 AAAAAAGGAA
1 AAAAAAGAAA
* *
1405987 AAAAGAGGAA
1 AAAAAAGAAA
* *
1405997 AAAAGAG-GA
1 AAAAAAGAAA
*
1406006 AAAAAGGAAA
1 AAAAAAGAAA
*
1406016 AAAAGAGAAA
1 AAAAAAGAAA
*
1406026 AATGAAAGAAA
1 AA-AAAAGAAA
1406037 A
1 A
1406038 GTTAAATTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
9 13 0.20
10 46 0.70
11 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1405990 original size:38 final size:38
Alignment explanation
Indices: 1405927--1406027 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
1405917 AACAGGCCAG
* *
1405927 AAAAAAGAGAGAAGAAAAAAGAAAAAAGA-AAAAAAAGA
1 AAAAAAAAGAGAA-AAAAAGGAAAAAAGAGAAAAAAAGA
*
1405965 AAAAAAAAGAGAAAAAAAGGAAAAAAGAGGAAAAAAGA
1 AAAAAAAAGAGAAAAAAAGGAAAAAAGAGAAAAAAAGA
**
1406003 GGAAAAAAG-GAAAAAAAGAGAAAAA
1 AAAAAAAAGAGAAAAAAAG-GAAAAA
1406028 TGAAAGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 23 0.41
38 33 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (38 bp):
AAAAAAAAGAGAAAAAAAGGAAAAAAGAGAAAAAAAGA
Found at i:1406038 original size:18 final size:17
Alignment explanation
Indices: 1405925--1406038 Score: 87
Period size: 18 Copynumber: 6.6 Consensus size: 17
1405915 GAAACAGGCC
1405925 AGAAAAAAGAGAGAAGAAA
1 AGAAAAAA-AGAGAA-AAA
1405944 A-AAGAAAAA-AGAAAAA
1 AGAA-AAAAAGAGAAAAA
* *
1405960 A-AAGAAAA-A-AAAAG
1 AGAAAAAAAGAGAAAAA
1405974 AGAAAAAAAG-GAAAAA
1 AGAAAAAAAGAGAAAAA
1405990 AGAGGAAAAAAGAGGAAAAA
1 AGA--AAAAAAGA-GAAAAA
1406010 AGGAAAAAAAGAGAAAAA
1 A-GAAAAAAAGAGAAAAA
*
1406028 TGAAAGAAAAG
1 AGAAA-AAAAG
1406039 TTAAATTTGT
Statistics
Matches: 80, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.06
15 11 0.14
16 13 0.16
17 8 0.10
18 21 0.26
19 13 0.16
20 7 0.09
21 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (17 bp):
AGAAAAAAAGAGAAAAA
Found at i:1406357 original size:13 final size:13
Alignment explanation
Indices: 1406339--1406363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1406329 TAATTGTCAT
1406339 TATTAAATATGAG
1 TATTAAATATGAG
1406352 TATTAAATATGA
1 TATTAAATATGA
1406364 AAGATAAATT
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:0.12, T:0.40
Consensus pattern (13 bp):
TATTAAATATGAG
Found at i:1411309 original size:2 final size:2
Alignment explanation
Indices: 1411298--1411330 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1411288 CATCACAAAA
1411298 AT AT -T 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
1411331 CCTTCTCCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1411923 original size:2 final size:2
Alignment explanation
Indices: 1411916--1411944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1411906 TAAGTTTAGA
1411916 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 A
1411945 GTTTTGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1425094 original size:14 final size:14
Alignment explanation
Indices: 1425075--1425110 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1425065 ACTAGATCAC
1425075 TCTCCCACTAAGCT
1 TCTCCCACTAAGCT
1425089 TCTCCCACTAAGCT
1 TCTCCCACTAAGCT
*
1425103 TCTTCCAC
1 TCTCCCAC
1425111 GAAAACTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (14 bp):
TCTCCCACTAAGCT
Found at i:1433423 original size:16 final size:17
Alignment explanation
Indices: 1433399--1433431 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1433389 AATTGGAATT
1433399 TAAAATAAA-TAAAAGG
1 TAAAATAAATTAAAAGG
*
1433415 TAAATTAAATTAAAAGG
1 TAAAATAAATTAAAAGG
