Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:565557 original size:20 final size:21
Alignment explanation
Indices: 565513--565570 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
565503 TGCATGGTAG
565513 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
565537 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
* *
565557 TGCACCGATCCACT
1 TGCATCGATGCACT
565571 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:566412 original size:21 final size:21
Alignment explanation
Indices: 566372--566451 Score: 146
Period size: 20 Copynumber: 3.9 Consensus size: 21
566362 GAGTCGAGGG
566372 TCTATGTGGTCCTT-GGGACA
1 TCTATGTGGTCCTTCGGGACA
566392 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
566413 TCTATGTGGT-CTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
566433 TCTATGTGGTCCTTCGGGA
1 TCTATGTGGTCCTTCGGGA
566452 AAAATTCTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
20 34 0.59
21 24 0.41
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.35
Consensus pattern (21 bp):
TCTATGTGGTCCTTCGGGACA
Found at i:566431 original size:41 final size:41
Alignment explanation
Indices: 566372--566451 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
566362 GAGTCGAGGG
566372 TCTATGTGGTCCTTGGGACATCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTGGGACATCTATGTGGTCCTTCGGGACA
566413 TCTATGTGGT-CTTCGGGACATCTATGTGGTCCTTCGGGA
1 TCTATGTGGTCCTT-GGGACATCTATGTGGTCCTTCGGGA
566452 AAAATTCTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 3 0.08
41 35 0.92
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.35
Consensus pattern (41 bp):
TCTATGTGGTCCTTGGGACATCTATGTGGTCCTTCGGGACA
Found at i:568787 original size:33 final size:33
Alignment explanation
Indices: 568745--568811 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
568735 AAGTTATGAG
568745 ATTTCATTAGCAAATATCTAGAGTACACAAATT
1 ATTTCATTAGCAAATATCTAGAGTACACAAATT
568778 ATTTCATTAGCAAATATCTAGAGTACACAAATT
1 ATTTCATTAGCAAATATCTAGAGTACACAAATT
568811 A
1 A
568812 AAAATATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (33 bp):
ATTTCATTAGCAAATATCTAGAGTACACAAATT
Found at i:572571 original size:18 final size:19
Alignment explanation
Indices: 572550--572608 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
572540 TGATATAAAA
*
572550 ATAAAACATATCA-ATAAT
1 ATAAAACAAATCATATAAT
*
572568 ATAAAATAAATCATATAAT
1 ATAAAACAAATCATATAAT
* * *
572587 AAAAATACAAAACATATCAT
1 ATAAA-ACAAATCATATAAT
572607 AT
1 AT
572609 GATATTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 11 0.34
19 9 0.28
20 12 0.38
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAACAAATCATATAAT
Found at i:574519 original size:2 final size:2
Alignment explanation
Indices: 574506--574551 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
574496 AGGAAAACAA
*
574506 AT AT AA 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
574548 AT AT
1 AT AT
574552 CAAAGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:575085 original size:18 final size:17
Alignment explanation
Indices: 575064--575106 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
575054 ATATATACAT
575064 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
575082 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
575099 ATAA-AATA
1 ATAATAATA
575107 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:575512 original size:37 final size:37
Alignment explanation
Indices: 575462--575566 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
575452 GTGCTTGTGG
* * * *
575462 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
575499 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
575536 ATCCCATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
575567 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:576411 original size:105 final size:105
Alignment explanation
Indices: 576109--576739 Score: 898
Period size: 105 Copynumber: 6.0 Consensus size: 105
576099 GCATTGTTCC
* * ** *
576109 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
576173 A-CTAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
576215 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
576275 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTATG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
576315 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
