Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 39
Found at i:2560865 original size:24 final size:26
Alignment explanation
Indices: 2560838--2560886 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2560828 CAAAACACAA
*
2560838 TAATTT-GAAAA-TTAACATTTTTTT
1 TAATTTCGAAAATTTAAAATTTTTTT
2560862 TAATTTCGAAAATTTAAAATTTTTT
1 TAATTTCGAAAATTTAAAATTTTTT
2560887 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TAATTTCGAAAATTTAAAATTTTTTT
Found at i:2561328 original size:20 final size:20
Alignment explanation
Indices: 2561299--2561336 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2561289 CCTCTTCAAA
*
2561299 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2561319 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2561337 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2567463 original size:9 final size:8
Alignment explanation
Indices: 2567433--2567470 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2567423 GGCTACCTCA
2567433 TTCTTCTT
1 TTCTTCTT
*
2567441 TTCTTCCT
1 TTCTTCTT
2567449 TT-TTCTT
1 TTCTTCTT
2567456 TTCCTTCTT
1 TT-CTTCTT
2567465 TTCTTC
1 TTCTTC
2567471 ATCATCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (8 bp):
TTCTTCTT
Found at i:2568490 original size:25 final size:24
Alignment explanation
Indices: 2568444--2568495 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
2568434 TTATTTTTAT
**
2568444 AAATATATTTAACTTACTTAAAACA
1 AAATATATTTAACTTAAAT-AAACA
2568469 AAAT-TATCTTAACTTAAATAAACA
1 AAATATAT-TTAACTTAAATAAACA
2568493 AAA
1 AAA
2568496 AAACGATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATATATTTAACTTAAATAAACA
Found at i:2568974 original size:59 final size:59
Alignment explanation
Indices: 2568896--2569404 Score: 813
Period size: 59 Copynumber: 8.6 Consensus size: 59
2568886 GTACAATCAA
* * * *
2568896 TATGATTTTCTTACTATTTTAGCACACAAAGTGCCGTATCTGGAAATTTATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* *
2568955 TATGATTTCCTTACCATTTTAGCACACAAAGTGACCTATTTGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* * * *
2569014 TATGATTTCCTTACTATTTTTGCACACAAAGTGCCATATCTGAAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
*
2569073 TATGATTTCCTTACCATTTTTGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
*
2569132 TATGATTTCCTTACCATTTTAGCACACAAAGTTCCCTATCTGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* * * *
2569191 TATGATTTACTTACCATTTTAGCACACAAAGTACCATATATGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
* **
2569250 TATGATTTCCTTACCATTTTAGCATATGAAGTGCCCTAAT-TGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT-ATCTGGAAATTCATACACTTAG
*
2569309 TATGATTTCCTTACCATTTTAACACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
*
2569368 TATGATTTCCTTACCATTTTACCACACAAAGTGCCCT
1 TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
2569405 TTGGTAATTT
Statistics
Matches: 416, Mismatches: 32, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
58 2 0.00
59 412 0.99
60 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAG
Found at i:2575499 original size:25 final size:24
Alignment explanation
Indices: 2575451--2575499 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2575441 TCATTTTTTT
**
2575451 ATAAAAATATTTAACTTACTTAAA
1 ATAAAAATATTTAACTTAAATAAA
*
2575475 ATAAAATTATCTTAACTTAAATAAA
1 ATAAAAATAT-TTAACTTAAATAAA
2575500 CAACAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAAAATATTTAACTTAAATAAA
Found at i:2575961 original size:59 final size:59
Alignment explanation
Indices: 2575905--2576337 Score: 737
Period size: 59 Copynumber: 7.4 Consensus size: 59
2575895 TAAGATTTTA
2575905 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
* *
2575964 TTACCA--TTAGCACACAAAGTGCCATATCTGGAAATTCATACACTTAGTATGATTTCT
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
* *
2576021 TTACCATTTTTGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCA
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
*
2576080 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTAC
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
* *
2576139 TTACCATTTTAGTACACAAAGTGCCCTATATGGAAATTCATACACTTAGTATGA-TTCC
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
* * *
2576197 TTACCATTTTAGAACACGAAGTGCCCTATCTAGAAATTCATACACTTAGTATGATTTCC
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
*
2576256 TTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACACTTAGTATGATTTCC
1 TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
*
2576315 TTACAATTTTAGCACACAAAGTG
1 TTACCATTTTAGCACACAAAGTG
2576338 ACCTTTGGTA
Statistics
Matches: 351, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
57 55 0.16
58 53 0.15
59 243 0.69
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (59 bp):
TTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCC
Found at i:2576273 original size:176 final size:177
Alignment explanation
Indices: 2575898--2576337 Score: 742
Period size: 176 Copynumber: 2.5 Consensus size: 177
2575888 CAATCAATAA
*
2575898 GATTTTATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTC
1 GATTTCATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTC
* *
2575963 CTTACCA--TTAGCACACAAAGTGCCATATCTGGAAATTCATACACTTAGTATGATTTCTTTACC
66 CTTACCATTTTAGCACACAAAGTGCCATATATGGAAATTCATACACTTAGTATGATTTCCTTACC
* * *
2576026 ATTTTTGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTAT
131 ATTTTAGAACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
*
2576073 GATTTCATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTA
1 GATTTCATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTC
* *
2576138 CTTACCATTTTAGTACACAAAGTGCCCTATATGGAAATTCATACACTTAGTATGA-TTCCTTACC
66 CTTACCATTTTAGCACACAAAGTGCCATATATGGAAATTCATACACTTAGTATGATTTCCTTACC
*
2576202 ATTTTAGAACACGAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
131 ATTTTAGAACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
* *
2576249 GATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGGAAATTCATACACTTAGTATGATTTC
1 GATTTCATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTC
*
2576314 CTTACAATTTTAGCACACAAAGTG
66 CTTACCATTTTAGCACACAAAGTG
2576338 ACCTTTGGTA
Statistics
Matches: 248, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
175 70 0.28
176 135 0.54
177 43 0.17
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (177 bp):
GATTTCATTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTC
CTTACCATTTTAGCACACAAAGTGCCATATATGGAAATTCATACACTTAGTATGATTTCCTTACC
ATTTTAGAACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
Found at i:2581110 original size:11 final size:11
Alignment explanation
Indices: 2581094--2581122 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2581084 TTGGTCCATT
2581094 CGTTGACCGAC
1 CGTTGACCGAC
2581105 CGTTGACCGAC
1 CGTTGACCGAC
2581116 CGTTGAC
1 CGTTGAC
2581123 TTTGACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:2583752 original size:15 final size:16
Alignment explanation
Indices: 2583732--2583761 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2583722 TTTATTAGAT
2583732 AAAAATAT-TAAATAA
1 AAAAATATATAAATAA
2583747 AAAAATATATAAATA
1 AAAAATATATAAATA
2583762 TTAAGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATATATAAATAA
Found at i:2586139 original size:3 final size:3
Alignment explanation
Indices: 2586131--2586183 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2586121 TTTTTATCCC
2586131 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2586179 AAT AA
1 AAT AA
2586184 AAAGAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2587766 original size:18 final size:18
Alignment explanation
Indices: 2587743--2587877 Score: 198
Period size: 18 Copynumber: 7.5 Consensus size: 18
2587733 TTTGTCTCGT
2587743 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
2587761 ATGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
* * *
2587779 AGGACTACTGTGTCCTGA
1 AGGACCACTATGTCCCGA
*
2587797 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
*
2587815 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
* *
2587833 AAGACCACTATGTTCCGA
1 AGGACCACTATGTCCCGA
2587851 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
2587869 AGGACCACT
1 AGGACCACT
2587878 GATAATCCCT
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 105 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:2591700 original size:34 final size:31
Alignment explanation
Indices: 2591672--2591740 Score: 66
Period size: 33 Copynumber: 2.1 Consensus size: 31
2591662 AGAGAAATAT
*
2591672 AAAGAAAAGAAAGGAAAGGAAAAAAGAGATAGATA
1 AAAGAAAACAAA--AAAGGAAAAAAGAGA-A-ATA
* * *
2591707 AAAGAATACAAAAAAGGAAAAAAAAGAAAGA
1 AAAGAAAACAAAAAAGGAAAAAAGAGAAATA
2591738 AAA
1 AAA
2591741 CATATCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
31 5 0.17
32 1 0.03
33 14 0.47
35 10 0.33
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.04
Consensus pattern (31 bp):
AAAGAAAACAAAAAAGGAAAAAAGAGAAATA
Found at i:2592416 original size:28 final size:28
Alignment explanation
Indices: 2592373--2592453 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
2592363 CAAAGAAGCC
*
2592373 AACCTGAAACATATTACCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
* *
2592401 AACCTAAAACACATTACCTCCTCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
*
2592429 AACCTGAAACACATTACCTTCCCAA