1433432 CAGAGGGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
TAAAATAAATTAAAAGG
Found at i:1433764 original size:19 final size:19
Alignment explanation
Indices: 1433739--1433847 Score: 164
Period size: 19 Copynumber: 5.7 Consensus size: 19
1433729 TCATATATTA
1433739 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
* **
1433758 GAAGATTATATATCATATC
1 TAAGATTGCATATCATATC
*
1433777 TAAGATTACATATCATATC
1 TAAGATTGCATATCATATC
*
1433796 TAAGATTGCATATCATATT
1 TAAGATTGCATATCATATC
*
1433815 TAGGATTGCATATCATATC
1 TAAGATTGCATATCATATC
1433834 TAAGATTGCATATC
1 TAAGATTGCATATC
1433848 CTCAAAAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:1434282 original size:182 final size:183
Alignment explanation
Indices: 1433975--1434339 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 183
1433965 TTTCATCAAT
1433975 AACTAAATATCATCAAGTATGATAACAAAGAAAAAGCCCTATTTTTGCTCAAATGGCCAAATGCC
1 AACTAAATATCATCAAGTATGATAACAAAGAAAAAGCCCTATTTTTGCTCAAATGGCCAAATGCC
1434040 AATTTTTTAATGGTAGAATGTCATTTTAAACTTTTGTAATGACCATATGGTCCTTTTTATTTAAA
66 AATTTTTTAATGGTAGAATGTCATTTTAAACTTTTGTAATGACCATATGGTCCTTTTTATTTAAA
1434105 CTATAGAAGTAGTTGTTTTTATAGGGAAAAAAACTTATATAT-TATATATATA
131 CTATAGAAGTAGTTGTTTTTATAGGGAAAAAAACTTATATATATATATATATA
1434157 AACTAAATATCATCAAGTATGATAACAAAGAAAAAGCCCTATTTTTGCTCAAATGGCCAAATGCC
1 AACTAAATATCATCAAGTATGATAACAAAGAAAAAGCCCTATTTTTGCTCAAATGGCCAAATGCC
1434222 AATTTTTTAATGGTAGAATGTCATTTTAAACTTTTGTAATGACCATATGGTCCTTTTTATTTAAA
66 AATTTTTTAATGGTAGAATGTCATTTTAAACTTTTGTAATGACCATATGGTCCTTTTTATTTAAA
1434287 CTATAGAAGTAGTTGTTTTTATAGGGAAAAAAACTTATATATATATATATATA
131 CTATAGAAGTAGTTGTTTTTATAGGGAAAAAAACTTATATATATATATATATA
1434340 TATGTAAACT
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 172 0.95
183 10 0.05
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37
Consensus pattern (183 bp):
AACTAAATATCATCAAGTATGATAACAAAGAAAAAGCCCTATTTTTGCTCAAATGGCCAAATGCC
AATTTTTTAATGGTAGAATGTCATTTTAAACTTTTGTAATGACCATATGGTCCTTTTTATTTAAA
CTATAGAAGTAGTTGTTTTTATAGGGAAAAAAACTTATATATATATATATATA
Found at i:1440815 original size:20 final size:21
Alignment explanation
Indices: 1440790--1440835 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
1440780 TTTTCAAAGC
1440790 TTTCATATGAGTTT-AATCAA
1 TTTCATATGAGTTTAAATCAA
1440810 TTTCATATGAGTTTAAATCAA
1 TTTCATATGAGTTTAAATCAA
1440831 TTTCA
1 TTTCA
1440836 ATGGGGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTCATATGAGTTTAAATCAA
Found at i:1440920 original size:27 final size:27
Alignment explanation
Indices: 1440882--1440942 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1440872 AAAAATAACT
1440882 AAAATATTATAACTTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
*
1440909 AAAATATTATAATTTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
1440936 AAAATAT
1 AAAATAT
1440943 ATCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATTATAACTTTTTTTATTTACC
Found at i:1441050 original size:27 final size:27
Alignment explanation
Indices: 1441012--1441076 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1441002 ATTGGCGGTT
*
1441012 TGGTGCCAAAGAGATTGGCGGCACCAA
1 TGGTGCCAAAGAGATTGGCAGCACCAA
*
1441039 TGGTGCCAAAGAGATTGGCAGCGCCAA
1 TGGTGCCAAAGAGATTGGCAGCACCAA
* *
1441066 TTGTGTCAAAG
1 TGGTGCCAAAG
1441077 GACTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.18
Consensus pattern (27 bp):
TGGTGCCAAAGAGATTGGCAGCACCAA