576380 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
576420 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
576485 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
576525 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
576590 CAGCGGTCCCTTCATCGTAAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
576630 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * ** * *
576695 CCAACCGTACCTTCGTTATGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
576736 GAGT
1 GAGT
576740 GTCACGATAT
Statistics
Matches: 483, Mismatches: 34, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
100 81 0.17
101 2 0.00
102 7 0.01
104 5 0.01
105 307 0.64
106 81 0.17
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:576986 original size:36 final size:36
Alignment explanation
Indices: 576939--577014 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
576929 TGTTTGGAGA
* * *
576939 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
576975 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
577011 GAAA
1 GAAA
577015 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:577190 original size:102 final size:101
Alignment explanation
Indices: 576924--577284 Score: 468
Period size: 101 Copynumber: 3.7 Consensus size: 101
576914 TGTTTTCAAA
** *
576924 GTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
*
576986 AAGCGAG-ATAAAATTCATTTCAAGGGAAATGTTTTCAAT
66 AAG-GAGAAAAAAATTCATTTCAAGGGAAATG-TTT--AT
*
577025 GTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
* *
577090 AAGAGAGAAAAAAAAATCATTTTAAGGGAAATGTTTAT
66 AAG-GAG-AAAAAAATTCATTTCAAGGGAAATGTTTAT
577128 GTTTATGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
*
577192 -AGGAGAGAAAAAATTAATTTCAAGGG-AA-----AT
66 AAGGAGA-AAAAAATTCATTTCAAGGGAAATGTTTAT
577222 G----T-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
577282 AAG
66 AAG
577285 CAAGATAAAA
Statistics
Matches: 240, Mismatches: 12, Indels: 26
0.86 0.04 0.09
Matches are distributed among these distances:
89 21 0.09
90 37 0.15
91 2 0.01
94 3 0.01
99 3 0.01
100 19 0.08
101 38 0.16
102 35 0.15
103 33 0.14
104 25 0.10
105 3 0.01
106 21 0.09
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (101 bp):
GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
AAGGAGAAAAAAATTCATTTCAAGGGAAATGTTTAT
Found at i:577418 original size:35 final size:35
Alignment explanation
Indices: 577364--577544 Score: 127
Period size: 35 Copynumber: 5.1 Consensus size: 35
577354 CTCAAGCGAG
* * *
577364 ATAAATCTTGTTTTAAGAAAAATAATCTTGAGTGAA
1 ATAAATATT-TTTCAAGAAAAACAATCTTGAGTGAA
* * * ** *
577400 ATAAATCTTTTTCGAGAAAAACAGTCTCAAGTGAG
1 ATAAATATTTTTCAAGAAAAACAATCTTGAGTGAA
*
577435 ACAAAGTATGTTTT-AAGAAAAACAATCTTGAGTGAA
1 ATAAA-TAT-TTTTCAAGAAAAACAATCTTGAGTGAA
* * * * *
577471 ATAAATATTTTTCGAGAAAAACAGTC-TCAATGAG
1 ATAAATATTTTTCAAGAAAAACAATCTTGAGTGAA
* *
577505 ACAAAGTATGTTTT-AAGAAAAACAAAT-TTGAGTGAG
1 ATAAA-TAT-TTTTCAAGAAAAAC-AATCTTGAGTGAA
577541 ATAA
1 ATAA
577545 TCATTGCATT
Statistics
Matches: 112, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
34 13 0.12
35 48 0.43
36 47 0.42
37 4 0.04
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (35 bp):
ATAAATATTTTTCAAGAAAAACAATCTTGAGTGAA
Found at i:577448 original size:71 final size:71
Alignment explanation
Indices: 577300--577544 Score: 300
Period size: 71 Copynumber: 3.4 Consensus size: 71
577290 TAAAATCTTC
* * * *
577300 TTAA-AAAAAAAAGCTTTGAGTGAAATAAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAG
1 TTAAGAAAAAAAATC-TTGAGTGAAAT-AAAT--CTT-TTTCGAG-AAAAACAGTCTCAAGTGAG
* *
577364 ATAAA-TCTTGTT
60 ACAAAGT-ATGTT
*
577376 TTAAGAAAAATAATCTTGAGTGAAATAAATCTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAG
1 TTAAGAAAAAAAATCTTGAGTGAAATAAATCTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAG
577441 TATGTT
66 TATGTT
* *
577447 TTAAGAAAAACAATCTTGAGTGAAATAAATATTTTTCGAGAAAAACAGTCTCAA-TGAGACAAAG
1 TTAAGAAAAAAAATCTTGAGTGAAATAAATCTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAG
577511 TATGTT
66 TATGTT
*
577517 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAA-AAATCTTGAGTGAAATAA
577545 TCATTGCATT
Statistics
Matches: 155, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
70 38 0.25
71 79 0.51
72 8 0.05
73 3 0.02
75 4 0.03
76 15 0.10
77 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (71 bp):