1 AACCTGAAACACATTACCTCCCCAA
2592454 GTCAGTCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.41, C:0.33, G:0.02, T:0.23
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAATT
Found at i:2594452 original size:18 final size:18
Alignment explanation
Indices: 2594429--2594463 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2594419 CCAAGAAGAG
2594429 AATGAAGACTACCCTTGT
1 AATGAAGACTACCCTTGT
*
2594447 AATGAAGACTACTCTTG
1 AATGAAGACTACCCTTG
2594464 CAACCATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (18 bp):
AATGAAGACTACCCTTGT
Found at i:2595559 original size:119 final size:117
Alignment explanation
Indices: 2595405--2595632 Score: 366
Period size: 119 Copynumber: 1.9 Consensus size: 117
2595395 TCACTCTAGA
*
2595405 TGGATCAACATTTCCAGTGGAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTT
1 TGGATCAACATTTACAGTGGAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTT
* * * * *
2595470 TATAATGAGAGGAACTTATTCAATCTTGGTTCGATTCCATCACAGATTGAGG
66 CATAATGAGAAGAACTTATTCAATCTTAGCTCGATTACATCACAGATTGAGG
*
2595522 TGGATCAACATTTACAGTGGAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAG
1 TGGATCAACATTTACAGTGGAG-G-GTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAG
*
2595587 TTCATAATGAGAAGAACTTGTTCAATCTTAGCTCGATTACATCACA
64 TTCATAATGAGAAGAACTTATTCAATCTTAGCTCGATTACATCACA
2595633 TAAAGAGTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 21 0.21
118 1 0.01
119 79 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (117 bp):
TGGATCAACATTTACAGTGGAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTT
CATAATGAGAAGAACTTATTCAATCTTAGCTCGATTACATCACAGATTGAGG
Found at i:2595611 original size:260 final size:260
Alignment explanation
Indices: 2595151--2595644 Score: 713
Period size: 259 Copynumber: 1.9 Consensus size: 260
2595141 ATAAACCAAA
** *
2595151 CAACATTTCCAGTGGAAGGGTTTGTAACAAGAAGAACTATCCGACGAGGAAGAATAAGTTCATAA
1 CAACATTTCCAGTGGAAGGGTTCATAACAAGAAGAACTATCCGACGAGGAAGAAAAAGTTCATAA
* * *
2595216 TGAGAAGAACTTGTTCAACCTTAATTCGCTTCCATCACAAAAGGAGGTGGATCAACATTTCCAAT
66 TGAGAAGAACTTATTCAACCTTAATTCGATTCCATCACAAAAGGAGGTGGATCAACATTTACAAT
* *
2595281 GGAAGGGTTCATATTGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAACTT
131 GGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAACTT
* *
2595346 GTTCAACCTCAGCTCGACT-CATCATATATAGAGTTGGATCAGGTACACCTCACTCTAGATGGAT
196 GTTCAACCTCAGCTCGACTACATCACATAAAGAGTTGGATCAGGTACACCTCACTCTAGATGGAT
** * * *
2595410 CAACATTTCCAGTGG-AGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTTATA
1 CAACATTTCCAGTGGAAGGGTTCATAACAAGAAGAACT-ATCCGACGAGGAAGAAAAAGTTCATA
* * ** * ** *
2595474 ATGAGAGGAACTTATTCAATCTTGGTTCGATTCCATCACAGATTGAGGTGGATCAACATTTACAG
65 ATGAGAAGAACTTATTCAACCTTAATTCGATTCCATCACAAAAGGAGGTGGATCAACATTTACAA
*
2595539 TGGAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAAC
130 TGGA-AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAAC
* * *
2595604 TTGTTCAATCTTAGCTCGATTACATCACATAAAGAGTTGGA
194 TTGTTCAACCTCAGCTCGACTACATCACATAAAGAGTTGGA
2595645 ATAACACCAA
Statistics
Matches: 205, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
258 18 0.09
259 95 0.46
260 75 0.37
261 17 0.08
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (260 bp):
CAACATTTCCAGTGGAAGGGTTCATAACAAGAAGAACTATCCGACGAGGAAGAAAAAGTTCATAA
TGAGAAGAACTTATTCAACCTTAATTCGATTCCATCACAAAAGGAGGTGGATCAACATTTACAAT
GGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAACTT
GTTCAACCTCAGCTCGACTACATCACATAAAGAGTTGGATCAGGTACACCTCACTCTAGATGGAT
Found at i:2595914 original size:117 final size:117
Alignment explanation
Indices: 2595705--2595959 Score: 320
Period size: 117 Copynumber: 2.2 Consensus size: 117
2595695 ATAACTTTGT
* * *
2595705 TCGATTCTATCACAGAAA-GAGGTGGATCAACATTTCCAATAAAGAGTTCATAATGAGAATAACT
1 TCGATTCCATCACA-AAAGGAGGAGGATCAACATTTCCAATAAAGAGTTCATAATGAGAAGAACT
* * *
2595769 CATCCGATGAAGGACAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGT
65 CATCCGATGAAGGACAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTAGC
* * * *
2595822 TTGATTCCATCACAAAAGGAGGAGGATCAATATTTCTAATAGAGAGTTCATAATGAGAAGAACTC
1 TCGATTCCATCACAAAAGGAGGAGGATCAACATTTCCAATAAAGAGTTCATAATGAGAAGAACTC
* *
2595887 ATCTGATTAGATA-GAC-A-AAGTTTATAATGAAAAGAACTTGTTCAACCTTAGC
66 ATCCGA-T-GA-AGGACAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTAGC
* *
2595939 TCGCTTCCATCACATAAGGAG
1 TCGATTCCATCACAAAAGGAG
2595960 TTGGAATAAC
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
116 3 0.03
117 108 0.91
118 2 0.02
119 5 0.04
120 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (117 bp):
TCGATTCCATCACAAAAGGAGGAGGATCAACATTTCCAATAAAGAGTTCATAATGAGAAGAACTC
ATCCGATGAAGGACAAGAAGTTCATAATGAAAAGAACTTGTTCAACCTTAGC
Found at i:2596042 original size:42 final size:42
Alignment explanation
Indices: 2595944--2596086 Score: 155
Period size: 42 Copynumber: 3.4 Consensus size: 42
2595934 TTAGCTCGCT
* * ** **
2595944 TCCATCACATAAGGAGTTGGAATAACACCGA-C-TTTGGCTTA
1 TCCATCACATAAGGAGTTGGAACAACATC-ATCATTTCACTCG
* * *
2595985 TCCATCTCATAAGGAGTTGGAACAATATCATCATTTTACTCG
1 TCCATCACATAAGGAGTTGGAACAACATCATCATTTCACTCG
* * *
2596027 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTCG
1 TCCATCACATAAGGAGTTGGAACAACATCATCATTTCACTCG
2596069 TCCATCACATAAGGAGTT
1 TCCATCACATAAGGAGTT
2596087 AGATCGATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.01
41 26 0.30
42 59 0.69
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGAACAACATCATCATTTCACTCG
Found at i:2596781 original size:20 final size:20
Alignment explanation
Indices: 2596756--2596798 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2596746 TCTAAGAGCA
* *
2596756 CATTTAGGACCATTTAGATG
1 CATTTAGGAACATATAGATG
*
2596776 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
2596796 CAT
1 CAT
2596799 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:2597069 original size:27 final size:27
Alignment explanation
Indices: 2597028--2597080 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2597018 TATTTTCACG
2597028 GGATCTCTGACCATGACCGAGAAATCT
1 GGATCTCTGACCATGACCGAGAAATCT
*
2597055 GGATCTCTGATCATGACCGAGAAATC
1 GGATCTCTGACCATGACCGAGAAATC
2597081 CGCCTGGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
GGATCTCTGACCATGACCGAGAAATCT
Found at i:2605432 original size:20 final size:20
Alignment explanation
Indices: 2605407--2605449 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2605397 TCTAAGAGCA
*
2605407 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2605427 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2605447 CAT
1 CAT
2605450 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2605720 original size:27 final size:27
Alignment explanation
Indices: 2605679--2605731 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2605669 TATTTTCACG
2605679 GGATCTCTGACCATGACCGAGAAATCT
1 GGATCTCTGACCATGACCGAGAAATCT
*
2605706 GGATCTCTGATCATGACCGAGAAATC
1 GGATCTCTGACCATGACCGAGAAATC
2605732 CGCCTGGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
GGATCTCTGACCATGACCGAGAAATCT
Found at i:2607907 original size:28 final size:28
Alignment explanation
Indices: 2607874--2607939 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
2607864 ACCCATTTAA
* *
2607874 AACATGTTATCGTATACTTAACC-TTTGT
1 AACATGTCATCGTATACTT-ACCAATTGT
* *
2607902 AACATGTCATCTTGTACTTACCAATTGT
1 AACATGTCATCGTATACTTACCAATTGT
*
2607930 AACATATCAT
1 AACATGTCAT
2607940 ATAATACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (28 bp):
AACATGTCATCGTATACTTACCAATTGT
Found at i:2608099 original size:30 final size:30
Alignment explanation
Indices: 2608079--2608286 Score: 165
Period size: 30 Copynumber: 7.0 Consensus size: 30
2608069 TATATACTTT
*
2608079 TGATATATTTTATAAGCCCATGTACATTAC
1 TGATATATTTTATAAGCCCATATACATTAC
* *
2608109 TGATATCTTTTATAAG-CCA-AGTACAATAC
1 TGATATATTTTATAAGCCCATA-TACATTAC
* *
2608138 TAATATCTTTTATAAGCCCATGA-ACATTAC
1 TGATATATTTTATAAGCCCAT-ATACATTAC
* ** * * *
2608168 TAATACCTTTTATAGGCCCATGTACAGTAC
1 TGATATATTTTATAAGCCCATATACATTAC
*
2608198 TGATATCTTTTATAAGCCCATGA-ACATTAC
1 TGATATATTTTATAAGCCCAT-ATACATTAC
* * * ** * *
2608228 TAATATCTTTTACACTCCCATGTACAGTAC
1 TGATATATTTTATAAGCCCATATACATTAC
*
2608258 TGATATCTTTTATAAGCCCATGAT-CATTA
1 TGATATATTTTATAAGCCCAT-ATACATTA
2608287 TTGAGAACTC
Statistics
Matches: 144, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
29 25 0.17
30 117 0.81
31 1 0.01
32 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (30 bp):
TGATATATTTTATAAGCCCATATACATTAC
Found at i:2608218 original size:60 final size:60
Alignment explanation
Indices: 2608079--2608286 Score: 301
Period size: 60 Copynumber: 3.5 Consensus size: 60
2608069 TATATACTTT
* * * * *
2608079 TGATATATTTTATAAGCCCATGTACATTACTGATATCTTTTATAAG-CCAAGTACAATAC
1 TGATATCTTTTATAAGCCCATGAACATTACTAATATCTTTTATAAGCCCATGTACAGTAC
* * *
2608138 TAATATCTTTTATAAGCCCATGAACATTACTAATACCTTTTATAGGCCCATGTACAGTAC
1 TGATATCTTTTATAAGCCCATGAACATTACTAATATCTTTTATAAGCCCATGTACAGTAC
* **
2608198 TGATATCTTTTATAAGCCCATGAACATTACTAATATCTTTTACACTCCCATGTACAGTAC
1 TGATATCTTTTATAAGCCCATGAACATTACTAATATCTTTTATAAGCCCATGTACAGTAC
*
2608258 TGATATCTTTTATAAGCCCATGATCATTA
1 TGATATCTTTTATAAGCCCATGAACATTA
2608287 TTGAGAACTC
Statistics
Matches: 134, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 40 0.30
60 94 0.70