Found at i:1448017 original size:22 final size:21
Alignment explanation
Indices: 1447992--1448061 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
1447982 AATTACATAG
1447992 AATTTTACTCTTAATAAACATT
1 AATTTTA-TCTTAATAAACATT
*
1448014 AATTTTAAT-GTATATCAAACTATT
1 AATTTT-ATCTTA-AT-AAAC-ATT
1448038 --TTTTATCTTAATAAACATT
1 AATTTTATCTTAATAAACATT
*
1448057 CATTT
1 AATTT
1448062 AATAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 9 0.23
22 15 0.38
23 5 0.13
24 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (21 bp):
AATTTTATCTTAATAAACATT
Found at i:1448724 original size:14 final size:14
Alignment explanation
Indices: 1448705--1448743 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1448695 TATCGTGTAA
1448705 AATAGAATTCAAAT
1 AATAGAATTCAAAT
1448719 AATAGAATTCAAAT
1 AATAGAATTCAAAT
1448733 AATAGAATTCA
1 AATAGAATTCA
1448744 TTATAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (14 bp):
AATAGAATTCAAAT
Found at i:1449600 original size:11 final size:11
Alignment explanation
Indices: 1449584--1449610 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1449574 CCTGTATGCA
1449584 TAGTACAAGAT
1 TAGTACAAGAT
1449595 TAGTACAAGAT
1 TAGTACAAGAT
1449606 TAGTA
1 TAGTA
1449611 TATTTAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (11 bp):
TAGTACAAGAT
Found at i:1453218 original size:51 final size:52
Alignment explanation
Indices: 1453158--1453259 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
1453148 CTAATGCATA
* * * *
1453158 CTTTAGCTTTGCAGCAAT-TT-TTTGTTTCAAAACGAGTGATGTAGGATAAGG
1 CTTTAGCTTTGCA-AAATGTTGTGTGTTTCAAAACAAGTGATGTAAGATAAGG
1453209 CTTTAGCTTTGCAAAATGTTGTGTGTTTCAAAACAAGTGATGTAAGATAAG
1 CTTTAGCTTTGCAAAATGTTGTGTGTTTCAAAACAAGTGATGTAAGATAAG
1453260 TAAGGAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 3 0.07
51 15 0.33
52 27 0.60
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (52 bp):
CTTTAGCTTTGCAAAATGTTGTGTGTTTCAAAACAAGTGATGTAAGATAAGG
Found at i:1453986 original size:6 final size:6
Alignment explanation
Indices: 1453966--1453996 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1453956 TTTATCAATC
1453966 TCTGAT TCATGAT TCTGAT TCTGAT TCTGAT
1 TCTGAT TC-TGAT TCTGAT TCTGAT TCTGAT
1453997 ATGCTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
TCTGAT
Found at i:1455457 original size:20 final size:20
Alignment explanation
Indices: 1455432--1455478 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1455422 CATCCAAACA
1455432 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
1455452 CTAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCATTTT
*
1455472 CCAGAAA
1 CTAGAAA
1455479 TCATTTTCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
CTAGAAAAGTAAATCATTTT
Found at i:1455498 original size:14 final size:14
Alignment explanation
Indices: 1455462--1455499 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1455452 CTAGAAAAGT
*
1455462 AAATCATTTTCCAG
1 AAATCATTTTCCAA
1455476 AAATCATTTTCCGAA
1 AAATCATTTTCC-AA
1455491 AAAT-ATTTT
1 AAATCATTTT
1455500 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:1456320 original size:9 final size:9
Alignment explanation
Indices: 1456306--1456333 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1456296 TTTTGTTACA
1456306 ACAATTAAT
1 ACAATTAAT
1456315 ACAATTAAT
1 ACAATTAAT
1456324 ACAATTAAT
1 ACAATTAAT
1456333 A
1 A