TTAAGAAAAAAAATCTTGAGTGAAATAAATCTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAG
TATGTT
Found at i:583592 original size:18 final size:17
Alignment explanation
Indices: 583571--583613 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
583561 ATACACACAT
*
583571 ATAATAATAATAGCATGA
1 ATAATAATAATA-AATGA
*
583589 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
583606 ATAA-AATA
1 ATAATAATA
583614 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:584020 original size:37 final size:37
Alignment explanation
Indices: 583970--584073 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
583960 GTGCTTGTGG
* * * * *
583970 ATCCTATCTTTAGGAATTTAAATCTTAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
584007 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
584044 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
584074 GGACGAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:584125 original size:20 final size:20
Alignment explanation
Indices: 584100--584151 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
584090 TGACACTTCA
* *
584100 GTATCGGTACTAACCTTTAG
1 GTATCGATACTAACCTATAG
584120 GTATCGATACTAACCTATAG
1 GTATCGATACTAACCTATAG
*
584140 GTATCAATACTA
1 GTATCGATACTA
584152 TTGACTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAACCTATAG
Found at i:584307 original size:15 final size:15
Alignment explanation
Indices: 584287--584317 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
584277 AAAATATATA
584287 AGTATCGATACCCCT
1 AGTATCGATACCCCT
584302 AGTATCGATACCCCT
1 AGTATCGATACCCCT
584317 A
1 A
584318 TTGGGGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (15 bp):
AGTATCGATACCCCT
Found at i:589000 original size:116 final size:116
Alignment explanation
Indices: 588794--589023 Score: 388
Period size: 116 Copynumber: 2.0 Consensus size: 116
588784 TATCTCTATC
* * *
588794 ACACACAATCAATTATAGTATCCCATGAAATCGAACTATTTTTCGAATATATGACTCAACATACT
1 ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
* *
588859 TATCCATAGAATTATTGGTTTGAATGGGAATGAAGTGTGTTAACTTAGTTA
66 TATCCATAGAATTATTAGTTCGAATGGGAATGAAGTGTGTTAACTTAGTTA
* * *
588910 ACACACAATCGATTCTAGTATCCCATGAAGTCAAACTATCTATCGAATATATGACTCAACATACT
1 ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
588975 TATCCATAGAATTATTAGTTCGAATGGGAATGAAGTGTGTTAACTTAGT
66 TATCCATAGAATTATTAGTTCGAATGGGAATGAAGTGTGTTAACTTAGT
589024 CAATTTATCA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 106 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (116 bp):
ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
TATCCATAGAATTATTAGTTCGAATGGGAATGAAGTGTGTTAACTTAGTTA
Found at i:590194 original size:16 final size:16
Alignment explanation
Indices: 590173--590222 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
590163 TGCACTGTTA
*
590173 TACATGAGCTATGTGT
1 TACATGACCTATGTGT
590189 TACATGTCATCCTATGTGT
1 TACATG--A-CCTATGTGT
*
590208 TACATGATCTATGTG
1 TACATGACCTATGTG
590223 GATATATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (16 bp):
TACATGACCTATGTGT
Found at i:590266 original size:15 final size:16
Alignment explanation
Indices: 590246--590284 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
590236 AAGATATAAG
590246 CTATGTGAA-A-ATGAT
1 CTATGTGAATACATG-T
590261 CTATGTGAATACATGT
1 CTATGTGAATACATGT
590277 CTATGTGA
1 CTATGTGA
590285 TAACCTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 10 0.45
17 3 0.14
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (16 bp):
CTATGTGAATACATGT
Found at i:590408 original size:23 final size:23
Alignment explanation
Indices: 590373--590416 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
590363 GAGTCGAGGT
590373 TCTACGAGGTCCTTTGGGACAAA
1 TCTACGAGGTCCTTTGGGACAAA
* *
590396 TCTACGTGTTCCTTTGGGACA
1 TCTACGAGGTCCTTTGGGACA
590417 TTTCTATGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
TCTACGAGGTCCTTTGGGACAAA
Found at i:590422 original size:23 final size:23
Alignment explanation
Indices: 590372--590441 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
590362 AGAGTCGAGG
590372 TTCTACGAGGTCCTTTGGGACAA
1 TTCTACGAGGTCCTTTGGGACAA
* * * *
590395 ATCTACGTGTTCCTTTGGGACAT
1 TTCTACGAGGTCCTTTGGGACAA
* * * *
590418 TTCTATGCGATCCTTCGGGACAA
1 TTCTACGAGGTCCTTTGGGACAA
590441 T
1 T
590442 ACTGTGTGGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGAGGTCCTTTGGGACAA
Found at i:590472 original size:23 final size:23
