Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_pilon, whole genome shotgun sequence
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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 19
Found at i:1281718 original size:38 final size:37
Alignment explanation
Indices: 1281652--1281728 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 37
1281642 GTTCATATGA
* * *
1281652 TTATATTATGTTCTAGTAAGATAGGTTGTAATTAGAGT
1 TTATATTATGTTCTAGTAAGACAAGTTGTAA-CAGAGT
* * *
1281690 TTATATTTTGTTCTATTCAGACAAGTTGTAACAGAGT
1 TTATATTATGTTCTAGTAAGACAAGTTGTAACAGAGT
1281727 TT
1 TT
1281729 GAATACTGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (37 bp):
TTATATTATGTTCTAGTAAGACAAGTTGTAACAGAGT
Found at i:1290555 original size:2 final size:2
Alignment explanation
Indices: 1290548--1290572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1290538 ATAATATCAC
1290548 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1290573 ATCATCAAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1297557 original size:22 final size:22
Alignment explanation
Indices: 1297532--1297584 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1297522 GTTAAACATA
1297532 GGGGAATCGATACCCCCTTGGG
1 GGGGAATCGATACCCCCTTGGG
1297554 GGGGAATCGATACCCCCTTGGG
1 GGGGAATCGATACCCCCTTGGG
*
1297576 AGGGAATCG
1 GGGGAATCG
1297585 GTTCCCTCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.25, G:0.38, T:0.17
Consensus pattern (22 bp):
GGGGAATCGATACCCCCTTGGG
Found at i:1300305 original size:23 final size:22
Alignment explanation
Indices: 1300280--1300383 Score: 120
Period size: 22 Copynumber: 4.7 Consensus size: 22
1300270 GAACCCCAGG
*
1300280 GGGGGTATCGGTTCCCCTACAA
1 GGGGGTATCGGTTCCCCTTCAA
* *
1300302 -GGGGAATCCGTTCCCCTTCAAA
1 GGGGGTATCGGTTCCCCTTC-AA
* *
1300324 GGGGGAATCGGTTCCCCTTTAA
1 GGGGGTATCGGTTCCCCTTCAA
* *
1300346 GGGGGTATCGATTCCCCTTTAA
1 GGGGGTATCGGTTCCCCTTCAA
*
1300368 GGGGGTATCGATTCCC
1 GGGGGTATCGGTTCCC
1300384 TCTGCACTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
21 16 0.22
22 40 0.55
23 17 0.23
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGGTTCCCCTTCAA
Found at i:1302251 original size:59 final size:59
Alignment explanation
Indices: 1302184--1302297 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
1302174 AGTTGTTACC
1302184 CCTTTGGATGGATCACCTATAATCTCACCATCCTTGACATAGTTGTATTCCCTTGAAGT
1 CCTTTGGATGGATCACCTATAATCTCACCATCCTTGACATAGTTGTATTCCCTTGAAGT
*
1302243 CCTTTGGATGGATCACCTATAATCTCACCATCCTTGATATAGTTGTATTCCCTTG
1 CCTTTGGATGGATCACCTATAATCTCACCATCCTTGACATAGTTGTATTCCCTTG
1302298 GGTAAGAGAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (59 bp):
CCTTTGGATGGATCACCTATAATCTCACCATCCTTGACATAGTTGTATTCCCTTGAAGT
Found at i:1307051 original size:14 final size:14
Alignment explanation
Indices: 1307028--1307060 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1307018 ATGACCAGTG
*
1307028 TGCTGTCATCTGCT
1 TGCTGCCATCTGCT
1307042 TGCTGCCATCTGCT
1 TGCTGCCATCTGCT
1307056 TGCTG
1 TGCTG
1307061 TCATGTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.24, T:0.39
Consensus pattern (14 bp):
TGCTGCCATCTGCT
Found at i:1307223 original size:21 final size:23
Alignment explanation
Indices: 1307190--1307232 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1307180 TAATTCAACA
1307190 AAACAAAAG-AAAAT-AAAAAAC
1 AAACAAAAGAAAAATGAAAAAAC
1307211 AAAC-AAAGTAAAAATGAAAAAA
1 AAACAAAAG-AAAAATGAAAAAA
1307233 AAAATGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 5 0.26
23 6 0.32
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (23 bp):
AAACAAAAGAAAAATGAAAAAAC
Found at i:1312322 original size:40 final size:39
Alignment explanation
Indices: 1312278--1312364 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
1312268 GCAAAGTTGA
* *
1312278 CATCTTTGGTTGGTGGCTAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACA-TGGAAAATT
* * *
1312318 CATCTTTGGTAGGTGGCCAACTTGTGCACATGGGAATTT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATGGAAAATT
1312357 CATCTTTG
1 CATCTTTG
1312365 ATCCCTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (39 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATGGAAAATT
Found at i:1313378 original size:21 final size:21
Alignment explanation
Indices: 1313332--1313379 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1313322 TTCCAATCGT
*
1313332 TTGTAACTCTTGTAATTACAC
1 TTGTAAATCTTGTAATTACAC
* * *
1313353 ATGTAAATGTTGTAATTACTC
1 TTGTAAATCTTGTAATTACAC
1313374 TTGTAA
1 TTGTAA
1313380 CTGGCACAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TTGTAAATCTTGTAATTACAC
Found at i:1315373 original size:22 final size:23
Alignment explanation
Indices: 1315327--1315386 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
1315317 TAAAGTATTA
1315327 ATTATTAAATATATTTCAAATATAT
1 ATTATT-AATAT-TTTCAAATATAT
1315352 -TTATTAATATTTTCAACA-ATAT
1 ATTATTAATATTTTCAA-ATATAT
*
1315374 AATATT-ATATTTT
1 ATTATTAATATTTT
1315387 TATATTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 17 0.53
23 10 0.31
24 5 0.16
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATTAATATTTTCAAATATAT
Found at i:1315434 original size:23 final size:23
Alignment explanation
Indices: 1315386--1315441 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
1315376 TATTATATTT
*
1315386 TTATATTATAATAATATAACCAA
1 TTATATTATAATAATATAACAAA
*
1315409 TTATATTTTAATAATATAA-AATA
1 TTATATTATAATAATATAACAA-A
1315432 TTATATTATA
1 TTATATTATA
1315442 TTTTAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATATTATAATAATATAACAAA
Found at i:1315440 original size:28 final size:28
Alignment explanation
Indices: 1315369--1315481 Score: 113
Period size: 28 Copynumber: 3.9 Consensus size: 28
1315359 TATTTTCAAC
* *
1315369 AATATAATATTATATTTTTATATTATAA
1 AATATAATATTATATTTTAATAATATAA
*
1315397 TAATATAACCAATTATATTTTAATAATATAA
1 -AATATAA--TATTATATTTTAATAATATAA
* *
1315428 AATATTATATTATATTTTAATAATATAT
1 AATATAATATTATATTTTAATAATATAA
*
1315456 AATA-AATTATTA-ATACTTAATAATAT
1 AATATAA-TATTATAT-TTTAATAATAT
1315482 TATTTATGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
27 3 0.04
28 38 0.53
29 7 0.10
30 6 0.08
31 18 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
AATATAATATTATATTTTAATAATATAA
Found at i:1330052 original size:13 final size:13
Alignment explanation
Indices: 1330034--1330082 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
1330024 CTTAGCATGT
1330034 TTAAAAAGAAAAC
1 TTAAAAAGAAAAC
*
1330047 TT-AAAA-TAAAC
1 TTAAAAAGAAAAC
1330058 -TAAAAACGAAAAC
1 TTAAAAA-GAAAAC
1330071 TTAAAAAGAAAA
1 TTAAAAAGAAAA
1330083 GAAATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 8 0.27
12 4 0.13
13 11 0.37
14 6 0.20
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.16
Consensus pattern (13 bp):
TTAAAAAGAAAAC
Found at i:1330321 original size:23 final size:25
Alignment explanation
Indices: 1330291--1330377 Score: 70
Period size: 27 Copynumber: 3.4 Consensus size: 25
1330281 GCTCGTCCAC
1330291 CTTCTAGAAA-G-CGCTGACTAGAT
1 CTTCTAGAAACGTCGCTGACTAGAT
* *
1330314 CTTCTAGAAAACTGTTGCTGACTGGAT
1 CTTCTAG-AAAC-GTCGCTGACTAGAT
* * * *
1330341 CTTCTAGAAAACTGTTGCTGATTGGAC
1 CTTCTAG-AAAC-GTCGCTGACTAGAT
1330368 CTTCTAGAAA
1 CTTCTAGAAA
1330378 TTGCTACGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
23 7 0.12
24 3 0.05
26 4 0.07
27 42 0.75
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (25 bp):
CTTCTAGAAACGTCGCTGACTAGAT
Found at i:1330341 original size:27 final size:27
Alignment explanation
Indices: 1330303--1330377 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
1330293 TCTAGAAAGC
*
1330303 GCTGACTAGATCTTCTAGAAAACTGTT
1 GCTGACTGGATCTTCTAGAAAACTGTT
1330330 GCTGACTGGATCTTCTAGAAAACTGTT
1 GCTGACTGGATCTTCTAGAAAACTGTT
* *
1330357 GCTGATTGGACCTTCTAGAAA
1 GCTGACTGGATCTTCTAGAAA
1330378 TTGCTACGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (27 bp):
GCTGACTGGATCTTCTAGAAAACTGTT
Found at i:1330413 original size:17 final size:18
Alignment explanation
Indices: 1330387--1330430 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1330377 ATTGCTACGT
1330387 CAGA-TCGTGT-CATGCC
1 CAGAGTCGTGTCCATGCC
*
1330403 CAGAGTCGTGTCCATGTC
1 CAGAGTCGTGTCCATGCC
*
1330421 TAGAGTCGTG
1 CAGAGTCGTG
1330431 ACCAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 14 0.58
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (18 bp):
CAGAGTCGTGTCCATGCC
Found at i:1331977 original size:2 final size:2
Alignment explanation
Indices: 1331970--1332004 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1331960 ATCCAAACAA
1331970 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 A
1332005 GCTTATCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1337088 original size:24 final size:24
Alignment explanation
Indices: 1337061--1337110 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1337051 TTGGAAATAG
*
1337061 GGTTAGTGATTTCAATTAAAGGGA
1 GGTTAGGGATTTCAATTAAAGGGA
* *
1337085 GGTTAGGGATTTTAATTAAGGGGA
1 GGTTAGGGATTTCAATTAAAGGGA
1337109 GG
1 GG
1337111 GGTGCTGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.32
Consensus pattern (24 bp):
GGTTAGGGATTTCAATTAAAGGGA
Found at i:1337154 original size:10 final size:10
Alignment explanation
Indices: 1337139--1337169 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1337129 GGAAGTCACG
1337139 CCAACAGCAC
1 CCAACAGCAC
1337149 CCAACAGCAC
1 CCAACAGCAC
1337159 CCAACAGCAC
1 CCAACAGCAC
1337169 C
1 C
1337170 AGCAAGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.52, G:0.10, T:0.00
Consensus pattern (10 bp):
CCAACAGCAC
Found at i:1337498 original size:154 final size:154
Alignment explanation
Indices: 1337218--1337531 Score: 601
Period size: 154 Copynumber: 2.0 Consensus size: 154
1337208 ATGTAAATGG
1337218 TTGGTACAATGTAAATGTATAAGCAATGTTCTAGGTAGGGCAAAAGGCATGAAATGAATGAATGA
1 TTGGTACAATGTAAATGTATAAGCAATGTTCTAGGTAGGGCAAAAGGCATGAAATGAATGAATGA
* *
1337283 AAACTTCTTCTTGTAATCTCTCTTATTTCTTCTTCTAAAACCTATTTTTTCTTCGATATTTCTTC
66 AAACTTCTTCCTGTAATCTCTCTTATTTCTTCTTCTAAAACCTATTTCTTCTTCGATATTTCTTC
1337348 TCTACTAAATCCAATCCATAACAA
131 TCTACTAAATCCAATCCATAACAA
1337372 TTGGTACAATGTAAATGTATAAGCAATGTTCTAGGTAGGGCAAAAGGCATGAAATGAATGAATGA
1 TTGGTACAATGTAAATGTATAAGCAATGTTCTAGGTAGGGCAAAAGGCATGAAATGAATGAATGA
1337437 AAACTTCTTCCTGTAATCTCTCTTATTTCTTCTTCTAAAACCTATTTCTTCTTCGATATTTCTTC
66 AAACTTCTTCCTGTAATCTCTCTTATTTCTTCTTCTAAAACCTATTTCTTCTTCGATATTTCTTC
*
1337502 TCTACTAAATCCAGTCCATAACAA
131 TCTACTAAATCCAATCCATAACAA
1337526 TTGGTA
1 TTGGTA
1337532 ATCAGAGCCA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 157 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (154 bp):
TTGGTACAATGTAAATGTATAAGCAATGTTCTAGGTAGGGCAAAAGGCATGAAATGAATGAATGA
AAACTTCTTCCTGTAATCTCTCTTATTTCTTCTTCTAAAACCTATTTCTTCTTCGATATTTCTTC
TCTACTAAATCCAATCCATAACAA
Found at i:1340529 original size:24 final size:24
Alignment explanation
Indices: 1340502--1340547 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1340492 GGAAATAGGA