1456334 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:1456355 original size:68 final size:66
Alignment explanation
Indices: 1456276--1456413 Score: 240
Period size: 68 Copynumber: 2.1 Consensus size: 66
1456266 TCAAGTTTGT
*
1456276 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1456341 AAA
64 AAA
1456344 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
1456409 T
66 A
1456410 TTTA
1 TTTA
1456414 TTAACAATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 23 0.34
67 1 0.01
68 44 0.65
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:1456427 original size:16 final size:16
Alignment explanation
Indices: 1456406--1456447 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1456396 AATAATTTGA
*
1456406 TAATTTTATTAACAAT
1 TAATTTTAATAACAAT
1456422 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
1456438 TAGTTTTAAT
1 TAATTTTAAT
1456448 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:1462670 original size:23 final size:23
Alignment explanation
Indices: 1462627--1462670 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1462617 GAAATTAAAT
* *
1462627 TGTAATTTTTATAATAGTAAAAC
1 TGTAATTTTTAAAAGAGTAAAAC
*
1462650 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAGTAAA
1462671 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAGTAAAAC
Found at i:1471853 original size:9 final size:9
Alignment explanation
Indices: 1471839--1471878 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1471829 TTTGGTTAAA
1471839 AATTAACCG
1 AATTAACCG
1471848 AATTAACCG
1 AATTAACCG
1471857 AATT-ACCTG
1 AATTAACC-G
*
1471866 AATTACCCG
1 AATTAACCG
1471875 AATT
1 AATT
1471879 GAATAACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 3 0.11
9 23 0.82
10 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:1473911 original size:17 final size:17
Alignment explanation
Indices: 1473875--1473907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1473865 AGACTGTGTG
*
1473875 ATTTAAATATTTTAAAT
1 ATTTAAATATTATAAAT
1473892 ATTTAAAT-TTATAAAT
1 ATTTAAATATTATAAAT
1473908 TATTGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAAATATTATAAAT
Found at i:1474513 original size:16 final size:16
Alignment explanation
Indices: 1474492--1474522 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1474482 TTTTGTTAAA
1474492 AATAATTAATTATATT
1 AATAATTAATTATATT
*
1474508 AATAATTTATTATAT
1 AATAATTAATTATAT
1474523 GACTAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATTAATTATATT
Found at i:1475621 original size:21 final size:22
Alignment explanation
Indices: 1475578--1475622 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1475568 CAAATGGCCA
* *
1475578 AATGCCATTTTTTTAATGGTAG
1 AATGCCATTTTTTAAATGATAG
*
1475600 AATGCCA-TTTTTAAATTATAG
1 AATGCCATTTTTTAAATGATAG
1475621 AA
1 AA
1475623 GTAGTTGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
AATGCCATTTTTTAAATGATAG
Found at i:1487781 original size:142 final size:143
Alignment explanation
Indices: 1487623--1487908 Score: 538
Period size: 142 Copynumber: 2.0 Consensus size: 143
1487613 TTATATAAAA
**
1487623 ATAATAATATAAAAAAATTTAATACAGGCGAGCAAGACTCAAGTTTTAATTTTTCTATCTAGGTT
1 ATAATAATATAAAAAAATTTAATACAGGCGAGCAAGACTCAAGTTTTAACATTTCTATCTAGGTT
1487688 AACTTGAGCAAAATTTTAAGTTCATTTTTCAAGTTGAACCTAGATCTAAAAAATAGGTCTAAA-T
66 AACTTGAGCAAAATTTTAAGTTCATTTTTCAAGTTGAACCTAGATCTAAAAAATAGGTCTAAATT
1487752 TTTTCGGTCCGAC
131 TTTTCGGTCCGAC