Alignment explanation
Indices: 590380--590477 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 23
590370 GGTTCTACGA
* ** *
590380 GGTCCTTTGGGACAAATCTACGT
1 GGTCCTTCGGGACATTTCTATGT
* * *
590403 GTTCCTTTGGGACATTTCTATGC
1 GGTCCTTCGGGACATTTCTATGT
* * * *
590426 GATCCTTCGGGACAATACTGTGT
1 GGTCCTTCGGGACATTTCTATGT
*
590449 GGTCCTTCGGAACATTTCTATGT
1 GGTCCTTCGGGACATTTCTATGT
590472 GG-CCTT
1 GGTCCTT
590478 TCGGTGCAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 4 0.07
23 55 0.93
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTATGT
Found at i:590694 original size:32 final size:32
Alignment explanation
Indices: 590631--590694 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
590621 GTGCATAGTA
* * *
590631 TTACATGTTCTTGTTTGGTTAAATGCGTGATG
1 TTACATGTTATTGTTTGGTTAAATACATGATG
* *
590663 TTACATGTTATTGTTTTGTTAAATATATGATG
1 TTACATGTTATTGTTTGGTTAAATACATGATG
590695 CATTCTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.50
Consensus pattern (32 bp):
TTACATGTTATTGTTTGGTTAAATACATGATG
Found at i:592938 original size:3 final size:3
Alignment explanation
Indices: 592930--592976 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
592920 TTTTTATCCA
*
592930 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
592977 ATAAATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:592991 original size:14 final size:14
Alignment explanation
Indices: 592972--593012 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
592962 TTATTATTAT
592972 TATTAATAAATATA
1 TATTAATAAATATA
592986 TATTAAATAAATATA
1 TATT-AATAAATATA
*
593001 TATAAATAAATA
1 TATTAATAAATA
593013 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:592996 original size:15 final size:15
Alignment explanation
Indices: 592972--593012 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
592962 TTATTATTAT
592972 TATT-AATAAATATA
1 TATTAAATAAATATA
592986 TATTAAATAAATATA
1 TATTAAATAAATATA
593001 TA-TAAATAAATA
1 TATTAAATAAATA
593013 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:593445 original size:20 final size:20
Alignment explanation
Indices: 593420--593462 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
593410 ACCCCAACCT
593420 GAAAAAAAAAAACAGAGACA
1 GAAAAAAAAAAACAGAGACA
* *
593440 GAAAAAAAAAGAGAGAGACA
1 GAAAAAAAAAAACAGAGACA
593460 GAA
1 GAA
593463 CCGAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.72, C:0.07, G:0.21, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAACAGAGACA
Found at i:599502 original size:43 final size:43
Alignment explanation
Indices: 599438--599810 Score: 451
Period size: 43 Copynumber: 8.7 Consensus size: 43
599428 CCGTATGCTT
* * * *
599438 CTTTGCTATGTACAAGGGTAAGACCTTACCATTTCCTAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * *
599481 CTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCCAGGTTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * *
599524 CTTTTCTATGTGCAAGGATAAGACTTTACCATTTCCCAAGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* *
599567 CTTTACTATGTGCAAGGATAAGACCTTACCGTTTACCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* *
599610 CTTTGCTATTTGCAAGGATAAGACCTTACCGTTTCTCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* **
599653 TTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCATACTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * *
599696 TTTTGTTATGTGTAAGGATAAGACCTTACTGTTTCCCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * ** *
599739 TTTTGCTATGTGCAAGGGTAAGACCTTATCGTTTTTGCAAGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCG-TTTCCCAGGCTC
*
599783 TTTTGCTATGTGCAAAGG-TAAGACCTTA
1 CTTTGCTATGTGC-AAGGATAAGACCTTA
599811 TTGTTTTTGT
Statistics
Matches: 287, Mismatches: 41, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
43 251 0.87
44 32 0.11
45 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (43 bp):
CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
Found at i:599832 original size:44 final size:44
Alignment explanation
Indices: 599560--599848 Score: 177
Period size: 43 Copynumber: 6.6 Consensus size: 44
599550 TACCATTTCC
* * * **
599560 CAAGCTCCTTTACTATGTGC-AAGGATAAGACCTTACCG-TTTAC
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * * *
599603 CAGGCTCCTTTGCTATTTGC-AAGGATAAGACCTTACCGTTTCT-
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * **
599646 CAGGCTCTTTTGCTATGTGC-AAGGATAAGACCTTACCG-TTTCC
