Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1261428 original size:23 final size:23
Alignment explanation
Indices: 1261366--1261455 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
1261356 CATAATTCAA
* *
1261366 GTCAAGTATCATATCAGAATTCAG
1 GTCAA-TATCAAATCAGAATCCAG
* * *
1261390 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAAATCAGAATCCAG
1261414 GTCAATATCAAATCAGAATCCAG
1 GTCAATATCAAATCAGAATCCAG
1261437 GTCAATATCATAA-CAGAAT
1 GTCAATATCA-AATCAGAAT
1261456 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (23 bp):
GTCAATATCAAATCAGAATCCAG
Found at i:1262612 original size:18 final size:18
Alignment explanation
Indices: 1262591--1262626 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1262581 CTGCCATCCG
*
1262591 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
1262609 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
1262627 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:1263915 original size:10 final size:9
Alignment explanation
Indices: 1263902--1263949 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
1263892 GTCAAAGTTT
1263902 TGGTCAACAG
1 TGGTCAAC-G
1263912 TGGTCAACG
1 TGGTCAACG
1263921 TGGGTCAA--
1 T-GGTCAACG
1263929 TGGTCAACG
1 TGGTCAACG
1263938 -GGTCAACG
1 TGGTCAACG
1263946 -GGTC
1 TGGTC
1263950 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.17
8 13 0.37
9 2 0.06
10 14 0.40
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (9 bp):
TGGTCAACG
Found at i:1263954 original size:13 final size:13
Alignment explanation
Indices: 1263936--1264003 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 13
1263926 CAATGGTCAA
1263936 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1263949 CGGGT---CGGGT
1 CGGGTCAACGGGT
*
1263959 CGGGTCAACTGGT
1 CGGGTCAACGGGT
* *
1263972 CGGGTAAACGGAT
1 CGGGTCAACGGGT
*
1263985 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1263998 CGGGTC
1 CGGGTC
1264004 GGGTCGGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
10 10 0.22
13 36 0.78
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1265231 original size:24 final size:25
Alignment explanation
Indices: 1265194--1265245 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
1265184 GTAGGAAATA
*
1265194 TTAGTTTTTTTAGAATTTAGAATGG
1 TTAGTTTTTTTAGAATCTAGAATGG
1265219 TTAG-TTTTTTAGAATCTAGAATGG
1 TTAGTTTTTTTAGAATCTAGAATGG
1265243 TTA
1 TTA
1265246 CTGAAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (25 bp):
TTAGTTTTTTTAGAATCTAGAATGG
Found at i:1268796 original size:14 final size:14
Alignment explanation
Indices: 1268773--1268813 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1268763 TATTTGAGTT
1268773 AAAAATTAAA-AAA
1 AAAAATTAAATAAA
1268786 AAAACATTAAATAAA
1 AAAA-ATTAAATAAA
1268801 ATAAAA-TAAATAA
1 A-AAAATTAAATAA
1268814 TAATAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.16
14 13 0.52
15 5 0.20
16 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAATTAAATAAA
Found at i:1272353 original size:26 final size:26
Alignment explanation
Indices: 1272313--1272387 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
1272303 CACTAAGTGC
*
1272313 ATGGTGGGCACGACCTTATGTGTATT
1 ATGGTGGGCAAGACCTTATGTGTATT
1272339 ATGGTGGGCAAGACCTTATGTGTATT
1 ATGGTGGGCAAGACCTTATGTGTATT
1272365 ATGGTGGGCAAGACCTTATGTGT
1 ATGGTGGGCAAGACCTTATGTGT
1272388 GTTAGCACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.33
Consensus pattern (26 bp):
ATGGTGGGCAAGACCTTATGTGTATT
Found at i:1273648 original size:13 final size:13
Alignment explanation
Indices: 1273623--1273687 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
1273613 GTCATAAATC
*
1273623 TATGACGCCCATT
1 TATGACGCACATT
* *
1273636 GATGACACACATT
1 TATGACGCACATT
*
1273649 TATGACTCACATT
1 TATGACGCACATT
* *
1273662 TATGGCGCGCATT
1 TATGACGCACATT
1273675 TATGACGCACATT
1 TATGACGCACATT
1273688 GAGCGTAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:1273920 original size:2 final size:2
Alignment explanation
Indices: 1273913--1273972 Score: 104
Period size: 2 Copynumber: 30.0 Consensus size: 2
1273903 CTCATAATAC
1273913 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
1273955 TA TA TCA TA T- TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA
1273973 AGCAATCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1274922 original size:29 final size:30
Alignment explanation
Indices: 1274901--1275031 Score: 132
Period size: 29 Copynumber: 4.6 Consensus size: 30
1274891 TTCGAAATGG
*
1274901 GTGCTATATT-GGAATTTAATTCGAAAAAG
1 GTGCTATATTAGGAATTTAATTCGAAAAAA
* * *
1274930 GTGCTAT-TTTGGTAATTTATTTTG-AAAAA
1 GTGCTATATTAGG-AATTTAATTCGAAAAAA
*
1274959 GTGCTATATTGGGAATTTAATT--AAAAAA
1 GTGCTATATTAGGAATTTAATTCGAAAAAA
*
1274987 GTGCTAT-TTAGGAATTTAATTCG-AAAAT
1 GTGCTATATTAGGAATTTAATTCGAAAAAA
* *
1275015 GTGCTATTTTAGTAATT
1 GTGCTATATTAGGAATT
1275032 ATTTTAAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
27 13 0.15
28 25 0.29
29 36 0.41
30 13 0.15
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (30 bp):
GTGCTATATTAGGAATTTAATTCGAAAAAA
Found at i:1275013 original size:28 final size:27
Alignment explanation
Indices: 1274901--1275023 Score: 140
Period size: 28 Copynumber: 4.3 Consensus size: 27
1274891 TTCGAAATGG
1274901 GTGCTATATTGGAATTTAATTCGAAAAA
1 GTGCTAT-TTGGAATTTAATTCGAAAAA
* *
1274929 GGTGCTATTTTGGTAATTTATTTTGAAAAA
1 -GTGCTA-TTTGG-AATTTAATTCGAAAAA
*
1274959 GTGCTATATTGGGAATTTAATT-AAAAAA
1 GTGCTAT-TT-GGAATTTAATTCGAAAAA
*
1274987 GTGCTATTTAGGAATTTAATTCGAAAAT
1 GTGCTATTT-GGAATTTAATTCGAAAAA
1275015 GTGCTATTT
1 GTGCTATTT
1275024 TAGTAATTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
27 13 0.16
28 26 0.32
29 26 0.32
30 17 0.21
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (27 bp):
GTGCTATTTGGAATTTAATTCGAAAAA
Found at i:1275041 original size:56 final size:57
Alignment explanation
Indices: 1274901--1275031 Score: 158
Period size: 56 Copynumber: 2.3 Consensus size: 57
1274891 TTCGAAATGG
* * * *
1274901 GTGCTATATT-GGAATTTAATTCGAAAAAGGTGCTATTTTGGTAATTTATTTTGAAAAA
1 GTGCTATATTAGGAATTTAATT--AAAAAAGTGCTATTTAGGTAATTTAATTCGAAAAA
* *
1274959 GTGCTATATTGGGAATTTAATTAAAAAAGTGCTATTTAGG-AATTTAATTCGAAAAT
1 GTGCTATATTAGGAATTTAATTAAAAAAGTGCTATTTAGGTAATTTAATTCGAAAAA
* *
1275015 GTGCTATTTTAGTAATT
1 GTGCTATATTAGGAATT
1275032 ATTTTAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 27 0.42
57 16 0.25
58 10 0.16
59 11 0.17
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (57 bp):
GTGCTATATTAGGAATTTAATTAAAAAAGTGCTATTTAGGTAATTTAATTCGAAAAA
Found at i:1282253 original size:30 final size:29
Alignment explanation
Indices: 1282204--1282355 Score: 175
Period size: 30 Copynumber: 5.2 Consensus size: 29
1282194 ACCGGGTGAC
1282204 ATTTTGGGAATTT-ATTCAAAATGAGTGCT
1 ATTTTGGGAATTTAATTCAAAA-GAGTGCT
* * *
1282233 ATTTTGGAAATTTAATTCAAAAAATGTGTT
1 ATTTTGGGAATTTAATTCAAAAGA-GTGCT
*
1282263 ATTTTGGGAATTTAATTTGAAAA-AGTGCT
1 ATTTTGGGAATTTAA-TTCAAAAGAGTGCT
* * *
1282292 ATATTGGGAATTTAATTCAAAAAAGGTGTT
1 ATTTTGGGAATTTAATTCAAAAGA-GTGCT
1282322 ATTTTGGGAATTTAATTCGAAAAG-GTGCT
1 ATTTTGGGAATTTAATTC-AAAAGAGTGCT
1282351 ATTTT
1 ATTTT
1282356 AGTAATTATT
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.06
29 41 0.39
30 48 0.46
31 10 0.10
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCAAAAGAGTGCT
Found at i:1282304 original size:59 final size:59
Alignment explanation
Indices: 1282204--1282352 Score: 212
Period size: 59 Copynumber: 2.5 Consensus size: 59
1282194 ACCGGGTGAC
* * *
1282204 ATTTTGGGAATTT-A-TTCAAAATGAGTGCTATTTTGGAAATTTAATTCAAAAAATGTGTT
1 ATTTTGGGAATTTAATTTGAAAA--AGTGCTATATTGGAAATTTAATTCAAAAAAGGTGTT
*
1282263 ATTTTGGGAATTTAATTTGAAAAAGTGCTATATTGGGAATTTAATTCAAAAAAGGTGTT
1 ATTTTGGGAATTTAATTTGAAAAAGTGCTATATTGGAAATTTAATTCAAAAAAGGTGTT
* *
1282322 ATTTTGGGAATTTAATTCGAAAAGGTGCTAT
1 ATTTTGGGAATTTAATTTGAAAAAGTGCTAT
1282353 TTTAGTAATT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 75 0.91
60 1 0.01
61 6 0.07
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (59 bp):
ATTTTGGGAATTTAATTTGAAAAAGTGCTATATTGGAAATTTAATTCAAAAAAGGTGTT
Found at i:1282362 original size:29 final size:29
Alignment explanation
Indices: 1282204--1282383 Score: 186
Period size: 29 Copynumber: 6.1 Consensus size: 29
1282194 ACCGGGTGAC
*
1282204 ATTTTGGGAATTT-ATTCAAAATGAGTGCT
1 ATTTTGGGAATTTAATTCAAAAAG-GTGCT
* * *
1282233 ATTTTGGAAATTTAATTCAAAAAATGTGTT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
*
1282263 ATTTTGGGAATTTAATTTGAAAAA-GTGCT
1 ATTTTGGGAATTTAA-TTCAAAAAGGTGCT
* *
1282292 ATATTGGGAATTTAATTCAAAAAAGGTGTT
1 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
*
1282322 ATTTTGGGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAGGTGCT
* * * *
1282351 ATTTTAGTAA-TTATTTTAAAAATGGTGCT
1 ATTTTGGGAATTTAATTCAAAAA-GGTGCT
1282380 ATTT
1 ATTT
1282384 CTGGAAAATG
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
28 11 0.09
29 62 0.49
30 48 0.38
31 6 0.05
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCAAAAAGGTGCT
Found at i:1283726 original size:32 final size:32
Alignment explanation
Indices: 1283685--1283752 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
1283675 TTGCTATCGT
1283685 TTTG-GATATATCTGTATTATTAAAATTTTGG
1 TTTGTGATATATCTGTATTATTAAAATTTTGG
1283716 TTTGTGATATATCTGTATTATTAAAATTTTGG
1 TTTGTGATATATCTGTATTATTAAAATTTTGG
1283748 TTTGT
1 TTTGT
1283753 ATTAATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.54
Consensus pattern (32 bp):
TTTGTGATATATCTGTATTATTAAAATTTTGG
Found at i:1289447 original size:24 final size:24
Alignment explanation
Indices: 1289411--1289490 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 24
1289401 CACCAAAGTG
* *