1340502 TTAGAGATTTTAATTAAAGGGAGG
1 TTAGAGATTTTAATTAAAGGGAGG
* *
1340526 TTAGGGATTTTAATTAAGGGGA
1 TTAGAGATTTTAATTAAAGGGA
1340548 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (24 bp):
TTAGAGATTTTAATTAAAGGGAGG
Found at i:1342378 original size:17 final size:16
Alignment explanation
Indices: 1342356--1342395 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1342346 TAAAGAAAAT
1342356 ATTTAAAATATATGATA
1 ATTTAAAATA-ATGATA
*
1342373 ATTTAAAATAATTATA
1 ATTTAAAATAATGATA
1342389 ATATTAA
1 AT-TTAA
1342396 GATTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTAAAATAATGATA
Found at i:1343681 original size:28 final size:30
Alignment explanation
Indices: 1343654--1343708 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1343644 CCGAAATCAT
*
1343654 TCAAAA-AATA-A-TTTATACACTTATTCA
1 TCAAAACAATATAGTTTAAACACTTATTCA
*
1343681 TGAAAACAATATAGTTTAAACACTTATT
1 TCAAAACAATATAGTTTAAACACTTATT
1343709 TTATAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 4 0.17
29 1 0.04
30 13 0.57
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (30 bp):
TCAAAACAATATAGTTTAAACACTTATTCA
Found at i:1343827 original size:9 final size:9
Alignment explanation
Indices: 1343813--1343841 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1343803 ACCTAGGTTC
1343813 CCTCATTTT
1 CCTCATTTT
1343822 CCTCATTTT
1 CCTCATTTT
1343831 CCTCATTTT
1 CCTCATTTT
1343840 CC
1 CC
1343842 ATACAGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.38, G:0.00, T:0.52
Consensus pattern (9 bp):
CCTCATTTT
Found at i:1348277 original size:23 final size:23
Alignment explanation
Indices: 1348251--1348302 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1348241 ACCAAAAGGA
*
1348251 AGAGAAAAACGTGCCACAAAGCC
1 AGAGAAAAACGTGCCACAAAGAC
* * * *
1348274 AGAGATAAATGTGTCATAAAGAC
1 AGAGAAAAACGTGCCACAAAGAC
1348297 AGAGAA
1 AGAGAA
1348303 CGTGTCACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.12
Consensus pattern (23 bp):
AGAGAAAAACGTGCCACAAAGAC
Found at i:1348745 original size:29 final size:29
Alignment explanation
Indices: 1348713--1348777 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
1348703 TGTCATGCAT
1348713 CATTTCTTCAAATATTA-TCGATCAAGCAC
1 CATTTCTTCAAATATTACT-GATCAAGCAC
*
1348742 CATTTCTTCAAATATTACTGATCTAGCAC
1 CATTTCTTCAAATATTACTGATCAAGCAC
*
1348771 CCTTTCT
1 CATTTCT
1348778 GACAGAGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (29 bp):
CATTTCTTCAAATATTACTGATCAAGCAC
Found at i:1354632 original size:20 final size:21
Alignment explanation
Indices: 1354599--1354640 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1354589 TTTATAATCA
1354599 TGTCTTTATGACACATTTTTT
1 TGTCTTTATGACACATTTTTT
*
1354620 TGTCTTT-TGACACGTTTTTT
1 TGTCTTTATGACACATTTTTT
1354640 T
1 T
1354641 AGTTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (21 bp):
TGTCTTTATGACACATTTTTT
Found at i:1355196 original size:19 final size:18
Alignment explanation
Indices: 1355157--1355198 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1355147 ATAGAATATA
**
1355157 AAATTTTAAATAATATTT
1 AAATTTTAAATAATAAAT
1355175 AAATTTTAATATAATAAAT
1 AAATTTTAA-ATAATAAAT
1355194 AAATT
1 AAATT
1355199 GGATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTTAAATAATAAAT
Found at i:1356599 original size:2 final size:2
Alignment explanation
Indices: 1356592--1356627 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1356582 TGCTCCACGC
1356592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1356628 AAGTGTGAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1358234 original size:29 final size:30
Alignment explanation
Indices: 1358188--1358255 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
1358178 TTTAAATAGT
* *
1358188 TATTATATTTTATATTAATATATTATGTAAA
1 TATTAT-TTTTATATTAAAATATTATATAAA
* *
1358219 TATTATTTTT-TATTAAAATATTTTATAAT
1 TATTATTTTTATATTAAAATATTATATAAA
1358248 TATTATTT
1 TATTATTT
1358256 AATTAGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 23 0.70
30 4 0.12
31 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTATTTTTATATTAAAATATTATATAAA
Found at i:1359994 original size:21 final size:21
Alignment explanation
Indices: 1359964--1360010 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1359954 GCAGGGGTAC
*
1359964 ATGCCCAGCCCTCCACTTCAT
1 ATGCCCAGCCCACCACTTCAT
* * *
1359985 ATGCCGAGCCCACCAGTTTAT
1 ATGCCCAGCCCACCACTTCAT
1360006 ATGCC
1 ATGCC
1360011 ATCTCCGCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.23
Consensus pattern (21 bp):
ATGCCCAGCCCACCACTTCAT
Found at i:1360045 original size:21 final size:20
Alignment explanation
Indices: 1360019--1360086 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 20
1360009 CCATCTCCGC
*
1360019 AGGGTTACATTCCGAGCCCG
1 AGGGTTACATTCCTAGCCCG
1360039 TAGGGTTACATTCCTAGCCCG
1 -AGGGTTACATTCCTAGCCCG
** *
1360060 CCGGTTACATGCCTAGCCCG
1 AGGGTTACATTCCTAGCCCG
1360080 CAGGGTT
1 -AGGGTT
1360087 TTATACCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.24
Consensus pattern (20 bp):
AGGGTTACATTCCTAGCCCG
Found at i:1360067 original size:20 final size:20
Alignment explanation
Indices: 1360021--1360080 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1360011 ATCTCCGCAG
* **
1360021 GGTTACATTCCGAGCCCGTAG
1 GGTTACATTCCTAGCCCG-CC
1360042 GGTTACATTCCTAGCCCGCC
1 GGTTACATTCCTAGCCCGCC
*
1360062 GGTTACATGCCTAGCCCGC
1 GGTTACATTCCTAGCCCGC
1360081 AGGGTTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (20 bp):
GGTTACATTCCTAGCCCGCC
Found at i:1360656 original size:33 final size:34
Alignment explanation
Indices: 1360618--1360686 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
1360608 ATATTATTCG
*
1360618 AAATTTAAAATA-AAAAAATAATTTTCGAAATTT
1 AAATTTAAAATATAAAAAATAATATTCGAAATTT
** *
1360651 AAATTTAAAATATAAATTATAGTATTCGAAATTT
1 AAATTTAAAATATAAAAAATAATATTCGAAATTT
1360685 AA
1 AA
1360687 CATTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (34 bp):
AAATTTAAAATATAAAAAATAATATTCGAAATTT
Found at i:1361474 original size:72 final size:75
Alignment explanation
Indices: 1361383--1361521 Score: 241
Period size: 75 Copynumber: 1.9 Consensus size: 75
1361373 ATAATAGGGC
1361383 ATGATAACATATCTCTGACAAAATAA-GGAAGGCGCG-CCCC-GGAACGCGCCTTCATGTGAATA
1 ATGATAACATATCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
1361445 GTGAAATGCA
66 GTGAAATGCA
1361455 ATGATAACATAT-TCTTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT
1 ATGATAACATATCTC-TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT
1361519 AGT
65 AGT
1361522 ACTCCGATTA
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
71 2 0.03
72 23 0.37
73 10 0.16
74 4 0.06
75 24 0.38
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (75 bp):
ATGATAACATATCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
GTGAAATGCA
Found at i:1361602 original size:8 final size:8
Alignment explanation
Indices: 1361589--1361629 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1361579 TCACAAGCTT
1361589 TCAAATTC
1 TCAAATTC
1361597 TCAAATTC
1 TCAAATTC
* *
1361605 CCAAACTC
1 TCAAATTC
1361613 T-AAATTC
1 TCAAATTC
1361620 TCAAATTC
1 TCAAATTC
1361628 TC
1 TC
1361630 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1367259 original size:25 final size:24
Alignment explanation
Indices: 1367231--1367281 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1367221 ACGGACGCAG
1367231 AAGTATGCCCACAA-TGGCAGAGAAA
1 AAGTATG-CCACAAGT-GCAGAGAAA
*
1367256 AAGTGTGCCACAAGTGCAGAGAAA
1 AAGTATGCCACAAGTGCAGAGAAA
1367280 AA
1 AA
1367282 CGTGTCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (24 bp):
AAGTATGCCACAAGTGCAGAGAAA
Found at i:1367286 original size:25 final size:24
Alignment explanation
Indices: 1367239--1367314 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
1367229 AGAAGTATGC
1367239 CCACAATGGCAGAGAAAAAGTGTG
1 CCACAATGGCAGAGAAAAAGTGTG
1367263 CCACAA-GTGCAGAGAAAAACGTGT-
1 CCACAATG-GCAGAGAAAAA-GTGTG
* *
1367287 -CACAAAGACAGAG-AAAAGTGTG
1 CCACAATGGCAGAGAAAAAGTGTG
*
1367309 TCACAA
1 CCACAA
1367315 GGACAAAGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 16 0.35
24 18 0.39
25 4 0.09
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (24 bp):
CCACAATGGCAGAGAAAAAGTGTG
Found at i:1367319 original size:23 final size:22
Alignment explanation
Indices: 1367240--1367316 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 22
1367230 GAAGTATGCC
*
1367240 CACAATGGCAGAGAAAAAGTGTGC
1 CACAA-GGCAGAG-AAAAGTGTGT
**
1367264 CACAAGTGCAGAGAAAAACGTGT
1 CACAAG-GCAGAGAAAAGTGTGT
*
1367287 CACAAAGACAGAGAAAAGTGTGT
1 CAC-AAGGCAGAGAAAAGTGTGT
1367310 CACAAGG
1 CACAAGG
1367317 ACAAAGATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
22 3 0.07
23 27 0.61
24 14 0.32
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (22 bp):
CACAAGGCAGAGAAAAGTGTGT
Found at i:1368485 original size:133 final size:131
Alignment explanation
Indices: 1368248--1368512 Score: 471
Period size: 133 Copynumber: 2.0 Consensus size: 131
1368238 TAATTGAATG
1368248 ACAACAATGTTATTGTTATTCATTGATATCAAAATAACTATCAAATCTATATTTAAATTTTCAAA
1 ACAACAATGTTATTGTTATTCATTGA-ATCAAAATAACTATCAAATCTATATTTAAATTTTCAAA
1368313 TAGATATTTAAATTTTTTTTGATTTATTATGTGTTTAATGTTACAAACGTTATCTATTTAAGTGT
65 TAGATATTTAAATTTTTTTTGATTTATTATGTGTTTAATGTTACAAACGTTATCTATTTAAGTGT
1368378 TT
130 TT
1368380 ACAACAATTGTTATTGTTATTCATTG-ATCAAAATAACTATCAAATCTATA-TTAAATTTTCAAA
1 ACAACAA-TGTTATTGTTATTCATTGAATCAAAATAACTATCAAATCTATATTTAAATTTTCAAA
1368443 TAGATATTTAAATTATTTTTTTGATTTATTTATGTGTTTAATGTTACAAACGTTATCTATTTAAG
65 TAGATATTTAAA-T-TTTTTTTGATTTA-TTATGTGTTTAATGTTACAAACGTTATCTATTTAAG
1368508 TGTTT
127 TGTTT
1368513 GGGCCGTCAA
Statistics
Matches: 129, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
130 25 0.19
131 25 0.19
132 20 0.16
133 59 0.46
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (131 bp):
ACAACAATGTTATTGTTATTCATTGAATCAAAATAACTATCAAATCTATATTTAAATTTTCAAAT
AGATATTTAAATTTTTTTTGATTTATTATGTGTTTAATGTTACAAACGTTATCTATTTAAGTGTT
T
Found at i:1374258 original size:2 final size:2
Alignment explanation
Indices: 1374251--1374306 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1374241 GTTTGAGCAT
1374251 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
1374293 TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
1374307 CTCCACACCT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1384181 original size:2 final size:2
Alignment explanation
Indices: 1384174--1384209 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1384164 AATTCTAATA
*
1384174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1384210 CTAACTTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1386787 original size:21 final size:21
Alignment explanation
Indices: 1386758--1386810 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1386748 ATTCTGACTA
*
1386758 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
1386779 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