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * **
599689 CATA-CTCTTTTGTTATGTG-TAAGGATAAGACCTTA-C-TGTTTCC
1 CA-AGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGT-TTTTG
* * *
599732 CAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTATCGTTTTTG
1 CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
* *
599776 CAAGCTCTTTTGCTATGTGCAAAGGTAAGACCTTATTGTTTTTG
1 CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
* * *
599820 -TAGTCTCATTTGCTTTGTTCACAAGGTAA
1 CAAG-CTCATTTGCTATGTGCA-AAGGTAA
599849 ATATGTTTTA
Statistics
Matches: 210, Mismatches: 24, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.01
43 135 0.64
44 64 0.30
45 8 0.04
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (44 bp):
CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
Found at i:603620 original size:16 final size:16
Alignment explanation
Indices: 603599--603648 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
603589 TGCACTGTTA
*
603599 TACATGAGCTATGTGT
1 TACATGACCTATGTGT
603615 TACATGTCATCCTATGTGT
1 TACATG--A-CCTATGTGT
*
603634 TACATGATCTATGTG
1 TACATGACCTATGTG
603649 GATATATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (16 bp):
TACATGACCTATGTGT
Found at i:603707 original size:16 final size:16
Alignment explanation
Indices: 603672--603710 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
603662 AAGATATAAG
603672 CTATGTG-ACAATGAT
1 CTATGTGAACAATGAT
603687 CTATGTGAACACATG-T
1 CTATGTGAACA-ATGAT
603703 CTATGTGA
1 CTATGTGA
603711 TAACCTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 12 0.55
17 3 0.14
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (16 bp):
CTATGTGAACAATGAT
Found at i:603918 original size:25 final size:25
Alignment explanation
Indices: 603889--603946 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
603879 CATTCGGGAC
* * *
603889 ATTTCTATGTGGCATTTCGGTGCAA
1 ATTTCTACGCGGCACTTCGGTGCAA
603914 ATTTCTACGCGGCACTTCGGTGC-A
1 ATTTCTACGCGGCACTTCGGTGCAA
*
603938 ATTTATACG
1 ATTTCTACG
603947 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (25 bp):
ATTTCTACGCGGCACTTCGGTGCAA
Found at i:605858 original size:72 final size:72
Alignment explanation
Indices: 605742--605897 Score: 174
Period size: 72 Copynumber: 2.1 Consensus size: 72
605732 TAAGTTCATC
* * * * * *
605742 CATTCATGCATATTCATGCAAGAAGCCAAATAGTCATGTTCACACAAGGG-GGAAGAATTTCAGC
1 CATTCATGAACATTCATCCAAGAAGACAAATAGACATGTTCACACAAGGGAGAAAGAA-TTCAGC
605806 C-AAGATA
65 CAAAGATA
* *
605813 CATTCATGAACATTCATCCATAGAAGACAAATCA-ACATGTTCACACATGGGAGAAAGGATTCAG
1 CATTCATGAACATTCATCCA-AGAAGACAAAT-AGACATGTTCACACAAGGGAGAAAGAATTCAG
605877 CCATGAAGATA
64 CCA--AAGATA
605888 CATTCATGAA
1 CATTCATGAA
605898 GATTTATTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 17 0.24
72 32 0.45
73 6 0.08
75 16 0.23
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (72 bp):
CATTCATGAACATTCATCCAAGAAGACAAATAGACATGTTCACACAAGGGAGAAAGAATTCAGCC
AAAGATA
Found at i:605941 original size:18 final size:18
Alignment explanation
Indices: 605920--605961 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
605910 TAATTCATCA
605920 TACATTCACAATTGATC-G
1 TACATTCACAATTG-TCTG
* *
605938 TACATTGACCATTGTCTG
1 TACATTCACAATTGTCTG
605956 TACATT
1 TACATT
605962 GTATTTCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (18 bp):
TACATTCACAATTGTCTG
Found at i:606836 original size:27 final size:27
Alignment explanation
Indices: 606798--606849 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
606788 AAAGGAATAG
606798 GCAGTTTACCTCTTTCAGAATGTTCAA
1 GCAGTTTACCTCTTTCAGAATGTTCAA
606825 GCAGTTTACCTCTTTCAGAATGTTC
1 GCAGTTTACCTCTTTCAGAATGTTC
606850 TTCATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (27 bp):
GCAGTTTACCTCTTTCAGAATGTTCAA
Found at i:607082 original size:18 final size:18
Alignment explanation
Indices: 607035--607085 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
607025 CAGATTTAGA
*
607035 TTTGGGTTTGGATTCGAG
1 TTTGGGTTTGGGTTCGAG
*
607053 TTCGGGTTTGGGTTCGAG
1 TTTGGGTTTGGGTTCGAG
607071 TTTGGGTTTGGGTTC
1 TTTGGGTTTGGGTTC
607086 AGGTTCAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.06, C:0.08, G:0.41, T:0.45
Consensus pattern (18 bp):
TTTGGGTTTGGGTTCGAG
Found at i:607132 original size:18 final size:18
Alignment explanation
Indices: 607035--607186 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 18