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (60 bp):
TGATATCTTTTATAAGCCCATGAACATTACTAATATCTTTTATAAGCCCATGTACAGTAC
Found at i:2608277 original size:90 final size:89
Alignment explanation
Indices: 2608079--2608279 Score: 276
Period size: 90 Copynumber: 2.2 Consensus size: 89
2608069 TATATACTTT
* * *
2608079 TGATATATTTTATAAGCCCATGTACATTACTGATATCTTTTATAAGCCAAGTACAATACTAATAT
1 TGATATCTTTTATAAGCCCATGTACAGTACTGATATCTTTTATAAGCCAAGAACAATACTAATAT
* *
2608144 CTTTTATAAGCCCATGAACATTAC
66 CTTTTACAAGCCCATGAACAGTAC
* * * * *
2608168 TAATACCTTTTATAGGCCCATGTACAGTACTGATATCTTTTATAAGCCCATGAACATTACTAATA
1 TGATATCTTTTATAAGCCCATGTACAGTACTGATATCTTTTATAAG-CCAAGAACAATACTAATA
** *
2608233 TCTTTTACACTCCCATGTACAGTAC
65 TCTTTTACAAGCCCATGAACAGTAC
2608258 TGATATCTTTTATAAGCCCATG
1 TGATATCTTTTATAAGCCCATG
2608280 ATCATTATTG
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 41 0.43
90 54 0.57
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (89 bp):
TGATATCTTTTATAAGCCCATGTACAGTACTGATATCTTTTATAAGCCAAGAACAATACTAATAT
CTTTTACAAGCCCATGAACAGTAC
Found at i:2608407 original size:38 final size:38
Alignment explanation
Indices: 2608356--2608443 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
2608346 CTCGTATAAA
* *
2608356 CTGTGTCCCGAAGGACCTATCATCCTGAAGGATGTCAT
1 CTGTGTCCCGAAGGACCTATCACCCTGAAGGATGTAAT
2608394 CTGTGTCCCGAAGGACCTATCACCCTGAAGGATGTAAT
1 CTGTGTCCCGAAGGACCTATCACCCTGAAGGATGTAAT
* *
2608432 ATGTGTCTCGAA
1 CTGTGTCCCGAA
2608444 TGGCTTGTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (38 bp):
CTGTGTCCCGAAGGACCTATCACCCTGAAGGATGTAAT
Found at i:2608653 original size:33 final size:33
Alignment explanation
Indices: 2608606--2608670 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
2608596 ATCATGTAGC
2608606 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
*
2608639 TTGTGTAACATTCTTGTATGATCTCATAGATC
1 TTGTATAACATTCTTGTATGATCTCATAGATC
2608671 CCTTTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGTATAACATTCTTGTATGATCTCATAGATCA
Found at i:2610682 original size:30 final size:31
Alignment explanation
Indices: 2610648--2610711 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
2610638 TTGGTCCTTG
* * *
2610648 AACTTTTCAAAGT-TTATACTTTGGTTACCA
1 AACTTTTCAAAATCTTATAATTTGGTCACCA
*
2610678 AAC-TTTCAAAATCTTATAATTTGGTCACTA
1 AACTTTTCAAAATCTTATAATTTGGTCACCA
2610708 AACT
1 AACT
2610712 AAATCCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTTTTCAAAATCTTATAATTTGGTCACCA
Found at i:2611562 original size:9 final size:9
Alignment explanation
Indices: 2611550--2611594 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
2611540 TTTCTTTGTT
2611550 TTTTTTTCA
1 TTTTTTTCA
2611559 TTTTTTTCA
1 TTTTTTTCA
*
2611568 TTTTTTCTTA
1 TTTTTT-TCA
2611578 TTCTTTTTCA
1 TT-TTTTTCA
2611588 TTTTTTT
1 TTTTTTT
2611595 ATAGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.62
10 8 0.25
11 4 0.12
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:2611571 original size:20 final size:20
Alignment explanation
Indices: 2611548--2611594 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2611538 TTTTTCTTTG
2611548 TTTTTTTTTCATT-TTTTTCA
1 TTTTTTTTT-ATTCTTTTTCA
*
2611568 TTTTTTCTTATTCTTTTTCA
1 TTTTTTTTTATTCTTTTTCA
2611588 TTTTTTT
1 TTTTTTT
2611595 ATAGTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTATTCTTTTTCA
Found at i:2614518 original size:30 final size:30
Alignment explanation
Indices: 2614459--2614630 Score: 222
Period size: 30 Copynumber: 5.8 Consensus size: 30
2614449 CTCATGTACT
* **
2614459 AGCCCATGTATATTTTTGATATC-TTTATA
1 AGCCCATGTACATTACTGATATCTTTTATA
*
2614488 AGCCCATGTACATTACTAATATCTTTTATA
1 AGCCCATGTACATTACTGATATCTTTTATA
* *
2614518 AG-CCATGTACAATACTTATATCTTTTATA
1 AGCCCATGTACATTACTGATATCTTTTATA
*
2614547 AGCCCATGAACATTACTGATATCTTTTATA
1 AGCCCATGTACATTACTGATATCTTTTATA
* *
2614577 GGCCCATGTACAATACTGATATCTTTTATA
1 AGCCCATGTACATTACTGATATCTTTTATA
* * *
2614607 AGCCCATGAACATTATTGAGATCT
1 AGCCCATGTACATTACTGATATCT
2614631 CAAGGTATGC
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
29 46 0.37
30 78 0.63
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (30 bp):
AGCCCATGTACATTACTGATATCTTTTATA
Found at i:2614743 original size:21 final size:21
Alignment explanation
Indices: 2614717--2614774 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 21
2614707 CTATCATCTC
2614717 GAAGGATGTCATCTGTGTCCT
1 GAAGGATGTCATCTGTGTCCT
** *
2614738 GAAGGACCT-ATC---ATCCT
1 GAAGGATGTCATCTGTGTCCT
2614755 GAAGGATGTCATCTGTGTCC
1 GAAGGATGTCATCTGTGTCC
2614775 CGAATGACCT
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
17 11 0.41
18 3 0.11
20 3 0.11
21 10 0.37
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (21 bp):
GAAGGATGTCATCTGTGTCCT
Found at i:2614743 original size:38 final size:37
Alignment explanation
Indices: 2614692--2614820 Score: 186
Period size: 38 Copynumber: 3.4 Consensus size: 37
2614682 TCATATAAAT
*
2614692 TGTGTCCCAAAGGACCTATCATCTCGAAGGATGTCATC
1 TGTGTCCCGAAGGACCTATCATC-CGAAGGATGTCATC
*
2614730 TGTGTCCTGAAGGACCTATCATCCTGAAGGATGTCATC
1 TGTGTCCCGAAGGACCTATCATCC-GAAGGATGTCATC
* *
2614768 TGTGTCCCGAATGACCTATCATCCCGAAGGATGTAATC
1 TGTGTCCCGAAGGACCTATCAT-CCGAAGGATGTCATC
*
2614806 TGTGTCCTGAAGGAC
1 TGTGTCCCGAAGGAC
2614821 TTGTCATATG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 79 0.96
39 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (37 bp):
TGTGTCCCGAAGGACCTATCATCCGAAGGATGTCATC
Found at i:2615010 original size:33 final size:33
Alignment explanation
Indices: 2614963--2615027 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
2614953 ATCATGTAGC
2614963 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
*
2614996 TTGTGTAACATTCTTGTATGATCTCATAGATC
1 TTGTATAACATTCTTGTATGATCTCATAGATC
2615028 CCTTTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGTATAACATTCTTGTATGATCTCATAGATCA
Found at i:2622620 original size:3 final size:3
Alignment explanation
Indices: 2622612--2622651 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2622602 CTATTGTTGC
2622612 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2622652 GGAGAAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2632465 original size:24 final size:24
Alignment explanation
Indices: 2632438--2632499 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2632428 CTTGAGTATC
*
2632438 CAAGGTGGTGTTGACTCTAATCTT
1 CAAGGTGGTGCTGACTCTAATCTT
*
2632462 CAAGGTGGTACTGACTCTAATCTT
1 CAAGGTGGTGCTGACTCTAATCTT
2632486 CAAGGTGGTGCTGA
1 CAAGGTGGTGCTGA
2632500 TTTAGCTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (24 bp):
CAAGGTGGTGCTGACTCTAATCTT
Found at i:2636617 original size:20 final size:20
Alignment explanation
Indices: 2636592--2636659 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2636582 CATGCATATG
2636592 TTATGTTACACATTCCTTGC
1 TTATGTTACACATTCCTTGC
** * *
2636612 TTATGTTATTCATGCATATG-
1 TTATGTTACACATTCCT-TGC
*
2636632 TTATGTTACACATTCCTTAC
1 TTATGTTACACATTCCTTGC
2636652 TTATGTTA
1 TTATGTTA
2636660 TCATATCATT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.92
21 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (20 bp):
TTATGTTACACATTCCTTGC
Found at i:2636622 original size:40 final size:40
Alignment explanation
Indices: 2636578--2636660 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
2636568 TAGCTTAATA
*
2636578 TATTCATGCATATGTTATGTTACACATTCCTTGCTTATGT
1 TATTCATGCATATGTTATGTTACACATTCCTTACTTATGT
2636618 TATTCATGCATATGTTATGTTACACATTCCTTACTTATGT
1 TATTCATGCATATGTTATGTTACACATTCCTTACTTATGT
2636658 TAT
1 TAT
2636661 CATATCATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (40 bp):
TATTCATGCATATGTTATGTTACACATTCCTTACTTATGT
Found at i:2637706 original size:31 final size:31
Alignment explanation
Indices: 2637668--2637730 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2637658 TGACCTATGT
*
2637668 AACTGTCCATATGTTTCAAAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
**
2637699 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
2637730 A
1 A
2637731 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:2638081 original size:139 final size:139
Alignment explanation
Indices: 2637831--2638122 Score: 548
Period size: 139 Copynumber: 2.1 Consensus size: 139
2637821 TCTCTTCTGT
* * *
2637831 CATATACCACATGTATGTATAACCATATGTCTCATATCATATCACATGTATCTCAAGTGCATTTA
1 CATATATCACATGTATGTATAACCATATGTCTCATATCATATCACATGTATCACAAGTGCATGTA
2637896 TTCACGTAGATCGTTTCATATAGCTTATATCATTTCTCATTTGTTCATGTAAACTCACATGTCAT
66 TTCACGTAGATCGTTTCATATAGCTTATATCATTTCTCATTTGTTCATGTAAACTCACATGTCAT
2637961 ATCATATAA
131 ATCATATAA
2637970 CATATATCACATGTATGTATAACCATATGTCTCATATCATATCACATGTATCACAAGTGCATGTA
1 CATATATCACATGTATGTATAACCATATGTCTCATATCATATCACATGTATCACAAGTGCATGTA
*
2638035 TTCACGTAGATCGTTTCATATTGCTTATATCATTTCTCATTTGTTCATGTAAACTCACATGTCAT
66 TTCACGTAGATCGTTTCATATAGCTTATATCATTTCTCATTTGTTCATGTAAACTCACATGTCAT
2638100 ATCATATAA
131 ATCATATAA
2638109 CATATATCACATGT
1 CATATATCACATGT
2638123 TGCATTCTTA
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 149 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (139 bp):
CATATATCACATGTATGTATAACCATATGTCTCATATCATATCACATGTATCACAAGTGCATGTA
TTCACGTAGATCGTTTCATATAGCTTATATCATTTCTCATTTGTTCATGTAAACTCACATGTCAT
ATCATATAA
Found at i:2643787 original size:31 final size:31
Alignment explanation