1289411 CCACATAG-ATTTGTCTCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
1289434 TCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* *
1289458 CCACATAGAA-ATGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
1289481 CCGCGTAGAA
1 CCACGTAGAA
1289491 CCATCGACTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:1289619 original size:15 final size:15
Alignment explanation
Indices: 1289597--1289673 Score: 75
Period size: 15 Copynumber: 5.1 Consensus size: 15
1289587 TCTTTTATTC
1289597 CACATAGAACACTTT
1 CACATAGAACACTTT
* *
1289612 CGCATAGAACATTTT
1 CACATAGAACACTTT
* * *
1289627 CACGTAGATCACATT
1 CACATAGAACACTTT
*
1289642 CACATA-AAGAACTTT
1 CACATAGAA-CACTTT
*
1289657 CACATAGAACACATT
1 CACATAGAACACTTT
1289672 CA
1 CA
1289674 TATGTAAATA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
14 1 0.02
15 44 0.94
16 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:1290797 original size:101 final size:101
Alignment explanation
Indices: 1290622--1290823 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
1290612 TCACTTAGTT
1290622 TCTCTTCATTTTTAAGCTTCCTTAATCTTATGTGCCAATCAAAGCTTCAAAACCAATCGGTAAAT
1 TCTCTTCATTTTTAAGCTTCCTTAATCTTATGTGCCAATCAAAGCTTCAAAACCAATCGGTAAAT
1290687 TAAAGAAACAACCAACTATAACGTATCTCACCTTAG
66 TAAAGAAACAACCAACTATAACGTATCTCACCTTAG
1290723 TCTCTTCATTTTTAAGCTTCCTTAATCTTATGTGCCAATCAAAGCTTCAAAACCAATCGGTAAAT
1 TCTCTTCATTTTTAAGCTTCCTTAATCTTATGTGCCAATCAAAGCTTCAAAACCAATCGGTAAAT
1290788 TAAAGAAACAACCAACTATAACGTATCTCACCTTAG
66 TAAAGAAACAACCAACTATAACGTATCTCACCTTAG
1290824 CAATGGAGTC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.32
Consensus pattern (101 bp):
TCTCTTCATTTTTAAGCTTCCTTAATCTTATGTGCCAATCAAAGCTTCAAAACCAATCGGTAAAT
TAAAGAAACAACCAACTATAACGTATCTCACCTTAG
Found at i:1296549 original size:23 final size:23
Alignment explanation
Indices: 1296521--1296565 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1296511 GTGTTGAATT
* *
1296521 TGTCCTGAAGGAGCGCGTAGAAA
1 TGTCCTGAAGGACCGCATAGAAA
1296544 TGTCCTGAAGGACCGCATAGAA
1 TGTCCTGAAGGACCGCATAGAA
1296566 CCCTTAACTC
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:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (23 bp):
TGTCCTGAAGGACCGCATAGAAA
Found at i:1296695 original size:15 final size:15
Alignment explanation
Indices: 1296675--1296743 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 15
1296665 TTTATTCCAT
*
1296675 ATAGAACACTTTCTC
1 ATAGAACACTTTCAC
*
1296690 ATAGAACATTTTCAC
1 ATAGAACACTTTCAC
* * * *
1296705 GTATATCACATTCAC
1 ATAGAACACTTTCAC
* *
1296720 ATATAGCACTTTCAC
1 ATAGAACACTTTCAC
1296735 ATAGAACAC
1 ATAGAACAC
1296744 ATTAATATGT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAGAACACTTTCAC
Found at i:1307988 original size:15 final size:15
Alignment explanation
Indices: 1307969--1308026 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
1307959 TTGCACGTAG
* *
1307969 AACATTTTCACTTAG
1 AACATTTTCACATAA
*
1307984 CACATTTTCACATAA
1 AACATTTTCACATAA
*
1307999 AACATTTTCATATAA
1 AACATTTTCACATAA
*
1308014 AACATATTCACAT
1 AACATTTTCACAT
1308027 GAAATAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (15 bp):
AACATTTTCACATAA
Found at i:1315094 original size:15 final size:15
Alignment explanation
Indices: 1315074--1315105 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1315064 TTGGATTGAA
*
1315074 GCTTGTTTCAGAGAG
1 GCTTGTTTCAAAGAG
1315089 GCTTGTTTCAAAGAG
1 GCTTGTTTCAAAGAG
1315104 GC
1 GC
1315106 CAGATTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (15 bp):
GCTTGTTTCAAAGAG
Found at i:1316962 original size:23 final size:24
Alignment explanation
Indices: 1316916--1316964 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1316906 AATTTTCCTT
1316916 AAGGACCACATAGAATTTGTCCCG
1 AAGGACCACATAGAATTTGTCCCG
* *
1316940 AAGGACCGCGTAGAA-TTGTCCCG
1 AAGGACCACATAGAATTTGTCCCG
1316963 AA
1 AA
1316965 TAACCGTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (24 bp):
AAGGACCACATAGAATTTGTCCCG
Found at i:1316970 original size:23 final size:24
Alignment explanation
Indices: 1316926--1316977 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1316916 AAGGACCACA
*
1316926 TAGAATTTGTCCCGAAGGACCGCG
1 TAGAATTTGTCCCGAAGAACCGCG
* *
1316950 TAGAA-TTGTCCCGAATAACCGTG
1 TAGAATTTGTCCCGAAGAACCGCG
1316973 TAGAA
1 TAGAA
1316978 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (24 bp):
TAGAATTTGTCCCGAAGAACCGCG
Found at i:1317154 original size:15 final size:15
Alignment explanation
Indices: 1317123--1317175 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1317113 TACGTAGAAA
**
1317123 ATTTTCACTTAGCAC
1 ATTTTCACTTAAAAC
1317138 ATTTTCACTTAAAAC
1 ATTTTCACTTAAAAC
*
1317153 ATTTCCA-TATAAAAC
1 ATTTTCACT-TAAAAC
*
1317168 ATATTCAC
1 ATTTTCAC
1317176 ATACAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 1 0.03
15 30 0.97
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTTTCACTTAAAAC
Found at i:1320287 original size:12 final size:12
Alignment explanation
Indices: 1320270--1320307 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
1320260 GAAAACTTAG
1320270 CCATTTCATGCT
1 CCATTTCATGCT
1320282 CCATTTCATGCT
1 CCATTTCATGCT
1320294 CCATTTCATGCT
1 CCATTTCATGCT
1320306 CC
1 CC
1320308 CCATGAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.37, G:0.08, T:0.39
Consensus pattern (12 bp):
CCATTTCATGCT
Found at i:1326720 original size:21 final size:22
Alignment explanation
Indices: 1326665--1326712 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
1326655 CCACAACTCG
1326665 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
1326687 T-ATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
1326708 TAATT
1 TAATT
1326713 ATCCCGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (22 bp):
TAATTTGCACCGAAGTGCCACA
Found at i:1326889 original size:21 final size:21
Alignment explanation
Indices: 1326860--1326908 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1326850 AAAGAGTATA
*
1326860 TTCACATTCAC-TGATTCAAAG
1 TTCATATTCACATG-TTCAAAG
1326881 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
1326902 TTCATAT
1 TTCATAT
1326909 ATTCCTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:1327317 original size:54 final size:55
Alignment explanation
Indices: 1327261--1327447 Score: 224
Period size: 52 Copynumber: 3.5 Consensus size: 55
1327251 ACTGGGGATT
* * * *
1327261 GATACACTCCTCAGTGTACCGATACACAAATTGTATTCGATG-TTTAAGGGCATT
1 GATACACTCCTCAGTGTACCGATACACAAATTGTATTCGATGTTTTGAGTGTATC
* * *
1327315 GATACACTCCTCAGTGTACTGATACATAAA-TGACATAT-GATGTTTTGAGTGTATC
1 GATACACTCCTCAGTGTACCGATACACAAATTG-TAT-TCGATGTTTTGAGTGTATC
* * *
1327370 GATACA---CTCAGTATACCGATACACAAATGGTATTCTATGTTTTGAGTGTATC
1 GATACACTCCTCAGTGTACCGATACACAAATTGTATTCGATGTTTTGAGTGTATC
1327422 GATACACTCCTCAGTGTACCGATACA
1 GATACACTCCTCAGTGTACCGATACA
1327448 TACTCATACA
Statistics
Matches: 111, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
51 1 0.01
52 42 0.38
53 3 0.03
54 34 0.31
55 31 0.28
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (55 bp):
GATACACTCCTCAGTGTACCGATACACAAATTGTATTCGATGTTTTGAGTGTATC
Found at i:1335780 original size:14 final size:16
Alignment explanation
Indices: 1335741--1335774 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1335731 CTATAATCTT
*
1335741 CTATCTTATTCTCTCA
1 CTATCTCATTCTCTCA
1335757 CTATCTCATTCTCTCA
1 CTATCTCATTCTCTCA
1335773 CT
1 CT
1335775 TTCATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (16 bp):
CTATCTCATTCTCTCA
Found at i:1337584 original size:31 final size:31
Alignment explanation
Indices: 1337531--1337590 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1337521 GCAACATTTT
* * *
1337531 AAATTTTTCATAATTAAAAGTTTATTTGAAC
1 AAATTTTTCAGAAATAAAAGTTTAATTGAAC
* *
1337562 AAATTTTTCGGAAATAAGAGTTTAATTGA
1 AAATTTTTCAGAAATAAAAGTTTAATTGA
1337591 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (31 bp):
AAATTTTTCAGAAATAAAAGTTTAATTGAAC
Found at i:1338271 original size:10 final size:10
Alignment explanation
Indices: 1338258--1338292 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1338248 AATCTAGTAA
1338258 ATTAATAATT
1 ATTAATAATT
*
1338268 ATTAATAATA
1 ATTAATAATT
1338278 ATTAATAACTT
1 ATTAATAA-TT
1338289 ATTA
1 ATTA
1338293 TTTTTAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTAATAATT
Found at i:1340663 original size:75 final size:75
Alignment explanation
Indices: 1340483--1340655 Score: 235
Period size: 75 Copynumber: 2.3 Consensus size: 75
1340473 GACGAGGCAC
* * *
1340483 TATCGATACCATTGTA-AG-GGTATCAATACCAAGCAACATCGAAGCTAAAATTGGTATCGATAC
1 TATCGATACCATAGTATAGAAGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
1340546 TGAAAGGGGG
66 TGAAAGGGGG
* * * *
1340556 TATCGATACCATAGTATGGTAGTCTCAATACCAGGCAACATCGAACCTAAAATTGGTATCGATAC
1 TATCGATACCATAGTATAGAAGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
1340621 T-AGAAGGGGG
66 TGA-AAGGGGG
* *
1340631 TATCGGTATCATAGTATAGAAGTAT
1 TATCGATACCATAGTATAGAAGTAT
1340656 GGGTACCATG
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 15 0.17
74 2 0.02
75 69 0.80
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (75 bp):
TATCGATACCATAGTATAGAAGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
TGAAAGGGGG
Found at i:1341445 original size:68 final size:68
Alignment explanation
Indices: 1341333--1341520 Score: 313
Period size: 68 Copynumber: 2.8 Consensus size: 68
1341323 AAAGATTAAT
*
1341333 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1341398 TGG
66 TGG
* *
1341401 AGGCCTAACTGTGCATTTGACAGGAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
1341466 TTG
66 TGG
* * *
1341469 AGGCCTAACTCTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
