Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_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: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:38 original size:19 final size:19
Alignment explanation
Indices: 10--46 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1 CAGAACCCA
*
10 GGGGGTATCGATTCCCCTG
1 GGGGGAATCGATTCCCCTG
*
29 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
47 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTG
Found at i:8167 original size:23 final size:23
Alignment explanation
Indices: 8133--8194 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
8123 GAGTCGAAGG
8133 TTCTACGCGGTCCTTCGGAACAA
1 TTCTACGCGGTCCTTCGGAACAA
* * * *
8156 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTCGGAACAA
8179 TTCTACGCGGTCCTTC
1 TTCTACGCGGTCCTTC
8195 AGGACATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.15, C:0.29, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGAACAA
Found at i:8199 original size:23 final size:22
Alignment explanation
Indices: 8133--8202 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
8123 GAGTCGAAGG
*
8133 TTCTACGCGGTCCTTCGGAACAA
1 TTCTACGCGGTCCTTCGG-ACAT
* *
8156 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGCGGTCC-TTCGGACAT
8179 TTCTACGCGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTC-GGACAT
8202 T
1 T
8203 CTATGTGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.05
23 34 0.85
24 4 0.10
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (22 bp):
TTCTACGCGGTCCTTCGGACAT
Found at i:9142 original size:2 final size:2
Alignment explanation
Indices: 9135--9196 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
9125 ATAAGTTGAA
9135 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
9177 AT AT AT -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9197 TGCATTTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20872 original size:13 final size:13
Alignment explanation
Indices: 20854--20879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20844 CAGCCTACAA
20854 GCATTATTAACAC
1 GCATTATTAACAC
20867 GCATTATTAACAC
1 GCATTATTAACAC
20880 CCGGAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GCATTATTAACAC
Found at i:24891 original size:34 final size:36
Alignment explanation
Indices: 24851--24937 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 36
24841 AAAACAATTA
* * * *
24851 ATATATATTTAAA-AATTATTATTATA-ATATCTTT
1 ATATATATTTAAATAATTACTAATATATATATATAT
24885 ATATATATTTAGGAATAATTACTAATATATATATATAT
1 ATATATATTTA--AATAATTACTAATATATATATATAT
24923 ATATATATATTAAAT
1 ATATATAT-TTAAAT
24938 TATCTCTCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 11 0.25
36 2 0.05
37 14 0.32
38 14 0.32
39 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (36 bp):
ATATATATTTAAATAATTACTAATATATATATATAT
Found at i:28859 original size:23 final size:23
Alignment explanation
Indices: 28833--28878 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28823 TTAGAACTGG
28833 AGGGTAACAAAAAAAAACTATCA
1 AGGGTAACAAAAAAAAACTATCA
28856 AGGGTAACAAAAAAAAACTATCA
1 AGGGTAACAAAAAAAAACTATCA
28879 TTTTTCGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (23 bp):
AGGGTAACAAAAAAAAACTATCA
Found at i:30241 original size:20 final size:20
Alignment explanation
Indices: 30218--30260 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
30208 AAAAGTCCTT
30218 AAATTGGATCTCAAATTTCA
1 AAATTGGATCTCAAATTTCA
* * *
30238 AAA-TGGTTCTTAAATTTTA
1 AAATTGGATCTCAAATTTCA
30257 AAAT
1 AAAT
30261 GCTCTAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATTGGATCTCAAATTTCA
Found at i:32037 original size:7 final size:7
Alignment explanation
Indices: 32025--32062 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
32015 GGGGGCGGTG
32025 GAAGAAA
1 GAAGAAA
32032 GAAGAAA
1 GAAGAAA
32039 GAAGAAA
1 GAAGAAA
32046 GAAGAAA
1 GAAGAAA
32053 GAAGAAA
1 GAAGAAA
32060 GAA
1 GAA
32063 TTGCATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:33344 original size:22 final size:22
Alignment explanation
Indices: 33310--33358 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
33300 ATAATTATTT
33310 AAAAA-ATTAAAT-AAAAATACA
1 AAAAATATTAAATAAAAAATA-A
*
33331 AAAAATATTTAATAAAAAATAA
1 AAAAATATTAAATAAAAAATAA
33353 AAAAAT
1 AAAAAT
33359 TAGGTTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 13 0.52
23 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAATATTAAATAAAAAATAA
Found at i:34670 original size:24 final size:24
Alignment explanation
Indices: 34639--34713 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
34629 TAATATATAA
34639 AAAATATTATTAATGAGTTATCTT
1 AAAATATTATTAATGAGTTATCTT
* * * *
34663 AAAGTATT-TT--TTA--TATATA
1 AAAATATTATTAATGAGTTATCTT
34682 AAAATATTATTAATGAGTTATCTT
1 AAAATATTATTAATGAGTTATCTT
34706 AAAATATT
1 AAAATATT
34714 TTTTATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
19 11 0.29
20 2 0.05
21 2 0.05
22 2 0.05
23 2 0.05
24 19 0.50
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (24 bp):
AAAATATTATTAATGAGTTATCTT
Found at i:34685 original size:44 final size:43
Alignment explanation
Indices: 34620--34721 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
34610 TTTTTCTTAA
**
34620 TAAAATATTTAATATATA-AAAAATATTATTAATGAGTTATCT
1 TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
*
34662 TAAAGTATTTTTTATATATAAAAATATTATTAATGAGTTATCT
1 TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
34705 TAAAATATTTTTTATAT
1 TAAAATATTTTTTATAT
34722 TTTTATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
42 15 0.27
43 40 0.73
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (43 bp):
TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
Found at i:37397 original size:21 final size:21
Alignment explanation
Indices: 37367--37442 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
37357 GATTTACATA
*
37367 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
37388 TTCGCGTTGCGATTTATTACAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
37411 TT--CGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
37430 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
37443 TTATTCCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 8 0.19
21 26 0.60
23 9 0.21
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:37462 original size:21 final size:21
Alignment explanation
Indices: 37436--37508 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
37426 GAAGTTCGCG
37436 TTGCGATTTATTCCAAATTCA
1 TTGCGATTTATTCCAAATTCA
*
37457 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCA
* * *
37478 TTGTGA--TAGTCCAAGTTCA
1 TTGCGATTTATTCCAAATTCA
37497 TTGCGATTTATT
1 TTGCGATTTATT
37509 TAGTTTTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 15 0.35
21 28 0.65
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCA
Found at i:38445 original size:320 final size:320
Alignment explanation
Indices: 37863--38465 Score: 1091
Period size: 320 Copynumber: 1.9 Consensus size: 320
37853 ACGTTAAATC
*
37863 TTGAACGGGTACTAAAATGGAACAAAAACTGGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
1 TTGAACGGGTACTAAAATGGAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
*
37928 AAACTAAACTTTAGGTATGATTTTGAAATAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTGA
66 AAACTAAACTTTAGGTATGATTTTGAAAAAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTGA
* *
37993 TAGTTTAGGTACTAAATACGTAGTTTACCCTTAAAAATATTTAATATCAACCGATACCAATACCA
131 TAGTTTAGATACTAAATACGTAATTTACCCTTAAAAATATTTAATATCAACCGATACCAATACCA
* *
38058 TATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCGGAATTTTTC
196 TATCAATTATTTTTTTGAATAGTCTAAGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTTC
38123 TTAATCAATAACACCACATACACGTAATTGCTCAAACCCAAGATCTTAAGAGAACAATAA
261 TTAATCAATAACACCACATACACGTAATTGCTCAAACCCAAGATCTTAAGAGAACAATAA
*
38183 TTGAACGGGTACTAAAATGGAA-AGAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAATA
1 TTGAACGGGTACTAAAATGGAACA-AAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACA
*
38247 AAAGCTAAACTTTAGGTATGATTTTGAAAAAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTG
65 AAAACTAAACTTTAGGTATGATTTTGAAAAAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTG
* *
38312 ATAGTTTAGATACTAAATACGTAATTTATCCTTAAAAATATTTAATATTAACCGATACCAATACC
130 ATAGTTTAGATACTAAATACGTAATTTACCCTTAAAAATATTTAATATCAACCGATACCAATACC
38377 ATATCAATTATTTTTTTGAATAGTCTAAGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
195 ATATCAATTATTTTTTTGAATAGTCTAAGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
*
38442 CTTAATCAATAACACTACATACAC
260 CTTAATCAATAACACCACATACAC
38466 ATTCTAACAA
Statistics
Matches: 271, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
319 1 0.00
320 270 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (320 bp):
TTGAACGGGTACTAAAATGGAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
AAACTAAACTTTAGGTATGATTTTGAAAAAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTGA
TAGTTTAGATACTAAATACGTAATTTACCCTTAAAAATATTTAATATCAACCGATACCAATACCA
TATCAATTATTTTTTTGAATAGTCTAAGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTTC
TTAATCAATAACACCACATACACGTAATTGCTCAAACCCAAGATCTTAAGAGAACAATAA
Found at i:41422 original size:29 final size:29
Alignment explanation
Indices: 41389--41464 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
41379 CTCTGGGGGT
41389 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
41418 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
41447 AGGTCGCCATGCACGCCC
1 AGGTCGCCATGCACGCCC
41465 CAACACGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.45, G:0.25, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:41503 original size:14 final size:14
Alignment explanation
Indices: 41480--41512 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41470 CGCTGGGCAT
41480 CCGAGACCATCCGA
1 CCGAGACCATCCGA
*
41494 CCGAGGCCATCCGA
1 CCGAGACCATCCGA
41508 CCGAG
1 CCGAG
41513 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.42, G:0.27, T:0.06
Consensus pattern (14 bp):
CCGAGACCATCCGA
Found at i:41533 original size:10 final size:10
Alignment explanation
Indices: 41518--41574 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
41508 CCGAGCTATG
41518 CGAGGGCATC
1 CGAGGGCATC
*
41528 CGAGGGCAAC
1 CGAGGGCATC
*
41538 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
41551 CGAGGGAATC
1 CGAGGGCATC
*
41561 CGAGGGCAAC
1 CGAGGGCATC
41571 CGAG
1 CGAG
41575 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:41546 original size:33 final size:33
Alignment explanation
Indices: 41494--41578 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
41484 GACCATCCGA
* * * *
41494 CCGAGGCCATCCGACCGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
41527 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
41560 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
41579 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:41665 original size:10 final size:10
Alignment explanation
Indices: 41623--41717 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 10
41613 CGCTCGGTTG
*
41623 CTCGGATTCC
1 CTCGGATGCC
*
41633 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
41645 GCTCGGTTGCC
1 -CTCGGATGCC
41656 CTCGGATGCC
1 CTCGGATGCC
*
41666 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
41678 GTTCGGATGGC
1 -CTCGGATGCC
*
41689 CTCGGATGCT
1 CTCGGATGCC
*
41699 CTCGGATGGC
1 CTCGGATGCC
41709 CTCGGATGC
1 CTCGGATGC
41718 TTTCAGATGG
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
10 44 0.69
11 5 0.08
12 5 0.08
13 10 0.16
ACGTcount: A:0.11, C:0.35, G:0.29, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:41668 original size:33 final size:32
Alignment explanation
Indices: 41611--41702 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
41601 GCGACCTACC
*
41611 CTCGCTCGGTTG-CTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
41642 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTG-CCTCGGATGCCCTCGCATAG
* * *
41675 CTCGTTCGGATGGCCTCGGATGCTCTCG
1 CTCGCTCGG-TTGCCTCGGATGCCCTCG
41703 GATGGCCTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.22
33 40 0.74
34 2 0.04
ACGTcount: A:0.09, C:0.36, G:0.28, T:0.27
Consensus pattern (32 bp):
CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
Found at i:41705 original size:20 final size:20
Alignment explanation
Indices: 41646--41730 Score: 89
Period size: 20 Copynumber: 4.1 Consensus size: 20
41636 GCATAGCTCG
* * *
41646 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
41666 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
41689 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
* *
41709 CTCGGATGCTTTCAGATGGC
1 CTCGGATGCTCTCGGATGGC
41729 CT
1 CT
41731 TGGTCGAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 34 0.62
21 3 0.05
22 4 0.07
23 14 0.25
ACGTcount: A:0.11, C:0.32, G:0.31, T:0.27
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:51525 original size:20 final size:20
Alignment explanation
Indices: 51500--51547 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
51490 GTCAGAGTGT
*
51500 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
51520 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
51540 GGCAGCGG
1 GGCGGCGG
51548 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:51537 original size:17 final size:16
Alignment explanation
Indices: 51517--51548 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
51507 GACGGCTGAC
51517 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
51534 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
51549 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:53906 original size:7 final size:7
Alignment explanation
Indices: 53894--53931 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
53884 AATTAACTGA
53894 AAATATT
1 AAATATT
53901 AAATATT
1 AAATATT
53908 AAATATT
1 AAATATT
53915 AAATATAT
1 AAATAT-T
53923 AATATATT
1 AA-ATATT
53931 A
1 A
53932 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 20 0.69
8 5 0.17
9 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATATT
Found at i:55551 original size:18 final size:18
Alignment explanation
Indices: 55528--55565 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55518 GACCCGACCC
55528 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
55546 AAAATATTATTTTTATTA
1 AAAATAATATATTTATTA
55564 AA
1 AA
55566 TAAAAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:60133 original size:18 final size:18
Alignment explanation
Indices: 60110--60150 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
60100 CTTCCTTAAA
60110 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
* * *
60128 ATTTTAGAGTTTTTATAT
1 ATTTTAAAATTATTATAT
60146 ATTTT
1 ATTTT
60151 TTATTAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:60811 original size:20 final size:20
Alignment explanation
Indices: 60763--60815 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
60753 TAATACAAAA
* *
60763 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
60783 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
60803 TCGCAACGCGATT
1 TCGCAACGCGATT
60816 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:61394 original size:19 final size:19
Alignment explanation
Indices: 61370--61411 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
61360 ACGAGAGAAT
*
61370 CGCAACCCGAAATAAAAAA
1 CGCAACCCGAAACAAAAAA
* *
61389 CGCAACGCGAAACAAAAAT
1 CGCAACCCGAAACAAAAAA
61408 CGCA
1 CGCA
61412 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.14, T:0.05
Consensus pattern (19 bp):
CGCAACCCGAAACAAAAAA
Found at i:61453 original size:20 final size:19
Alignment explanation
Indices: 61407--61572 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
61397 GAAACAAAAA
*
61407 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
61426 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
61445 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