1487765 ATAATAATATAAAAAAATTTAATACAGGCGAGCAAGACTCAAGTTTTAACATTTCTATCTAGGTT
1 ATAATAATATAAAAAAATTTAATACAGGCGAGCAAGACTCAAGTTTTAACATTTCTATCTAGGTT
1487830 AACTTGAGCAAAATTTTAAGTTCATTTTTCAAGTTGAACCTAGATCTAAAAAATAGGTCTAAATT
66 AACTTGAGCAAAATTTTAAGTTCATTTTTCAAGTTGAACCTAGATCTAAAAAATAGGTCTAAA-T
1487895 TTTTTCGGTCCGAC
130 TTTTTCGGTCCGAC
1487909 GGCCATGATC
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
142 126 0.90
144 14 0.10
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (143 bp):
ATAATAATATAAAAAAATTTAATACAGGCGAGCAAGACTCAAGTTTTAACATTTCTATCTAGGTT
AACTTGAGCAAAATTTTAAGTTCATTTTTCAAGTTGAACCTAGATCTAAAAAATAGGTCTAAATT
TTTTCGGTCCGAC
Found at i:1488590 original size:17 final size:17
Alignment explanation
Indices: 1488541--1488592 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1488531 TTTTTTTTTG
*
1488541 TAAATTTTCATAAATCTC
1 TAAATTTTCATAAA-ATC
* * *
1488559 TAAAATTTAAAAAAATC
1 TAAATTTTCATAAAATC
1488576 TAAATTTTCATAAAATC
1 TAAATTTTCATAAAATC
1488593 AGTATCCTAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTTCATAAAATC
Found at i:1490687 original size:51 final size:50
Alignment explanation
Indices: 1490611--1490788 Score: 163
Period size: 51 Copynumber: 3.6 Consensus size: 50
1490601 ACTAGACCTG
1490611 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCTC-TA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTA-AAATCTTATTTC-CGTA
* * *
1490662 AAGTTTCAGTGGAGCAGATTGAAGCTACAAG------TCTTATTTCCGTA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTAAAATCTTATTTCCGTA
* * * * * *
1490706 AAGTTGAAGTGGAACAAATTAAAGATACAAGTTATAAATCTTATCTCCTTG
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTA-AAATCTTATTTCCGTA
* * * *
1490757 AAGTTACAGTGGAGCAGATTGAAGTTACAAGT
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGT
1490789 CTTATCTCCC
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 36 0.36
51 64 0.63
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (50 bp):
AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTAAAATCTTATTTCCGTA
Found at i:1490708 original size:44 final size:43
Alignment explanation
Indices: 1490643--1490830 Score: 142
Period size: 44 Copynumber: 4.1 Consensus size: 43
1490633 AGCTACAAGT
* * *
1490643 TACAAATCTTATTTCTCTAAAGTTTCAGTGGAGCAGATTGAAGC
1 TACAAGTCTTATCTC-CTAAAGTTGCAGTGGAGCAGATTGAAGC
* * * * * *
1490687 TACAAGTCTTATTTCCGTAAAGTTGAAGTGGAACAAATTAAAGA
1 TACAAGTCTTATCTCC-TAAAGTTGCAGTGGAGCAGATTGAAGC
* * *
1490731 TACAAGTTATAAATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGT
1 TACAAG-------TCTTATCTCC-TAAAGTTGCAGTGGAGCAGATTGAAGC
* * *
1490782 TACAAGTCTTATCTCCCTAAAGTAGCAGTGGAGTAGATTGAAAC
1 TACAAGTCTTATCT-CCTAAAGTTGCAGTGGAGCAGATTGAAGC
1490826 TACAA
1 TACAA
1490831 TTCCTATACC
Statistics
Matches: 113, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.01
44 75 0.66
45 2 0.02
51 35 0.31
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (43 bp):
TACAAGTCTTATCTCCTAAAGTTGCAGTGGAGCAGATTGAAGC
Found at i:1490830 original size:95 final size:95
Alignment explanation
Indices: 1490611--1490830 Score: 291
Period size: 95 Copynumber: 2.3 Consensus size: 95
1490601 ACTAGACCTG
* *
1490611 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTTCTCTAAAGTTTCAGTGGAG
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTCCTCTAAAGTTACAGTGGAG
* *
1490676 CAGATTGAAGCTACAAGTCTTATTTCCGTA
66 CAGATTGAAGCTACAAGTCTTATCTCCCTA
* * * * *