*
1386800 TCGCGATGCGA
1 TCGCGTTGCGA
1386811 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:1386876 original size:60 final size:59
Alignment explanation
Indices: 1386779--1387054 Score: 217
Period size: 61 Copynumber: 4.6 Consensus size: 59
1386769 TTTCCCAAAT
* * * * *
1386779 TCGCGTTGCGATTTTCCTAATTCGCGATGCGAATACGTAAATCGCGATGCGATTACGTAAA
1 TCGCATTGCGATTTACGTAA-TCGCGATGCGATTACGTAAATCGCGATGCGAATACGT-AA
*
1386840 TCGCGA-TGCGA-TTACGTAAATCGCGATGCGATTACGTAAATCGCGATGTGAATACGTAA
1 TCGC-ATTGCGATTTACGT-AATCGCGATGCGATTACGTAAATCGCGATGCGAATACGTAA
* * * *
1386899 TCGCATTGCGATTTACGTAATCGC-ATTGCGATTTTCCTAATTCGC-ATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAATCGCGA-TGCGA-TTACGTAAATCGCGA-TGCGA-ATACGTAA
* * * * *
1386960 TCGCATTGCGATTTTCCTAATTCGC-ATTGCGATTTACGT-AATCGC-ATTGCGATTTTCCTAA
1 TCGCATTGCGATTTACGTAA-TCGCGA-TGCGA-TTACGTAAATCGCGA-TGCGA-ATACGTAA
*
1387021 TTCGCATTGCGATTTACATAATCGC-ATTGCGATT
1 -TCGCATTGCGATTTACGTAATCGCGA-TGCGATT
1387055 TTCCTAATTC
Statistics
Matches: 185, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
58 2 0.01
59 23 0.12
60 60 0.32
61 66 0.36
62 34 0.18
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (59 bp):
TCGCATTGCGATTTACGTAATCGCGATGCGATTACGTAAATCGCGATGCGAATACGTAA
Found at i:1386932 original size:20 final size:20
Alignment explanation
Indices: 1386757--1387055 Score: 258
Period size: 20 Copynumber: 14.8 Consensus size: 20
1386747 GATTCTGACT
* **
1386757 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
1386777 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACGTA
*
1386798 ATTCGCGA-TGCGA-ATACGTAA
1 A-TCGC-ATTGCGATTTACGT-A
1386819 ATCGCGA-TGCGA-TTACGTAA
1 ATCGC-ATTGCGATTTACGT-A
1386839 ATCGCGA-TGCGA-TTACGTAA
1 ATCGC-ATTGCGATTTACGT-A
1386859 ATCGCGA-TGCGA-TTACGTAA
1 ATCGC-ATTGCGATTTACGT-A
* *
1386879 ATCGCGA-TGTGA-ATACGTA
1 ATCGC-ATTGCGATTTACGTA
1386898 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* *
1386918 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
1386938 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
1386959 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
1386979 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
1387000 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
*
1387020 ATTCGCATTGCGATTTACATA
1 A-TCGCATTGCGATTTACGTA
1387041 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
1387056 TCCTAATTCG
Statistics
Matches: 247, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
18 1 0.00
19 10 0.04
20 153 0.62
21 83 0.34
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:1387087 original size:41 final size:41
Alignment explanation
Indices: 1386899--1387067 Score: 329
Period size: 41 Copynumber: 4.1 Consensus size: 41
1386889 GAATACGTAA
1386899 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1386940 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1386981 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
*
1387022 TCGCATTGCGATTTACATAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1387063 TCGCA
1 TCGCA
1387068 ACGAGATTCT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:1387105 original size:82 final size:82
Alignment explanation
Indices: 1386908--1387108 Score: 246
Period size: 82 Copynumber: 2.5 Consensus size: 82
1386898 ATCGCATTGC
* * * * *
1386908 GATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATT
1 GATTTACGTAATCGCAATACGAATTTCCAAATTCGCATTGCGATTTACATAATCGCATTGCGATT
** *
1386973 TTCCTAATTCGCATTGC
66 TTCCTAATTCGCAACGA
* * * *
1386990 GATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACATAATCGCATTGCGATT
1 GATTTACGTAATCGCAATACGAATTTCCAAATTCGCATTGCGATTTACATAATCGCATTGCGATT
1387055 TTCCTAATTCGCAACGA
66 TTCCTAATTCGCAACGA
1387072 GATTCTGAC-T-ATCGCAATACTGAATTT-CAAATTCGCA
1 GATT-T-ACGTAATCGCAATAC-GAATTTCCAAATTCGCA
1387109 ACTCGATTTC
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
82 99 0.92
83 7 0.06
84 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (82 bp):
GATTTACGTAATCGCAATACGAATTTCCAAATTCGCATTGCGATTTACATAATCGCATTGCGATT
TTCCTAATTCGCAACGA
Found at i:1387937 original size:24 final size:24
Alignment explanation
Indices: 1387910--1387963 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1387900 GTATTCGAAA
1387910 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1387934 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1387958 TTTGAT
1 TTTGAT
1387964 GATTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1390515 original size:19 final size:19
Alignment explanation
Indices: 1390473--1390551 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
1390463 CTTAATGTCT
* **
1390473 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
1390493 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1390512 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1390526 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1390545 ATCGCAA
1 ATCGCAA
1390552 CGAGGGAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 24 0.51
20 8 0.17
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1390530 original size:33 final size:33
Alignment explanation
Indices: 1390493--1390586 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1390483 GGAAATGACT
*
1390493 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1390526 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1390559 ATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1390587 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1390589 original size:19 final size:18
Alignment explanation
Indices: 1390473--1390590 Score: 63
Period size: 19 Copynumber: 6.7 Consensus size: 18
1390463 CTTAATGTCT
**
1390473 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
*
1390493 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1390512 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
1390526 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
1390545 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
1390559 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
1390578 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
1390591 TTTAGTTTCG
Statistics
Matches: 74, Mismatches: 13, Indels: 23
0.67 0.12 0.21
Matches are distributed among these distances:
14 16 0.22
15 4 0.05
16 4 0.05
17 3 0.04
18 4 0.05
19 35 0.47
20 8 0.11
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1390618 original size:14 final size:14
Alignment explanation
Indices: 1390601--1390640 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1390591 TTTAGTTTCG
*
1390601 CGTTGCGATTTTGT
1 CGTTGCGATTTTAT
*
1390615 CGTTGCGATTCTAT
1 CGTTGCGATTTTAT
1390629 CGTTGCGATTTT
1 CGTTGCGATTTT
1390641 CATTTCGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:1390795 original size:14 final size:14
Alignment explanation
Indices: 1390762--1390797 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1390752 CATCAATTAA
1390762 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1390776 AC-AATCATCTTTT
1 ACAAATCAACTTTT
1390789 ACAAATCAA
1 ACAAATCAA
1390798 TTAACAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1392212 original size:42 final size:41
Alignment explanation
Indices: 1392127--1392249 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1392117 GTGAATCGGG
* * * *
1392127 CTCTTGAATGGTGGGA-GGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1392169 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1392211 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1392250 CGAGTTAAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1392695 original size:90 final size:88
Alignment explanation
Indices: 1392552--1392773 Score: 311
Period size: 91 Copynumber: 2.4 Consensus size: 88
1392542 CAAACTTGCA
* * * *
1392552 ACACAATTTAGCAGAATTAGCAGTAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAG
1 ACACAGTTTAGC--AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAG
1392616 ACAAATACTAACTTCACAGTGTTAAGAAT
63 ACAAATACTAACTTCACAGTGTT---AAT
*
1392645 ACACAGTTTAGCAATTGGCAGCAACCTAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACA
1 ACACAGTTTAGCAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACA
1392710 AATACTAACTTCACAGTGTTAAT
66 AATACTAACTTCACAGTGTTAAT
*
1392733 AAACAGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
1 ACACAGTTTAGCA--ATTGGCAGCAACCGAATAAATTTACT
1392774 AAGCAATCTA
Statistics
Matches: 119, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
88 15 0.13
90 44 0.37
91 49 0.41
93 11 0.09
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (88 bp):
ACACAGTTTAGCAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACA
AATACTAACTTCACAGTGTTAAT
Found at i:1394544 original size:19 final size:19
Alignment explanation
Indices: 1394455--1394586 Score: 157
Period size: 19 Copynumber: 7.1 Consensus size: 19
1394445 TCTTTTGGTT
*
1394455 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1394474 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1394494 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1394512 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1394528 GAAATGAAAATCTCAACGC
1 GAAATGAAAATCGCAACGC
1394547 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1394566 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1394585 GA
1 GA
1394587 TAGTCATTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 52 0.54
20 28 0.29
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1408971 original size:28 final size:28
Alignment explanation
Indices: 1408938--1409016 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
1408928 TTCGAATCAG
* * *
1408938 ATCATGCCATATGTCACTAATATCAAAT
1 ATCATGACACATGTCACTAATACCAAAT
*
1408966 ATCATGACACGTGTCACTAATACCAAAT
1 ATCATGACACATGTCACTAATACCAAAT
* *
1408994 ATCATAACACGTGTCACTAATAC
1 ATCATGACACATGTCACTAATAC
1409017 TTAATTTAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (28 bp):
ATCATGACACATGTCACTAATACCAAAT
Found at i:1411535 original size:11 final size:10
Alignment explanation
Indices: 1411519--1411584 Score: 64
Period size: 11 Copynumber: 6.4 Consensus size: 10
1411509 ACGACAAAGA
1411519 AAAATAATAAT
1 AAAATAA-AAT
*
1411530 AAAAT-AAGT
1 AAAATAAAAT
1411539 AAAAATAAAAAT
1 -AAAAT-AAAAT
*
1411551 AAAATAAAAAC
1 AAAAT-AAAAT
1411562 AAAATAAAAT
1 AAAATAAAAT
1411572 -AAATAAAAT
1 AAAATAAAAT
1411581 AAAA
1 AAAA
1411585 ACAAAACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 11 0.23
10 13 0.28
11 20 0.43
12 3 0.06
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1411543 original size:21 final size:20
Alignment explanation
Indices: 1411518--1411697 Score: 91
Period size: 21 Copynumber: 8.4 Consensus size: 20
1411508 AACGACAAAG
**
1411518 AAAAATAATAATAAAATAAGT
1 AAAAATAA-AATAAAATAAAA
1411539 AAAAATAAAAATAAAATAAAA
1 AAAAAT-AAAATAAAATAAAA
1411560 ACAAAATAAAAT-AAATAAAA
1 A-AAAATAAAATAAAATAAAA
* *
1411580 TAAAAACAAAACAAAA-AAACA
1 -AAAAATAAAATAAAATAAA-A