607025 CAGATTTAGA
*
607035 TTTGGGTTTGGATTC-GAG
1 TTTGGGTTTGGGTTCAG-G
*
607053 TTCGGGTTTGGGTTC-GAG
1 TTTGGGTTTGGGTTCAG-G
607071 TTTGGGTTTGGGTTCAGG
1 TTTGGGTTTGGGTTCAGG
** * * *
607089 TTCAGGATCGGGTTCATG
1 TTTGGGTTTGGGTTCAGG
** *
607107 TTCAGGTTTGGTTTCAGG
1 TTTGGGTTTGGGTTCAGG
* * **
607125 TTTGGGTTTAGATTCATA
1 TTTGGGTTTGGGTTCAGG
* * **
607143 TTTGGGTTCGAGTTTGGG
1 TTTGGGTTTGGGTTCAGG
607161 TTAT-GGTTTGGGTTC-GAG
1 TT-TGGGTTTGGGTTCAG-G
607179 TTTGGGTT
1 TTTGGGTT
607187 ATGGTTTGGG
Statistics
Matches: 101, Mismatches: 29, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
17 2 0.02
18 97 0.96
19 2 0.02
ACGTcount: A:0.11, C:0.08, G:0.38, T:0.44
Consensus pattern (18 bp):
TTTGGGTTTGGGTTCAGG
Found at i:607157 original size:24 final size:24
Alignment explanation
Indices: 607130--607198 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
607120 TCAGGTTTGG
607130 GTTTAGATTCAT-ATTTGGGTTCGA
1 GTTTAGATT-ATGATTTGGGTTCGA
* * *
607154 GTTTGGGTTATGGTTTGGGTTCGA
1 GTTTAGATTATGATTTGGGTTCGA
* * *
607178 GTTTGGGTTATGGTTTGGGTT
1 GTTTAGATTATGATTTGGGTT
607199 TGCGTTTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.12, C:0.04, G:0.36, T:0.48
Consensus pattern (24 bp):
GTTTAGATTATGATTTGGGTTCGA
Found at i:607174 original size:6 final size:6
Alignment explanation
Indices: 607143--607216 Score: 62
Period size: 6 Copynumber: 12.3 Consensus size: 6
607133 TAGATTCATA
* * * *
607143 TTTGGG TTCGAG TTTGGG TTAT-GG TTTGGG TTCGAG TTTGGG TTAT-GG
1 TTTGGG TTTGGG TTTGGG TT-TGGG TTTGGG TTTGGG TTTGGG TT-TGGG
* *
607191 TTTGGG TTTGCG TTTGTG TTTGGG TT
1 TTTGGG TTTGGG TTTGGG TTTGGG TT
607217 AAGGTTAGAT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
5 2 0.04
6 49 0.92
7 2 0.04
ACGTcount: A:0.05, C:0.04, G:0.41, T:0.50
Consensus pattern (6 bp):
TTTGGG
Found at i:607205 original size:12 final size:11
Alignment explanation
Indices: 607143--607213 Score: 70
Period size: 12 Copynumber: 6.0 Consensus size: 11
607133 TAGATTCATA
*
607143 TTTGGGTTCGAG
1 TTTGGGTTTG-G
607155 TTTGGGTTATGG
1 TTTGGGTT-TGG
*
607167 TTTGGGTTCGAG
1 TTTGGGTTTG-G
607179 TTTGGGTTATGG
1 TTTGGGTT-TGG
607191 TTTGGGTTTGCG
1 TTTGGGTTTG-G
*
607203 TTTGTGTTTGG
1 TTTGGGTTTGG
607214 GTTAAGGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.08
12 45 0.88
13 2 0.04
ACGTcount: A:0.06, C:0.04, G:0.41, T:0.49
Consensus pattern (11 bp):
TTTGGGTTTGG
Found at i:607206 original size:24 final size:24
Alignment explanation
Indices: 607143--607198 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
607133 TAGATTCATA
607143 TTTGGGTTCGAGTTTGGGTTATGG
1 TTTGGGTTCGAGTTTGGGTTATGG
607167 TTTGGGTTCGAGTTTGGGTTATGG
1 TTTGGGTTCGAGTTTGGGTTATGG
607191 TTTGGGTT
1 TTTGGGTT
607199 TGCGTTTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.07, C:0.04, G:0.41, T:0.48
Consensus pattern (24 bp):
TTTGGGTTCGAGTTTGGGTTATGG
Found at i:607672 original size:93 final size:93
Alignment explanation
Indices: 607539--607733 Score: 268
Period size: 93 Copynumber: 2.1 Consensus size: 93
607529 GGATGCACAC
*
607539 GGATGAACAAGGGTTGAATTTTGGGAATTTGATTGAAAAAAACACGAAATGGTTTGGGTTTCAGT
1 GGATGAACAAGGGTTGAATTTTGGGAATTTGATTGAAAAAAACACGAAATGGCTTGGGTTTCAGT
*
607604 GTTTGTGAAGATC-AATTGAGTGATTTTG
66 GTTTGTGAAGATCAAATT-AGGGATTTTG
* * ** * **
607632 GGATGAACAAGTGTTGAGTTTTTGGGTGTTTGGTTG-AAAAAACACGAAATGGCTTGGGTTTTGG
1 GGATGAACAAGGGTTGA-ATTTTGGGAATTTGATTGAAAAAAACACGAAATGGCTTGGGTTTCAG
*
607696 TGTTTGTGAAGATCAAATTAGGGTTTTTG
65 TGTTTGTGAAGATCAAATTAGGGATTTTG
607725 GGATGAACA
1 GGATGAACA
607734 CAGATGAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
93 72 0.80
94 18 0.20
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.35
Consensus pattern (93 bp):
GGATGAACAAGGGTTGAATTTTGGGAATTTGATTGAAAAAAACACGAAATGGCTTGGGTTTCAGT
GTTTGTGAAGATCAAATTAGGGATTTTG
Found at i:607764 original size:22 final size:21
Alignment explanation
Indices: 607734--607774 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
607724 GGGATGAACA
607734 CAGATGAATTTCTAGAGAGAAGT
1 CAGATGAATTT-T-GAGAGAAGT
607757 CAGA-GAATTTTGAGAGAA
1 CAGATGAATTTTGAGAGAA
607775 TCGAAGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 6 0.33
23 4 0.22
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.24
Consensus pattern (21 bp):
CAGATGAATTTTGAGAGAAGT
Found at i:607884 original size:13 final size:13
Alignment explanation