Indices: 2643751--2643813 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
2643741 GGACCTATGT
2643751 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
2643782 AACTGTCCATATGTTCTGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
2643813 A
1 A
2643814 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:2648388 original size:21 final size:19
Alignment explanation
Indices: 2648332--2648420 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
2648322 TATTTAATTT
**
2648332 TTAAAAAATAATTAAAA-A
1 TTAAAAAATAAAAAAAATA
**
2648350 TT-AAAAATATTCAAAAATA
1 TTAAAAAATA-AAAAAAATA
*
2648369 TTCAAAAATAAAAATTAAATTA
1 TTAAAAAATAAAAA--AAA-TA
2648391 TTAAAAAATAAAAAAAATA
1 TTAAAAAATAAAAAAAATA
*
2648410 TATTAAAAATA
1 T-TAAAAAATA
2648421 CTAAAAATAG
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.12
18 6 0.11
19 8 0.14
20 18 0.32
21 3 0.05
22 15 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TTAAAAAATAAAAAAAATA
Found at i:2648397 original size:22 final size:22
Alignment explanation
Indices: 2648366--2648429 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
2648356 ATATTCAAAA
*
2648366 ATATTCAAAAATAAAAATTAAAT
1 ATATTAAAAAATAAAAA-TAAAT
2648389 -TATTAAAAAATAAAAA-AAAT
1 ATATTAAAAAATAAAAATAAAT
2648409 ATATTAAAAATACTAAAAATA
1 ATATTAAAAA-A-TAAAAATA
2648430 GTATTCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 4 0.11
21 9 0.25
22 16 0.44
23 6 0.17
24 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (22 bp):
ATATTAAAAAATAAAAATAAAT
Found at i:2648426 original size:21 final size:20
Alignment explanation
Indices: 2648362--2648434 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
2648352 AAAAATATTC
*
2648362 AAAAATAT-TCAAAAATAAA
1 AAAAATATATTAAAAATAAA
2648381 AATTAAAT-TATTAAAAAATAAA
1 AA--AAATATATT-AAAAATAAA
**
2648403 AAAAATATATTAAAAATACT
1 AAAAATATATTAAAAATAAA
2648423 AAAAATAGTATT
1 AAAAATA-TATT
2648435 CATATTAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 19 0.42
21 13 0.29
22 11 0.24
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (20 bp):
AAAAATATATTAAAAATAAA
Found at i:2648827 original size:7 final size:7
Alignment explanation
Indices: 2648807--2648853 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
2648797 TAATTTAATA
2648807 TTTAT-T
1 TTTATAT
2648813 TTTGATAT
1 TTT-ATAT
2648821 TTTATAT
1 TTTATAT
*
2648828 TTAATAGT
1 TTTATA-T
2648836 TTTATAT
1 TTTATAT
*
2648843 TTTAAAT
1 TTTATAT
2648850 TTTA
1 TTTA
2648854 AATATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
6 3 0.09
7 22 0.63
8 10 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (7 bp):
TTTATAT
Found at i:2648840 original size:15 final size:14
Alignment explanation
Indices: 2648799--2648853 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
2648789 ACTTTTAGTA
2648799 ATTTAATA-TTTAT
1 ATTTAATATTTTAT
* *
2648812 TTTTGATATTTTAT
1 ATTTAATATTTTAT
2648826 ATTTAATAGTTTTAT
1 ATTTAATA-TTTTAT
2648841 ATTTTAA-ATTTTA
1 A-TTTAATATTTTA
2648854 AATATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.17
14 16 0.46
15 8 0.23
16 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
ATTTAATATTTTAT
Found at i:2649208 original size:13 final size:13
Alignment explanation
Indices: 2649192--2649222 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2649182 TTTAATTGCG
2649192 AAAATTAAAAATT
1 AAAATTAAAAATT
2649205 AAAATTAAAAATT
1 AAAATTAAAAATT
2649218 AAAAT
1 AAAAT
2649223 ACCCGATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:2649222 original size:6 final size:7
Alignment explanation
Indices: 2649192--2649221 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2649182 TTTAATTGCG
2649192 AAAATTA
1 AAAATTA
2649199 AAAATT-
1 AAAATTA
2649205 AAAATTA
1 AAAATTA
2649212 AAAATTA
1 AAAATTA
2649219 AAA
1 AAA
2649222 TACCCGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:2649363 original size:27 final size:26
Alignment explanation
Indices: 2649303--2649409 Score: 76
Period size: 27 Copynumber: 3.9 Consensus size: 26
2649293 CATAAGAATG
* * *
2649303 AAAAAAAATGATAATAACAATAAATCAA
1 AAAAAAAATAATAA-AATAATAAAAC-A
2649331 AGAAAAAAATCAAT-AAATCAATAAAA-A
1 A-AAAAAAAT-AATAAAAT-AATAAAACA
2649358 TAAAAATAAA-AATAAAATAAATAAAACA
1 -AAAAA-AAATAATAAAAT-AATAAAACA
*
2649386 AAAATAAATAAATAAAATAATAAA
1 AAAAAAAAT-AATAAAATAATAAA
2649410 TAACCTAGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.09
27 26 0.40
28 16 0.25
29 15 0.23
30 2 0.03
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (26 bp):
AAAAAAAATAATAAAATAATAAAACA
Found at i:2649371 original size:26 final size:26
Alignment explanation
Indices: 2649354--2649409 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
2649344 TAAATCAATA
*
2649354 AAAATAAAAATAAAAATAAAATAAAT
1 AAAACAAAAATAAAAATAAAATAAAT
2649380 AAAACAAAAATAAATAAATAAAAT-AAT
1 AAAACAAAAAT-AA-AAATAAAATAAAT
2649407 AAA
1 AAA
2649410 TAACCTAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 8 0.30
28 9 0.33
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (26 bp):
AAAACAAAAATAAAAATAAAATAAAT
Found at i:2649381 original size:4 final size:4
Alignment explanation
Indices: 2649321--2649412 Score: 52
Period size: 4 Copynumber: 23.2 Consensus size: 4
2649311 TGATAATAAC
* * * * *
2649321 AATA AATCA AAGA AAAA AATC AATA AATC AAT- AA-A AATA AA-A ATAAA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA
2649368 AATAA AATA AATA AA-A CAA-A AATA AATA AATA AA-A TAATA AATA A
1 AAT-A AATA AATA AATA -AATA AATA AATA AATA AATA -AATA AATA A
2649413 CCTAGAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
3 10 0.14
4 51 0.72
5 10 0.14
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (4 bp):
AATA
Found at i:2649383 original size:20 final size:20
Alignment explanation
Indices: 2649355--2649412 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
2649345 AAATCAATAA
2649355 AAATAAAAATAAAAATAAAAT
1 AAAT-AAAATAAAAATAAAAT
*
2649376 AAATAAAACAAAAAT-AAAT
1 AAATAAAATAAAAATAAAAT
2649395 AAATAAAATAATAAATAA
1 AAATAAAATAA-AAATAA
2649413 CCTAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.42
20 14 0.42
21 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAATAAAAT
Found at i:2649408 original size:31 final size:31
Alignment explanation
Indices: 2649313--2649412 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 31
2649303 AAAAAAAATG
*
2649313 ATAATAACAATAAATCAAAGAAAAAAATCAATAA
1 ATAATAACAA-AAAT-AAATAAAAAAAT-AATAA
2649347 ATCAATAA-AAATAA-AAATAAAAATAA-AATAA
1 AT-AATAACAAA-AATAAATAAAAA-AATAATAA
2649378 ATAA-AACAAAAATAAATAAATAAAATAATAA
1 ATAATAACAAAAATAAATAAA-AAAATAATAA
2649409 ATAA
1 ATAA
2649413 CCTAGAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 17
0.76 0.01 0.22
Matches are distributed among these distances:
29 4 0.07
30 14 0.24
31 18 0.31
32 8 0.14
33 3 0.05
34 6 0.10
35 5 0.09
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.19
Consensus pattern (31 bp):
ATAATAACAAAAATAAATAAAAAAATAATAA
Found at i:2649411 original size:35 final size:33
Alignment explanation
Indices: 2649334--2649412 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 33
2649324 AAATCAAAGA
* * *
2649334 AAAAAATCAATAAATCAATAAAAAT-AA-AAAT
1 AAAAAATAAATAAATAAACAAAAATAAATAAAT
2649365 -AAAAATAAAATAAATAAAACAAAAATAAATAAAT
1 AAAAAAT-AAATAAAT-AAACAAAAATAAATAAAT
2649399 AAAATAATAAATAA
1 AAAA-AATAAATAA
2649413 CCTAGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 6 0.15
31 7 0.18
32 8 0.21
33 2 0.05
34 4 0.10
35 9 0.23
36 3 0.08
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (33 bp):
AAAAAATAAATAAATAAACAAAAATAAATAAAT
Found at i:2650128 original size:27 final size:28
Alignment explanation
Indices: 2650098--2650164 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
2650088 GTGTGGGGCC
2650098 AATAAAAATAATAAAATAAA-AAATAT-T
1 AATAAAAATAA-AAAATAAATAAATATAT
* *
2650125 AATAATAATAAGAAATAAATAAATATAT
1 AATAAAAATAAAAAATAAATAAATATAT
*
2650153 AAT-ATAATAAAA
1 AATAAAAATAAAA
2650165 TGTTTTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.20
27 24 0.69
28 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (28 bp):
AATAAAAATAAAAAATAAATAAATATAT
Found at i:2650140 original size:19 final size:18
Alignment explanation
Indices: 2650106--2650165 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 18
2650096 CCAATAAAAA
2650106 TAATAAAATAAAAAATAT
1 TAATAAAATAAAAAATAT
*
2650124 TAATAATAATAAGAAATA-
1 TAATAA-AATAAAAAATAT
* *
2650142 -AAT-AAATATATAATA-
1 TAATAAAATAAAAAATAT
2650157 TAATAAAAT
1 TAATAAAAT
2650166 GTTTTTGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 8 0.23
16 4 0.11
17 7 0.20
18 6 0.17
19 10 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAATAAAATAAAAAATAT
Found at i:2650598 original size:81 final size:81
Alignment explanation
Indices: 2650489--2650688 Score: 321
Period size: 81 Copynumber: 2.5 Consensus size: 81
2650479 CGGTTGATAC
* * * *
2650489 GCCCTCG-AGCTGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGTGTT
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTATAGCCTTGAGTT
2650553 ATGCTGCAAATGATGT
66 ATGCTGCAAATGATGT
* * *
2650569 GCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCTGATAACCCTTATAGCCTTGAGTT
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTATAGCCTTGAGTT
2650634 ATGCTGCAAATGATGT
66 ATGCTGCAAATGATGT
*