61465 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
61481 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
61498 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
61512 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
61531 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
61551 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
61571 TC
1 TC
61573 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:61488 original size:39 final size:39
Alignment explanation
Indices: 61412--61488 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
61402 AAAAATCGCA
* **
61412 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
61451 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
61489 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:61497 original size:33 final size:33
Alignment explanation
Indices: 61460--61547 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
61450 GTTGCGATTT
* *
61460 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
61493 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
61526 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
61548 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:63644 original size:21 final size:21
Alignment explanation
Indices: 63620--63686 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
63610 TCATTCCTCG
63620 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
63641 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
63662 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
63683 AGAG
1 AGAG
63687 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:63644 original size:42 final size:42
Alignment explanation
Indices: 63568--63686 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
63558 GACTCGCCTG
* * * * * * *
63568 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
63610 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
63652 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
63687 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:65063 original size:14 final size:14
Alignment explanation
Indices: 65044--65079 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
65034 ATTGTTTAAT
65044 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
65058 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
65072 TGATTTGT
1 TGATTTGT
65080 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:65239 original size:32 final size:34
Alignment explanation
Indices: 65196--65281 Score: 115
Period size: 32 Copynumber: 2.6 Consensus size: 34
65186 ATCGCAATGT
65196 GATTTTCATTTCGCATTGCGAAAT-TAGCGTTGC
1 GATTTTCATTTCGCATTGCGAAATCTAGCGTTGC
* **
65229 G-TTTTCATTTCGCATTGCG-ATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGAAATCTAGCGTTGC
*
65261 GATTTTCATTTCGTATTGCGA
1 GATTTTCATTTCGCATTGCGA
65282 TAGTAATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 2 0.04
32 26 0.57
33 18 0.39
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (34 bp):
GATTTTCATTTCGCATTGCGAAATCTAGCGTTGC
Found at i:65281 original size:19 final size:18
Alignment explanation
Indices: 65225--65282 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
65215 GAAATTAGCG
65225 TTGCG-TTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
*
65243 TTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGA
65257 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCG-A
65276 TTGCGAT
1 TTGCGAT
65283 AGTAATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 6 0.19
16 7 0.22
17 7 0.22
18 5 0.16
19 7 0.22
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:67591 original size:12 final size:12
Alignment explanation
Indices: 67574--67598 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67564 TCTTCGGGGA
67574 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67586 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67598 C
1 C
67599 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:67807 original size:24 final size:24
Alignment explanation
Indices: 67773--67826 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
67763 CTGAAACATC
* *
67773 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
67797 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
67821 ATCAAA
1 ATCAAA
67827 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:68908 original size:20 final size:20
Alignment explanation
Indices: 68883--68920 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
68873 ATTTATTTGA
68883 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
68903 CTATCGCAACGCGAAAAT
1 CTATCGCAACGCGAAAAT
68921 CGCAATGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:68963 original size:14 final size:16
Alignment explanation
Indices: 68943--69016 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
68933 TGAAAATCGC
68943 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
68958 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
68975 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
68994 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
69010 -TTGCGAT
1 ATTGCGAT
69017 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:68980 original size:19 final size:19
Alignment explanation
Indices: 68939--69006 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
68929 GAAATGAAAA
68939 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
68955 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
68972 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
68991 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
69007 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:68982 original size:52 final size:52
Alignment explanation
Indices: 68920--69034 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
68910 AACGCGAAAA
* ***
68920 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
68972 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
69024 TCGCGTTGCGA
1 TCGCATTGCGA
69035 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:69143 original size:14 final size:14
Alignment explanation
Indices: 69124--69159 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
69114 ATCAATTAAG
69124 CAAATCAACATTTA
1 CAAATCAACATTTA
* *
69138 CAAATCATCTTTTA
1 CAAATCAACATTTA
69152 CAAATCAA
1 CAAATCAA
69160 TTAAACAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
CAAATCAACATTTA
Found at i:71033 original size:20 final size:20
Alignment explanation
Indices: 71008--71060 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
70998 TAGTTTACTT
*
71008 TCGCAACACGAAACTTAA-AA
1 TCGCAACGCGAAA-TTAACAA
*
71028 TCGCAACGCGAAATTAACTA
1 TCGCAACGCGAAATTAACAA
71048 TCGCAACGCGAAA
1 TCGCAACGCGAAA
71061 ATGGCTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAATTAACAA
Found at i:71102 original size:14 final size:14
Alignment explanation
Indices: 71083--71140 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
71073 ATGCGAAATG
*
71083 AAAATCGCAACGAC
1 AAAATCGCAACGAA
71097 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
71113 ATGAAATCGCAACGAT
1 A--AAATCGCAACGAA
71129 AAAATCGCAACG
1 AAAATCGCAACG
71141 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:71125 original size:32 final size:33
Alignment explanation
Indices: 71070--71145 Score: 127
Period size: 32 Copynumber: 2.3 Consensus size: 33
71060 AATGGCTATT
*
71070 GCAATGCGAAATGAAAATCGCAACGACAAAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
*
71103 GCAACGCGAAATG-AAATCGCAACGATAAAATC
1 GCAACGCGAAATGAAAATCGCAACGACAAAATC
71135 GCAACGCGAAA
1 GCAACGCGAAA
71146 CACAAATCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 29 0.71
33 12 0.29
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGACAAAATC
Found at i:71193 original size:14 final size:14
Alignment explanation
Indices: 71174--71231 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
71164 TTTCATTTCG
71174 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
71188 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