1341521 CGATTAAACA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
68 111 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TGG
Found at i:1341609 original size:81 final size:81
Alignment explanation
Indices: 1341503--1341892 Score: 521
Period size: 81 Copynumber: 4.8 Consensus size: 81
1341493 AATGTGTCAT
* *
1341503 TTATGCCAGTTAGATGAACGATTAAACACCGTTGAGTAAAAGAATAATGTCCTAACTGTGCAATT
1 TTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATT
* *
1341568 GGTAGAAAGGTTCCAG
66 GGTAGAAAGGTGCCAA
* * *** *
1341584 TTATGCTAGTTAGATGAAAGGTTAAACACCGTTGAGTAAAAGAATAACAACCTAATTGTGCAATT
1 TTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATT
*
1341649 AGTAGAAAGGTGCCAA
66 GGTAGAAAGGTGCCAA
* * * * * *
1341665 TTAAT-CCAGTTAGATGAAAGATTAAACATCGTTGAGTAAAAGAACATTGGCCTAGCTGTGCAAT
1 TT-ATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAAT
* *
1341729 TGGTAGAAATGTTCCAA
65 TGGTAGAAAGGTGCCAA
* * *
1341746 TTATGTCAGTTAGATGAACGGTTAGACACCGTTGAGTAAAAGAATAATGGCCTAACTGTACAATT
1 TTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATT
*
1341811 GGTAGAAATGTGCCAA
66 GGTAGAAAGGTGCCAA
* * * *
1341827 TTATTCCAGTTAGATGAACGGTTAAACACCGTTAAGTAAAATAATAATGGCCTAACTGTACAATT
1 TTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATT
1341892 G
66 G
1341893 TTTAACCGAT
Statistics
Matches: 269, Mismatches: 38, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
80 2 0.01
81 265 0.99
82 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (81 bp):
TTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATT
GGTAGAAAGGTGCCAA
Found at i:1345522 original size:57 final size:57
Alignment explanation
Indices: 1345418--1345525 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
1345408 CAAACAGCCC
* * * *
1345418 CTAAGTGTATGAATTTCCATATTGGGCAATTTATGTGCAAAAGATAAGAAACTCATA
1 CTAAGTGTATAAATTTCCATATTGGGAAATATATGTGCAAAACATAAGAAACTCATA
* *
1345475 CTAAGTGTATAAATTTCCATA-TGGGAAATATATGTGTATGAACATAAGAAA
1 CTAAGTGTATAAATTTCCATATTGGGAAATATATGTGCA-AAACATAAGAAA
1345526 TTTATAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 14 0.32
57 30 0.68
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (57 bp):
CTAAGTGTATAAATTTCCATATTGGGAAATATATGTGCAAAACATAAGAAACTCATA
Found at i:1345831 original size:68 final size:68
Alignment explanation
Indices: 1345722--1345854 Score: 230
Period size: 68 Copynumber: 2.0 Consensus size: 68
1345712 TATGCTTAAC
* * * *
1345722 TGTGCATTTGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGTCTAAGTGTCTTTGAGGCCT
1 TGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
1345787 AAT
66 AAT
1345790 TGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
1 TGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
1345855 GTCGCAACCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (68 bp):
TGTGCATTTGACAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
AAT
Found at i:1346240 original size:14 final size:15
Alignment explanation
Indices: 1346221--1346254 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1346211 ATATATATAT
*
1346221 ATATAATAA-AAATA
1 ATATAATAATAAAAA
1346235 ATATAATAATAAAAA
1 ATATAATAATAAAAA
1346250 ATATA
1 ATATA
1346255 TGTAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATAATAATAAAAA
Found at i:1346260 original size:19 final size:19
Alignment explanation
Indices: 1346207--1346265 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
1346197 CATATATGAG
1346207 AAAAATATATATATATATAAT
1 AAAAA-ATATATATA-ATAAT
1346228 -AAAAATA-ATATAATAAT
1 AAAAAATATATATAATAAT
*
1346245 AAAAAATATATGTAATAAT
1 AAAAAATATATATAATAAT
1346264 AA
1 AA
1346266 TAATAAACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 5 0.14
18 12 0.34
19 14 0.40
20 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATATATATAATAAT
Found at i:1346265 original size:22 final size:20
Alignment explanation
Indices: 1346207--1346268 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 20
1346197 CATATATGAG
1346207 AAAAATATATATATATATAAT-
1 AAAAATATAT-TATA-ATAATA
1346228 AAAAATA-A-TATAATAATA
1 AAAAATATATTATAATAATA
1346246 AAAAATATATGTAATAATAATA
1 AAAAATATAT-T-ATAATAATA
1346268 A
1 A
1346269 TAAACGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.14
18 11 0.31
19 1 0.03
20 1 0.03
21 8 0.22
22 10 0.28
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAATATATTATAATAATA
Found at i:1346267 original size:15 final size:15
Alignment explanation
Indices: 1346221--1346267 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1346211 ATATATATAT
1346221 ATATAATAA-AAATA
1 ATATAATAATAAATA
*
1346235 ATATAATAATAAAAA
1 ATATAATAATAAATA
*
1346250 ATATATGTAAT-AATA
1 ATATA-ATAATAAATA
1346265 ATA
1 ATA
1346268 ATAAACGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.32
15 15 0.54
16 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
ATATAATAATAAATA
Found at i:1346271 original size:25 final size:25
Alignment explanation
Indices: 1346233--1346282 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1346223 ATAATAAAAA
1346233 TAATATAATAATAAA-AAATATATG
1 TAATATAATAATAAACAAATATATG
1346257 TAATAATAATAATAAACGAAATATAT
1 TAAT-ATAATAATAAAC-AAATATAT
1346283 TTAAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
27 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (25 bp):
TAATATAATAATAAACAAATATATG
Found at i:1347963 original size:106 final size:106
Alignment explanation
Indices: 1347777--1348454 Score: 1088
Period size: 106 Copynumber: 6.4 Consensus size: 106
1347767 TGTTTCGAGG
* * * *
1347777 CCAATATCCTTCGTTGTGAAGTTTAAATTGGATCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
*
1347842 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
1347883 CCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
* *
1347948 CGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTAGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * ** *
1347989 CAAATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAGGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
*
1348054 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAAT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
1348095 CCAATATCCTTCGCTATGAAGTTAAAATTGGCTCCGAAATTGGGAAGTTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
*
1348160 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
1348201 CCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAGGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
*
1348266 CGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1348307 CCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
*
1348372 CGGTCCCTTAGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
1348413 CCAATATCCTTCGTTGTGAAGTT-AATATCGGCTCCGAGATTG
1 CCAATATCCTTCGCTGTGAAGTTGAA-ATTGGCTCCGAAATTG
1348455 TTATTGACAA
Statistics
Matches: 527, Mismatches: 44, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
105 2 0.00
106 525 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:1359688 original size:22 final size:21
Alignment explanation
Indices: 1359657--1359718 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 21
1359647 ATGAGAAAAA
1359657 AAATAT-ATATATATATATAAT
1 AAATATAATATATATA-ATAAT
1359678 AAATATAATATA-ATAATAAT
1 AAATATAATATATATAATAAT
*
1359698 -AATA-AATATATGTAATAAT
1 AAATATAATATATATAATAAT
1359717 AA
1 AA
1359719 TAATAAACGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 6 0.16
19 11 0.30
20 6 0.16
21 9 0.24
22 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATAATATATATAATAAT
Found at i:1359719 original size:22 final size:22
Alignment explanation
Indices: 1359657--1359725 Score: 97
Period size: 22 Copynumber: 3.1 Consensus size: 22
1359647 ATGAGAAAAA
1359657 AAATATATAT-AT-ATATATAAT
1 AAATATATATAATAATA-ATAAT
1359678 AAATATAATATAATAATAATAAT
1 AAATAT-ATATAATAATAATAAT
*
1359701 AAATATATGTAATAATAATAAT
1 AAATATATATAATAATAATAAT
1359723 AAA
1 AAA
1359726 CGAAATATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 6 0.14
22 22 0.50
23 13 0.30
24 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (22 bp):
AAATATATATAATAATAATAAT
Found at i:1361461 original size:81 final size:81
Alignment explanation
Indices: 1360836--1361447 Score: 873
Period size: 81 Copynumber: 7.6 Consensus size: 81
1360826 GCGTCTACAA
* ** * * *
1360836 GGCCTAACTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTACATGAACGGTTAAACACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1360901 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* *
1360917 GGTCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAACACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1360982 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * *
1360998 GGCCTAACTGTGCAATTGGTAGAAATGTGCCAATTATGCCAGTTAGATGAATGATTAAACATCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1361063 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * **
1361079 GGTCTAACTGTGCAATTGGTAGAAATGTGCCAATTATGTGAGTTAGATGAACGGTTAAACACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
*
1361144 TAAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
** * * * *
1361160 GGCCTAACTGTGCAATTGGTAGAAAGGCATCAATTATGCCTGTTAGATGAGCGGTTAAATAGCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1361225 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* *
1361241 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAACATCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
*
1361306 TGAGTAAAAGATTAAT
66 TGAGTAAAAGAATAAT
* *
1361322 GGCCTAACTGTGCAATTTGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
1361387 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
** * * ** * * *
1361403 GGATTAGCTGTGCATTTTATAGAAAAGTGTCAAATATGCAAGTTA
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTA
1361448 AATAAAAAGT
Statistics
Matches: 477, Mismatches: 54, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 477 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGT
TGAGTAAAAGAATAAT
Found at i:1370743 original size:29 final size:30
Alignment explanation
Indices: 1370701--1370767 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
1370691 ATATTACTTT
* *
1370701 CTAAACTT-TAAAAAATTTCAATTCACTAA
1 CTAAACTTAAAAAAAAATTCAATTCACTAA
*
1370730 CTAAACTTAAAAAAAAATTCAATTTACTAA
1 CTAAACTTAAAAAAAAATTCAATTCACTAA
1370760 CTAAACTT
1 CTAAACTT
1370768 TCGAATTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 8 0.24
30 26 0.76
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (30 bp):
CTAAACTTAAAAAAAAATTCAATTCACTAA
Found at i:1379604 original size:18 final size:18
Alignment explanation
Indices: 1379583--1379617 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1379573 ATTCTTGGCG
1379583 TGGCAGAGATTCCTGACC
1 TGGCAGAGATTCCTGACC
* *
1379601 TGGCAGATATTCTTGAC
1 TGGCAGAGATTCCTGAC
1379618 GTACAAGCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (18 bp):
TGGCAGAGATTCCTGACC
Found at i:1380285 original size:17 final size:17
Alignment explanation
Indices: 1380260--1380311 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1380250 TTGTTCAACG
*
1380260 ATAACTTAAACAAATTA
1 ATAATTTAAACAAATTA
**
1380277 ATAATTTAAAGTTGAA-TA
1 ATAATTTAAA--CAAATTA
1380295 ATAATTTAAACAAATTA
1 ATAATTTAAACAAATTA
1380312 TAAAAAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 12 0.44
19 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAATTTAAACAAATTA
Found at i:1380698 original size:27 final size:27
Alignment explanation
Indices: 1380660--1380714 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1380650 TGTCGGTGGG
1380660 GCCATATACTGAAATAATGATAGAGTC
1 GCCATATACTGAAATAATGATAGAGTC
* * *
1380687 GCCATATTCTGAAATATTGATTGAGTC
1 GCCATATACTGAAATAATGATAGAGTC
1380714 G
1 G
1380715 AGCGGGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (27 bp):
GCCATATACTGAAATAATGATAGAGTC
Found at i:1387301 original size:63 final size:61
Alignment explanation
Indices: 1387145--1387307 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 61
1387135 ATGAATTAAA
* * * *
1387145 TTGAACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGTACTGAGGAGTT
1 TTGAACATCGAATGCATTTGATGCATCGATGCAC-TACCATGCACCAATGCACTCAGGAGTT
* * *
1387207 TATGAAAACCTCGAATGCATTTGATGCATCGATGCACTAGCCATGCATCAATGCACTCTGGCTA-
1 T-TG--AACATCGAATGCATTTGATGCATCGATGCACTA-CCATGCACCAATGCACTCAGG--AG
1387271 TT
60 TT
*
1387273 TTGAACATCGAATGCACTTGATGCATCGATGCACT
1 TTGAACATCGAATGCATTTGATGCATCGATGCACT
1387308 CTTAGTGCAC
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
62 1 0.01
63 32 0.37
64 2 0.02
65 47 0.55
66 3 0.03
67 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (61 bp):
TTGAACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCAATGCACTCAGGAGTT
Found at i:1395742 original size:65 final size:63
Alignment explanation
Indices: 1395626--1395815 Score: 190
Period size: 65 Copynumber: 3.0 Consensus size: 63
1395616 ATCCACCAAT
* ** *
1395626 CCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCATTTCATGCATCGATGCACAT
1 CCATGCACCGATGCACTCA-GAA-TATTTTGAAACATCGAATGCATTTGATGCATCGATGCACA-
1395689 A
63 A
*
1395690 CCACT-CACCGATGCACTGAGAAT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCACC
1 CCA-TGCACCGATGCACTCAGAATATTT-TG-AAACATCGAATGCATTTGATGCATCGATGCA-C
*
1395753 AG
62 AA
* * ** *
1395755 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 CCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTGATGCATCGATGCAC
1395816 TCTTAGTGCA
Statistics
Matches: 106, Mismatches: 12, Indels: 17
0.79 0.09 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 47 0.44
65 49 0.46
66 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
CCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTGATGCATCGATGCACAA
Found at i:1395815 original size:17 final size:19
Alignment explanation
Indices: 1395787--1395835 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1395777 TATTTTGAAA
1395787 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1395805 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1395824 CACCGATGCACT
1 CATCGATGCACT
1395836 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1399012 original size:15 final size:16
Alignment explanation
Indices: 1398992--1399026 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1398982 GGGTTTTCAA
*
1398992 ATTAATTTGT-TAACC
1 ATTAATTGGTATAACC
1399007 ATTAATTGGTATAACC
1 ATTAATTGGTATAACC
1399023 ATTA
1 ATTA
1399027 TTTTTTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (16 bp):
ATTAATTGGTATAACC
Found at i:1401085 original size:2 final size:2
Alignment explanation
Indices: 1401078--1401438 Score: 173
Period size: 2 Copynumber: 187.5 Consensus size: 2
1401068 AATTGAAAAC
1401078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1401120 AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT TT AT AT -T AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * * *
1401161 AA AC A- AT AT A- AT -T AT -T AT A- AG CT AT AT AT AA AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1401197 AT GT TT AT GT GA- AT -T AT AT AT AT AA ACT AT AT A- AGT AT A-
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* * * * *
1401236 AA AT AT AA AA AGT AT AT AGT TT AT AT -T AT TT AT AT -T A- AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1401277 AGT AT AT AT AT AT TT AT AT AT AT AT A- AA AT AT AT GT AT AA ACT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
1401320 AT AT A- AA AT AT AT AGT TT AT AT AT -T AT A- AT TT AT AT -T A-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1401358 AT AT AGT AT AT AT AT GT AT GT AT A- ACT A- AT AT A- AGT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
1401397 A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1401438 A
1 A
1401439 AAGAAATATT
Statistics
Matches: 276, Mismatches: 43, Indels: 80
0.69 0.11 0.20
Matches are distributed among these distances:
1 27 0.10
2 236 0.86
3 13 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1401663 original size:16 final size:16
Alignment explanation
Indices: 1401644--1401704 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 16
1401634 CAATAGTTAA
1401644 TATATGTAACTTATAG
1 TATATGTAACTTATAG
1401660 TATATGTATACATTTAAACTA-
1 TATATGTA-AC--TT--A-TAG
1401681 TATATGTAACTTATAG
1 TATATGTAACTTATAG
*
1401697 TACATGTA
1 TATATGTA
1401705 TGTATACTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
15 2 0.05
16 16 0.43
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 9 0.24
22 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (16 bp):
TATATGTAACTTATAG
Found at i:1401723 original size:2 final size:2
Alignment explanation
Indices: 1401716--1401796 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
1401706 GTATACTATG
1401716 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
1401758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1401797 CTAACATATA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1401891 original size:7 final size:7
Alignment explanation
Indices: 1401881--1401918 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1401871 TAGTTTATAA
1401881 AAACCCT
1 AAACCCT
1401888 AAACCCT
1 AAACCCT
1401895 AAA-CCT
1 AAACCCT
1401901 AAACCCT
1 AAACCCT
*
1401908 AAATCCT
1 AAACCCT
1401915 AAAC
1 AAAC
1401919 ACTATCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:1401903 original size:13 final size:14
Alignment explanation
Indices: 1401885--1401918 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1401875 TTATAAAAAC
1401885 CCTAAACCCTAAA-
1 CCTAAACCCTAAAT
1401898 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
1401912 CCTAAAC
1 CCTAAAC
1401919 ACTATCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:1401906 original size:20 final size:20
Alignment explanation
Indices: 1401881--1401918 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1401871 TAGTTTATAA
1401881 AAACCCTAAACCCTAAACCT
1 AAACCCTAAACCCTAAACCT
*
1401901 AAACCCTAAATCCTAAAC
1 AAACCCTAAACCCTAAAC
1401919 ACTATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (20 bp):
AAACCCTAAACCCTAAACCT
Found at i:1402026 original size:22 final size:20
Alignment explanation
Indices: 1402001--1402105 Score: 67
Period size: 22 Copynumber: 5.1 Consensus size: 20
1401991 CTTATAGTAC
1402001 ATGTATCATATATGTATAAACT
1 ATGTAT-ATATAT-TATAAACT
1402023 ATGTATAGTATA-TATAAACT
1 ATGTATA-TATATTATAAACT
*
1402043 ATG-A-ATATA-TATAACCT
1 ATGTATATATATTATAAACT
*
1402060 ATAGTATATGTATATATACAATCT
1 AT-GTATATATAT-TATA-AA-CT
* *
1402084 ATTTATATGT-TATATAAACT
1 ATGTATATATAT-TATAAACT
1402104 AT
1 AT
1402106 ATATGTAACC
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
17 13 0.18
18 2 0.03
19 2 0.03
20 19 0.27
21 3 0.04
22 20 0.28
23 8 0.11
24 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
ATGTATATATATTATAAACT
Found at i:1402085 original size:24 final size:22
Alignment explanation
Indices: 1402048--1402106 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1402038 AAACTATGAA
*
1402048 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
1402070 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
1402093 T-TATATAAACTATA
1 TATATATAAACTATA
1402107 TATGTAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:1402140 original size:21 final size:21
Alignment explanation
Indices: 1402116--1402204 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
1402106 ATATGTAACC
*
1402116 TATAGTTTATAATCAATAGTT
1 TATAATTTATAATCAATAGTT
* *
1402137 TATAATATTGTACT-ATATAGTT
1 TATAAT-TTATAATCA-ATAGTT
* * * *