2650650 GCCCTCGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTTG
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
2650689 TGTTTCAAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 6 0.06
81 103 0.94
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (81 bp):
GCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTATAGCCTTGAGTT
ATGCTGCAAATGATGT
Found at i:2650760 original size:34 final size:34
Alignment explanation
Indices: 2650685--2650807 Score: 185
Period size: 34 Copynumber: 3.6 Consensus size: 34
2650675 CTCGAAGGTC
2650685 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGG--TTTT
*
2650721 TTTGTGTTTCAATAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
2650755 TTTGTGTTTCAAGAGAAACGATTTCAATGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
2650789 TTTGTGTTTAAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
2650808 TGTCTCCAGG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
34 54 0.66
36 27 0.33
37 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:2650840 original size:37 final size:36
Alignment explanation
Indices: 2650793--2650944 Score: 115
Period size: 37 Copynumber: 4.3 Consensus size: 36
2650783 GGTTTTTTTG
* *
2650793 TGTTTAAAGAGAAACTGTCTCCAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCT-CAGAGAGACAAAATTT
* * *
2650830 TGTTTCAAGAGAAACATAT-TTA-A-AG-----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAGAGAGACAAAATT-T
* *
2650860 TGTTTCAAGAGAAATTGTCTCGAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTC-AGAGAGACAAAATTT
* *
2650897 TGTTTCAAGGGAAACTCTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTC-AGAGAGACAAAATTT
2650933 TGTTTCAAGAGA
1 TGTTTCAAGAGA
2650945 GACAAAACTT
Statistics
Matches: 89, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
29 5 0.06
30 15 0.17
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
36 14 0.16
37 45 0.51
38 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAGAGAGACAAAATTT
Found at i:2650942 original size:21 final size:22
Alignment explanation
Indices: 2650916--2650959 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2650906 GGAAACTCTC
2650916 TCAAGAGAGACAAAA-TTTGTT
1 TCAAGAGAGACAAAACTTTGTT
2650937 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAACTTTGTT
2650959 T
1 T
2650960 TGAGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (22 bp):
TCAAGAGAGACAAAACTTTGTT
Found at i:2651668 original size:73 final size:73
Alignment explanation
Indices: 2651549--2651696 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
2651539 CTTGAATATC
2651549 CTTCGTCGTGAAGTTGAAATTCAAGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTT
1 CTTCGTCGTGAAGTTGAAATTCAAGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTT
2651614 GAAATTGG
66 GAAATTGG
2651622 CTTCGTCGTGAAGTTGAAATTCAAGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTT
1 CTTCGTCGTGAAGTTGAAATTCAAGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTT
2651687 GAAATTGG
66 GAAATTGG
2651695 CT
1 CT
2651697 CTGAATGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (73 bp):
CTTCGTCGTGAAGTTGAAATTCAAGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTT
GAAATTGG
Found at i:2651911 original size:110 final size:110
Alignment explanation
Indices: 2651645--2652412 Score: 1100
Period size: 110 Copynumber: 7.0 Consensus size: 110
2651635 TTGAAATTCA
* * * * *
2651645 AGCTTGTATTGTTTTGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACT-
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* *
2651709 AGGAAGTTGTTTGTTGACAGCCAG-CTGCCCCTTCGCTGTG-AGTTG
66 A-AAAGTTGTTTGTTGACAGTCAGTC-GCCCCTTCGCTGTGAAGTTG
* * *
2651754 AGCTTGTGTTGTCTCGAGTTCAATATCCTTCACTATGAAGTTGAAATTGACTCTGAATGAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* * *
2651819 AAAAGTTGTTTGTTGACAGTCAGTCACCCCTTTGTTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
* ** *
2651864 AGCTTGTGTTGTCTCGAGTCTAATATCCTTCTTTGTGAAGTTGAAATTGACTCTAAATGAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* *
2651929 AAAAGTTGTTTGTTGACAGTCAGTCACCCATTCGCTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
** * *
2651974 AGCTTGCATTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* * *
2652039 AAAAGTTATTTATTGACAATCAGTCGCCCCTTCGCTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
* * *
2652084 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTTTAAATGAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* * *
2652149 AAAAGTTGTTTGTTGATAATCAGTCTCCCCTTCGCTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
* * * *
2652194 AGCTTGTGTTTTCTCAAGTCTAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* *
2652259 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTTGGTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
*
2652304 AGCTTGGGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
1 AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
* *
2652369 AAAAGTTATTTGTTGACAGTCA----CTCCTTCGCTGTGAAGTTG
66 AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
2652410 AGC
1 AGC
2652413 AACCACCACC
Statistics
Matches: 594, Mismatches: 62, Indels: 9
0.89 0.09 0.01
Matches are distributed among these distances:
106 19 0.03
109 89 0.15
110 486 0.82
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (110 bp):
AGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG
AAAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTG
Found at i:2656087 original size:13 final size:13
Alignment explanation
Indices: 2656071--2656101 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2656061 TTTAACTGCG
2656071 AAAATTAAAAATT
1 AAAATTAAAAATT
*
2656084 AAAATTAAAATTT
1 AAAATTAAAAATT
2656097 AAAAT
1 AAAAT
2656102 ACCCGATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:2656234 original size:29 final size:28
Alignment explanation
Indices: 2656202--2656292 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 28
2656192 TAATAACAAT
2656202 AAATCAA-AGAAAAAAACAATAAAAAAATA
1 AAATCAATA-AAAAAAA-AATAAAAAAATA
2656231 AAATCAATAAAAATAAAAATAAAAATAATAA
1 AAATCAATAAAAA-AAAAATAAAAA-AAT-A
*
2656262 AAAT-AATAAAAATAAAATAAAATAAATA
1 AAATCAATAAAAAAAAAATAAAA-AAATA
2656290 AAA
1 AAA
2656293 CAAAATAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
28 4 0.07
29 31 0.55
30 16 0.29
31 5 0.09
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.16
Consensus pattern (28 bp):
AAATCAATAAAAAAAAAATAAAAAAATA
Found at i:2656244 original size:15 final size:13
Alignment explanation
Indices: 2656219--2656354 Score: 94
Period size: 14 Copynumber: 9.5 Consensus size: 13
2656209 AGAAAAAAAC
2656219 AATAAAAAAATAA
1 AATAAAAAAATAA
2656232 AATCAATAAAAATAAA
1 AAT-AA-AAAAAT-AA
2656248 AATAAAAATAATAAA
1 AATAAAAA-AAT-AA
2656263 AATAATAAAAATAA
1 AATAA-AAAAATAA
2656277 AATAAAATAAATAA
1 AATAAAA-AAATAA
* *
2656291 AACAAAATAATAAA
1 AATAAAAAAAT-AA
* *
2656305 TAATACCAGAAAATAT
1 -AATA--AAAAAATAA
2656321 AATAAAAGAAAT-A
1 AATAAAA-AAATAA
* *
2656334 TATAAAAATAGTAA
1 AATAAAAA-AATAA
2656348 AATAAAA
1 AATAAAA
2656355 TAAAGGGACA
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.01
13 18 0.18
14 37 0.37
15 29 0.29
16 9 0.09
17 5 0.05
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:2656245 original size:6 final size:6
Alignment explanation
Indices: 2656236--2656307 Score: 69
Period size: 6 Copynumber: 11.8 Consensus size: 6
2656226 AAATAAAATC
*
2656236 AATAAA AATAAA AATAAA AATAATA AA-AAT AATAAA AAT-AA AAT-AA
1 AATAAA AATAAA AATAAA AATAA-A AATAAA AATAAA AATAAA AATAAA
*
2656282 AATAAA TAAAACAA AATAATA AATAA
1 AATAAA -AATA-AA AATAA-A AATAA
2656308 TACCAGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 12 0.21
6 27 0.48
7 15 0.27
8 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:2656260 original size:9 final size:9
Alignment explanation
Indices: 2656213--2656309 Score: 81
Period size: 9 Copynumber: 10.1 Consensus size: 9
2656203 AATCAAAGAA
*
2656213 AAAAACAAT
1 AAAAATAAT
2656222 AAAAA-AAT
1 AAAAATAAT
2656230 -AAAATCAAT
1 AAAAAT-AAT
2656239 AAAAATAAAAAT
1 AAAAAT---AAT
2656251 AAAAATAAT
1 AAAAATAAT
2656260 AAAAATAAT
1 AAAAATAAT
*
2656269 AAAAATAAA
1 AAAAATAAT
2656278 ATAAAATAAAT
1 A-AAAAT-AAT
*
2656289 AAAACAAAAT
1 AAAA-ATAAT
2656299 AATAAATAAT
1 AA-AAATAAT
2656309 A
1 A
2656310 CCAGAAAATA
Statistics
Matches: 74, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
7 4 0.05
8 3 0.04
9 29 0.39
10 23 0.31
11 6 0.08
12 9 0.12
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:2656291 original size:44 final size:42
Alignment explanation
Indices: 2656219--2656358 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 42
2656209 AGAAAAAAAC
2656219 AATAA-AAAAATAAAATCAATAAAAATAAAAATAAAAATAATAAA
1 AATAATAAAAATAAAAT-AA-AAAAAT-AAAATAAAAATAATAAA
*
2656263 AATAATAAAAATAAAATAAAATAAATAAAA-CAAAATAATAAA
1 AATAATAAAAATAAAATAAAA-AAATAAAATAAAAATAATAAA
** * * *
2656305 TAATACCAGAAAATATAATAAAAGAAAT-ATATAAAAATAGTAAA
1 -AATAATA-AAAATAAAATAAAA-AAATAAAATAAAAATAATAAA
*
2656349 ATAAAATAAA
1 A-ATAATAAA
2656359 GGGACAAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 13
0.77 0.11 0.13
Matches are distributed among these distances:
42 11 0.14
43 16 0.20
44 41 0.52
45 11 0.14
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (42 bp):
AATAATAAAAATAAAATAAAAAAATAAAATAAAAATAATAAA
Found at i:2656309 original size:29 final size:28