71204 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
71220 CGTTGCGATTTT
1 CGTTGCGATTTT
71232 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:71238 original size:33 final size:33
Alignment explanation
Indices: 71157--71243 Score: 158
Period size: 32 Copynumber: 2.7 Consensus size: 33
71147 ACAAATCGCA
*
71157 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
71190 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
71222 TTGCGATTTTCATTTCGCATTG
1 TTGCGATTTTCATTTCGCATTG
71244 TGATAGCCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 31 0.60
33 21 0.40
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:71274 original size:20 final size:19
Alignment explanation
Indices: 71220--71286 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
71210 GCGATTTTGT
**
71220 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
71239 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
71259 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
71279 TGTTGCGA
1 CGTTGCGA
71287 AAGTAAACTA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 12 0.32
20 22 0.59
21 3 0.08
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:71787 original size:18 final size:18
Alignment explanation
Indices: 71761--71805 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
71751 GTCGATCAGA
*
71761 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
71779 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
71797 TGATGGCTC
1 TGATGGCTC
71806 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:73450 original size:22 final size:22
Alignment explanation
Indices: 73420--73463 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
73410 GATGGAGATA
*
73420 GACGAATTTCGCCGGAGATGGG
1 GACGAATTTCGCCAGAGATGGG
* *
73442 GACGGATTTCGTCAGAGATGGG
1 GACGAATTTCGCCAGAGATGGG
73464 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCAGAGATGGG
Found at i:73678 original size:20 final size:20
Alignment explanation
Indices: 73652--73765 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
73642 GATTATGTAT
73652 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
73672 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
73692 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
73712 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
73733 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
73753 TATCGCATTGCGA
1 TATCGCGTTGCGA
73766 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:73769 original size:41 final size:41
Alignment explanation
Indices: 73632--73767 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
73622 TGCTTTGAAA
*
73632 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
73673 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
73713 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
73754 ATCGCATTGCGATT
1 ATCGCATTGCGATT
73768 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:73788 original size:21 final size:21
Alignment explanation
Indices: 73755--73847 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
73745 ATAGTCAGTA
73755 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
73776 TCGCGTTGTGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
73796 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
73817 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
73837 TCGCATTGCGA
1 TCGCATTGCGA
73848 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:73800 original size:41 final size:41
Alignment explanation
Indices: 73755--73847 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
73745 ATAGTCAGTA
*
73755 TCGCATTGCGATTTTCCCAATTCGCGTTGTGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
73796 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
73837 TCGCATTGCGA
1 TCGCATTGCGA
73848 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:80906 original size:205 final size:205
Alignment explanation
Indices: 80545--80918 Score: 667
Period size: 205 Copynumber: 1.8 Consensus size: 205
80535 TTTTGACACC
* * * *
80545 ATAACGTTCTAAATTTTTAATTTCTTAAATTATTCCACATTAATGTTGTAAATTATTTTTTAAAA
1 ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAATGTTCTAAATTATTTTTTAAAA
*
80610 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATTTTAATAAAT
66 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
* *
80675 TTTATTTCAATTATGTATTTTGAATTTTTAAAAATTTTAAATTTTAACTTTTAGATTTTTTATAT
131 TTTATTTCAATTATATATTGTGAATTTTTAAAAATTTTAAATTTTAACTTTTAGATTTTTTATAT
80740 AATTTTTTTA
196 AATTTTTTTA
*
80750 ATAACATTCTAAATTCTTAATTTCATAAATTATTTCACATTAATGTTCTAAATTATTTTTTAAAA
1 ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAATGTTCTAAATTATTTTTTAAAA
80815 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
66 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
*
80880 TTTATTTCAATTATATATTGTGAATTTTTAAAACTTTTA
131 TTTATTTCAATTATATATTGTGAATTTTTAAAAATTTTA
80919 TATATATTAA
Statistics
Matches: 160, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 160 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (205 bp):
ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAATGTTCTAAATTATTTTTTAAAA
TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
TTTATTTCAATTATATATTGTGAATTTTTAAAAATTTTAAATTTTAACTTTTAGATTTTTTATAT
AATTTTTTTA
Found at i:80976 original size:25 final size:25
Alignment explanation
Indices: 80933--80997 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
80923 TATTAACTTG
80933 AAATATTTTTATTTCAACTT-A-TT
1 AAATATTTTTATTTCAACTTAATTT
*
80956 AAATATATTTTATTATTAACTTAATTT
1 AAATAT-TTTTATT-TCAACTTAATTT
*
80983 AAAGATGTTTTATTT
1 AAATAT-TTTTATTT
80998 TTTTATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 6 0.17
24 7 0.20
25 6 0.17
26 2 0.06
27 14 0.40
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (25 bp):
AAATATTTTTATTTCAACTTAATTT
Found at i:86800 original size:131 final size:130
Alignment explanation
Indices: 86533--86925 Score: 680
Period size: 131 Copynumber: 3.0 Consensus size: 130
86523 AAAGCAAACC
*
86533 CCGTATCTTCGATGCAATCACCGCAGAGATTCTACAGCTGCGTCTTAGAGTCCAACCACTAAGA-
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAA-CACTAAGAC
* *
86597 CTTGTTTGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCACGTGCAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
86662 A
130 A
*
86663 CTGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAAGCACTAAGAC
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAA-CACTAAGAC
* *
86728 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACAAGGACCAAGTGAAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
86793 A
130 A
*
86794 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCGACAACTAAGAC
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAAC-ACTAAGAC
*
86859 CTTGTTCGAACAAAGGAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
86924 A
130 A
86925 C
1 C
86926 ACTAATTTAT
Statistics
Matches: 249, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
130 62 0.25
131 187 0.75
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (130 bp):
CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAACACTAAGACC
TTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATTA
Found at i:101586 original size:37 final size:37
Alignment explanation
Indices: 101513--101587 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
101503 GTTGGAAAAT
* *
101513 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
101550 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
101587 A
1 A
101588 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:102228 original size:24 final size:24
Alignment explanation
Indices: 102195--102241 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
102185 TTTATTAGTT
*
102195 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
102219 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
102242 TATATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:106636 original size:24 final size:23
Alignment explanation