1402159 TATACTTTATAACCTATAGTA
1 TATAATTTATAATCAATAGTT
* *
1402180 TATAATTTATAAACTATAGTT
1 TATAATTTATAATCAATAGTT
1402201 TATA
1 TATA
1402205 TTAATGTACT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 37 0.70
22 16 0.30
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAATTTATAATCAATAGTT
Found at i:1402190 original size:14 final size:14
Alignment explanation
Indices: 1402116--1402190 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
1402106 ATATGTAACC
*
1402116 TATAGTTTATAATC
1 TATAGTTTATAATT
*
1402130 AATAGTTTATAATAT
1 TATAGTTTATAAT-T
* * * *
1402145 TGTACTATATAGTT
1 TATAGTTTATAATT
* **
1402159 TATACTTTATAACC
1 TATAGTTTATAATT
*
1402173 TATAGTATATAATT
1 TATAGTTTATAATT
1402187 TATA
1 TATA
1402191 AACTATAGTT
Statistics
Matches: 44, Mismatches: 16, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
14 36 0.82
15 8 0.18
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATT
Found at i:1402217 original size:20 final size:21
Alignment explanation
Indices: 1402131--1402233 Score: 75
Period size: 22 Copynumber: 4.8 Consensus size: 21
1402121 TTTATAATCA
* *
1402131 ATAGTTTATAATATTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
1402153 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
1402174 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
1402195 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
1402217 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
1402234 TAATTATCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 7 0.11
21 23 0.35
22 34 0.52
23 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:1402252 original size:15 final size:14
Alignment explanation
Indices: 1402222--1402438 Score: 97
Period size: 15 Copynumber: 14.4 Consensus size: 14
1402212 ACTATATAGT
*
1402222 TTATATTAATGTTAA
1 TTATATTAAT-ATAA
*
1402237 TTATCTTAACTATAA
1 TTATATTAA-TATAA
1402252 TTTATATTAATATAA
1 -TTATATTAATATAA
*
1402267 TATATAGTTTATA-AA
1 T-TATA-TTAATATAA
* *
1402282 CTATACT-ATATAA
1 TTATATTAATATAA
*
1402295 TT-TATAACATATAA
1 TTATATTA-ATATAA
1402309 TTTATATTAATATTAA
1 -TTATATTAATA-TAA
*
1402325 TGT-TA-TAGACTATATT
1 T-TATATTA-A-TATA-A
1402341 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
1402356 TTATAAATTATAAACTATA
1 TTAT--ATTA-ATA-TA-A
1402375 TTATATTAATATAA
1 TTATATTAATATAA
1402389 GTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
*
1402406 TTATAAT-ATATAA
1 TTATATTAATATAA
1402419 TTA-ATATAATATTAA
1 TTATAT-TAATA-TAA
1402434 TTATA
1 TTATA
1402439 AATAGTTAAT
Statistics
Matches: 157, Mismatches: 17, Indels: 55
0.69 0.07 0.24
Matches are distributed among these distances:
12 6 0.04
13 11 0.07
14 20 0.13
15 54 0.34
16 44 0.28
17 13 0.08
18 4 0.03
19 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:1402271 original size:7 final size:7
Alignment explanation
Indices: 1402247--1402439 Score: 57
Period size: 7 Copynumber: 26.7 Consensus size: 7
1402237 TTATCTTAAC
*
1402247 TATAATT
1 TATAATA
*
1402254 TATATTAA
1 TATAAT-A
1402262 TATAATA
1 TATAATA
* *
1402269 TATAGTT
1 TATAATA
1402276 TATAA-A
1 TATAATA
*
1402282 CTATACTA
1 -TATAATA
*
1402290 TATAATT
1 TATAATA
*
1402297 TATAACA
1 TATAATA
1402304 TATAATTTA
1 TATAA--TA
1402313 TATTAATA
1 TA-TAATA
*
1402321 T-TAATGT
1 TATAAT-A
1402328 TATAGACTA
1 TATA-A-TA
**
1402337 TATTTTA
1 TATAATA
1402344 TATTAATA
1 TA-TAATA
1402352 T-TAAT-
1 TATAATA
1402357 TATAA-A
1 TATAATA
1402363 TTATAA-A
1 -TATAATA
*
1402370 CTATATTA
1 -TATAATA
1402378 TATTAATA
1 TA-TAATA
1402386 TAAGTTAATA
1 T-A--TAATA
1402396 T-TAATA
1 TATAATA
1402402 T-TAAT-
1 TATAATA
1402407 TATAATA
1 TATAATA
1402414 TATAATTAA
1 TATAA-T-A
1402423 TATAATA
1 TATAATA
1402430 T-TAAT-
1 TATAATA
1402435 TATAA
1 TATAA
1402440 ATAGTTAATT
Statistics
Matches: 141, Mismatches: 22, Indels: 47
0.67 0.10 0.22
Matches are distributed among these distances:
5 3 0.02
6 32 0.23
7 58 0.41
8 23 0.16
9 14 0.10
10 11 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (7 bp):
TATAATA
Found at i:1402291 original size:21 final size:21
Alignment explanation
Indices: 1402247--1402314 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1402237 TTATCTTAAC
1402247 TATAATTTATATTAA-TATAATA
1 TATAATTTATA--AACTATAATA
* *
1402269 TATAGTTTATAAACTATACTA
1 TATAATTTATAAACTATAATA
*
1402290 TATAATTTAT-AACATATAATT
1 TATAATTTATAAAC-TATAATA
1402311 TATA
1 TATA
1402315 TTAATATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.13
21 24 0.62
22 10 0.26
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (21 bp):
TATAATTTATAAACTATAATA
Found at i:1402316 original size:88 final size:89
Alignment explanation
Indices: 1402173--1402384 Score: 240
Period size: 88 Copynumber: 2.4 Consensus size: 89
1402163 CTTTATAACC
* * * * * *
1402173 TATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAAT
1 TATAATATATAATTTATAAACTATACTATATATTAATGAACTATATAATTTATATTAATATTAAT
*
1402238 -TATCTTA-ACTATAATTTATATTAA
66 GT-T-ATAGACTATAATTTATATTAA
* *
1402262 TATAATATATAGTTTATAAACTATACTATATAATTTAT-AAC-ATATAATTTATATTAATATTAA
1 TATAATATATAATTTATAAACTATACTATAT-ATTAATGAACTATATAATTTATATTAATATTAA
*
1402325 TGTTATAGACTATATTTTATATTAA
65 TGTTATAGACTATAATTTATATTAA
*
1402350 TATTAAT-TATAAATTATAAACTATA-T-TATATTAAT
1 TA-TAATATATAATTTATAAACTATACTATATATTAAT
1402385 ATAAGTTAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
85 5 0.05
86 3 0.03
87 3 0.03
88 56 0.53
89 34 0.32
90 5 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (89 bp):
TATAATATATAATTTATAAACTATACTATATATTAATGAACTATATAATTTATATTAATATTAAT
GTTATAGACTATAATTTATATTAA
Found at i:1402323 original size:6 final size:6
Alignment explanation
Indices: 1402312--1402448 Score: 54
Period size: 6 Copynumber: 22.3 Consensus size: 6
1402302 CATATAATTT
* * * * *
1402312 ATATTA ATATTA ATGTTA TAGACT- ATATTTT ATATTA ATATTA ATTATAA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA A-TATTA
* * *
1402362 ATTATAA ACTATATT ATATTA ATA-TA A-GTTA ATATTA ATATTA AT-TATA
1 A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA
*
1402411 ATA-T- ATAATTA ATA-TA ATATTA ATTATAA ATAGTTA AT
1 ATATTA AT-ATTA ATATTA ATATTA A-TATTA ATA-TTA AT
1402449 TAATAAAAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.02
5 16 0.16
6 47 0.47
7 34 0.34
8 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
ATATTA
Found at i:1402344 original size:31 final size:30
Alignment explanation
Indices: 1402215--1402439 Score: 128
Period size: 28 Copynumber: 8.0 Consensus size: 30
1402205 TTAATGTACT
* * *
1402215 ATATAGTTTATATTAATGTTAATTATCTTAAC
1 ATATAATTTATATTAATATTAATT-T-ATAAC
* **
1402247 -TATAATTTATATTAATA-TAATATATAGT
1 ATATAATTTATATTAATATTAATTTATAAC
* ** *
1402275 TTATAAACTATACT-ATA-TAATTTATAAC
1 ATATAATTTATATTAATATTAATTTATAAC
1402303 ATATAATTTATATTAATATTAATGTTATAGAC
1 ATATAATTTATATTAATATTAAT-TTATA-AC
*
1402335 -TATATTTTATATTAATATTAA-TTATAA-
1 ATATAATTTATATTAATATTAATTTATAAC
**
1402362 ATTATAAACTATATT-ATATTAA--TATAA-
1 A-TATAATTTATATTAATATTAATTTATAAC
* *
1402389 GT-T-A---ATATTAATATTAA-TTATAAT
1 ATATAATTTATATTAATATTAATTTATAAC
*
1402413 ATATAATTAATA-TAATATTAA-TTATAA
1 ATATAATTTATATTAATATTAATTTATAA
1402440 ATAGTTAATT
Statistics
Matches: 156, Mismatches: 22, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
21 5 0.03
22 7 0.04
23 5 0.03
24 2 0.01
25 2 0.01
26 2 0.01
27 5 0.03
28 46 0.29
29 32 0.21
30 8 0.05
31 40 0.26
32 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (30 bp):
ATATAATTTATATTAATATTAATTTATAAC
Found at i:1402361 original size:110 final size:109
Alignment explanation
Indices: 1402159--1402367 Score: 237
Period size: 110 Copynumber: 1.9 Consensus size: 109
1402149 CTATATAGTT
* * *
1402159 TATACTTTATAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTT
1 TATACTTTATAAACTATACTATATAATTTATAAACTATAATTTATATTAA-GTACTATATAGTTT
* * * *
1402224 ATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAATA
65 AGACTAATGTTAATTATATTAACTATAAATTATATTAATATAATA
* *
1402269 TATAGTTTATAAACTATACTATATAATTTAT-AACATATAATTTATATTAA-TATTA-AT-GTTA
1 TATACTTTATAAACTATACTATATAATTTATAAAC-TATAATTTATATTAAGTACTATATAGTT-
* *
1402330 TAGACTATATTTTATATTAATATTAATTATAAATTATA
64 TAGACTA-ATGTTA-ATT-ATATTAACTATAAATTATA
1402368 AACTATATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
106 3 0.04
107 7 0.08
108 9 0.11
109 6 0.07
110 58 0.70
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (109 bp):
TATACTTTATAAACTATACTATATAATTTATAAACTATAATTTATATTAAGTACTATATAGTTTA
GACTAATGTTAATTATATTAACTATAAATTATATTAATATAATA
Found at i:1402421 original size:23 final size:23
Alignment explanation
Indices: 1402351--1402425 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
1402341 TTATATTAAT
*
1402351 ATTAATTATAAATTATAA-ACTAT-
1 ATTAA-TATTAATTATAATA-TATA
1402374 ATT-ATATTAA-TATAAGT-TA-A
1 ATTAATATTAATTATAA-TATATA
1402394 TATTAATATTAATTATAATATATA
1 -ATTAATATTAATTATAATATATA
1402418 ATTAATAT
1 ATTAATAT
1402426 AATATTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
20 7 0.16
21 8 0.19
22 9 0.21
23 18 0.42
24 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTAATATTAATTATAATATATA
Found at i:1402430 original size:44 final size:44
Alignment explanation
Indices: 1402346--1402427 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 44
1402336 ATATTTTATA
1402346 TTAATATTAATTATAAATTATAAACTATATTATATTAATATAAG
1 TTAATATTAATTATAAATTATAAACTATATTATATTAATATAAG
*
1402390 TTAATATTAA-TATTAATTAT-AA-TATA-TA-ATTAATATAA
1 TTAATATTAATTATAAATTATAAACTATATTATATTAATATAA
1402428 TATTAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 10 0.27
40 2 0.05
41 4 0.11
42 2 0.05
43 9 0.24
44 10 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (44 bp):
TTAATATTAATTATAAATTATAAACTATATTATATTAATATAAG