Alignment explanation
Indices: 2656219--2656309 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 28
2656209 AGAAAAAAAC
*
2656219 AATAAAAAAATAAAATCAATAAAAATAAA-
1 AATAAAAAAATAAAA-CAA-AATAATAAAT
*
2656248 AATAAAAATAATAAAA-ATAATAA-AAAT
1 AATAAAAA-AATAAAACAAAATAATAAAT
2656275 AAAATAAAATAAATAAAACAAAATAATAAAT
1 --AATAAAA-AAATAAAACAAAATAATAAAT
2656306 AATA
1 AATA
2656310 CCAGAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
26 3 0.06
27 4 0.08
28 1 0.02
29 26 0.50
30 14 0.27
31 4 0.08
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (28 bp):
AATAAAAAAATAAAACAAAATAATAAAT
Found at i:2656319 original size:17 final size:16
Alignment explanation
Indices: 2656199--2656327 Score: 61
Period size: 16 Copynumber: 7.7 Consensus size: 16
2656189 TGATAATAAC
* *
2656199 AATAAATCAAAGAAAA
1 AATAAATAAAACAAAA
*
2656215 AA-ACAATAAAAAAATAA
1 AATA-AATAAAACAA-AA
*
2656232 AATCAATAAAA-ATAAA
1 AATAAATAAAACA-AAA
*
2656248 AATAAAAATAATAA-AAAT
1 AAT--AAATAA-AACAAAA
2656266 AATAAA-AATAA-AATAA
1 AATAAATAA-AACAA-AA
2656282 AATAAATAAAACAAAA
1 AATAAATAAAACAAAA
* *
2656298 TAATAAATAATACCAGAA
1 -AATAAATAA-AACAAAA
2656316 AATATAATAAAA
1 AATA-AATAAAA
2656328 GAAATATATA
Statistics
Matches: 91, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.09
16 30 0.33
17 30 0.33
18 20 0.22
19 3 0.03
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (16 bp):
AATAAATAAAACAAAA
Found at i:2657003 original size:7 final size:8
Alignment explanation
Indices: 2656984--2657042 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
2656974 GGGCCTGTAG
2656984 AAATAATA
1 AAATAATA
2656992 AAATAA-A
1 AAATAATA
2656999 AAATAATA
1 AAATAATA
*
2657007 ATAATAGTA
1 A-AATAATA
*
2657016 ATA-AAT-
1 AAATAATA
2657022 AAATATATA
1 AAATA-ATA
*
2657031 ATATAATA
1 AAATAATA
2657039 AAAT
1 AAAT
2657043 GTTTTGTAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
6 2 0.05
7 10 0.25
8 17 0.43
9 11 0.28
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (8 bp):
AAATAATA
Found at i:2657020 original size:27 final size:26
Alignment explanation
Indices: 2656987--2657038 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2656977 CCTGTAGAAA
2656987 TAATAAAATAAA-AAATAATAATAATAG
1 TAAT-AAATAAATAAATAAT-ATAATAG
*
2657014 TAATAAATAAATATATAATATAATA
1 TAATAAATAAATAAATAATATAATA
2657039 AAATGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
TAATAAATAAATAAATAATATAATAG
Found at i:2658065 original size:74 final size:76
Alignment explanation
Indices: 2657940--2658131 Score: 271
Period size: 75 Copynumber: 2.6 Consensus size: 76
2657930 TAAATATCCC
* * *
2657940 AAAAAAGCATAAACTCTAAATCATTATCCCTAAAAATCATAAGATTCATTTTTTAGAATGAATTT
1 AAAAAATCATAAACTCTAAATCGTAATCCCTAAAAATCATAAGATTCATTTTTTAGAATGAATTT
*
2658005 AGGGATTA-CA
66 AGGGATCACCA
* * * *
2658015 AAAAAATCCTAAACTCTTAATCGTAATCCCT-AAAATCATAAGATTTATTTTTTTGAATGAATTT
1 AAAAAATCATAAACTCTAAATCGTAATCCCTAAAAATCATAAGATTCATTTTTTAGAATGAATTT
2658079 AGGGATCACCA
66 AGGGATCACCA
* * *
2658090 AAAAATTCATAAACTCTAAATTGTAATCCTTAAAAATCATAA
1 AAAAAATCATAAACTCTAAATCGTAATCCCTAAAAATCATAA
2658132 AAATCATAAG
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 38 0.37
75 54 0.53
76 10 0.10
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (76 bp):
AAAAAATCATAAACTCTAAATCGTAATCCCTAAAAATCATAAGATTCATTTTTTAGAATGAATTT
AGGGATCACCA
Found at i:2658295 original size:27 final size:27
Alignment explanation
Indices: 2658239--2658298 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
2658229 GAGTTTATGC
*
2658239 TTTTTGGGATTTTTAGGAATCTAGTAGT
1 TTTTTGAGATTTTTAGGAATCTAG-AGT
2658267 TTTTTGAGATTTTCT-GGAATCTA-AGGT
1 TTTTTGAGATTTT-TAGGAATCTAGA-GT
2658294 TTTTT
1 TTTTT
2658299 TTGGGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 7 0.24
28 20 0.69
29 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.53
Consensus pattern (27 bp):
TTTTTGAGATTTTTAGGAATCTAGAGT
Found at i:2664479 original size:34 final size:36
Alignment explanation
Indices: 2664436--2664518 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
2664426 TCAATTTATG
*
2664436 TTTGTTGTTCTTGAT-TGGTATG-GCATACTGCTTC
1 TTTGTTGTTCTTGATCTGCTATGCGCATACTGCTTC
** * *
2664470 TTTGTTGTTCTTTTTCTGCTTTGCTGCTTACTGCTTC
1 TTTGTTGTTCTTGATCTGCTATGC-GCATACTGCTTC
2664507 TTTGTTGTTCTT
1 TTTGTTGTTCTT
2664519 TTTCTGCTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 13 0.32
35 5 0.12
37 23 0.56
ACGTcount: A:0.06, C:0.17, G:0.19, T:0.58
Consensus pattern (36 bp):
TTTGTTGTTCTTGATCTGCTATGCGCATACTGCTTC
Found at i:2664502 original size:37 final size:37
Alignment explanation
Indices: 2664461--2664534 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2664451 TGGTATGGCA
2664461 TACTGCTTCTTTGTTGTTCTTTTTCTGCTTTGCTGCT
1 TACTGCTTCTTTGTTGTTCTTTTTCTGCTTTGCTGCT
2664498 TACTGCTTCTTTGTTGTTCTTTTTCTGCTTTGCTGCT
1 TACTGCTTCTTTGTTGTTCTTTTTCTGCTTTGCTGCT
2664535 CACATTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.03, C:0.22, G:0.16, T:0.59
Consensus pattern (37 bp):
TACTGCTTCTTTGTTGTTCTTTTTCTGCTTTGCTGCT
Found at i:2667457 original size:21 final size:22
Alignment explanation
Indices: 2667433--2667485 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
2667423 TCATTGAAAT
*
2667433 TCATCATCTTCTACACCA-TTA
1 TCATCATCTTCTACACCACATA
* * *
2667454 TCATCGTCATCTTCACCACATA
1 TCATCATCTTCTACACCACATA
2667476 T-ATCATCTTC
1 TCATCATCTTC
2667486 ATCTTAACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.26, C:0.34, G:0.02, T:0.38
Consensus pattern (22 bp):
TCATCATCTTCTACACCACATA
Found at i:2667465 original size:24 final size:24
Alignment explanation
Indices: 2667436--2667490 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2667426 TTGAAATTCA
2667436 TCATCTTCTA-CACCAT-TATCATCG
1 TCATCTTC-ACCA-CATATATCATCG
*
2667460 TCATCTTCACCACATATATCATCT
1 TCATCTTCACCACATATATCATCG
2667484 TCATCTT
1 TCATCTT
2667491 AACAATTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.40
Consensus pattern (24 bp):
TCATCTTCACCACATATATCATCG
Found at i:2667612 original size:21 final size:21
Alignment explanation
Indices: 2667561--2667626 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2667551 CATCACCATT
*
2667561 ACCATCACCATCTCCACCTCC
1 ACCATCACCACCTCCACCTCC
* * * *
2667582 ATCATTACCACCTCTACCTTC
1 ACCATCACCACCTCCACCTCC
* *
2667603 ACCATCACCACCACCATCTCC
1 ACCATCACCACCTCCACCTCC
2667624 ACC
1 ACC
2667627 TCGGTTAGTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (21 bp):
ACCATCACCACCTCCACCTCC
Found at i:2675041 original size:24 final size:23
Alignment explanation
Indices: 2675014--2675062 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2675004 TTTTGTATAT
* *
2675014 TCAAATTCGAATTTGAATTCGAGC
1 TCAAAATCGAATTTCAATT-GAGC
*
2675038 TCAAAATCGAGTTTCAATTGAGC
1 TCAAAATCGAATTTCAATTGAGC
2675061 TC
1 TC
2675063 GAGTCTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (23 bp):
TCAAAATCGAATTTCAATTGAGC
Found at i:2680976 original size:3 final size:3
Alignment explanation
Indices: 2680968--2681020 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2680958 TTGTTTTTAA
* *
2680968 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
2681013 TAT TAT TA
1 TAT TAT TA
2681021 CAAACAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2680999 original size:25 final size:27
Alignment explanation
Indices: 2680965--2681018 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2680955 CATTTGTTTT
2680965 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
2680990 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
2681018 T
1 T
2681019 TACAAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:2681013 original size:10 final size:10
Alignment explanation
Indices: 2680971--2681018 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
2680961 TTTTTAATAT
2680971 TATTATTAATA
1 TATTATT-ATA
2680982 TATTATTATA
1 TATTATTATA
*
2680992 -ATT-TTATT
1 TATTATTATA
2681000 TATTATTATA
1 TATTATTATA
2681010 TATTATTAT
1 TATTATTAT
2681019 TACAAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:2682315 original size:3 final size:3
Alignment explanation
Indices: 2682307--2682336 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2682297 TTTACTTTTA
*
2682307 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2682337 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2682563 original size:119 final size:117
Alignment explanation
Indices: 2682425--2682659 Score: 267
Period size: 120 Copynumber: 2.0 Consensus size: 117
2682415 TTTAATCCTA
* * * * * * *
2682425 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAATTGGATGTTCAT
1 TTTTAATAATTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAG-TCAT
* *
2682488 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
** * ** * *
2682543 TTTTAATTAATTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TTTTAA-TAATTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*
2682608 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATT
2682660 AATATATATT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
118 17 0.18
119 26 0.27
120 36 0.37
121 18 0.19
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (117 bp):
TTTTAATAATTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:2686521 original size:15 final size:15
Alignment explanation
Indices: 2686501--2686532 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2686491 GATCAATACC