Indices: 106609--106676 Score: 54
Period size: 24 Copynumber: 3.0 Consensus size: 23
106599 GTAAATGCGA
106609 ATTTTTAAAAGTTATATAAAAAAT
1 ATTTTTAAAA-TTATATAAAAAAT
** *
106633 ATTTAAAAAAAATTA-ATATAAAAT
1 ATTT--TTAAAATTATATAAAAAAT
106657 A--TTT-AAATTATATAAAAAAT
1 ATTTTTAAAATTATATAAAAAAT
106677 CTAAAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 6 0.17
20 8 0.23
22 1 0.03
24 13 0.37
25 3 0.09
26 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
ATTTTTAAAATTATATAAAAAAT
Found at i:106681 original size:18 final size:19
Alignment explanation
Indices: 106642--106686 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
106632 TATTTAAAAA
* *
106642 AAATTAATATAAAATATTT
1 AAATTAATATAAAAAATCT
106661 AAATT-ATATAAAAAATCT
1 AAATTAATATAAAAAATCT
106679 AAAATTAA
1 -AAATTAA
106687 CGAGAGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 11 0.50
19 10 0.45
20 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTAATATAAAAAATCT
Found at i:106683 original size:19 final size:18
Alignment explanation
Indices: 106641--106685 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
106631 ATATTTAAAA
*
106641 AAAATTAATATAAAATATT
1 AAAATT-ATATAAAAAATT
*
106660 TAAATTATATAAAAAATCT
1 AAAATTATATAAAAAAT-T
106679 AAAATTA
1 AAAATTA
106686 ACGAGAGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATATAAAAAATT
Found at i:113945 original size:2 final size:2
Alignment explanation
Indices: 113938--113972 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
113928 GTCAAAAGTT
113938 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 T
113973 TAATATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:113978 original size:6 final size:6
Alignment explanation
Indices: 113969--114083 Score: 97
Period size: 6 Copynumber: 18.3 Consensus size: 6
113959 ATATATATAT
* *
113969 ATATTA ATATTA TTATTA ATATTA ATGTTA GGA-ACTTGA TACTATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA --ATA-TT-A -A-TATTA
* * * *
114016 ATATTA ATATTA ATATTA ATATTA TTATTA TTATTA TTATTA TTATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
* *
114064 TTATTA TTATTA ATATTA AT
1 ATATTA ATATTA ATATTA AT
114084 TCGAAAATTC
Statistics
Matches: 96, Mismatches: 7, Indels: 12
0.83 0.06 0.10
Matches are distributed among these distances:
6 86 0.90
7 1 0.01
8 5 0.05
9 3 0.03
10 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
ATATTA
Found at i:113978 original size:12 final size:13
Alignment explanation
Indices: 113938--113990 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
113928 GTCAAAAGTT
113938 TATATATATA-TA
1 TATATATATATTA
113950 TATATATATA-TA
1 TATATATATATTA
113962 TATATATATATTA
1 TATATATATATTA
113975 -ATAT-TATTATTA
1 TATATATA-TATTA
113987 -ATAT
1 TATAT
113991 TAATGTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATATATTA
Found at i:115119 original size:2 final size:2
Alignment explanation
Indices: 115112--115149 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
115102 TTATTAAAGA
115112 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
115150 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115456 original size:39 final size:37
Alignment explanation
Indices: 115413--115507 Score: 124
Period size: 34 Copynumber: 2.6 Consensus size: 37
115403 TATTATATAA
115413 GATATGATATTAAAAATTAATTAAAACAGGTTATGAG
1 GATATGATATTAAAAATTAATTAAAACAGGTTATGAG
115450 G---TGATATTAAAAATTAATTAAAACAGGTTATGAGG
1 GATATGATATTAAAAATTAATTAAAACAGGTTATGA-G
* *
115485 TGATATAATAATAAAAAATTAAT
1 -GATATGAT-ATTAAAAATTAAT
115508 CGATTAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
34 32 0.64
35 1 0.02
36 1 0.02
37 1 0.02
39 3 0.06
40 12 0.24
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.33
Consensus pattern (37 bp):
GATATGATATTAAAAATTAATTAAAACAGGTTATGAG
Found at i:115460 original size:34 final size:34
Alignment explanation
Indices: 115417--115490 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
115407 ATATAAGATA
115417 TGATATTAAAAATTAATTAAAACAGGTTATGAGG
1 TGATATTAAAAATTAATTAAAACAGGTTATGAGG
115451 TGATATTAAAAATTAATTAAAACAGGTTATGAGG
1 TGATATTAAAAATTAATTAAAACAGGTTATGAGG
115485 TGATAT
1 TGATAT
115491 AATAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.34
Consensus pattern (34 bp):
TGATATTAAAAATTAATTAAAACAGGTTATGAGG
Found at i:122094 original size:38 final size:38
Alignment explanation
Indices: 122026--122101 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
122016 ACCCGACCCG
* * *
122026 ACCCGACCCGAGAAGTATACACCCTTCATCTGAACCTA
1 ACCCGACCCGAGAAGTATACAACATCCATCTGAACCTA
* * *
122064 ACCCGACCTGAGAAGTATATAACATCCATCTGACCCTA
1 ACCCGACCCGAGAAGTATACAACATCCATCTGAACCTA
122102 CACTACTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.20
Consensus pattern (38 bp):
ACCCGACCCGAGAAGTATACAACATCCATCTGAACCTA
Found at i:145874 original size:20 final size:20
Alignment explanation
Indices: 145849--145983 Score: 99
Period size: 19 Copynumber: 7.0 Consensus size: 20
145839 GGCTGCTGGA
145849 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGG-TTTC
*
145869 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTAACCGGTTTC
* *
145889 AACCGGTTCGAACTGGTTT-
1 AACCGGTTCTAACCGGTTTC
*
145908 GACCGG-TCTGAACCGGTTT-
1 AACCGGTTCT-AACCGGTTTC
*
145927 GACCGG-TCTGAACCGGTTT-
1 AACCGGTTCT-AACCGGTTTC
*
145946 GACCGG-TCTGAACCGGTTT-
1 AACCGGTTCT-AACCGGTTTC
*
145965 GACCGG-TCTGAACCGGTTT
1 AACCGGTTCT-AACCGGTTT
145984 GACCGGTCTG
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
18 2 0.02
19 70 0.66
20 28 0.26
21 6 0.06
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTC
Found at i:145914 original size:19 final size:19
Alignment explanation
Indices: 145870--145994 Score: 191
Period size: 19 Copynumber: 6.5 Consensus size: 19
145860 CCGGTTTTCA
*
145870 ACCGGTTCTG-ACCGGTTTCA
1 ACCGG-TCTGAACCGGTTT-G
*
145890 ACCGGT-TCGAACTGGTTTG
1 ACCGGTCT-GAACCGGTTTG
145909 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
145928 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
145947 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
145966 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
145985 ACCGGTCTGA
1 ACCGGTCTGA
145995 CCCGACCCGA
Statistics
Matches: 99, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.01
19 85 0.86
20 13 0.13
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:146003 original size:5 final size:5
Alignment explanation
Indices: 145993--146062 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
145983 TGACCGGTCT
* *
145993 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
146042 GACCGTT GACCC GACCC GACC
1 GACC--C GACCC GACCC GACC
146063 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 41 0.77
7 12 0.23
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:146007 original size:57 final size:57
Alignment explanation
Indices: 145890--146007 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
145880 ACCGGTTTCA
* ****
145890 ACCGGTTCGAACTGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGAACCGACCCG
*
145947 ACCGG-TCTGAACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGACCCGACCCG
1 ACCGGTTC-GAACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGAACCGACCCG
146004 ACCG
1 ACCG
146008 TTGACCCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 2 0.04
57 52 0.96
ACGTcount: A:0.16, C:0.30, G:0.31, T:0.24
Consensus pattern (57 bp):
ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGAACCGACCCG
Found at i:146014 original size:17 final size:17
Alignment explanation
Indices: 145992--146069 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 17
145982 TTGACCGGTC
145992 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
146009 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
146031 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
146048 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
146065 TGACC
1 TGACC
146070 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 39 0.70