Found at i:1402431 original size:50 final size:51
Alignment explanation
Indices: 1402343--1402439 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 51
1402333 ACTATATTTT
*
1402343 ATATTAATATTAATTATAAATTATAAACTATATTATATTAA-TATAAGTTA
1 ATATTAATATTAATTATAAATTATAAACTATATAATATTAATTATAAGTTA
*
1402393 ATATTAATATTAATTAT-AA-TATATAATTAATATAATATTAATTATAA
1 ATATTAATATTAATTATAAATTATA-AACT-ATATAATATTAATTATAA
1402440 ATAGTTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
48 4 0.10
49 5 0.12
50 28 0.67
51 5 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (51 bp):
ATATTAATATTAATTATAAATTATAAACTATATAATATTAATTATAAGTTA
Found at i:1402442 original size:29 final size:29
Alignment explanation
Indices: 1402374--1402453 Score: 101
Period size: 28 Copynumber: 2.7 Consensus size: 29
1402364 TATAAACTAT
*
1402374 ATTATATTAATATAAGTTAATATTAATATTA
1 ATTATAAT-ATATAA-TTAATATTAATATTA
1402405 ATTATAATATATAATTAATA-TAATATTA
1 ATTATAATATATAATTAATATTAATATTA
1402433 ATTATAA-ATAGTTAATTAATA
1 ATTATAATATA--TAATTAATA
1402454 AAAATTATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 3 0.07
28 15 0.33
29 15 0.33
30 6 0.13
31 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (29 bp):
ATTATAATATATAATTAATATTAATATTA
Found at i:1403174 original size:19 final size:19
Alignment explanation
Indices: 1403136--1403186 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1403126 ATCTTCTATC
*
1403136 ACCC-AACCCT-AACTTGA
1 ACCCGAACCCTAAACCTGA
*
1403153 ACCTGAACCCTAAACCTGA
1 ACCCGAACCCTAAACCTGA
1403172 ACCCGAACCC-AAACC
1 ACCCGAACCCTAAACC
1403187 CGAATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 15 0.52
ACGTcount: A:0.37, C:0.43, G:0.08, T:0.12
Consensus pattern (19 bp):
ACCCGAACCCTAAACCTGA
Found at i:1403218 original size:43 final size:43
Alignment explanation
Indices: 1403158--1403261 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
1403148 CTTGAACCTG
* * **
1403158 AACCCTAAACCT-GAACCCGAACCCAAACCCGAATTCAAATCTA
1 AACCCT-AACCTAAAACCCGAACCCAAACCCAAACCCAAATCTA
* *
1403201 TA-CCTGAATCTAAAACCCGAACCCAAACCCAAACCCAAATCTA
1 AACCCT-AACCTAAAACCCGAACCCAAACCCAAACCCAAATCTA
1403244 AACCCTAACCTAAAACCC
1 AACCCTAACCTAAAACCC
1403262 TTAACCCTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
42 7 0.14
43 40 0.80
44 3 0.06
ACGTcount: A:0.43, C:0.38, G:0.05, T:0.13
Consensus pattern (43 bp):
AACCCTAACCTAAAACCCGAACCCAAACCCAAACCCAAATCTA
Found at i:1403550 original size:17 final size:17
Alignment explanation
Indices: 1403528--1403569 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1403518 AAACTGTTTA
*
1403528 ATTTGTTTCTATTGTTG
1 ATTTGTTTCTACTGTTG
1403545 ATTTGTTTCTACTGTTG
1 ATTTGTTTCTACTGTTG
1403562 ATTTGTTT
1 ATTTGTTT
1403570 GCGTTGTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (17 bp):
ATTTGTTTCTACTGTTG
Found at i:1403721 original size:102 final size:102
Alignment explanation
Indices: 1403557--1403765 Score: 382
Period size: 102 Copynumber: 2.0 Consensus size: 102
1403547 TTGTTTCTAC
*
1403557 TGTTGATTTGTTTGCGTTGTTGGTTGTTCATTCGGATTGCTTTTATAAGGTTGTTAGGTGCCTTT
1 TGTTGATTTGTTTGCGTTGTTGGTTGTTCATTCGGATTGCTTTTATAAGGTTGTTAGCTGCCTTT
*
1403622 ATTTAGAGTTTAAATAAACTGTTTAATTTGTAGCTAT
66 ATTTACAGTTTAAATAAACTGTTTAATTTGTAGCTAT
*
1403659 TGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTTTATAAGGTTGTTAGCTGCCTTT
1 TGTTGATTTGTTTGCGTTGTTGGTTGTTCATTCGGATTGCTTTTATAAGGTTGTTAGCTGCCTTT
*
1403724 ATTTACAGTTTAAATAAACTGTTTAATTTGTAGCTTT
66 ATTTACAGTTTAAATAAACTGTTTAATTTGTAGCTAT
1403761 TGTTG
1 TGTTG
1403766 GTTGTTCATT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.51
Consensus pattern (102 bp):
TGTTGATTTGTTTGCGTTGTTGGTTGTTCATTCGGATTGCTTTTATAAGGTTGTTAGCTGCCTTT
ATTTACAGTTTAAATAAACTGTTTAATTTGTAGCTAT
Found at i:1406328 original size:20 final size:20
Alignment explanation
Indices: 1406303--1406361 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1406293 CTACATGTTG
*
1406303 CTGCTTCCTACTGACTGCTA
1 CTGCTTCCTACTGCCTGCTA
1406323 CTGCTTCCTACTGCCTGCTA
1 CTGCTTCCTACTGCCTGCTA
*
1406343 CTGCTTCCTGCTGCCTGCT
1 CTGCTTCCTACTGCCTGCT
1406362 TGTTGTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.08, C:0.39, G:0.17, T:0.36
Consensus pattern (20 bp):
CTGCTTCCTACTGCCTGCTA
Found at i:1406356 original size:10 final size:10
Alignment explanation
Indices: 1406303--1406356 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
1406293 CTACATGTTG
1406303 CTGCTTCCTA
1 CTGCTTCCTA
*
1406313 CTGAC-TGCTA
1 CTG-CTTCCTA
1406323 CTGCTTCCTA
1 CTGCTTCCTA
* *
1406333 CTGCCTGCTA
1 CTGCTTCCTA
*
1406343 CTGCTTCCTG
1 CTGCTTCCTA
1406353 CTGC
1 CTGC
1406357 CTGCTTGTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 1 0.03
10 33 0.94
11 1 0.03
ACGTcount: A:0.09, C:0.39, G:0.17, T:0.35
Consensus pattern (10 bp):
CTGCTTCCTA
Found at i:1406950 original size:14 final size:14
Alignment explanation
Indices: 1406931--1406977 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1406921 TTTTTTTCTT
1406931 TATATAAATTAAAC
1 TATATAAATTAAAC
1406945 TATAT-AATT----
1 TATATAAATTAAAC
1406954 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1406968 TATATTAATT
1 TATATAAATT
1406978 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1406955 original size:23 final size:24
Alignment explanation
Indices: 1406929--1406978 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1406919 TATTTTTTTC
1406929 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1406952 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1406976 TTT
1 TTT
1406979 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1407274 original size:16 final size:15
Alignment explanation
Indices: 1407253--1407297 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
1407243 TTTGCAGGTT
1407253 AGGTTAAAAACAGATC
1 AGGTTAAAAACAG-TC
1407269 AGGTTAAAAACATGTC
1 AGGTTAAAAACA-GTC
*
1407285 AGGTTGAAAACAG
1 AGGTTAAAAACAG
1407298 GTCGGGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (15 bp):
AGGTTAAAAACAGTC
Found at i:1407629 original size:28 final size:28
Alignment explanation
Indices: 1407597--1407688 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
1407587 GTTGCGACTA
1407597 CTTTCTTCTCTAGGTTCAGTGTTCCTTG
1 CTTTCTTCTCTAGGTTCAGTGTTCCTTG
* * ***
1407625 CTTTCTTATATA--TCTCAACCTTCTTCTAT-
1 CTTTCTTCTCTAGGT-TCAGTGTTC--CT-TG
*
1407654 ATTTCTTCTCTAGGTTCAGTGTTCCTTG
1 CTTTCTTCTCTAGGTTCAGTGTTCCTTG
1407682 CTTTCTT
1 CTTTCTT
1407689 ATATATCTCA
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
26 1 0.02
27 7 0.16
28 18 0.40
29 11 0.24
30 7 0.16
31 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.11, T:0.52
Consensus pattern (28 bp):
CTTTCTTCTCTAGGTTCAGTGTTCCTTG
Found at i:1411815 original size:3 final size:3
Alignment explanation
Indices: 1411807--1411841 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1411797 AAGGCACTGC
*
1411807 AGA AGA AGA AGC AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1411842 CTATCGGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1412238 original size:53 final size:54
Alignment explanation
Indices: 1412170--1412272 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
1412160 ACCTTGGTAA
*
1412170 ATCCAACTTAATA-TTTTTTAGTAAATTACGTTTTATATCCCTCAATTTTGGGG
1 ATCCAACTTAATATTTTTTTAGTAAATTACGTTTTATATCACTCAATTTTGGGG
* * *
1412223 ATCCCACTTAATATTTTTTTAGTAAATTATGTTTTTTATCACTCAATTTT
1 ATCCAACTTAATATTTTTTTAGTAAATTACGTTTTATATCACTCAATTTT
1412273 AACCTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 12 0.27
54 33 0.73
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.50
Consensus pattern (54 bp):
ATCCAACTTAATATTTTTTTAGTAAATTACGTTTTATATCACTCAATTTTGGGG
Found at i:1413785 original size:27 final size:27
Alignment explanation
Indices: 1413755--1413809 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1413745 TTTGTGTTAG
1413755 CGTCTAAAAGATTTATCTTTGTTTATA
1 CGTCTAAAAGATTTATCTTTGTTTATA
1413782 CGTCTAAAAGATTTATCTTTGTTTATA
1 CGTCTAAAAGATTTATCTTTGTTTATA
1413809 C
1 C
1413810 TCGGTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (27 bp):
CGTCTAAAAGATTTATCTTTGTTTATA
Found at i:1414631 original size:38 final size:39
Alignment explanation
Indices: 1414537--1414633 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 39
1414527 GGGTATGTCC
* *
1414537 ATGAGATTCAACATCAATCTAGCACCAATGAACAAGATA
1 ATGAGATTCAACATCAACCTAACACCAATGAACAAGATA
* ** **
1414576 GTGAGATTCAATGTCAACCTAACACCGCTGAACAAGA-A
1 ATGAGATTCAACATCAACCTAACACCAATGAACAAGATA
*
1414614 ATGAGATTAAACATCAACCT
1 ATGAGATTCAACATCAACCT
1414634 GGCATTGATG
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
38 17 0.36
39 30 0.64
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (39 bp):
ATGAGATTCAACATCAACCTAACACCAATGAACAAGATA
Found at i:1415970 original size:42 final size:43
Alignment explanation
Indices: 1415918--1416032 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 43
1415908 CATTTTTGGA
*
1415918 AAAAACGCCGCTAAATACTAGTACTTTAGTGGC-TTTTTCTAT
1 AAAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTCTAT
* * * * *
1415960 AAAAATGCCGCTATAGACTTGTATTTTAGTGGCA-TTTT-TGT
1 AAAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTCTAT
* * *
1416001 ACAAACACCGCTATAGACTCA-TACTTTAGTGG
1 AAAAACGCCGCTAAAGACT-AGTACTTTAGTGG
1416033 GTTGTTAGAC
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 28 0.47
42 32 0.53
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTCTAT
Found at i:1416029 original size:41 final size:40
Alignment explanation
Indices: 1415939--1416071 Score: 124
Period size: 40 Copynumber: 3.2 Consensus size: 40
1415929 TAAATACTAG
* * **
1415939 TACTTTAGTGGCTTTTTCTATAAAAATGCCGCTATAGACTTG
1 TACTTTAGTGGCTTTTTGTACAAAAA--CCGCTATAGACTCA
* *