1490706 AAGTTGAAGTGGAACAAATTAAAGATACAAGTTATAAATCTTATCTCCT-TGAAGTTACAGTGGA
1 AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTAT-TCCTCTAAAGTTACAGTGGA
*
1490770 GCAGATTGAAGTTACAAGTCTTATCTCCCTA
65 GCAGATTGAAGCTACAAGTCTTATCTCCCTA
* **
1490801 AAGTAGCAGTGGAGTAGATTGAAA-CTACAA
1 AAGTTGCAGTGGAACAGATT-AAAGCTACAA
1490831 TTCCTATACC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 101 0.94
96 6 0.06
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (95 bp):
AAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATTCCTCTAAAGTTACAGTGGAG
CAGATTGAAGCTACAAGTCTTATCTCCCTA
Found at i:1491377 original size:26 final size:26
Alignment explanation
Indices: 1491347--1491410 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
1491337 AACTTTTGAA
*
1491347 AAATTTAGTTATACCTTTAA-TTTTTT
1 AAATTTA-TTATACCTTCAATTTTTTT
* *
1491373 AAATTTAATTAAATCTTCAATTTTTTT
1 AAATTT-ATTATACCTTCAATTTTTTT
1491400 AAATTTATTAT
1 AAATTTATTAT
1491411 TGAACATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (26 bp):
AAATTTATTATACCTTCAATTTTTTT
Found at i:1491502 original size:17 final size:17
Alignment explanation
Indices: 1491453--1491504 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1491443 TTTTTTTTTG
*
1491453 TAAATTTTCATAAATCTC
1 TAAATTTTCATAAA-ATC
* * *
1491471 TAAAATTTAAAAAAATC
1 TAAATTTTCATAAAATC
1491488 TAAATTTTCATAAAATC
1 TAAATTTTCATAAAATC
1491505 AGTATCCTAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTTCATAAAATC
Found at i:1492629 original size:30 final size:31
Alignment explanation
Indices: 1492595--1492678 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 31
1492585 CCAATATCTC
*
1492595 GATACTCATATCTTTGACTTTCCAAAT-TTT
1 GATACCCATATCTTTGACTTTCCAAATATTT
* *
1492625 GATACCCATATCTTTGACTTT-CTATTATTT
1 GATACCCATATCTTTGACTTTCCAAATATTT
1492655 GATACCCATATCTTTGACTTTCCA
1 GATACCCATATCTTTGACTTTCCA
1492679 TAAATATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
29 3 0.06
30 44 0.92
31 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (31 bp):
GATACCCATATCTTTGACTTTCCAAATATTT
Found at i:1492640 original size:15 final size:15
Alignment explanation
Indices: 1492595--1492671 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
1492585 CCAATATCTC
*
1492595 GATACTCATATCTTT
1 GATACCCATATCTTT
** *
1492610 GACTTTCCAAAT-TTT
1 GA-TACCCATATCTTT
1492625 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
1492640 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
1492655 GATACCCATATCTTT
1 GATACCCATATCTTT
1492670 GA
1 GA
1492672 CTTTCCATAA
Statistics
Matches: 43, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
14 10 0.23
15 24 0.56
16 9 0.21
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:1494822 original size:22 final size:24
Alignment explanation
Indices: 1494794--1494837 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1494784 TATGGCAAGA
1494794 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
1494816 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
1494838 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:1496155 original size:2 final size:2
Alignment explanation
Indices: 1496150--1496202 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1496140 TATATATATA
1496150 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1496192 TG TG TG TG TG T
1 TG TG TG TG TG T
1496203 TTTGGGCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.