22 17 0.30
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:146019 original size:22 final size:22
Alignment explanation
Indices: 145993--146076 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
145983 TGACCGGTCT
145993 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
146015 GACCCGACCCGACCGTT-----
1 GACCCGACCCGACCGTTGACCC
146032 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
146054 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
146077 GTTGATTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
17 17 0.31
22 26 0.48
24 11 0.20
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:153258 original size:9 final size:9
Alignment explanation
Indices: 153244--153308 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
153234 GGCTGCTGGA
153244 AACCGGTTT
1 AACCGGTTT
153253 AACCGGTTTT
1 AACCGG-TTT
153263 CAACCGGTTCT
1 -AACCGGTT-T
*
153274 GACCGGTTT
1 AACCGGTTT
* *
153283 GACCGGTCTG
1 AACCGGT-TT
153293 AACCGGTTT
1 AACCGGTTT
*
153302 GACCGGT
1 AACCGGT
153309 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 21 0.45
10 19 0.40
11 7 0.15
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:153269 original size:20 final size:21
Alignment explanation
Indices: 153244--153282 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
153234 GGCTGCTGGA
153244 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
153264 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
153283 GACCGGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:153289 original size:19 final size:18
Alignment explanation
Indices: 153265--153314 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
153255 CCGGTTTTCA
153265 ACCGGTTCTGACCGGTTTG
1 ACCGG-TCTGACCGGTTTG
153284 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTG-ACCGGTTTG
153303 ACCGGTCTGACC
1 ACCGGTCTGACC
153315 CGACCCGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:153313 original size:9 final size:9
Alignment explanation
Indices: 153265--153314 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
153255 CCGGTTTTCA
153265 ACCGGTTCTG
1 ACCGG-TCTG
*
153275 ACCGGTTTG
1 ACCGGTCTG
153284 ACCGGTCTG
1 ACCGGTCTG
*
153293 AACCGGTTTG
1 -ACCGGTCTG
153303 ACCGGTCTG
1 ACCGGTCTG
153312 ACC
1 ACC
153315 CGACCCGACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 22 0.63
10 13 0.37
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:153336 original size:5 final size:5
Alignment explanation
Indices: 153328--153385 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
153318 CCCGACTGTT
* *
153328 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
153377 GACCC GACC
1 GACCC GACC
153386 GTTGACCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:153339 original size:22 final size:22
Alignment explanation
Indices: 153328--153392 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
153318 CCCGACTGTT
153328 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
153350 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
153372 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
153393 ATTGACTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:153392 original size:17 final size:17
Alignment explanation
Indices: 153310--153358 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
153300 TTGACCGGTC
*
153310 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
153327 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
153344 TGACCCGACCCGACC
1 TGACCCGACCCGACC
153359 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:154912 original size:2 final size:2
Alignment explanation
Indices: 154905--154965 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
154895 ATAGGCCGGG
154905 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
154947 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
154966 TAAATTATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:158338 original size:27 final size:27
Alignment explanation
Indices: 158292--158355 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
158282 GAGGAGCTTT
*
158292 TGGAGAAGCAGCTCGCGGGGGTGGAGG
1 TGGAGAAGCAGATCGCGGGGGTGGAGG
*
158319 TGGAGAAGCAGATCGTGGGGGTGGAGG
1 TGGAGAAGCAGATCGCGGGGGTGGAGG
158346 TGGAGAAGCA
1 TGGAGAAGCA
158356 ACCCTAGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.53, T:0.12
Consensus pattern (27 bp):
TGGAGAAGCAGATCGCGGGGGTGGAGG
Found at i:158365 original size:27 final size:27
Alignment explanation
Indices: 158292--158365 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
158282 GAGGAGCTTT
158292 TGGAGAAGCAG-CTCGC-GGGGGTGGAGG
1 TGGAGAAGCAGAC-C-CTGGGGGTGGAGG
* *
158319 TGGAGAAGCAGATCGTGGGGGTGGAGG
1 TGGAGAAGCAGACCCTGGGGGTGGAGG
*
158346 TGGAGAAGCA-ACCCTAGGGG
1 TGGAGAAGCAGACCCTGGGGG
158366 AGGCCCTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 7 0.17
27 33 0.82
ACGTcount: A:0.23, C:0.14, G:0.51, T:0.12
Consensus pattern (27 bp):
TGGAGAAGCAGACCCTGGGGGTGGAGG
Found at i:162356 original size:20 final size:20
Alignment explanation
Indices: 162300--162359 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
162290 ATTGAATTTC
* **
162300 TTATTATTTGTTAAACATTTT
1 TTATT-TTTGTTAAAAATTCG
*
162321 TATATTTTTTTATAAAAATTCG
1 T-TATTTTTGT-TAAAAATTCG
162343 TTATTTTTGTTAAAAAT
1 TTATTTTTGTTAAAAAT
162360 ATAAAATATC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.22
21 13 0.41
22 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TTATTTTTGTTAAAAATTCG
Found at i:162774 original size:14 final size:14
Alignment explanation
Indices: 162754--162786 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
162744 TTCAACCCTG
162754 AAAAAAAA-GATAA
1 AAAAAAAACGATAA
162767 ACAAAAAAACGATAA
1 A-AAAAAAACGATAA
162782 AAAAA
1 AAAAA
162787 CCGTAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 11 0.61
15 6 0.33
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (14 bp):
AAAAAAAACGATAA
Found at i:163945 original size:185 final size:182
Alignment explanation
Indices: 163469--163957 Score: 475
Period size: 184 Copynumber: 2.7 Consensus size: 182
163459 GCCCTTAAAA
* * * * * *
163469 TTTT-AATTTTATAAAATAATTCTTATTTTCTATTTTTATAATTAAAAACCTATAATTTAATATT
1 TTTTCAATTTTATAAAATAATACCTACTTTCTATCTTTATAATTAAGAGCC-ATAATTTAATATT
** * * * *
163533 TTTATGCTTTATTGATGTAATATTAAATTAATTATTCAAAATAATATAACATATTTTCGTTTTAC
65 TTTATTATTTATTAATGTAATATTAAATTAATTATTCAAAATAATAAAATATATTTTCATTTTAC
* * ** * * * * * *
163598 AGGGCTTATTTTTTGAGTTTTAGCTCAAAATTTGTAGCTAGGAGTCCCTATTC
130 AAGACCCATTCTTTGAATTTTAGATCAAAATTTATAACTAAGAGTCCCTATTC
* * * * * *
163651 TTTTCAATTTTATAAAAAAAATACGTACTTTATA-CTTTTATAATTAAGGGCCCACAATGTAATA
1 TTTTCAATTTTAT-AAAATAATACCTACTTTCTATC-TTTATAATTAAGAG-CCATAATTTAATA
* * *
163715 TTTTTA-TAGTTTATTAATGTAATATTAAATTATTTTTTTAAAATAATAAAATATATTTT-ATTT
63 TTTTTATTA-TTTATTAATGTAATATTAAATTAATTATTCAAAATAATAAAATATATTTTCATTT
* * * * *
163778 TATAAGACCCATTCTTT-AATTTTCGATCAAAGTTTATAATTAAGAGTCCCTATTTT
127 TACAAGACCCATTCTTTGAATTTTAGATCAAAATTTATAACTAAGAGTCCCTA-TTC
* * *
163834 TTTCTCAATTTTATAAAATAATCCCTACTTTCTATCTTTATAAATGAGAGCTCATAATTTAATTA
1 TTT-TCAATTTTATAAAATAATACCTACTTTCTATCTTTATAATTAAGAGC-CATAATTTAA-T-
* * *
163899 ATTTTTATTATTTATTAATATAATATTAAAATAATTGTTCAAAATAATAAAATATATTT
62 ATTTTTATTATTTATTAATGTAATATTAAATTAATTATTCAAAATAATAAAATATATTT
163958 CCGTTCTATA
Statistics
Matches: 246, Mismatches: 49, Indels: 21
0.78 0.16 0.07
Matches are distributed among these distances:
182 32 0.13
183 62 0.25
184 97 0.39
185 53 0.22
186 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.47
Consensus pattern (182 bp):
TTTTCAATTTTATAAAATAATACCTACTTTCTATCTTTATAATTAAGAGCCATAATTTAATATTT
TTATTATTTATTAATGTAATATTAAATTAATTATTCAAAATAATAAAATATATTTTCATTTTACA
AGACCCATTCTTTGAATTTTAGATCAAAATTTATAACTAAGAGTCCCTATTC
Found at i:164541 original size:2 final size:2
Alignment explanation
Indices: 164534--164575 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
164524 TATAAATTGT
164534 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