Indices: 607866--607891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
607856 ATACGGGTTC
607866 GTTTGGGTTTTGA
1 GTTTGGGTTTTGA
607879 GTTTGGGTTTTGA
1 GTTTGGGTTTTGA
607892 CCTACGTATT
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:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (13 bp):
GTTTGGGTTTTGA
Found at i:608015 original size:61 final size:61
Alignment explanation
Indices: 607943--608079 Score: 220
Period size: 61 Copynumber: 2.2 Consensus size: 61
607933 TCTTAGTTTT
* *
607943 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAATCTTCATATTTA
1 AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
* *
608004 AAATTTATTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTAAACTTCATATTTA
1 AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
* *
608065 AATTTTTTTCAATTT
1 AAATTTATTCAATTT
608080 GATCCTTATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (61 bp):
AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
Found at i:608181 original size:18 final size:18
Alignment explanation
Indices: 608158--608309 Score: 112
Period size: 18 Copynumber: 8.3 Consensus size: 18
608148 ACTAATAAAC
608158 TATATAATATATAATTTA
1 TATATAATATATAATTTA
*** *
608176 TATATACCGTATAGTTTA
1 TATATAATATATAATTTA
**
608194 TATAT-ATATATTAATGAA
1 TATATAATATA-TAATTTA
*
608212 TTATATAATATATAGTTTA
1 -TATATAATATATAATTTA
*
608231 TATAT-ATATAT-ATATA
1 TATATAATATATAATTTA
**
608247 TATATATATATACTAATGAA
1 TATATA-ATATA-TAATTTA
*
608267 CTATATAATATATAGTTTA
1 -TATATAATATATAATTTA
** *
608286 TATATACCATATACTTTA
1 TATATAATATATAATTTA
608304 TATATA
1 TATATA
608310 TAATTTTTAT
Statistics
Matches: 103, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
16 8 0.08
17 8 0.08
18 54 0.52
19 14 0.14
20 13 0.13
21 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATAATATATAATTTA
Found at i:608197 original size:2 final size:2
Alignment explanation
Indices: 608192--608324 Score: 77
Period size: 2 Copynumber: 67.0 Consensus size: 2
608182 CCGTATAGTT
*
608192 TA TA TA TA TA TA T- TA -A TGA -A T- TA TA TA -A TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA -TA TA
608231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA -A TGA -A CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA -TA TA
* * *
608272 TA -A TA TA TA GTT TA TA TA TA CCA TA TA CTT TA TA TA TA TA -A
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* *
608313 TT TT TA TA TA TA
1 TA TA TA TA TA TA
608325 GTTCATATGT
Statistics
Matches: 104, Mismatches: 10, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
1 9 0.09
2 86 0.83
3 9 0.09
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:608217 original size:55 final size:54
Alignment explanation
Indices: 608148--608311 Score: 231
Period size: 55 Copynumber: 3.0 Consensus size: 54
608138 ATATATAACC
* * *
608148 ACTAATAAACTATATAATATATAATTTATATATACCGTATAGTTTATATATATAT
1 ACTAATGAACTATATAATATATAGTTTATATATACCATATA-TTTATATATATAT
* * *
608203 ATTAATGAATTATATAATATATAGTTTATATATA-TATATATATATATATATATAT
1 ACTAATGAACTATATAATATATAGTTTATATATACCATATAT-T-TATATATATAT
608258 ACTAATGAACTATATAATATATAGTTTATATATACCATATACTTTATATATATA
1 ACTAATGAACTATATAATATATAGTTTATATATACCATATA-TTTATATATATA
608312 ATTTTTATAT
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
53 1 0.01
54 5 0.05
55 83 0.86
56 6 0.06
57 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (54 bp):
ACTAATGAACTATATAATATATAGTTTATATATACCATATATTTATATATATAT
Found at i:608351 original size:110 final size:108
Alignment explanation
Indices: 608148--608361 Score: 247
Period size: 110 Copynumber: 2.0 Consensus size: 108
608138 ATATATAACC
* *
608148 ACTAATAAACTATATAATATATAATTTATATATACCGTATAGTTTATATATATATATTAATGAAT
1 ACTAATAAACTATATAATATATAATTTATATATACCATATACTTTATATATATATATT-ATGAAT
** *
608213 TATATAATATATAGTTTATATATATATATATATATATATATATAT
65 TATATAATATATAGTAAATATAAATATATATAT-TATATATATAT
* * **
608258 ACTAATGAACTATATAATATATAGTTTATATATACCATATACTTTATATATATA-ATT-TTTA-T
1 ACTAATAAACTATATAATATATAATTTATATATACCATATACTTTATATATATATATTATGAATT
*
608320 ATATAGT-TCATATGTAAACTACTAAACTATATATATTATATA
66 ATATAATAT-ATA-GTAAA-TA-TAAA-TATATATATTATATA
608362 GTTTACATAG
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
105 1 0.01
106 10 0.11
107 5 0.06
108 2 0.02
109 12 0.13
110 59 0.66
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (108 bp):