1411601 AAACCAA-AAAA-AGAAATAAAA
1 AAA--AATAAAATA-AAATAAAA
*
1411622 TAAAAATAAAAGAAAA-AATGGAA
1 -AAAAATAAAATAAAATAA---AA
* * *
1411645 TTAAATAGAAAATAAAACAGAAA
1 --AAAAATAAAATAAAATA-AAA
*
1411668 CAAAAATAAAAATAAAACAAAA
1 -AAAAAT-AAAATAAAATAAAA
1411690 AAAAATAA
1 AAAAATAA
1411698 TAAACGAAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 39
0.73 0.06 0.22
Matches are distributed among these distances:
20 29 0.22
21 48 0.37
22 23 0.18
23 15 0.12
24 13 0.10
25 1 0.01
26 1 0.01
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAATAAAATAAAATAAAA
Found at i:1411547 original size:6 final size:6
Alignment explanation
Indices: 1411518--1411701 Score: 78
Period size: 6 Copynumber: 29.5 Consensus size: 6
1411508 AACGACAAAG
* *
1411518 AAAAAT AATAAT AAAATAAGT AAAAAT AAAAAT -AAAAT AAAAA- CAAAAT
1 AAAAAT AAAAAT -AAA-AA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * * **
1411567 AAAATAA ATAAAAT AAAAAC AAAACAA AAAAAC AAAACC AAAAA- AAGAAAT
1 AAAA-AT A-AAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AA-AAAT
*
1411618 -AAAAT AAAAAT AAAAGA- AAAAAT GGAATTAAAT AGAAAAT -AAAAC
1 AAAAAT AAAAAT AAAA-AT AAAAAT --AA--AAAT A-AAAAT AAAAAT
* *
1411663 AGAAAC AAAAAT AAAAAT AAAACA- AAAAA- AAATAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAA-AAT AAA
1411702 CGAAAAATAA
Statistics
Matches: 141, Mismatches: 15, Indels: 43
0.71 0.08 0.22
Matches are distributed among these distances:
5 24 0.17
6 78 0.55
7 22 0.16
8 11 0.08
9 2 0.01
10 4 0.03
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:1411577 original size:4 final size:5
Alignment explanation
Indices: 1411519--1411584 Score: 64
Period size: 5 Copynumber: 12.8 Consensus size: 5
1411509 ACGACAAAGA
* *
1411519 AAAAT AATAAT AAAAT -AAGT AAAAAT AAAAAT AAAAT AAAAAC AAAAT
1 AAAAT AA-AAT AAAAT AAAAT -AAAAT -AAAAT AAAAT -AAAAT AAAAT
1411567 AAAAT -AAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
1411585 ACAAAACAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 7 0.13
5 27 0.52
6 18 0.35
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1411581 original size:25 final size:25
Alignment explanation
Indices: 1411547--1411625 Score: 97
Period size: 25 Copynumber: 3.1 Consensus size: 25
1411537 GTAAAAATAA
1411547 AAATAAAATAAAAACAAAATAAAAT
1 AAATAAAATAAAAACAAAATAAAAT
*
1411572 AAATAAAATAAAAACAAAACAAAA-
1 AAATAAAATAAAAACAAAATAAAAT
* * *
1411596 AAACAAAACCAAAAAAAGAAATAAAAT
1 AAATAAAA-TAAAAACA-AAATAAAAT
1411623 AAA
1 AAA
1411626 AATAAAAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 7 0.15
25 29 0.63
26 7 0.15
27 3 0.07
ACGTcount: A:0.81, C:0.08, G:0.01, T:0.10
Consensus pattern (25 bp):
AAATAAAATAAAAACAAAATAAAAT
Found at i:1411598 original size:14 final size:14
Alignment explanation
Indices: 1411557--1411639 Score: 55
Period size: 15 Copynumber: 5.8 Consensus size: 14
1411547 AAATAAAATA
*
1411557 AAAACAAAATAAAAT
1 AAAACAAAA-AAAAC
1411572 AAATA-AAATAAAAAC
1 AAA-ACAAA-AAAAAC
1411587 AAAAC-AAAAAAAC
1 AAAACAAAAAAAAC
* *
1411600 AAAACCAAAAAAAG
1 AAAACAAAAAAAAC
*
1411614 AAATA-AAATAAAAAT
1 AAA-ACAAA-AAAAAC
*
1411629 AAAAGAAAAAA
1 AAAACAAAAAA
1411640 TGGAATTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
13 11 0.19
14 19 0.33
15 25 0.44
16 2 0.04
ACGTcount: A:0.82, C:0.07, G:0.02, T:0.08
Consensus pattern (14 bp):
AAAACAAAAAAAAC
Found at i:1411599 original size:13 final size:14
Alignment explanation
Indices: 1411581--1411612 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1411571 TAAATAAAAT
1411581 AAAAACAAAA-CAA
1 AAAAACAAAACCAA
1411594 AAAAACAAAACCAA
1 AAAAACAAAACCAA
1411608 AAAAA
1 AAAAA
1411613 GAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAACCAA
Found at i:1411618 original size:42 final size:43
Alignment explanation
Indices: 1411557--1411639 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
1411547 AAATAAAATA
*
1411557 AAAACAAAATAAAATAAATAAAATAAAAACAAAACAAAAAAAC
1 AAAACAAAATAAAAGAAATAAAATAAAAACAAAACAAAAAAAC
* * *
1411600 AAAACCAAA-AAAAGAAATAAAATAAAAATAAAAGAAAAAA
1 AAAACAAAATAAAAGAAATAAAATAAAAACAAAACAAAAAA
1411640 TGGAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.82, C:0.07, G:0.02, T:0.08
Consensus pattern (43 bp):
AAAACAAAATAAAAGAAATAAAATAAAAACAAAACAAAAAAAC
Found at i:1411708 original size:18 final size:17
Alignment explanation
Indices: 1411545--1411701 Score: 75
Period size: 17 Copynumber: 8.8 Consensus size: 17
1411535 AAGTAAAAAT
*
1411545 AAAAATAAAATAAAAACA
1 AAAAAAAAAAT-AAAACA
*
1411563 AAATAAAATAAATAAAATA
1 AAA-AAAA-AAATAAAACA
*
1411582 AAAACAAAACAAAAAAACA
1 AAAA-AAAA-AATAAAACA
* *
1411601 AAACCAAAAAAA-GAAA-T
1 AAA--AAAAAAATAAAACA
* *
1411618 AAAATAAAAATAAAAGA
1 AAAAAAAAAATAAAACA
*** * *
1411635 AAAAATGGAATTAAATA
1 AAAAAAAAAATAAAACA
* * *
1411652 GAAAATAAAACAGAAACA
1 AAAAAAAAAATA-AAACA
*
1411670 AAAATAAAAATAAAACA
1 AAAAAAAAAATAAAACA
1411687 AAAAAAAATAATAAA
1 AAAAAAAA-AATAAA
1411702 CGAAAAATAA
Statistics
Matches: 103, Mismatches: 26, Indels: 20
0.69 0.17 0.13
Matches are distributed among these distances:
15 6 0.06
16 3 0.03
17 33 0.32
18 26 0.25
19 26 0.25
20 8 0.08
21 1 0.01
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAATAAAACA
Found at i:1411725 original size:29 final size:28
Alignment explanation
Indices: 1411675--1411730 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1411665 AAACAAAAAT
1411675 AAAAATAAAACAAAAAAAAATAATAAACG
1 AAAAATAAAACAAAAAAAAAT-ATAAACG
**
1411704 AAAAATAATAA-AAAAATTAATATAAAC
1 AAAAATAA-AACAAAAAAAAATATAAAC
1411731 ATATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 16 0.67
30 2 0.08
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (28 bp):
AAAAATAAAACAAAAAAAAATATAAACG
Found at i:1411939 original size:18 final size:17
Alignment explanation
Indices: 1411916--1411968 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
1411906 TTGTAGGTAT
1411916 ATAATATAATATTAAATA
1 ATAATATAA-ATTAAATA
* *
1411934 ATAATAAAAATAAAATAA
1 ATAATATAAATTAAAT-A
*
1411952 AAAATATAAA-TAAATA
1 ATAATATAAATTAAATA
1411968 A
1 A
1411969 ATAAAAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 2 0.07
17 10 0.34
18 17 0.59
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAATATAAATTAAATA
Found at i:1411952 original size:21 final size:19
Alignment explanation
Indices: 1411928--1411974 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1411918 AATATAATAT
1411928 TAAATAATAATAAAAATAAA
1 TAAATAA-AATAAAAATAAA
*
1411948 -ATAA-AAAATATAAATAAA
1 TA-AATAAAATAAAAATAAA
1411966 TAAATAAAA
1 TAAATAAAA
1411975 AAGAGTAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
18 13 0.57
19 8 0.35
20 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAATAAAATAAAAATAAA
Found at i:1412034 original size:2 final size:2
Alignment explanation
Indices: 1412027--1412059 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1412017 AATAAAAATA
*
1412027 AT AT AT AT AT AT AT AT AA 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 A
1412060 CACGTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1412143 original size:5 final size:5
Alignment explanation
Indices: 1412135--1412159 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1412125 ATTAAAACAA
1412135 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1412160 GAACAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1412197 original size:25 final size:23
Alignment explanation
Indices: 1412138--1412202 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
1412128 AAAACAAAAA
* *
1412138 ATAAAATAAAATAAAATAAAATG
1 ATAAAATAAAAGAAAATAAAAGG
1412161 A-ACAAATAAAAAGAATAATAAAAGG
1 ATA-AAAT-AAAAGAA-AATAAAAGG
*
1412186 ATTAAAATAAAATAAAA
1 A-TAAAATAAAAGAAAA
1412203 AATAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 1 0.03
23 5 0.15
24 8 0.24
25 15 0.44
26 4 0.12
27 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (23 bp):
ATAAAATAAAAGAAAATAAAAGG
Found at i:1414006 original size:84 final size:83
Alignment explanation
Indices: 1413919--1414736 Score: 827
Period size: 84 Copynumber: 9.8 Consensus size: 83
1413909 ATTTTCCTCT
* * * * * *
1413919 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAGCCTTTCTCA-ATTTAAGCTAT
1 GAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCT-AGACTTAAGTTAT
* *
1413983 GCTGCAAAGGATGTGCCTTT
64 GCTGCAAATGATGTGCCTTC
* * * * * **
1414003 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACATATAACCCTCCTAGCCTTGGGTTATGC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
1414068 TGTAAATGATGTGCCCTC
66 TGCAAATGATGTGCCTTC
* * * * * * * *
1414086 GAAGCTGAGTGTAATCAAACCCGAGGGTC--T-TTGGTAGATAGCCCTTCTCGACTTAAGCTATG
1 G-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
1414148 CTGCAAATTATGTGCCTTG
65 CTGCAAATGATGTGCCTTC
* * * * *
1414167 GAGCTGAGCATAGTCGAACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * *
1414232 TTGTAAATGATATGCCTTG
65 CTGCAAATGATGTGCCTTC
* *
1414251 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAG-CATTGAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGAC-TTAAGTTATG
* *
1414315 CTGCAAATGATGTACCCTC
65 CTGCAAATGATGTGCCTTC
* * *
1414334 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTAT
1 G-AGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* *
1414399 GTTGCAAATGATGTGCCTTT
64 GCTGCAAATGATGTGCCTTC
* * * * * *
1414419 GAGCTGAGCGTAGTCGAGCTCGAAGGTCTTTATTGGCAGATAACCATTCTAGCCTTGAGTTATGC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
1414484 TGCAAATGATTTGCCCTC
66 TGCAAATGATGTGCCTTC
* * * * * *
1414502 GAAGCTGAGTGTAATCAAACTCGAAGGGCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 G-AGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
*
1414567 GCTGCAAATGATGTGCCTTT
64 GCTGCAAATGATGTGCCTTC
* * * * *
1414587 GAGCTGAGCATAGTCGAACTTCGAAGGTCTTTGTTGGTATATAACCCTTCTAGCCTTAAGTTATG
1 GAGCTGAGCGTAATCGAAC-TCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * * *
1414652 ATGTAAATAATATGCCCTC
65 CTGCAAATGATGTGCCTTC
* * * *
1414671 GAAGTTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTAT
1 G-AGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTAT
1414736 G
64 G
1414737 GTACCAATAG
Statistics
Matches: 597, Mismatches: 122, Indels: 29
0.80 0.16 0.04
Matches are distributed among these distances:
80 20 0.03
81 38 0.06
82 4 0.01
83 127 0.21
84 265 0.44
85 142 0.24
86 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (83 bp):
GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATGTGCCTTC
Found at i:1414383 original size:168 final size:168
Alignment explanation
Indices: 1413870--1414736 Score: 917
Period size: 168 Copynumber: 5.2 Consensus size: 168
1413860 AATTTATTGA
* * * * * * *
1413870 CAGATAGCCCTTCTTGCTTTGAGCTATGCTGTAAATGTAATTTTCCTCT-GAGCTGAGTGTAATC
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATG--ATGTGCCT-TGGAGCTGAGCGTAGTC
* * * *
1413934 GAACTCGAAGGTCTTTTGTTGGTAGATAGCCTTTCT--CAATTTAAGCTATGCTGCAAAGGATGT
63 GAACTCGAAGGTC-TTTGTTGGTAGATAACCCTTCTAGC-A-TTAAGTTATGCTGCAAATGATGT