164576 AAGTTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171618 original size:21 final size:21
Alignment explanation
Indices: 171560--171623 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
171550 AGTTGAAGTT
*
171560 ACTGTAGCAGTGCATCAGTAC
1 ACTGTAGCAGTGCATCGGTAC
171581 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGGTAC
* *
171602 ACTGTAGCAGTACATCGATAC
1 ACTGTAGCAGTGCATCGGTAC
171623 A
1 A
171624 TAATTTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGGTAC
Found at i:171726 original size:19 final size:19
Alignment explanation
Indices: 171698--171747 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
171688 ACTGTTCACG
* *
171698 GTACTGTTCATACCGTATA
1 GTACTATTCATACCATATA
171717 GTACTATTCATACCATATA
1 GTACTATTCATACCATATA
171736 GTACTATTCATA
1 GTACTATTCATA
171748 AAAATGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (19 bp):
GTACTATTCATACCATATA
Found at i:174327 original size:13 final size:14
Alignment explanation
Indices: 174309--174342 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
174299 TTCATTGAAA
174309 AACCGAAAAA-CCG
1 AACCGAAAAACCCG
174322 AACCGAAAAACCCG
1 AACCGAAAAACCCG
174336 AACCGAA
1 AACCGAA
174343 CCGAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.53, C:0.32, G:0.15, T:0.00
Consensus pattern (14 bp):
AACCGAAAAACCCG
Found at i:174354 original size:14 final size:14
Alignment explanation
Indices: 174309--174342 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
174299 TTCATTGAAA
174309 AACCG-AAAAACCG
1 AACCGAAAAAACCG
*
174322 AACCGAAAAACCCG
1 AACCGAAAAAACCG
174336 AACCGAA
1 AACCGAA
174343 CCGAAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.53, C:0.32, G:0.15, T:0.00
Consensus pattern (14 bp):
AACCGAAAAAACCG
Found at i:186964 original size:36 final size:36
Alignment explanation
Indices: 186814--186992 Score: 136
Period size: 36 Copynumber: 4.9 Consensus size: 36
186804 TATATATATA
*
186814 TTGACAATTATGAATACTGA--TTTTTTACAATTAT
1 TTGACAATTATGAATCCTGATTTTTTTTACAATTAT
* * *
186848 TTGACAATTATGAATCTTGATTTTTTTGAAAATTCCTTATT
1 TTGACAATTATGAATCCTGATTTTTTTTACAA----TTA-T
* * * * * *
186889 TCTTA-AATT-T-AA-ACTTATATATATTGACAATTAT
1 T-TGACAATTATGAATCCTGAT-TTTTTTTACAATTAT
*
186923 ATGACAATTATGAATCCTGATTTTTTTTACAATTAT
1 TTGACAATTATGAATCCTGATTTTTTTTACAATTAT
* *
186959 TTGACAATCATGAATCCTGATTTTTTTTAGAATT
1 TTGACAATTATGAATCCTGATTTTTTTTACAATT
186993 CCTTATTTCT
Statistics
Matches: 111, Mismatches: 21, Indels: 24
0.71 0.13 0.15
Matches are distributed among these distances:
33 2 0.02
34 23 0.21
35 4 0.04
36 53 0.48
37 4 0.04
38 3 0.03
39 10 0.09
40 4 0.04
41 6 0.05
42 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (36 bp):
TTGACAATTATGAATCCTGATTTTTTTTACAATTAT
Found at i:186993 original size:111 final size:111
Alignment explanation
Indices: 186733--187070 Score: 454
Period size: 111 Copynumber: 3.0 Consensus size: 111
186723 ACCTTTATAA
* *
186733 AATTATTTGACAATTATGAATCCTGA-TTTTTTGAAAATTTCTTATTTCTTAAATTTAAAATTAT
1 AATTATTTGACAATTATGAATCCTGATTTTTTTGAAAATTCCTTATTTCTTAAATTTAAACTTAT
* *
186797 -TAATATAT-A-TATATATATTGACAATTATGAATACTGA--TTTTTTAC
66 AT-ATAT-TGACAAT-TATA-TGACAATTATGAATCCTGATTTTTTTTAC
*
186842 AATTATTTGACAATTATGAATCTTGATTTTTTTGAAAATTCCTTATTTCTTAAATTTAAACTTAT
1 AATTATTTGACAATTATGAATCCTGATTTTTTTGAAAATTCCTTATTTCTTAAATTTAAACTTAT
186907 ATATATTGACAATTATATGACAATTATGAATCCTGATTTTTTTTAC
66 ATATATTGACAATTATATGACAATTATGAATCCTGATTTTTTTTAC
* * *
186953 AATTATTTGACAATCATGAATCCTGATTTTTTTTAGAATTCCTTATTTCTTAAATTTAAACTTAT
1 AATTATTTGACAATTATGAATCCTGATTTTTTTGAAAATTCCTTATTTCTTAAATTTAAAC-T-T
* * * *
187018 ATACATATATTGACAATTATTTGACAATTGTGAAGCCTGATTTTTTTGAC
64 AT--ATATATTGACAATTATATGACAATTATGAATCCTGATTTTTTTTAC
187068 AAT
1 AAT
187071 CATGAATCCT
Statistics
Matches: 206, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
109 44 0.21
110 45 0.22
111 68 0.33
112 1 0.00
113 3 0.01
115 45 0.22
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (111 bp):
AATTATTTGACAATTATGAATCCTGATTTTTTTGAAAATTCCTTATTTCTTAAATTTAAACTTAT
ATATATTGACAATTATATGACAATTATGAATCCTGATTTTTTTTAC
Found at i:187076 original size:25 final size:25
Alignment explanation
Indices: 187037--187089 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
187027 TTGACAATTA
**
187037 TTTGACAATTGTGAAGCCTGATTTT
1 TTTGACAATCATGAAGCCTGATTTT
* *
187062 TTTGACAATCATGAATCCTTATTTT
1 TTTGACAATCATGAAGCCTGATTTT
187087 TTT
1 TTT
187090 ATTTCCTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTGACAATCATGAAGCCTGATTTT
Found at i:187147 original size:107 final size:104
Alignment explanation
Indices: 186958--187172 Score: 274
Period size: 107 Copynumber: 2.0 Consensus size: 104
186948 TTTACAATTA
186958 TTTGACAATCATGAATCCTGATTTTTTTTAGAATTCCTTATTTCTTAAATTTAAACTTATATACA
1 TTTGACAATCATGAATCCTGATTTTTTTTA-AATTCCTTATTTCTTAAATTTAAACTTATATACA
**
187023 TATATTGACAATTATTTGACAATTGTGAAGCC-TGATTTT
65 TATATTGACAATTATTTGACAATTACGAAGCCTTGATTTT
* * * *
187062 TTTGACAATCATGAATCCTTA-TTTTTTT-ATTTCCTTATTTGTTAACTTTAAACTTCTATATAT
1 TTTGACAATCATGAATCCTGATTTTTTTTAAATTCCTTATTTCTTAAATTTAAA---C--T-TAT
* *
187125 ATATATATATTGACAATTATTTGACAATTACGAATCCTTGATTTT
60 ATACATATATTGACAATTATTTGACAATTACGAAGCCTTGATTTT
187170 TTT
1 TTT
187173 TTGAAAATTC
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
101 21 0.22
103 7 0.07
104 21 0.22
106 1 0.01
107 36 0.38
108 10 0.10
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (104 bp):
TTTGACAATCATGAATCCTGATTTTTTTTAAATTCCTTATTTCTTAAATTTAAACTTATATACAT
ATATTGACAATTATTTGACAATTACGAAGCCTTGATTTT
Found at i:187162 original size:82 final size:79
Alignment explanation
Indices: 187062--187254 Score: 244
Period size: 84 Copynumber: 2.3 Consensus size: 79
187052 GCCTGATTTT
* * * *
187062 TTTGACAATCATGAATCCTTATTTTTTT-ATTTCCTTATTTGTTAACTTTAAACTTCTATATATA
1 TTTGACAATTATGAATCCTTATTTTTTTAAATTCCTTATTTCTTAAATTTAAA---CT-TATATA
187126 TATATATATTGACAATTA
62 TATATATATTGACAATTA
*
187144 TTTGACAATTACGAATCCTTGATTTTTTTTTGAAAATTCCTTATTTCTTAAATTTAAACTTATAT
1 TTTGACAATTATGAATCCTT-A--TTTTTTT--AAATTCCTTATTTCTTAAATTTAAACTTATAT
187209 ATATATATATTGACAATTA
61 ATATATATATTGACAATTA
*
187228 TTTGACAATTATGAATCCTGATTTTTT
1 TTTGACAATTATGAATCCTTATTTTTT
187255 AAGCTATCCT
Statistics
Matches: 98, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
81 6 0.06
82 18 0.18
83 2 0.02
84 42 0.43
85 9 0.09
88 21 0.21
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.50
Consensus pattern (79 bp):
TTTGACAATTATGAATCCTTATTTTTTTAAATTCCTTATTTCTTAAATTTAAACTTATATATATA
TATATTGACAATTA
Found at i:187227 original size:84 final size:85
Alignment explanation
Indices: 187092--187254 Score: 258
Period size: 84 Copynumber: 1.9 Consensus size: 85
187082 ATTTTTTTAT
* *
187092 TTCCTTATTTGTTAACTTTAAACTTCTATATATATATATATATTGACAATTATTTGACAATTACG
1 TTCCTTATTTCTTAAATTTAAA--TCTATATATATATATATATTGACAATTATTTGACAATTACG
187157 AATCCTTGATTTTTTTTTGAAAA
64 AATCC-TGATTTTTTTTTGAAAA
*
187180 TTCCTTATTTCTTAAATTTAAA-CT-TATATATATATATATTGACAATTATTTGACAATTATGAA
1 TTCCTTATTTCTTAAATTTAAATCTATATATATATATATATTGACAATTATTTGACAATTACGAA
187243 TCCTGATTTTTT
66 TCCTGATTTTTT
187255 AAGCTATCCT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
83 9 0.12
84 41 0.57
85 2 0.03
88 20 0.28
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (85 bp):
TTCCTTATTTCTTAAATTTAAATCTATATATATATATATATTGACAATTATTTGACAATTACGAA
TCCTGATTTTTTTTTGAAAA
Found at i:189312 original size:36 final size:35
Alignment explanation
Indices: 189256--189331 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
189246 TTCATGTTCA
*
189256 AAATTCCAAAATACTTTAATTACACTCTAAACCCT
1 AAATTCCAAAATACTCTAATTACACTCTAAACCCT
*
189291 AAATTCCAAAAATACTCTAATTACATTCTAAACCCT
1 AAATTCC-AAAATACTCTAATTACACTCTAAACCCT
189327 AAATT
1 AAATT
189332 AAAGTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 7 0.18
36 31 0.82
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAATACTCTAATTACACTCTAAACCCT
Found at i:202715 original size:12 final size:12