1415981 TATTTTAGTGGCATTTTTGTACAAACACCGCTATAGACTCA
1 TACTTTAGTGGC-TTTTTGTACAAAAACCGCTATAGACTCA
* * ** *
1416022 TACTTTAGTGGGTTGTTAG-ACAAATGCCGCTAAAGACTCA
1 TACTTTAGTGGCTT-TTTGTACAAAAACCGCTATAGACTCA
1416062 TACTTTAGTG
1 TACTTTAGTG
1416072 TCGGTTTTAG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 30 0.39
41 25 0.32
42 11 0.14
43 11 0.14
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (40 bp):
TACTTTAGTGGCTTTTTGTACAAAAACCGCTATAGACTCA
Found at i:1416059 original size:40 final size:40
Alignment explanation
Indices: 1416008--1416088 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
1415998 TGTACAAACA
*
1416008 CCGCTATAGACTCATACTTTAGTG-GGTTGTTAGACAAATG
1 CCGCTAAAGACTCATACTTTAGTGCGGTT-TTAGACAAATG
1416048 CCGCTAAAGACTCATACTTTAGTGTCGGTTTTAGACAAATG
1 CCGCTAAAGACTCATACTTTAGTG-CGGTTTTAGACAAATG
1416089 TCACTATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 23 0.61
41 11 0.29
42 4 0.11
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (40 bp):
CCGCTAAAGACTCATACTTTAGTGCGGTTTTAGACAAATG
Found at i:1418441 original size:21 final size:21
Alignment explanation
Indices: 1418417--1418457 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1418407 TTTATTTCCT
* *
1418417 TTTTAATTTTTTTTCTAATTC
1 TTTTAATTCTCTTTCTAATTC
1418438 TTTTAATTCTCTTTCTAATT
1 TTTTAATTCTCTTTCTAATT
1418458 TGTGAATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAATTCTCTTTCTAATTC
Found at i:1423960 original size:16 final size:16
Alignment explanation
Indices: 1423939--1423998 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
1423929 CAGATCGAGA
*
1423939 AAACATACATCAATAC
1 AAACATACATCAACAC
1423955 AAACATACATCAACAC
1 AAACATACATCAACAC
* *
1423971 ATACATATATACATACAC
1 AAACATACAT-CA-ACAC
*
1423989 ATACATACAT
1 AAACATACAT
1423999 GACACATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 23 0.61
17 2 0.05
18 13 0.34
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (16 bp):
AAACATACATCAACAC
Found at i:1423996 original size:14 final size:15
Alignment explanation
Indices: 1423973--1424005 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1423963 ATCAACACAT
*
1423973 ACATATATACAT-AC
1 ACATACATACATGAC
1423987 ACATACATACATGAC
1 ACATACATACATGAC
1424002 ACAT
1 ACAT
1424006 GAAATTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (15 bp):
ACATACATACATGAC
Found at i:1424390 original size:31 final size:32
Alignment explanation
Indices: 1424347--1424444 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 32
1424337 TTTCTCTGAA
*
1424347 AAACCAATTTTGTCTCGCTTGAGAATTTTTTC
1 AAACAAATTTTGTCTCGCTTGAGAATTTTTTC
* *
1424379 -CACAAATTTTGTCTCGCTTGAGACAATTTCTCTC
1 AAACAAATTTTGTCTCGCTTGAG--AATTT-TTTC
*
1424413 AAAACAAATTTTGTCTCGCTTCAGACATTTTT
1 -AAACAAATTTTGTCTCGCTTGAGA-ATTTTT
1424445 CTCTAAGATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 20 0.37
33 5 0.09
34 5 0.09
35 4 0.07
36 20 0.37
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (32 bp):
AAACAAATTTTGTCTCGCTTGAGAATTTTTTC
Found at i:1424420 original size:36 final size:36
Alignment explanation
Indices: 1424318--1424461 Score: 147
Period size: 36 Copynumber: 4.0 Consensus size: 36
1424308 TTTAAAAAAA
* *
1424318 TTGTCTCGCTTGAGACAACTTTCTCTGAAAAACCAATT
1 TTGTCTCGCTTGAGACAA-TTTCTCT-CAAAACAAATT
* *
1424356 TTGTCTCGCTTGAG--AATTT-TTTC--CACAAATT
1 TTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATT
1424387 TTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATT
1 TTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATT
* *
1424423 TTGTCTCGCTTCAGAC-ATTTTTCTCTAAGATACAAATT
1 TTGTCTCGCTTGAGACAATTTCTCTC-AA-A-ACAAATT
1424461 T
1 T
1424462 AAATTTTTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
31 20 0.22
33 5 0.06
34 5 0.06
35 11 0.12
36 26 0.29
37 1 0.01
38 22 0.24
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.40
Consensus pattern (36 bp):
TTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATT
Found at i:1424723 original size:66 final size:66
Alignment explanation
Indices: 1424584--1424744 Score: 186
Period size: 66 Copynumber: 2.5 Consensus size: 66
1424574 AAAATTTATA
* * * *
1424584 ATCTTTGGGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAATT
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAT
*
1424649 T
66 C
* * *
1424650 TTTTTTGAGTTTGTTTCTTTGGATAC-AAA-GTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTGAGACAATTTCTTTTG--AAAA
1424713 ATC
64 ATC
*
1424716 ATCTTTGAG-TTGTTTATCTT-GAAACAAAA
1 ATCTTTGAGTTTGTTTCT-TTGGAAACAAAA
1424745 ATCTTGGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
64 27 0.34
65 14 0.18
66 38 0.48
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (66 bp):
ATCTTTGAGTTTGTTTCTTTGGAAACAAAATGTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAT
C
Found at i:1424817 original size:30 final size:31
Alignment explanation
Indices: 1424783--1424871 Score: 90
Period size: 34 Copynumber: 2.8 Consensus size: 31
1424773 ATTTTGTCTC
*
1424783 TTGAGACAGTTTCTTTTGAAA-AAAAAATCT
1 TTGAGACAGTTTCCTTTGAAACAAAAAATCT
* *
1424813 TTGAGTCTGTTTCCTTTGAAACAAAAAAACATCT
1 TTGAGACAGTTTCCTTTGAAAC--AAAAA-ATCT
** *
1424847 TTGAGATTGTTTCCCTTGAAACAAA
1 TTGAGACAGTTTCCTTTGAAACAAA
1424872 TTTTATCTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 18 0.37
32 3 0.06
33 5 0.10
34 23 0.47
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGAGACAGTTTCCTTTGAAACAAAAAATCT
Found at i:1424847 original size:34 final size:34
Alignment explanation
Indices: 1424801--1424871 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1424791 GTTTCTTTTG
*
1424801 AAAAAAAAATCTTTGAG-TCTGTTTCCTTTGAAAC
1 AAAAAAAAATCTTTGAGAT-TGTTTCCCTTGAAAC
*
1424835 AAAAAAACATCTTTGAGATTGTTTCCCTTGAAAC
1 AAAAAAAAATCTTTGAGATTGTTTCCCTTGAAAC
1424869 AAA
1 AAA
1424872 TTTTATCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (34 bp):
AAAAAAAAATCTTTGAGATTGTTTCCCTTGAAAC
Found at i:1425564 original size:14 final size:14
Alignment explanation
Indices: 1425545--1425580 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1425535 AACCCGGTTC
1425545 TGACCCATTACAAG
1 TGACCCATTACAAG
1425559 TGACCCATTACAAG
1 TGACCCATTACAAG
1425573 TGACCCAT
1 TGACCCAT
1425581 CACTTAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (14 bp):
TGACCCATTACAAG
Found at i:1426079 original size:14 final size:13
Alignment explanation
Indices: 1426046--1426070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1426036 AAAGCAAAGA
1426046 AAAAAGATTTGAG
1 AAAAAGATTTGAG
1426059 AAAAAGATTTGA
1 AAAAAGATTTGA
1426071 ACCAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
AAAAAGATTTGAG
Found at i:1426902 original size:30 final size:29
Alignment explanation
Indices: 1426868--1427029 Score: 139
Period size: 30 Copynumber: 5.4 Consensus size: 29
1426858 TTAATACCAG
1426868 TTTAGTCCTTTAACTTTCTATTTTTGCTAT
1 TTTAGTCCTTTAACTTT-TATTTTTGCTAT
* *
1426898 TTTAGTCCTGTAACTTTT-TGTTTTTCTAT
1 TTTAGTCCTTTAACTTTTAT-TTTTGCTAT
* * * * *
1426927 TTT-GACCCTTAAGTTTTTTTTTTACTAT
1 TTTAGTCCTTTAACTTTTATTTTTGCTAT
* * * *
1426955 TTTAGCCCTTTAAATTTCTATTTGTGCCAT
1 TTTAGTCCTTTAACTTT-TATTTTTGCTAT
*
1426985 TTTAGTCCTTTAAGTTTTAGTTTTTTTGCTAT
1 TTTAGTCCTTTAACTTTTA---TTTTTGCTAT
*
1427017 TTTGGTCCTTTAA
1 TTTAGTCCTTTAA
1427030 GTTGTTGTTT
Statistics
Matches: 106, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 22 0.21
29 25 0.24
30 39 0.37
32 20 0.19
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.59
Consensus pattern (29 bp):
TTTAGTCCTTTAACTTTTATTTTTGCTAT
Found at i:1426963 original size:28 final size:28
Alignment explanation
Indices: 1426868--1426964 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
1426858 TTAATACCAG
* * *
1426868 TTTAGTCCTTTAACTTTCTATTTTTGCTAT
1 TTTAG-CCCTTAACTTTTTGTTTTT-CTAT
*
1426898 TTTAGTCCTGTAACTTTTTGTTTTTCTAT
1 TTTAGCCCT-TAACTTTTTGTTTTTCTAT
*
1426927 TTT-GACCCTTAAGTTTTT-TTTTTACTAT
1 TTTAG-CCCTTAACTTTTTGTTTTT-CTAT
1426955 TTTAGCCCTT
1 TTTAGCCCTT
1426965 TAAATTTCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 5 0.09
28 21 0.37
29 13 0.23
30 18 0.32
ACGTcount: A:0.15, C:0.16, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTAGCCCTTAACTTTTTGTTTTTCTAT
Found at i:1427050 original size:29 final size:31
Alignment explanation
Indices: 1426982--1427064 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
1426972 CTATTTGTGC
* *
1426982 CATTTTAGTCCTTTAAGTTTTAGTTTTTTTG
1 CATTTTGGTCCTTTAAGTTTTAGTTTTTCTG
1427013 CTATTTTGGTCCTTTAAGTTGTT-G-TTTTCT-
1 C-ATTTTGGTCCTTTAAGTT-TTAGTTTTTCTG
1427043 CATTTTGGTCCTTGTAA-TTTTA
1 CATTTTGGTCCTT-TAAGTTTTA
1427065 AAGATTTACT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
28 2 0.04
29 14 0.30
30 4 0.09
31 6 0.13
32 18 0.39
33 2 0.04
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.59
Consensus pattern (31 bp):
CATTTTGGTCCTTTAAGTTTTAGTTTTTCTG
Found at i:1429133 original size:40 final size:41
Alignment explanation
Indices: 1429037--1429143 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
1429027 CCTGAATGCT
*
1429037 ATCCTTAATCCCCTCAGATAAGCCATCTTTGTTGCAAACCAA
1 ATCCTTAAT-TCCTCAGATAAGCCATCTTTGTTGCAAACCAA
1429079 ATCCTTAATTCCTCAGATAAGCCATCTTTGTTGCAAACC-A
1 ATCCTTAATTCCTCAGATAAGCCATCTTTGTTGCAAACCAA
1429119 ATCCTTAATTCCTCAGATAAGCCAT
1 ATCCTTAATTCCTCAGATAAGCCAT
1429144 TTCTCCCTCG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 26 0.41
41 29 0.45
42 9 0.14
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (41 bp):
ATCCTTAATTCCTCAGATAAGCCATCTTTGTTGCAAACCAA
Found at i:1429596 original size:15 final size:15
Alignment explanation
Indices: 1429535--1429617 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 15
1429525 TTTTATAAAT
1429535 ATATATATAATATTA
1 ATATATATAATATTA
* *
1429550 ATAAATTTAAT-TTA