* * * *
1413997 GCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGA
125 GCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
* * * * * * * * *
1414039 CATATAACCCTCCTAGCCTTGGGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* * * * * *
1414104 ACCCGAGGGTC--T-TTGGTAGATAGCCCTTCTCG-ACTTAAGCTATGCTGCAAATTATGTG-CC
65 ACTCGAAGGTCTTTGTTGGTAGATAACCCTTCTAGCA-TTAAGTTATGCTGCAAATGATGTGCCC
* * * * *
1414164 TTGGAGCTGAGCATAGTCGAACTCGAATGTCTTTGGTTGG
129 TCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
* * *
1414204 CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1414269 CTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTGCAAATGATGTACCCTC
66 CTCGAAGGTCTTTGTTGGTAGATAACCCTTCTAGCATTAAGTTATGCTGCAAATGATGTGCCCTC
*
1414334 GAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGG
131 GAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
* * * * * * *
1414372 CAGATAACCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAG
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
1414437 CTCGAAGGTCTTTATTGGCAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGATTTGCCCTC
66 CTCGAAGGTCTTTGTTGGTAGATAACCCTTCTAGCATTAAGTTATGCTGCAAATGATGTGCCCTC
* * *
1414502 GAAGCTGAGTGTAATCAAACTCGAAGGGCTTTGGTTGG
131 GAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
* * * * * * *
1414540 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
1414605 CTTCGAAGGTCTTTGTTGGTATATAACCCTTCTAGCCTTAAGTTATGATGTAAATAATATGCCCT
66 C-TCGAAGGTCTTTGTTGGTAGATAACCCTTCTAGCATTAAGTTATGCTGCAAATGATGTGCCCT
*
1414670 CGAAGTTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
130 CGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
* *
1414709 CAGATAACCCTTCTTGCCTTGAGTTATG
1 CAGATAACCCTTCTAGCCTTGAGCTATG
1414737 GTACCAATAG
Statistics
Matches: 602, Mismatches: 84, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
163 4 0.01
164 94 0.16
165 42 0.07
166 1 0.00
167 40 0.07
168 279 0.46
169 142 0.24
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (168 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGTTGGTAGATAACCCTTCTAGCATTAAGTTATGCTGCAAATGATGTGCCCTC
GAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGG
Found at i:1414594 original size:252 final size:251
Alignment explanation
Indices: 1413919--1414736 Score: 880
Period size: 248 Copynumber: 3.3 Consensus size: 251
1413909 ATTTTCCTCT
* * * * * * ** * *
1413919 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGATAGCCTTTCTCA-ATTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT-AGCCTTGAGTTAT
* * * * * * * *
1413983 GCTGCAAAGGATGTGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACATATAAC
65 GCTGCAAATGATATGCC-TCGAAGCTGAGCGTAATCAAACTCGAAGGGCTTTGTTGGCAGATAAC
* * ** * * * * *
1414047 CCTCCTAGCCTTGGGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACCCGAGG
129 CCTTCTAGCATTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAG
* * * *
1414112 GTCTTTGG-T--AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATTATGTGCCTTG
194 GTCTTTGGTTGGAGATAACCCTTCTCGACTTAAGCTATGATGCAAATAATGTGCCTTC
* *
1414167 GAGCTGAGCATAGTCGAACTCGAATGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* * * * * * *
1414232 TTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCC
66 CTGCAAATGATATGCCTCGAAGCTGAGCGTAATCAAACTCGAAGGGCTTTGTTGGCAGATAACCC
* * *
1414297 TTCTAGCATTGAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAAGGT
131 TTCTAGCATTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGT
* * *
1414362 CTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTT
196 CTTTGGTTGG-AGATAACCCTTCTCGACTTAAGCTATGATGCAAATAATGTGCCTTC
* * *
1414419 GAGCTGAGCGTAGTCGAGCTCGAAGGTCTTT-ATTGGCAGATAACCATTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* * *
1414483 CTGCAAATGATTTGCCCTCGAAGCTGAGTGTAATCAAACTCGAAGGGCTTTGGTTGGCAGATAGC
66 CTGCAAATGATATG-CCTCGAAGCTGAGCGTAATCAAACTCGAAGGGCTTT-GTTGGCAGATAAC
* * * ** *
1414548 CCTTCTCG-ACTTAAGCTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCATAGTCGAACTTCGA
129 CCTTCTAGCA-TTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC-TCGA
* * * * * * *
1414611 AGGTCTTT-GTTGGTATATAACCCTTCTAGCCTTAAGTTATGATGTAAATAATATGCCCTC
192 AGGTCTTTGGTTGG-AGATAACCCTTCTCGACTTAAGCTATGATGCAAATAATGTGCCTTC
* * *
1414671 GAAGTTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTAT
1 G-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
1414736 G
65 G
1414737 GTACCAATAG
Statistics
Matches: 487, Mismatches: 71, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
247 4 0.01
248 169 0.35
249 1 0.00
251 42 0.09
252 158 0.32
253 83 0.17
254 30 0.06
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (251 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
CTGCAAATGATATGCCTCGAAGCTGAGCGTAATCAAACTCGAAGGGCTTTGTTGGCAGATAACCC
TTCTAGCATTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGT
CTTTGGTTGGAGATAACCCTTCTCGACTTAAGCTATGATGCAAATAATGTGCCTTC
Found at i:1416054 original size:95 final size:94
Alignment explanation
Indices: 1415927--1416119 Score: 316
Period size: 95 Copynumber: 2.0 Consensus size: 94
1415917 TATTGTATAG
1415927 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCAGGGAG-TTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAG-CAGGG-GCTTTAACCAAT
*
1415991 TGCTCTAGAGGGACAACTCAAGCTTTATTGT
64 TGCTCTACAGGGACAACTCAAGCTTTATTGT
* *
1416022 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCTTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCAGGGGC-TTTAACCAATT
*
1416087 GCTCTACAGGGACAATTCAAGCTTTATTGT
65 GCTCTACAGGGACAACTCAAGCTTTATTGT
1416117 ATA
1 ATA
1416120 CATAATATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
93 1 0.01
94 4 0.04
95 87 0.95
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (94 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCAGGGGCTTTAACCAATTG
CTCTACAGGGACAACTCAAGCTTTATTGT
Found at i:1420082 original size:21 final size:19
Alignment explanation
Indices: 1420051--1420162 Score: 82
Period size: 21 Copynumber: 5.5 Consensus size: 19
1420041 AAACGGAACG
1420051 ACAAAGAAAAATAATAATAAA
1 ACAAA-AAAAATAA-AATAAA
* *
1420072 ATAAGTAAAAATAAAAATAAA
1 ACAA-AAAAAAT-AAAATAAA
1420093 ACAAAAAAAATAAAATAAAA
1 ACAAAAAAAATAAAAT-AAA
** *
1420113 ACAAAACAAAACCAAA-AGA
1 ACAAAA-AAAATAAAATAAA
* *
1420132 AGAAATAAAATAAAAATAAA
1 ACAAAAAAAAT-AAAATAAA
1420152 ACAATAAAAAA
1 ACAA-AAAAAA
1420163 ATGGAATTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
18 4 0.06
19 14 0.20
20 20 0.29
21 30 0.43
22 2 0.03
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.12
Consensus pattern (19 bp):
ACAAAAAAAATAAAATAAA
Found at i:1420086 original size:6 final size:6
Alignment explanation
Indices: 1420057--1420258 Score: 60
Period size: 6 Copynumber: 32.7 Consensus size: 6
1420047 AACGACAAAG
* *
1420057 AAAAAT AATAAT AAAATAAGT AAAAAT AAAAAT AAAACA- AAAAAA ATAAAAT
1 AAAAAT AAAAAT -AAA-AA-T AAAAAT AAAAAT AAAA-AT AAAAAT A-AAAAT
* * ** *
1420109 AAAAA- CAAAAC AAAACC AAAAGA- AGAAAT -AAAAT AAAAAT AAAACAAT
1 AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT -AAA-AAT
* * * * * * *
1420157 AAAAA- AATGGAAT -TAAAT AGAAAAT -AAAAC AGAAAC AAAAAC AAAAAC
1 AAAAAT AA--AAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
1420205 AAAAAT AAAAAT AAAACAA AAAAAT AATAAAC GAAAA- AATAAT AAAAAAT
1 AAAAAT AAAAAT AAAA-AT AAAAAT AA-AAAT AAAAAT AAAAAT -AAAAAT
1420255 AAAA
1 AAAA
1420259 TTAATATATA
Statistics
Matches: 150, Mismatches: 24, Indels: 44
0.69 0.11 0.20
Matches are distributed among these distances:
5 22 0.15
6 83 0.55
7 36 0.24
8 8 0.05
9 1 0.01
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:1420099 original size:12 final size:12
Alignment explanation
Indices: 1420057--1420258 Score: 50
Period size: 11 Copynumber: 16.8 Consensus size: 12
1420047 AACGACAAAG
*
1420057 AAAAATAATAATA
1 AAAAATAA-AACA
1420070 AAATAAGTAAAA-A
1 AAA-AA-TAAAACA
1420083 TAAAAATAAAACAAA
1 -AAAAATAAAAC--A
*
1420098 AAAAATAAAA-T
1 AAAAATAAAACA
*
1420109 AAAAACAAAAC-
1 AAAAATAAAACA
** *
1420120 AAAACCAAAAGA
1 AAAAATAAAACA
* *
1420132 AGAAATAAAA-T
1 AAAAATAAAACA
1420143 AAAAATAAAAC-
1 AAAAATAAAACA
*
1420154 AATAA-AAAA-A
1 AAAAATAAAACA
*** * *
1420164 TGGAATTAAATA
1 AAAAATAAAACA
*
1420176 GAAAATAAAACA
1 AAAAATAAAACA
*
1420188 GAAACA-AAAACA
1 -AAAAATAAAACA
*
1420200 AAAACA-AAAA-T
1 AAAA-ATAAAACA
1420211 AAAAATAAAACAA
1 AAAAATAAAAC-A
1420224 AAAAATAATAAACGA
1 AAAAAT-A-AAAC-A
*
1420239 AAAAAT--AATA
1 AAAAATAAAACA
1420249 AAAAATAAAA
1 AAAAATAAAA
1420259 TTAATATATA
Statistics
Matches: 142, Mismatches: 26, Indels: 43
0.67 0.12 0.20
Matches are distributed among these distances:
10 14 0.10
11 47 0.33
12 33 0.23
13 15 0.11
14 18 0.13
15 15 0.11
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (12 bp):
AAAAATAAAACA
Found at i:1420143 original size:5 final size:5
Alignment explanation
Indices: 1420058--1420112 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
1420048 ACGACAAAGA
* *
1420058 AAAAT AATAAT AAAAT -AAGT AAAAAT AAAAAT AAAAC AAAA- AAAAT
1 AAAAT AA-AAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
1420104 AAAAT AAAA
1 AAAAT AAAA
1420113 ACAAAACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 7 0.16
5 22 0.51
6 14 0.33
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:1420258 original size:16 final size:15
Alignment explanation
Indices: 1420069--1420264 Score: 68
Period size: 16 Copynumber: 12.6 Consensus size: 15
1420059 AAATAATAAT
*
1420069 AAAATAAGTAAAAATA
1 AAAATAA-TAAAAAAA
*
1420085 AAAATAA-AACAAAA
1 AAAATAATAAAAAAA
1420099 AAAATAA-AATAAAAA
1 AAAATAATAA-AAAAA
* *
1420114 CAAAACAA-AACCAAAAG
1 -AAAATAATAA--AAAAA
* *
1420131 AAGA-AAT-AAAATA
1 AAAATAATAAAAAAA
1420144 AAAATAA-AACAATAAA
1 AAAATAATAA-AA-AAA
* * *
1420160 AAAATGGAATTAAATAG
1 AAAAT--AATAAAAAAA
1420177 AAAATAA-AACAGAAACA
1 AAAATAATAA-A-AAA-A
*
1420194 AAAACAA-AAACAAAA
1 AAAATAATAAA-AAAA
1420209 ATAAA-AATAAAACAAA
1 A-AAATAATAAAA-AAA
**
1420225 AAAATAATAAACGAA
1 AAAATAATAAAAAAA
1420240 AAAATAATAAAAAATA
1 AAAATAATAAAAAA-A
*
1420256 AAATTAATA
1 AAAATAATA
1420265 TATACGTATA
Statistics
Matches: 137, Mismatches: 24, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
13 6 0.04
14 18 0.13
15 34 0.25
16 56 0.41
17 18 0.13
18 4 0.03
19 1 0.01
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (15 bp):
AAAATAATAAAAAAA
Found at i:1420514 original size:21 final size:22
Alignment explanation
Indices: 1420479--1420530 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1420469 AATATAGTAT
*
1420479 TAAAT-AATAGTAAAAATAAAA
1 TAAATAAATAGAAAAAATAAAA
1420500 T-AATAAATAGAAAAAATAAAA
1 TAAATAAATAGAAAAAATAAAA
1420521 TAAATAAATA
1 TAAATAAATA
1420531 AATAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.11
21 17 0.61
22 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (22 bp):
TAAATAAATAGAAAAAATAAAA
Found at i:1420524 original size:26 final size:25
Alignment explanation