2686501 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2686516 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2686531 TT
1 TT
2686533 ATTCATTGCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2693890 original size:10 final size:9
Alignment explanation
Indices: 2693862--2693891 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2693852 ATGCTTGAAG
2693862 GAAAAAAAA
1 GAAAAAAAA
2693871 GAAAAAAAA
1 GAAAAAAAA
2693880 GAGAAAAAAA
1 GA-AAAAAAA
2693890 GA
1 GA
2693892 TGGGGTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2694754 original size:114 final size:114
Alignment explanation
Indices: 2694554--2694775 Score: 354
Period size: 114 Copynumber: 1.9 Consensus size: 114
2694544 CACGTTCTCG
** *
2694554 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * * * *
2694619 GGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTAA
66 GGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTAA
*
2694668 TAGTAGAAATAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
2694733 GGTAAGAACCACAGAACCAATCATTGGAATTAAAAGATGAATT
66 GGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAATT
2694776 GCATGATCGT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAAAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTAA
Found at i:2695670 original size:113 final size:112
Alignment explanation
Indices: 2695475--2696268 Score: 800
Period size: 112 Copynumber: 7.0 Consensus size: 112
2695465 GCAAAGACTC
* * * *
2695475 AAATCCATCACTTGATAGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
* * *
2695540 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
*
2695588 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
* *
2695653 AAGAAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTT
66 AAG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * * *
2695701 AAATTCATCATTTGATGGATCAA-TATTGCCA-AGTAGAGTTCATAATGAGAATAACTAGTCATC
1 AAATCCATCACTTGATGGATCAACT-TTTCCAGAG-AAAGTTCATAATGAGAAGAACT--T-ATC
* *
2695764 T---GAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTT
61 TGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * *
2695813 AAATCCATCATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACT--T-ATCT
* *
2695877 ---GAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTTT
62 GAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * *
2695925 GAATTCATCACTCGATGAATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
* * * * *
2695990 AAGAAGAATAAGCTCATAATGAAAAGAGCTTGTTCAACCTTTTGCTT
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * * * * ** *
2696037 GACTCTATCACATAAGAAGATAGATCAGCATTAACATTTCCAGTTAGAGTTCATAATGAGAAGAA
1 AAATCCATCAC-T-------T-GAT--GGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* * * * *
2696102 CTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGGTCAAACCTTTTGTTT
55 CTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTGTTT
* *
2696162 GAATTCATCA-TTCGATGGATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAA
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA
* * * **
2696225 GAAGGAAAAAGAAGTTCATAAGGAGCAGAACTTACTCAACCTTT
65 GAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
2696269 ACATGATTAT
Statistics
Matches: 583, Mismatches: 74, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
109 4 0.01
110 1 0.00
112 252 0.43
113 213 0.37
114 13 0.02
115 1 0.00
116 8 0.01
121 3 0.01
123 44 0.08
124 26 0.04
125 18 0.03
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
Found at i:2695790 original size:20 final size:20
Alignment explanation
Indices: 2695737--2695793 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2695727 TGCCAAGTAG
* *
2695737 AGTTCATAATGAGAATAACT
1 AGTTCATAATGAGAAGAACA
* *
2695757 AG-TCAT-CTGAAGAAGAAGA
1 AGTTCATAATG-AGAAGAACA
2695776 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
2695794 TTTGTTCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.41
20 13 0.45
21 2 0.07
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACA
Found at i:2695913 original size:20 final size:20
Alignment explanation
Indices: 2695849--2695905 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
2695839 TGCCAAGTAG
2695849 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * **
2695869 CG-TCAT-CTGAAGAAGAAGA
1 AGTTCATAATG-AGAAGAACT
2695888 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
2695906 TTTGTTCAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 12 0.43
21 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:2696507 original size:3 final size:3
Alignment explanation
Indices: 2696499--2696551 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2696489 TTGTTTTTAA
* *
2696499 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
2696544 TAT TAT TA
1 TAT TAT TA
2696552 CAAACAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2696530 original size:25 final size:27
Alignment explanation
Indices: 2696496--2696549 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2696486 CATTTGTTTT
2696496 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
2696521 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
2696549 T
1 T
2696550 TACAAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:2696544 original size:10 final size:10
Alignment explanation
Indices: 2696502--2696549 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
2696492 TTTTTAATAT
2696502 TATTATTAATA
1 TATTATT-ATA
2696513 TATTATTATA
1 TATTATTATA
*
2696523 -ATT-TTATT
1 TATTATTATA
2696531 TATTATTATA
1 TATTATTATA
2696541 TATTATTAT
1 TATTATTAT
2696550 TACAAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:2697850 original size:3 final size:3
Alignment explanation
Indices: 2697842--2697871 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2697832 TTTACTTTTA
*
2697842 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2697872 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2698089 original size:20 final size:19
Alignment explanation
Indices: 2698064--2698105 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2698054 TTATTTTATA
2698064 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
2698084 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2698103 AAT
1 AAT
2698106 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2698098 original size:119 final size:117
Alignment explanation
Indices: 2697962--2698196 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 117
2697952 TTTAATCCTA
* * * * *
2697962 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-T
* *
2698025 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
** * ** *
2698080 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCT
*
2698145 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATT
2698197 AATATATATT
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 17 0.17
119 27 0.27
120 34 0.34
121 22 0.22
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (117 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTT
TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:2698194 original size:29 final size:31
Alignment explanation
Indices: 2698158--2698219 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
2698148 CTGATATTTC
* *
2698158 TAAATAAATAAATATTTTATTTATAAATATATA
1 TAAATTAATATATA-TTT-TTTATAAATATATA
*
2698191 TAAATTAATATATATTTTTTATAATTATA
1 TAAATTAATATATATTTTTTATAAATATA
2698220 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
32 3 0.12
33 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TAAATTAATATATATTTTTTATAAATATATA
Found at i:2698233 original size:33 final size:31
Alignment explanation
Indices: 2698163--2698233 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
2698153 ATTTCTAAAT
2698163 AAATAA-ATATTTTATTTATAAATATATATA
1 AAATAATATATTTTATTTATAAATATATATA
* * *
2698193 AATTAATATATATTT-TTTATAATTATAATTTTA
1 AAATAATATAT-TTTATTTATAAATAT-A-TATA
2698226 AAATAATA
1 AAATAATA
2698234 GGATTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
30 5 0.15
31 14 0.42
32 4 0.12
33 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATAATATATTTTATTTATAAATATATATA
Found at i:2701232 original size:37 final size:36
Alignment explanation
Indices: 2701157--2701232 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
2701147 TTTTTATATT
*
2701157 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
2701193 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
2701230 TTT
1 TTT
2701233 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:2701367 original size:9 final size:10
Alignment explanation
Indices: 2701349--2701412 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 10
2701339 GTCTTTTTTA
2701349 TATTATTTAAT
1 TATTA-TTAAT
2701360 T-TTATTAAT
1 TATTATTAAT
2701369 TATTATT-AT
1 TATTATTAAT
2701378 TATTATT-AT
1 TATTATTAAT
2701387 TATTATT-AT
1 TATTATTAAT
2701396 TATTA--AAT
1 TATTATTAAT
2701404 TATATATTA
1 TAT-TATTA
2701413 CAAATTTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.10
9 33 0.69
10 8 0.17
11 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:2701373 original size:3 final size:3
Alignment explanation
Indices: 2701349--2701400 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2701339 GTCTTTTTTA
*
2701349 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