1 ATATATATAATATTA
* * *
1429564 ATTTAAATTATA-TA
1 ATATATATAATATTA
*
1429578 TATATATATAATATTT
1 -ATATATATAATATTA
*
1429594 ATATATTTAAT-TTAA
1 ATATATATAATATT-A
1429609 ATATATATA
1 ATATATATA
1429618 CCGACCCGAT
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
14 13 0.26
15 36 0.72
16 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATAATATTA
Found at i:1441588 original size:31 final size:31
Alignment explanation
Indices: 1441494--1441589 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
1441484 AGAGTCGAGG
1441494 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* ** **
1441525 GCTTACCTATGTTCTAAGAAACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
1441556 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
1441587 GTT
1 GTT
1441590 GCCGAGGTTC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:1441609 original size:30 final size:31
Alignment explanation
Indices: 1441494--1441601 Score: 76
Period size: 31 Copynumber: 3.5 Consensus size: 31
1441484 AGAGTCGAGG
* * * *
1441494 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCGAGGTTCTTCAGGACCTATGGACA
* * * * * *
1441525 GCTTACCTATGTTC-TAAGAAACATATGGACA
1 GTTTACCGAGGTTCTTCAG-GACCTATGGACA
* *
1441556 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCGAGGTTCTTCAGGACCTATGGACA
*
1441587 G-TTGCCGAGGTTCTT
1 GTTTACCGAGGTTCTT
1441602 TATGACCTCT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
30 14 0.22
31 47 0.75
32 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (31 bp):
GTTTACCGAGGTTCTTCAGGACCTATGGACA
Found at i:1447405 original size:30 final size:27
Alignment explanation
Indices: 1447369--1447432 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 27
1447359 TAGGGCCGAG
1447369 TATATATTTAAATTAAATATAAATATTAT
1 TATATATTTAAATTAAAT-TAAAT-TTAT
1447398 ATATATATTTAAATTAAATTAAATTTAT
1 -TATATATTTAAATTAAATTAAATTTAT
1447426 TA-ATATT
1 TATATATT
1447433 ATATATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 4 0.12
29 5 0.15
30 18 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATATTTAAATTAAATTAAATTTAT
Found at i:1447450 original size:37 final size:35
Alignment explanation
Indices: 1447376--1447447 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
1447366 GAGTATATAT
**
1447376 TTAAATTAAATATAAATATTATATATATATTTAAA
1 TTAAATTAAATATAAATATTATATATATAAATAAA
*
1447411 TTAAATTAAATTTATTAATATTATATATATACAATAA
1 TTAAATTAAA--TATAAATATTATATATATA-AATAA
1447448 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.32
37 18 0.58
38 3 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
TTAAATTAAATATAAATATTATATATATAAATAAA
Found at i:1457326 original size:280 final size:282
Alignment explanation
Indices: 1456732--1457525 Score: 871
Period size: 280 Copynumber: 2.8 Consensus size: 282
1456722 ATTAAGATGT
* * * * *
1456732 TAAACTTTTGTTTACTAACATTTAAAATGAATTTAATTTATTCCAATTTGATATTAATTTCAAAT
1 TAAACTTTTGTTCACTAACTTTTAAAATGAATTCAATTTAGTCCAATTTGATATTAATTTCAACT
* * * *
1456797 TTACATTTTACAATTATTTCAATTTGATCCTTGTATGTTATTTAATTTATTCAAATTTCA-TATT
66 TTACATTTTACAATTATTTCAATTTGATCCTTGTGTGTTGTTTAATTTATTTAAATTTTAGT-TT
* * * ** * * *
1456861 GTAGTTTCATGTTTGTTCAATTTAGTACGCAAAAGTTTGTTTTGATCCAAAATTAACCCATATAT
130 CTAATTTCATG-TTGTTCAATTTAGTTCTTAATA--TT-TTTT-ATCCTAAATTAGCCCATA-A-
* * * * * *
1456926 TTTTTTTATTTTTTTCTATAATCTACTCCAAACCCTATAAACCATATCATAAATTTCAATTCAAA
188 -TTATTTATATTTTT-T-TAATTTACTCCAAACCATATAAACCACATCATAAACTTCAATTCAAA
* * *
1456991 CCCTATAAATTATATCATAATCTCTAAATCTTA
250 CCCTATAAATTATATCATAATATCTAAACCATA
* * * *
1457024 TAAACTTTTGTTCAATAACTTTTCAAATGAATGCAATTTAGTCCAATTTGATATTAATTTCAGCT
1 TAAACTTTTGTTCACTAACTTTTAAAATGAATTCAATTTAGTCCAATTTGATATTAATTTCAACT
* ** * * *
1457089 TTACATTTTACAA-TATTTCAATTCGATCCAGGCGTTTTGTTTAATTTATTTGAATTTTAGTTTC
66 TTACATTTTACAATTATTTCAATTTGATCCTTGTGTGTTGTTTAATTTATTTAAATTTTAGTTTC
*
1457153 TAATTTCATGTGTGTTCAA-TTAGTTCTTAATATTTTTTATCCTAAATTAGCCCATAATTATTTC
131 TAATTTCATGT-TGTTCAATTTAGTTCTTAATATTTTTTATCCTAAATTAGCCCATAATTATTTA
* * *
1457217 TA-TTTTTTAATTTACTCCAAACCATATAAATCACATCATAAACTTCATTTCAAACTCTATAAAT
195 TATTTTTTTAATTTACTCCAAACCATATAAACCACATCATAAACTTCAATTCAAACCCTATAAAT
1457281 TATATCATAATATCTAAACCATA
260 TATATCATAATATCTAAACCATA
* * * *
1457304 TAAACTTTTGTTCACCAACTTTTAAAATGAATTCAATTTTGT-CAATTTTTATATTAATTTTAAC
1 TAAACTTTTGTTCACTAACTTTTAAAATGAATTCAATTTAGTCCAA-TTTGATATTAATTTCAAC
* * * * **
1457368 TTCACATTTTATAATTGTTTTAATTTGATCCTTGTGTGTTGTTTAATTCGTTTAAATTTTAGTTT
65 TTTACATTTTACAATTATTTCAATTTGATCCTTGTGTGTTGTTTAATTTATTTAAATTTTAGTTT
* * ** *
1457433 TTAATTTAATGTTGGTTCAATTTAG-TCTTTAATAGTATATTTTTATTTTAAATAAGCCCATAAT
130 CTAATTTCATGTT-GTTCAATTTAGTTC-TT-A-A-TAT-TTTTTATCCTAAATTAGCCCATAAT
*
1457497 TATTTATATTTTTTTAATTTACTGCAAAC
189 TATTTATATTTTTTTAATTTACTCCAAAC
1457526 TCTATACAAT
Statistics
Matches: 423, Mismatches: 67, Indels: 29
0.82 0.13 0.06
Matches are distributed among these distances:
279 3 0.01
280 135 0.32
281 59 0.14
282 10 0.02
283 7 0.02
284 1 0.00
285 4 0.01
286 45 0.11
287 23 0.05
288 2 0.00
290 10 0.02
291 54 0.13
292 70 0.17
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (282 bp):
TAAACTTTTGTTCACTAACTTTTAAAATGAATTCAATTTAGTCCAATTTGATATTAATTTCAACT
TTACATTTTACAATTATTTCAATTTGATCCTTGTGTGTTGTTTAATTTATTTAAATTTTAGTTTC
TAATTTCATGTTGTTCAATTTAGTTCTTAATATTTTTTATCCTAAATTAGCCCATAATTATTTAT
ATTTTTTTAATTTACTCCAAACCATATAAACCACATCATAAACTTCAATTCAAACCCTATAAATT
ATATCATAATATCTAAACCATA
Found at i:1459399 original size:79 final size:79
Alignment explanation
Indices: 1459268--1459433 Score: 305
Period size: 79 Copynumber: 2.1 Consensus size: 79
1459258 CTTTTATAAA
* *
1459268 TTATAGTACGAATAATATTATATTAGTGGTCCATGTATAAAACGTGCAGGTGTCTTATCATTTTA
1 TTATAGTACAAATAATATTATATTAGTGGTCCATGTATAAAACGTACAGGTGTCTTATCATTTTA
1459333 TATAAAACAAAATT
66 TATAAAACAAAATT
1459347 TTATAGTACAAATAATATTATATTAGTGGTCCATGTATAAAACGTACAGGTGTCTTATCATTTTA
1 TTATAGTACAAATAATATTATATTAGTGGTCCATGTATAAAACGTACAGGTGTCTTATCATTTTA
1459412 TATAAAACAAAATT
66 TATAAAACAAAATT
*
1459426 TGATAGTA
1 TTATAGTA
1459434 GGTCCGGCAT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 84 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (79 bp):
TTATAGTACAAATAATATTATATTAGTGGTCCATGTATAAAACGTACAGGTGTCTTATCATTTTA
TATAAAACAAAATT
Found at i:1460080 original size:180 final size:182
Alignment explanation
Indices: 1459678--1460145 Score: 661
Period size: 180 Copynumber: 2.6 Consensus size: 182
1459668 GATCCAAATT
* * * * **
1459678 AAAAATGTATCAATCCACAACGATATAACAGGTAAAATTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
1459743 AAACCGGTAAAGCGGTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * ** *
1459808 GTTAATTTAAAAGAGAAGCGGTTTTAGCGCCTATAAACTGTCGATACTTTAA
131 ATGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAACAGTCGATACTTTAA
* * * * *
1459860 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAATCGATATCAAAATGATG
1 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
1459925 AAACCGGTAAAACGCTACCGGATATATTGAAATTGTCGATACTTT-ATATAAGGATCGATACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
1459989 ATGAATTTAAAAGAGAATCAATTTTAGTGCCTATAAA-AGTCGATACTTTAA
131 ATGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAACAGTCGATACTTTAA
* * * *
1460040 AAAAATATATTGATCCAAAATGATATAACAGGTAAAAATATAATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1460105 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATA
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATA
1460146 TTTTCGTAAG
Statistics
Matches: 253, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
180 109 0.43
181 48 0.19
182 96 0.38
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
ATGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAACAGTCGATACTTTAA
Found at i:1460105 original size:20 final size:19
Alignment explanation
Indices: 1460055--1460113 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1460045 TATATTGATC
* *
1460055 CAAAATGATATAACAGGTA
1 CAAAATGATAAAACCGGTA
* *
1460074 AAAATATAATAAAACCGGTA
1 CAAA-ATGATAAAACCGGTA
1460094 TCAAAATGATAAAACCGGTA
1 -CAAAATGATAAAACCGGTA
1460114 AAACGCTACC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.20
Consensus pattern (19 bp):
CAAAATGATAAAACCGGTA
Found at i:1462451 original size:33 final size:33
Alignment explanation
Indices: 1462408--1462473 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1462398 AAATAGATGG
* * *
1462408 AGTGGTGAAAGGAGTAGAGGTGTTGAGGGGTGA
1 AGTGGCGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1462441 AGTGGCGAAAGAAGTTGAGGTGTTAATGGGTGA
1 AGTGGCGAAAGAAGTAGAGGTGTTAAGGGGTGA
1462474 TCTTAAGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGCGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1462699 original size:33 final size:33
Alignment explanation
Indices: 1462661--1462748 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
1462651 AAAATATGAA
*
1462661 GAAGAAAATAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
*
1462694 GAAGAAAAGAGGGATGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
*
1462727 GAAGAAATGA-GGAGGAAGGAAG
1 GAAGAAAAGAGGGAGG-AGGAAG
1462749 TCGATGTCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 4 0.08
33 46 0.92
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.06
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:1464323 original size:19 final size:19
Alignment explanation
Indices: 1464299--1464347 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1464289 AATGTAGGGT
1464299 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1464318 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1464337 TAATTTTGTAT
1 TAATTTTGTAT
1464348 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Done.