Alignment explanation
Indices: 202698--202729 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
202688 GCGATTACGG
202698 TTCGATTCGGTT
1 TTCGATTCGGTT
202710 TTCGATTCGGTT
1 TTCGATTCGGTT
202722 TTCGATTC
1 TTCGATTC
202730 TCTTAACTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.50
Consensus pattern (12 bp):
TTCGATTCGGTT
Found at i:203090 original size:18 final size:19
Alignment explanation
Indices: 203051--203090 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
203041 ACGTGATAAG
*
203051 TTTATTTAAATAATATTTT
1 TTTATTTAAATAATATTAT
*
203070 TTTATTTAAAT-TTATTAT
1 TTTATTTAAATAATATTAT
203088 TTT
1 TTT
203091 GATGTGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTAAATAATATTAT
Found at i:203771 original size:15 final size:15
Alignment explanation
Indices: 203751--203780 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
203741 GTATAGTCCA
*
203751 TTTTATACATGGACG
1 TTTTATACAAGGACG
203766 TTTTATACAAGGACG
1 TTTTATACAAGGACG
203781 GACGCATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (15 bp):
TTTTATACAAGGACG
Found at i:214489 original size:45 final size:45
Alignment explanation
Indices: 214425--214515 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
214415 ATGTTTGACA
*
214425 GCATCCACTGCTTCGAATTGAAGTAGAGAGTGAATAAAACGAACT
1 GCATCCACTGCTTCGAATTGAAGTAAAGAGTGAATAAAACGAACT
214470 GCATCCACTGCTTCGAATTGAAGTAAAGAGTGAATAAAACGAACT
1 GCATCCACTGCTTCGAATTGAAGTAAAGAGTGAATAAAACGAACT
214515 G
1 G
214516 AGAGAAGCAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (45 bp):
GCATCCACTGCTTCGAATTGAAGTAAAGAGTGAATAAAACGAACT
Found at i:215904 original size:9 final size:9
Alignment explanation
Indices: 215890--215916 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
215880 AGAGAGTGCT
215890 GCAGCAATG
1 GCAGCAATG
215899 GCAGCAATG
1 GCAGCAATG
215908 GCAGCAATG
1 GCAGCAATG
215917 CTAAGACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.11
Consensus pattern (9 bp):
GCAGCAATG
Found at i:226460 original size:2 final size:2
Alignment explanation
Indices: 226453--226483 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
226443 AAATTGTATG
226453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
226484 TAGAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:236521 original size:20 final size:20
Alignment explanation
Indices: 236496--236569 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
236486 TTTTCCCAAT
*
236496 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
236516 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
236536 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
236557 TCGCAACGCGAAT
1 TCGCAACGCGAAT
236570 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:236538 original size:41 final size:41
Alignment explanation
Indices: 236493--236585 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
236483 CGATTTTCCC
236493 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
236534 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
236575 AAATCGCAATG
1 AATTCGCAATG
236586 TGATACTGAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:236542 original size:21 final size:20
Alignment explanation
Indices: 236496--236583 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
236486 TTTTCCCAAT
* *
236496 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGGAAA
**
236516 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGGAAA
* *
236536 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGGAAA
**
236557 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATAAGG-AAA
236578 TCGCAA
1 TCGCAA
236584 TGTGATACTG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
20 29 0.54
21 25 0.46
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGGAAA
Found at i:236659 original size:28 final size:28
Alignment explanation
Indices: 236619--236672 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
236609 TAATAAAAAA
*
236619 TCGCAACGAGATACTTACTTTCGCAATT
1 TCGCAACGAGATACTGACTTTCGCAATT
*
236647 TCGCAACGCGATACTGACTTTCGCAA
1 TCGCAACGAGATACTGACTTTCGCAA
236673 CGCGATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (28 bp):
TCGCAACGAGATACTGACTTTCGCAATT
Found at i:237257 original size:19 final size:19
Alignment explanation
Indices: 237197--237277 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
237187 TTCAAGAATG
237197 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
237217 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
237233 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
237250 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
237269 AAAATCGCA
1 AAAATCGCA
237278 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:237319 original size:20 final size:19
Alignment explanation
Indices: 237273--237438 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
237263 GAAACCAAAA
*
237273 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
237292 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
237311 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
237331 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
237347 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
237364 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
237378 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
237397 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
237417 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
237437 TC
1 TC
237439 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:237354 original size:39 final size:39
Alignment explanation
Indices: 237278--237354 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
237268 CAAAATCGCA
* **
237278 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
237317 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
237355 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:237363 original size:33 final size:33
Alignment explanation
Indices: 237326--237413 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
237316 GTTGCGATTT
* **
237326 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
237359 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
237392 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
237414 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:239503 original size:21 final size:21
Alignment explanation
Indices: 239479--239545 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
239469 TCATTCCTCG
239479 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
239500 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
239521 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
239542 AGAG
1 AGAG
239546 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:239503 original size:42 final size:42
Alignment explanation
Indices: 239423--239545 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
239413 GCCCGACTCG
* * * * * * *
239423 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
239465 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
239507 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
239546 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:240924 original size:14 final size:14
Alignment explanation
Indices: 240905--240940 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
240895 ATTGTTTAAT
240905 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
240919 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
240933 TGATTTGT
1 TGATTTGT
240941 TTAATTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:241109 original size:19 final size:19
Alignment explanation
Indices: 241047--241100 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
241037 AAAAAGTACT
*
241047 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
241066 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
241086 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
241101 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Done.