Indices: 1420491--1420539 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
1420481 AATAATAGTA
1420491 AAAATAAA-ATAATAAATAGAAAAAAT
1 AAAATAAATA-AATAAATA-AAAAAAT
1420517 AAAATAAATAAATAAATAAAAAA
1 AAAATAAATAAATAAATAAAAAA
1420540 GAGTAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.23
26 16 0.73
27 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAATAAATAAATAAATAAAAAAAT
Found at i:1420538 original size:18 final size:18
Alignment explanation
Indices: 1420501--1420537 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1420491 AAAATAAAAT
1420501 AATAAATAGAAAAAATAA
1 AATAAATAGAAAAAATAA
*
1420519 AATAAATA-AATAAATAA
1 AATAAATAGAAAAAATAA
1420536 AA
1 AA
1420538 AAGAGTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
AATAAATAGAAAAAATAA
Found at i:1420647 original size:2 final size:2
Alignment explanation
Indices: 1420642--1420666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1420632 CAAAAAATGA
1420642 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
1420667 ATAACGTTTA
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:1420719 original size:18 final size:19
Alignment explanation
Indices: 1420687--1420723 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1420677 AACAAAACAT
1420687 TAAAAAAAACAAAATAAAA
1 TAAAAAAAACAAAATAAAA
*
1420706 TAAAATAAAC-AAATAAAA
1 TAAAAAAAACAAAATAAAA
1420724 AGAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (19 bp):
TAAAAAAAACAAAATAAAA
Found at i:1420759 original size:2 final size:2
Alignment explanation
Indices: 1420752--1420788 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1420742 AAATAAAATA
1420752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1420789 CGTATAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1420838 original size:11 final size:11
Alignment explanation
Indices: 1420818--1420855 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1420808 AATAAAATAA
*
1420818 ATAAATAAAAC
1 ATAAAAAAAAC
1420829 ATAAAAAAAAC
1 ATAAAAAAAAC
*
1420840 ATAAAAATAA-
1 ATAAAAAAAAC
1420850 ATAAAA
1 ATAAAA
1420856 GGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (11 bp):
ATAAAAAAAAC
Found at i:1425115 original size:42 final size:42
Alignment explanation
Indices: 1424854--1425122 Score: 243
Period size: 41 Copynumber: 6.5 Consensus size: 42
1424844 CGTTTTATGA
* * * *
1424854 ATAAACGCCGGTAAATAAT-GTACTTTAGTGGCATTTTTATA-
1 ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-AC
* * * *
1424895 AAAAACGCCGCTAAATACTC-TACTTTAATGGCATTTTTATAC
1 ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-AC
* * * *
1424937 --AAACCCCGCTAACG-GTCGTATTTTAGTGGCG-TTTTAAGC
1 ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAA-C
* * **
1424976 ACAAACGACGCTAATTACAT-GTACTTTAGTGGCGTTTTTAA-
1 ATAAACGCCGCTAAAGAC-TCGTACTTTAGTGGCGTTTTTAAC
* *
1425017 ATAAACGCCGATAAATACT-GTACTTTAGTGGCGTTTTTAAC
1 ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAAC
* *
1425058 ATAAACGCAGCTAAAGACTCGTACTTTTGTGGCGTTTTTAAC
1 ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAAC
*
1425100 ATAAATGCCGCTAAAGACTCGTA
1 ATAAACGCCGCTAAAGACTCGTA
1425123 GTGGGTTTTC
Statistics
Matches: 190, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 8 0.04
40 43 0.23
41 76 0.40
42 55 0.29
43 7 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (42 bp):
ATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAAC
Found at i:1426119 original size:42 final size:39
Alignment explanation
Indices: 1426066--1426166 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 39
1426056 ACGGTCATAT
** *
1426066 TTTAGTGGCGTTTTAAGCACAAACGACGCTAATTACATGTAC
1 TTTAGTGGCGTTTTAA--ACAAACGACAATAAATAC-TGTAC
* *
1426108 TTTAGTGGCGTTTTTAAATAAACGCCAATAAATACTGTAC
1 TTTAGTGGCG-TTTTAAACAAACGACAATAAATACTGTAC
*
1426148 TTTAGTGGCGTTTTTAACA
1 TTTAGTGGCGTTTTAAACA
1426167 TAAACGCAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
39 7 0.14
40 15 0.29
41 13 0.25
42 10 0.20
43 6 0.12
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (39 bp):
TTTAGTGGCGTTTTAAACAAACGACAATAAATACTGTAC
Found at i:1426131 original size:41 final size:41
Alignment explanation
Indices: 1426066--1426212 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 41
1426056 ACGGTCATAT
* ** *
1426066 TTTAGTGGCG-TTTTAAGCACAAACGACGCTAATTACATGTAC
1 TTTAGTGGCGTTTTTAA-CATAAACGACAATAAATAC-TGTAC
*
1426108 TTTAGTGGCGTTTTTAA-ATAAACGCCAATAAATACTGTAC
1 TTTAGTGGCGTTTTTAACATAAACGACAATAAATACTGTAC
* * * *
1426148 TTTAGTGGCGTTTTTAACATAAACG-CAGCTAAAGACTCATAA
1 TTTAGTGGCGTTTTTAACATAAACGACA-ATAAATACT-GTAC
*
1426190 TTTTGTGGCGTTTTTAACATAAA
1 TTTAGTGGCGTTTTTAACATAAA
1426213 TGCCGCTAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
40 24 0.26
41 27 0.30
42 34 0.37
43 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTAACATAAACGACAATAAATACTGTAC
Found at i:1426204 original size:42 final size:42
Alignment explanation
Indices: 1426108--1426227 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
1426098 TTACATGTAC
* * * *
1426108 TTTAGTGGCGTTTTTAA-ATAAACGCCA-ATAAATACT-GTAC
1 TTTAGTGGCGTTTTTAACATAAACG-CAGCTAAAGACTCATAA
1426148 TTTAGTGGCGTTTTTAACATAAACGCAGCTAAAGACTCATAA
1 TTTAGTGGCGTTTTTAACATAAACGCAGCTAAAGACTCATAA
* * *
1426190 TTTTGTGGCGTTTTTAACATAAATGCCGCTAAAGACTC
1 TTTAGTGGCGTTTTTAACATAAACGCAGCTAAAGACTC
1426228 GTAGTGGGTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 19 0.27
41 14 0.20
42 37 0.53
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTAGTGGCGTTTTTAACATAAACGCAGCTAAAGACTCATAA
Found at i:1432031 original size:85 final size:86
Alignment explanation
Indices: 1431941--1432167 Score: 233
Period size: 86 Copynumber: 2.7 Consensus size: 86
1431931 TTTGAAATCG
* * * * * *
1431941 CTGCTATAAATCTCGACCTTTTGCGACATTTATTCCAAAAACGTCGCTATAGATCT-GATCTTTT
1 CTGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGACGCTATAGATCTAGACCTTTT
** *
1432005 GTGGCGTTTCATTCAAAAACA
66 ACGGCATTTCATTCAAAAACA
* * * * *
1432026 TTGCTATAGATCACAATCTTTTGCGGCGTTTGTTCCAAAAAC-ACAGCTATAGATATAGACCTTT
1 CTGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGAC-GCTATAGATCTAGACCTTT
** *
1432090 TACGGCATTTGTTTCAAAAATA
65 TACGGCATTTCATTCAAAAACA
* * * * *
1432112 CCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCT
1 CTGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGACGCTATAGATCT
1432168 TGACATATTG
Statistics
Matches: 112, Mismatches: 27, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
84 1 0.01
85 44 0.39
86 66 0.59
87 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (86 bp):
CTGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGACGCTATAGATCTAGACCTTTT
ACGGCATTTCATTCAAAAACA
Found at i:1432171 original size:43 final size:43
Alignment explanation
Indices: 1431883--1432171 Score: 206
Period size: 43 Copynumber: 6.8 Consensus size: 43
1431873 CTTTTGTAGA
* * * * *
1431883 GTTTGTTCTAAAAATGTCGTTATAGAT-TTGACCTTTTGCGAC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
* *** * * * * *
1431925 GTTTATTTTGAAATCGCTGCTATAAATCTCGACCTTTTGCGAC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
* * * * *
1431968 ATTTATTCCAAAAACGTCGCTATAGATC-TGATCTTTTGTGGC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
* *** *** *
1432010 GTTTCATT-CAAAAACATTGCTATAGATCACAATCTTTTGCGGC
1 GTTT-GTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
* * * * *
1432053 GTTTGTTCCAAAAACACAGCTATAGATATAGACCTTTTACGGC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
* * ** *
1432096 ATTTGTTTCAAAAATACCGCTATAGATATTGACCTTTTGCGGC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
*
1432139 GTTTGTTCCAAAAACGCCGCTATATATCTTGAC
1 GTTTGTTCCAAAAACGCCGCTATAGATCTTGAC
1432172 ATATTGCGAC
Statistics
Matches: 194, Mismatches: 49, Indels: 7
0.78 0.20 0.03
Matches are distributed among these distances:
42 51 0.26
43 143 0.74
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (43 bp):
GTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGC
Found at i:1439564 original size:18 final size:18
Alignment explanation
Indices: 1439541--1439579 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1439531 GTTGAGTAAT
*
1439541 AATAATGTAGTAGGTGTA
1 AATAATATAGTAGGTGTA
1439559 AATAATATAGTAGGTGTA
1 AATAATATAGTAGGTGTA
1439577 AAT
1 AAT
1439580 CATGAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (18 bp):
AATAATATAGTAGGTGTA
Found at i:1440225 original size:172 final size:173
Alignment explanation
Indices: 1439708--1440295 Score: 688
Period size: 182 Copynumber: 3.3 Consensus size: 173
1439698 ATTTAATTAA
* * * * * * *
1439708 GACAAAA-CTGGTAAAACGCTACCAGATATGTTGAAAGTATCGATTAGATTGAA-ATAAATATCG
1 GACAAAATC-GGTAAAGCGCTACCGGATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCG
* *
1439771 ATACTTTGGGAATTTAAAAGAGAAGCAGTAA-ATCACCTATAAAGTGTTGATA-TTATATAAAAA
63 ATACTTTGGGAATTTAAAAGAGAAGCAGTAATAACACCTATAAAGTGTCGATACTT-TATAAAAA
* *
1439834 TGTATCGATCTATAAC-AATATAACATGTAAAAATATGACAAAATGGGTCTCGAAAA
127 TGTATCGATCCATAACGAA-ATAACATGTAAAAATATGAC---A---G---CGAAAT
* *
1439890 GACAAAA-CTGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
1 GACAAAATC-GGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAT
* * * *
1439954 ACTTTGGGAA-TTAAAAGAGAAGCAGCAATAACGCCTATAAAGTATCGATACTTTATAAAAATAT
65 ACTTTGGGAATTTAAAAGAGAAGCAGTAATAACACCTATAAAGTGTCGATACTTTATAAAAATGT
* *
1440018 ATCGATCCATAACGATATAACAGGTAAAAATATGACA-CGAAAT
130 ATCGATCCATAACGAAATAACATGTAAAAATATGACAGCGAAAT
* *
1440061 GACAAAATCGGTAAAGCGTTACCGGATATATTAAAAGTGTCGATACTTTAATATAAGTATCGATA
1 GACAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGATA
*
1440126 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCACCTATAAAGTGTCGATACTTTATAAAAATGTA
66 CTTTGGGAATTTAAAAGAGAAGCAGTAATAACACCTATAAAGTGTCGATACTTTATAAAAATGTA
*
1440191 TCGGTCCATAACGAAATAACATGTAAAAATATGACAAAACCAGTCTTGAAAT
131 TCGATCCATAACGAAATAACATGTAAAAATATG-----A-CAG-C--GAAAT
*
1440243 GAAAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
1 GACAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
1440296 AGTACACGTA
Statistics
Matches: 358, Mismatches: 32, Indels: 32
0.85 0.08 0.08
Matches are distributed among these distances:
171 73 0.20
172 81 0.23
177 1 0.00
178 3 0.01
180 22 0.06
181 80 0.22
182 98 0.27
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (173 bp):
GACAAAATCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGATA
CTTTGGGAATTTAAAAGAGAAGCAGTAATAACACCTATAAAGTGTCGATACTTTATAAAAATGTA
TCGATCCATAACGAAATAACATGTAAAAATATGACAGCGAAAT
Found at i:1442303 original size:22 final size:23
Alignment explanation
Indices: 1442252--1442307 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1442242 AATGTTTTTG
* *
1442252 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
*
1442275 TAGTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
1442298 TTTTATTATA
1 TTTTATTATA
1442308 AATACAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:1445628 original size:201 final size:201
Alignment explanation
Indices: 1445017--1445989 Score: 1428