2701393 TAT TAT TA
1 TAT TAT TA
2701401 AATTATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2701411 original size:12 final size:12
Alignment explanation
Indices: 2701349--2701412 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
2701339 GTCTTTTTTA
2701349 TATTATT-TAAT
1 TATTATTATAAT
2701360 T-TTA-T-TAAT
1 TATTATTATAAT
*
2701369 TATTATTATTAT
1 TATTATTATAAT
*
2701381 TATTATTATTAT
1 TATTATTATAAT
2701393 TATTATTA-AAT
1 TATTATTATAAT
2701404 TATATATTA
1 TAT-TATTA
2701413 CAAATTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
9 6 0.13
10 6 0.13
11 7 0.15
12 28 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:2704365 original size:20 final size:20
Alignment explanation
Indices: 2704309--2704359 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2704299 ATCCTATTCC
2704309 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
2704329 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
2704349 CTGGTAATCTT
1 CTGGTAATCTT
2704360 ACATTCTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:2706818 original size:21 final size:21
Alignment explanation
Indices: 2706776--2706818 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2706766 TTTTTGGGCT
*
2706776 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2706797 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2706818 A
1 A
2706819 ACGAACATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2706891 original size:23 final size:22
Alignment explanation
Indices: 2706847--2706891 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2706837 AATTCCAGAG
*
2706847 GGGAACCAATACCCCCACAGGA
1 GGGAACCAATACCCCCAAAGGA
* *
2706869 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCAATACCCCC-AAAGGA
2706892 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (22 bp):
GGGAACCAATACCCCCAAAGGA
Found at i:2708592 original size:103 final size:103
Alignment explanation
Indices: 2708366--2708584 Score: 438
Period size: 103 Copynumber: 2.1 Consensus size: 103
2708356 AGTCGATGGT
2708366 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
2708431 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
2708469 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
2708534 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
2708572 ATATGTGGTCCTT
1 ATATGTGGTCCTT
2708585 ATGGACATTA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
Found at i:2708631 original size:23 final size:23
Alignment explanation
Indices: 2708601--2708657 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2708591 ATTATTATAT
2708601 GGCACTACGGTTCAATTCTACGC
1 GGCACTACGGTTCAATTCTACGC
* *
2708624 GGCACTACGGTTCAATTCTATGT
1 GGCACTACGGTTCAATTCTACGC
*
2708647 GGCACTTCGGT
1 GGCACTACGGT
2708658 GCATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTTCAATTCTACGC
Found at i:2708668 original size:23 final size:23
Alignment explanation
Indices: 2708591--2708668 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
2708581 CCTTATGGAC
* *
2708591 ATTATTATATGGCACTACGGTTCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2708615 ATTCTACGCGGCACTACGGTTCA
1 ATTATATGTGGCACTACGGTGCA
* *
2708638 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2708661 TTTATATG
1 ATTATATG
2708669 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2710078 original size:35 final size:36
Alignment explanation
Indices: 2710022--2710095 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
2710012 GCCCTCAGGC
* *
2710022 ACATAAGGAATTACCATCTTGATCGG-TCTGAACCT
1 ACATAAGGAATTACCAGCTTGATCGGAGCTGAACCT
*
2710057 ACATGAGGAATTACCAGCTTGATCGGAGCTGAACCT
1 ACATAAGGAATTACCAGCTTGATCGGAGCTGAACCT
2710093 ACA
1 ACA
2710096 GAGACTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 24 0.69
36 11 0.31
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (36 bp):
ACATAAGGAATTACCAGCTTGATCGGAGCTGAACCT
Found at i:2710896 original size:36 final size:37
Alignment explanation
Indices: 2710849--2710924 Score: 136
Period size: 38 Copynumber: 2.1 Consensus size: 37
2710839 TTGGATAACT
2710849 CACCTTGTAATTTCTC-TCTCACTTTATCACAAATTC
1 CACCTTGTAATTTCTCTTCTCACTTTATCACAAATTC
2710885 CACCTTGTAATTTCTCTTTCTCACTTTATCACAAATTC
1 CACCTTGTAATTTCTC-TTCTCACTTTATCACAAATTC
2710923 CA
1 CA
2710925 AAACCACGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 16 0.42
38 22 0.58
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.42
Consensus pattern (37 bp):
CACCTTGTAATTTCTCTTCTCACTTTATCACAAATTC
Found at i:2711737 original size:15 final size:15
Alignment explanation
Indices: 2711719--2711750 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2711709 CACTACATTA
2711719 TAGGGGAGTTTGGTT
1 TAGGGGAGTTTGGTT
2711734 TAGGGGAGTTTGGTT
1 TAGGGGAGTTTGGTT
2711749 TA
1 TA
2711751 AGGTTTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.41
Consensus pattern (15 bp):
TAGGGGAGTTTGGTT
Found at i:2712157 original size:32 final size:34
Alignment explanation
Indices: 2712112--2712199 Score: 167
Period size: 34 Copynumber: 2.6 Consensus size: 34
2712102 TTATTTTGTA
2712112 AAAAAAATTATATAAATATTATTAATTTAATTTTT
1 AAAAAAA-TATATAAATATTATTAATTTAATTTTT
2712147 AAAAAAATATATAAATATTATTAATTTAATTTTT
1 AAAAAAATATATAAATATTATTAATTTAATTTTT
2712181 AAAAAAATATATAAATATT
1 AAAAAAATATATAAATATT
2712200 TTACAATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 46 0.87
35 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAAAAATATATAAATATTATTAATTTAATTTTT
Found at i:2727358 original size:63 final size:61
Alignment explanation
Indices: 2727242--2727441 Score: 219
Period size: 60 Copynumber: 3.3 Consensus size: 61
2727232 AACCAACAAA
* * * * * * *
2727242 TTCGCAACAC-AGTTTCCAAATTTGTAACT-TAGTTTTCAGATTCGCAACTCGAATTTCTTT
1 TTCGCAACACGATTTTCCAAATTCGCAACTCGATTTTTGA-ATTCGCAACACGAATTTCTTT
*
2727302 TTCGCAACGCGATTTTCCAAATTCGCAACTCGA-TTTTGACAATTTCGCAACACGAATTTCTTT
1 TTCGCAACACGATTTTCCAAATTCGCAACTCGATTTTTG--AA-TTCGCAACACGAATTTCTTT
* * * *
2727365 TTCGCAACACGATTTT-TAATTTTGCAACTCGATTTTTGAATTCGCAAAACGAATTTCTTT
1 TTCGCAACACGATTTTCCAAATTCGCAACTCGATTTTTGAATTCGCAACACGAATTTCTTT
*
2727425 TTCGCAACACGAATTTC
1 TTCGCAACACGATTTTC
2727442 TTTTTCACAA
Statistics
Matches: 120, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
60 43 0.36
61 22 0.18
62 15 0.12
63 40 0.33
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (61 bp):
TTCGCAACACGATTTTCCAAATTCGCAACTCGATTTTTGAATTCGCAACACGAATTTCTTT
Found at i:2727369 original size:20 final size:20
Alignment explanation
Indices: 2727282--2727480 Score: 163
Period size: 20 Copynumber: 9.8 Consensus size: 20
2727272 AGTTTTCAGA
*
2727282 TTCGCAACTCGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
* * ***
2727302 TTCGCAACGCGATTTTCCAAA
1 TTCGCAACACGAATTT-CTTT
* * **
2727323 TTCGCAACTCGATTTTGACAAT
1 TTCGCAACACGAATTT--CTTT
2727345 TTCGCAACACGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
2727365 TTCGCAACACG-ATTT-TTAAT
1 TTCGCAACACGAATTTCTT--T
* * *
2727385 TTTGCAACTCG-ATTT-TTGAA
1 TTCGCAACACGAATTTCTT--T
*
2727405 TTCGCAAAACGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
2727425 TTCGCAACACGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
* *
2727445 TTCACAACTCGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
2727465 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
2727481 TTTGGGTATA
Statistics
Matches: 148, Mismatches: 25, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
18 2 0.01
19 4 0.03
20 103 0.70
21 20 0.14
22 19 0.13
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCGCAACACGAATTTCTTT
Found at i:2727453 original size:60 final size:60
Alignment explanation
Indices: 2727281--2727480 Score: 199
Period size: 60 Copynumber: 3.3 Consensus size: 60
2727271 TAGTTTTCAG
* * * ***
2727281 ATTCGCAACTCGAATTTCTTTTTCGCAACGCGATTTTCCAAATTCGCAACTCGATTTTGACA
1 ATTCGCAACACGAATTTCTTTTTCGCAACACGAATTT-CTTTTTCGCAACTCGATTTTGA-A
*
2727343 ATTTCGCAACACGAATTTCTTTTTCGCAACACG-ATTT-TTAATTTTGCAACTCGATTTTTG-A
1 A-TTCGCAACACGAATTTCTTTTTCGCAACACGAATTTCTT--TTTCGCAACTCGA-TTTTGAA
* * * ***
2727404 ATTCGCAAAACGAATTTCTTTTTCGCAACACGAATTTCTTTTTCACAACTCGAATTTCTT
1 ATTCGCAACACGAATTTCTTTTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTGAA
*
2727464 TTTCGCAACACGAATTT
1 ATTCGCAACACGAATTT
2727481 TTTGGGTATA
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
59 3 0.03
60 56 0.48
61 6 0.05
62 17 0.15
63 34 0.29
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (60 bp):
ATTCGCAACACGAATTTCTTTTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTGAA
Found at i:2727642 original size:16 final size:15
Alignment explanation
Indices: 2727607--2727645 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2727597 TCCCCATCTC
*
2727607 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
2727622 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2727638 TAATTTTT
1 TAATTTTT
2727646 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2728406 original size:24 final size:24
Alignment explanation
Indices: 2728379--2728432 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2728369 GTATTCGAAA
*
2728379 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCAGAC
* * *
2728403 TTTGATTTTTGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
2728427 TTTGAT
1 TTTGAT
2728433 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Done.