Period size: 201 Copynumber: 4.8 Consensus size: 201
1445007 GTAAACATAT
* *
1445017 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
* *
1445082 AGTAATTTTTCAATGTAACCGGTATAAATCTACCGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
*
1445147 ATCGACACTTTTTAAGTTTAAGTTTCTGTCGATACGTTTTGTCCAGAATGAATGCCCAAACTAGG
131 ATCGACACTTTTTAAGTTT--G----TGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGG
1445212 TGCACGCATAAA
190 TGCACGCATAAA
* * *
1445224 GTGTCGATACATTTACAAAAGGTATCAATCCCAAAAACGTCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
* *
1445289 GGTAATTTTTCAATGTAACCGGTATAATTCTACC-GTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * *
1445353 ATCAACAATTTTTAAGTTTGTGTCGATACTTTTTTTCCATAATGAATGCCCAAACTAGGTGCACA
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
*
1445418 AATAAA
196 CATAAA
* *
1445424 GTGTCAATACATTTACAAAAGGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
* * * *
1445489 TGTAATTTTTCAATGTAACCGGTATGAATATACCGGTTTTATTTGATAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * ** * *
1445554 ATCGACACTTTTTAATTTTGTGTCGATACTCTTCATCCAGAATGAATCCCCAAACTAGGTGCACT
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
1445619 CATAAA
196 CATAAA
** * *
1445625 GTGTCGATACATTTATGAAACGTATCGATCCCAAAAATATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
* * *
1445690 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTAAGAT-AGAATAGGTCTACATAATA
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATG-TGAGAATAGGTCTACATAATG
*
1445754 TATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCAC
130 TATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
1445819 GCATAAA
195 GCATAAA
* * * * * *
1445826 GTGCCGATACATTGATAAAAAATATCGATCCCAAAAACATTGAAACTCATAATTAAAATGTAATA
1 GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
* * * * *
1445891 GGTAAATTTCCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAATAGGTGTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* *
1445956 ATCGACACTTTTTAAATTTGGGTCGATACTTTTT
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTT
1445990 TTAAATTTCG
Statistics
Matches: 695, Mismatches: 68, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
200 138 0.20
201 416 0.60
202 1 0.00
204 1 0.00
206 47 0.07
207 92 0.13
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (201 bp):
GTGTCGATACATTTACAAAAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
CATAAA
Found at i:1446226 original size:23 final size:23
Alignment explanation
Indices: 1446200--1446244 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1446190 GACTCTTTAT
*
1446200 TTTTCCTTAATATGTTTATGTTA
1 TTTTCATTAATATGTTTATGTTA
* *
1446223 TTTTCATTAATGTGTTTGTGTT
1 TTTTCATTAATATGTTTATGTT
1446245 CCAATGTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.07, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTCATTAATATGTTTATGTTA
Found at i:1446336 original size:15 final size:15
Alignment explanation
Indices: 1446312--1446355 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
1446302 CTCTTTCTCA
*
1446312 AAGCTCTTCTCAACC
1 AAGCTATTCTCAACC
1446327 AAGCTATTCTCAACC
1 AAGCTATTCTCAACC
1446342 AAGCTATTCTCAAC
1 AAGCTATTCTCAAC
1446356 GACAACCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (15 bp):
AAGCTATTCTCAACC
Found at i:1448625 original size:11 final size:11
Alignment explanation
Indices: 1448609--1448633 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1448599 TGTGGGTTTG
1448609 ATTATTTGAAC
1 ATTATTTGAAC
1448620 ATTATTTGAAC
1 ATTATTTGAAC
1448631 ATT
1 ATT
1448634 GTTATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTATTTGAAC
Found at i:1448976 original size:18 final size:18
Alignment explanation
Indices: 1448955--1448991 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1448945 GTAATTGGAG
1448955 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1448973 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1448991 T
1 T
1448992 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1448998 original size:24 final size:24
Alignment explanation
Indices: 1448947--1448999 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1448937 TTTCATATGT
* * *
1448947 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1448971 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1448995 AATTT
1 AATTT
1449000 TGGCTTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1450612 original size:199 final size:199
Alignment explanation
Indices: 1450253--1451850 Score: 2067
Period size: 199 Copynumber: 8.0 Consensus size: 199
1450243 CAGTAATCTC
* *
1450253 CAGAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCC
1 CAGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
**
1450318 CAAAAACATCGTATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTA-AATATA
65 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAA-ATA
* * *
1450382 TACCGGTTAATTAGAAAACATGTCTACATAATATATCGACACTTTTTAAA-TTGTGTCGATACTT
129 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
*
1450446 TTTATA
194 TTTGTA
* * * * * * *
1450452 AATAATGTATGATCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTATCGATAC
1 CAGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
* *
1450517 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACAGGTAGATATAT
65 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
* * *
1450582 ACCAGTTAATTAGAAAATAGGTCTACATAATATATCAACACTTTTTAAA-TTGTGTCGATACTTT
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
*
1450646 TTGTC
195 TTGTA
* *
1450651 CAGAATGAATGACCAACTGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCGAT-T
1 CAGAATGAATGACCAAC-GAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
* * * * *
1450715 CAAAAACATCGAATACGATAATTATAATGTAATAGGTAATTTTACAATGTAACTGGTAGATATAT
65 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
* * *
1450780 ACCGGTTAATTAGAAAATAGGTCTACATAATATATCGATAATTTTTAAA-TTGTGTCGATACTTT
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
*
1450844 TTGTC
195 TTGTA
* *
1450849 CAGAATGAATGACCAACCGAGGTGCGCGAATAAAGTGTCGATACATTTATAAAATGTATCGATCC
1 CAGAATGAATGACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
** * *
1450914 CAAAAACATTGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATAT
65 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
* * *
1450979 ACCGGTTAATTAGAAAATAAGTCTACATAATGTATCGATACTTTTTAAATTTGTGTCGATA-TGA
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT-T
1451043 TTTG-A
194 TTTGTA
*
1451048 CCAGAATGACTGAATGAATGCCCAACGAGGTGAACGAATAAAGTGTCGATACATTTATAAAAAGT
1 -CAG-A--A-TGAATG-A---CCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGT
* *
1451113 ATCGATCTCAAAAACATCAAATAAGATAATTATAATGTAATAGGTCAATTTACAATGTAACCGGT
57 ATCGATCCCAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGT
*
1451178 AGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTC
122 AGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTC
* *
1451243 GATACATTTTGTC
187 GATACTTTTTGTA
* * * *
1451256 CAGAATGAATG-CCTAACAACGTGCATGAATAAAGTGTCGATACATTTATAAAAAGTATCAATCC
1 CAGAATGAATGACC-AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
* * * * **
1451320 CAAAAACATCGAATAAGGTAATTATAATGTAATAGGTCAATTTCCAATGTAACAAGTAGAAATAT
65 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
*
1451385 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATAGACACTTTTTAAATTTGTGTCGATACTTT
130 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
*
1451450 TTGTC
195 TTGTA
* * **
1451455 CAGAATGAATG-CCTAA-AAGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATC
1 CAGAATGAATGACC-AACGAG-GTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* * * * * * *
1451517 CCAAAAAATATCAAA-ACCGATAATTAAAATGTAATTGGTAAATTTCCATTGTAACCGGTATAAA
64 CC-AAAAACATCAAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAA
*
1451581 TATACCGGTT--TTAAGAGAGAATAGGTCTACATAATGTATCGGCACTTTTTAAATTTGTGTCGA
127 TATACCGGTTAATT-AGA-A-AATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGA
* *
1451644 TGCGTTTTG-A
189 TACTTTTTGTA
* * * * *
1451654 CCAGAAAGAATGTCCAACGAGGTGTACGAATAAAGTGTAGATACATTTATAAAAAGTATCGATTC
1 -CAGAATGAATGACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
* ** * * *
1451719 CATAAACATCGAAA-CCGATAAATATAATGTAGTAGGTAAATTTCCAATGTAACCGGTAGAAATA
65 CAAAAACATC-AAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATA
* * * *
1451783 TACCGATTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAAGTTGTGTTGATACTT
129 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
1451848 TTT
194 TTT
1451851 TAAATTACGC
Statistics
Matches: 1247, Mismatches: 121, Indels: 62
0.87 0.08 0.04
Matches are distributed among these distances:
197 2 0.00
198 208 0.17
199 657 0.53
200 163 0.13
201 24 0.02
202 2 0.00
203 7 0.01
204 7 0.01
205 1 0.00
206 1 0.00
207 171 0.14
208 4 0.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (199 bp):
CAGAATGAATGACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
AAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATA
CCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTT
TGTA
Found at i:1451299 original size:406 final size:402
Alignment explanation
Indices: 1450257--1451850 Score: 2118
Period size: 397 Copynumber: 4.0 Consensus size: 402
1450247 AATCTCCAGA
* *
1450257 ATGAATG-CCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAA
1 ATGAATGAACCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAA
**
1450321 AAACATCGTATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTA-AATATATAC
65 AAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAA-ATATAC
* * * *
1450385 CGGTTAATTAGAAAACATGTCTACATAATATATCGACACTTTTTAAATTGTGTCGATACTTTTTA
129 CGGTTAATTAGAAAATAGGTCTACATAATATATCGACAATTTTTAAATTGTGTCGATACTTTTTG
** * * * *
1450450 TAAATAATGTATGATCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTATCGAT
194 TCCAGAATGAATGACCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGAT
* * * *
1450515 ACCAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACAGGTAGATAT
259 CCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACAGGTAGAAAT
* *
1450580 ATACCAGTTAATTAGAAAATAGGTCTACATAATATATCAACACTTTTTAAA-TTGTGTCGATACT
324 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACT
1450644 TTTTGTCCAG-A--
389 TTTTGTCCAGAATG
* *
1450655 ATGAATG-ACCAACTGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCGAT-TCAA
1 ATGAATGAACCAAC-GAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAA
* * * * *
1450718 AAACATCGAATACGATAATTATAATGTAATAGGTAATTTTACAATGTAACTGGTAGATATATACC
65 AAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACC
*
1450783 GGTTAATTAGAAAATAGGTCTACATAATATATCGATAATTTTTAAATTGTGTCGATACTTTTTGT
130 GGTTAATTAGAAAATAGGTCTACATAATATATCGACAATTTTTAAATTGTGTCGATACTTTTTGT
* * *
1450848 CCAGAATGAATGACCAACCGAGGTGCGCGAATAAAGTGTCGATACATTTATAAAATGTATCGATC
195 CCAGAATGAATGACCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* * *
1450913 CCAAAAACATTGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATA
260 CCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACAGGTAGAAATA
* * *
1450978 TACCGGTTAATTAGAAAATAAGTCTACATAATGTATCGATACTTTTTAAATTTGTGTCGATA-TG
325 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACT-
* *
1451042 ATTTGACCAGAATG
389 TTTTGTCCAGAATG
* *
1451056 ACTGAATGAATGCCCAACGAGGTGAACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCT
1 A-TGAATGAA---CCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
*
1451121 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTCAATTTACAATGTAACCGGTAGAAATAT
62 CAAAAACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
* *
1451186 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTCGATACATT
127 ACCGGTTAATTAGAAAATAGGTCTACATAATATATCGACAATTTTTAAA-TTGTGTCGATACTTT
* *
1451251 TTGTCCAGAATGAATG-CCTAA-CAACGTGCATGAATAAAGTGTCGATACATTTATAAAAAGTAT
191 TTGTCCAGAATGAATGACC-AACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTAT
* * * *
1451314 CAATCCCAAAAACATCGAATAAGGTAATTATAATGTAATAGGTCAATTTCCAATGTAACAAGTAG
255 CGATCCCAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACAGGTAG
1451379 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTAT-AGACACTTTTTAAATTTGTGTCG
320 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCA-ACACTTTTTAAATTTGTGTCG
1451443 ATACTTTTTGTCCAGAATG
384 ATACTTTTTGTCCAGAATG
** * **
1451462 AATGCCT-AA--AA-GA-GTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATCCCAA
1 -ATGAATGAACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC-A
* * * * * * *
1451521 AAAATATCAAA-ACCGATAATTAAAATGTAATTGGTAAATTTCCATTGTAACCGGTATAAATATA
64 AAAACATCAAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATA
* * * * *
1451585 CCGGTT--TTAAGAGAGAATAGGTCTACATAATGTATCGGCACTTTTTAAATTTGTGTCGATGCG
128 CCGGTTAATT-AGA-A-AATAGGTCTACATAATATATCGACAATTTTTAAA-TTGTGTCGATACT
* * * * * *
1451648 TTTTGACCAGAAAGAATGTCCAA-CGAGGTGTACGAATAAAGTGTAGATACATTTATAAAAAGTA
189 TTTTGTCCAGAATGAATGACCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTA
* * * * * *
1451712 TCGATTCCATAAACATCGAA-ACCGATAAATATAATGTAGTAGGTAAATTTCCAATGTAACCGGT
254 TCGATCCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTCCAATGTAACAGGT
* * *
1451776 AGAAATATACCGATTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAAGTTGTGTT
318 AGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTC
1451841 GATACTTTTT
383 GATACTTTTT
1451851 TAAATTACGC
Statistics
Matches: 1069, Mismatches: 101, Indels: 51
0.88 0.08 0.04
Matches are distributed among these distances:
396 2 0.00
397 300 0.28
398 163 0.15
399 223 0.21
400 5 0.00
401 1 0.00
402 6 0.01
403 1 0.00
405 45 0.04
406 289 0.27
407 34 0.03
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (402 bp):
ATGAATGAACCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAA
AACATCAAATAAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCG
GTTAATTAGAAAATAGGTCTACATAATATATCGACAATTTTTAAATTGTGTCGATACTTTTTGTC
CAGAATGAATGACCAACCAAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
CAAAAACATCGAATAAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACAGGTAGAAATAT
ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTT
TTGTCCAGAATG
Found at i:1453758 original size:23 final size:23
Alignment explanation
Indices: 1453727--1453818 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
1453717 CACCACAGCT
* *
1453727 CGTATAATTTCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1453750 CGTAGAATTGCACCGGAGTG-CA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1453772 GCGTAGAATTGTACCGAAGTGCCG
1 -CGTAGAATTGCACCGAAGTGCCA
*
1453796 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1453819 TATAATAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
22 2 0.03
23 55 0.95
24 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1453962 original size:103 final size:103
Alignment explanation
Indices: 1453837--1454051 Score: 412
Period size: 103 Copynumber: 2.1 Consensus size: 103
1453827 TGTCCATATA
*
1453837 GACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1453902 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
1453940 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1454005 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1454043 GACCACATA
1 GACCACATA
1454052 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:1458594 original size:16 final size:16
Alignment explanation
Indices: 1458575--1458627 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1458565 CCATAACCCC
1458575 TATCACACATATATCA
1 TATCACACATATATCA
** * *
1458591 TATCATGCACACATCA
1 TATCACACATATATCA
1458607 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1458625 TAT
1 TAT
1458628 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1458988 original size:23 final size:23
Alignment explanation
Indices: 1458962--1459025 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1458952 CAGCTCATAT
*
1458962 AATTACACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1458985 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1459008 AATTGTACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1459026 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1459212 original size:103 final size:103
Alignment explanation
Indices: 1459043--1459258 Score: 396
Period size: 103 Copynumber: 2.1 Consensus size: 103
1459033 ATGTCCATAT
* *
1459043 GGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
1459108 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
* *
1459146 GGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTAGA
1 GGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
1459211 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
1459249 GGACCACATA
1 GGACCACATA
1459259 GAACCTCGAC
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
GGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCCGAA
Found at i:1461506 original size:19 final size:19
Alignment explanation
Indices: 1461484--1461520 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1461474 ATTTTATATG
1461484 CGATTCATAATTATGTATA
1 CGATTCATAATTATGTATA
* *
1461503 CGATTTATAATTTTGTAT
1 CGATTCATAATTATGTAT
1461521 GTGAATGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (19 bp):
CGATTCATAATTATGTATA
Found at i:1464613 original size:185 final size:184
Alignment explanation
Indices: 1464312--1464650 Score: 468
Period size: 185 Copynumber: 1.8 Consensus size: 184
1464302 AATTATAATG
* *
1464312 TAATAGGTAAATTAACAATGTAACCGGTATAAATATACCGGTTAATTACAAAATAGGTAAACATA
1 TAATAGGTAAATTAACAATGTAACCGGTATAAACATACCGGTTAATGACAAAATAGGTAAACATA
* * *
1464377 TTGTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTG
66 TTGTATCGACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAAAGA-GTG
1464442 CACGCATAAAGTGCCGATACATTTATTAAAAGTATCGAAATTGATAATTATGGTA
130 CACGCATAAAGTGCCGATACATTTATTAAAAGTATCGAAATTGATAATTATGGTA
* * * *
1464497 TAATAGGTAAATTTAA-AATGTAACTGGTATAAACATACCGGTTTTATGAGAAAATAGGTTAACA
1 TAATAGGTAAA-TTAACAATGTAACCGGTATAAACATACCGG-TTAATGACAAAATAGGTAAACA
* * * * ** *
1464561 T-TATGTATCGACATTTTTTAAATATGTGTCGATACTT-TTTTCCATCATGAATGCCTAAAAGAG
64 TAT-TGTATCGACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAAAGAG
*
1464624 TGCACGCATAAAGTGTCGATACATTTA
128 TGCACGCATAAAGTGCCGATACATTTA
1464651 AAATTGTATC
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
184 27 0.20
185 55 0.41
186 52 0.39
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (184 bp):
TAATAGGTAAATTAACAATGTAACCGGTATAAACATACCGGTTAATGACAAAATAGGTAAACATA
TTGTATCGACACTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAAAGAGTGC
ACGCATAAAGTGCCGATACATTTATTAAAAGTATCGAAATTGATAATTATGGTA
Found at i:1464890 original size:23 final size:23
Alignment explanation
Indices: 1464840--1464884 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1464830 TGCCTATTTT
*
1464840 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1464863 ATTATATAAGCGCTGCCTAATA
1 ATTATATAAGCGCTACCTAATA
1464885 TGTTATTGAA
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:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1464906 original size:87 final size:87
Alignment explanation
Indices: 1464756--1464918 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1464746 AAATAGGTCA
*
1464756 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
*
1464821 CTGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
1464843 ATATAAGCGCTACCTATTACATTATATAAGCGCTGCCTAATATGTTATTGAACTTGATGATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
1464908 CCGGTTAAATG
66 CCGGTTAAATG
1464919 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1468394 original size:16 final size:16
Alignment explanation
Indices: 1468373--1468403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1468363 AAACTTAATT
*
1468373 AAAATAATTAAAATAA
1 AAAATAATAAAAATAA
1468389 AAAATAATAAAAATA
1 AAAATAATAAAAATA
1468404 GTAAAACAAC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATAAAAATAA
Found at i:1468622 original size:11 final size:11
Alignment explanation
Indices: 1468590--1468629 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1468580 TAAATTGAAA
*
1468590 TAAAACAAAAT
1 TAAAATAAAAT
1468601 TAAGTAATAAAAT
1 TAA--AATAAAAT
1468614 TAAAATAAAAT
1 TAAAATAAAAT
1468625 TAAAA
1 TAAAA
1468630 AGAAAGGTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (11 bp):
TAAAATAAAAT
Found at i:1469789 original size:3 final size:3
Alignment explanation
Indices: 1469781--1469822 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1469771 AAAATAAATA
1469781 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT AATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
1469823 TTTTTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1469800 original size:23 final size:24
Alignment explanation
Indices: 1469773--1469822 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1469763 AAAAATGTAA
1469773 AATAAATAA-ATAATAATAA-TAAT
1 AATAAATAATATAAT-ATAATTAAT
1469796 AAT-AATAATATAATATAATTAAT
1 AATAAATAATATAATATAATTAAT
1469819 AATA
1 AATA
1469823 TTTTTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATAAATAATATAATATAATTAAT
Found at i:1470054 original size:15 final size:15
Alignment explanation
Indices: 1470029--1470073 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
1470019 CTATCGAGGT
1470029 AAATTGATTCGTGAC
1 AAATTGATTCGTGAC
1470044 AAATT-ATTTCGTGAC
1 AAATTGA-TTCGTGAC
1470059 AAATTGATTCGTGAC
1 AAATTGATTCGTGAC
1470074 TATACATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (15 bp):
AAATTGATTCGTGAC
Found at i:1471960 original size:21 final size:21
Alignment explanation
Indices: 1471934--1471976 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1471924 CCAAAGCCTC
*
1471934 CTACAAATACACCCACTGTTG
1 CTACAAATACACCCACCGTTG
1471955 CTACAAATACACCCACCGTTG
1 CTACAAATACACCCACCGTTG
1471976 C
1 C
1471977 CTTCTTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.09, T:0.21
Consensus pattern (21 bp):
CTACAAATACACCCACCGTTG
Done.