ACTAATAAACTATATAATATATAATTTATATATACCATATACTTTATATATATATATTATGAATT
ATATAATATATAGTAAATATAAATATATATATTATATATATAT
Found at i:608385 original size:9 final size:9
Alignment explanation
Indices: 608355--608386 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
608345 ACTATATATA
608355 TTATATAGT
1 TTATATAGT
*
608364 TTACATAGT
1 TTATATAGT
608373 TTATATAGT
1 TTATATAGT
608382 TTATA
1 TTATA
608387 CATATAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (9 bp):
TTATATAGT
Found at i:608507 original size:18 final size:18
Alignment explanation
Indices: 608497--608531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
608487 ATATAGTTTA
608497 TACATAATATATATATAG
1 TACATAATATATATATAG
*
608515 TTCATAATATATATATA
1 TACATAATATATATATA
608532 TATATATATT
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:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TACATAATATATATATAG
Found at i:608511 original size:22 final size:22
Alignment explanation
Indices: 608486--608535 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
608476 ATCTATAAAC
*
608486 TATATAGTTTATACATA-ATATA
1 TATATAGTTCATA-ATATATATA
608508 TATATAGTTCATAATATATATA
1 TATATAGTTCATAATATATATA
608530 TATATA
1 TATATA
608536 TATATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAGTTCATAATATATATA
Found at i:610944 original size:15 final size:16
Alignment explanation
Indices: 610926--610960 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
610916 ATCGTCATTT
610926 AAAAT-AATTTTAAGA
1 AAAATCAATTTTAAGA
*
610941 AAAATCATTTTTAAGA
1 AAAATCAATTTTAAGA
610957 AAAA
1 AAAA
610961 AAAATGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAATCAATTTTAAGA
Found at i:613015 original size:20 final size:20
Alignment explanation
Indices: 612966--613015 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
612956 AGAAAAACGT
*
612966 CAACGATCAAAGTCAATGGC
1 CAACGATCAAAGTCAATAGC
* * *
612986 CAATGTTCAAAGTCAATAGT
1 CAACGATCAAAGTCAATAGC
*
613006 TAACGATCAA
1 CAACGATCAA
613016 CAAGTCGAGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (20 bp):
CAACGATCAAAGTCAATAGC
Found at i:616590 original size:14 final size:14
Alignment explanation
Indices: 616565--616600 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
616555 CATTACTATG
*
616565 AAATCCTCCTCCTT
1 AAATCATCCTCCTT
*
616579 ACATCATCCTCCTT
1 AAATCATCCTCCTT
616593 AAATCATC
1 AAATCATC
616601 AAATTCAAAT
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:0.28, C:0.39, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATCATCCTCCTT
Found at i:618258 original size:20 final size:20
Alignment explanation
Indices: 618235--618279 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
618225 TCAGTATCTG
* *
618235 TACTAACCTATGGGTATCGA
1 TACTAACCTATGGATATCAA
*
618255 TACTAGCCTATGGATATCAA
1 TACTAACCTATGGATATCAA
618275 TACTA
1 TACTA
618280 CTGACTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (20 bp):
TACTAACCTATGGATATCAA
Found at i:618338 original size:20 final size:21
Alignment explanation
Indices: 618313--618361 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
618303 AAAGGGCTAG
618313 TATTGATAC-TCTAGT-TTGAA
1 TATTGATACTTCTAGTCTTG-A
*
618333 TATTGATACTTCTAGTCTTGG
1 TATTGATACTTCTAGTCTTGA
618354 TATTGATA
1 TATTGATA
618362 TTGTCTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 14 0.54
22 3 0.12
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (21 bp):
TATTGATACTTCTAGTCTTGA
Found at i:618446 original size:20 final size:20
Alignment explanation
Indices: 618421--618458 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
618411 CTTAATAACA
618421 ATACTCTACCCCCAGTATTT
1 ATACTCTACCCCCAGTATTT
618441 ATACTCTACCCCCAGTAT
1 ATACTCTACCCCCAGTAT
618459 CGACACACCC
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:0.26, C:0.37, G:0.05, T:0.32
Consensus pattern (20 bp):
ATACTCTACCCCCAGTATTT
Found at i:622225 original size:11 final size:10
Alignment explanation
Indices: 622195--622224 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
622185 GTAATAAATT
622195 ATTATTTTTA
1 ATTATTTTTA
622205 ACTTATTTTTA
1 A-TTATTTTTA
622216 ATTATTTTT
1 ATTATTTTT
622225 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTATTTTTA
Found at i:623598 original size:79 final size:78
Alignment explanation
Indices: 623431--623598 Score: 237
Period size: 79 Copynumber: 2.1 Consensus size: 78
623421 TTAAATGCAG
* * * ** *
623431 GAAATGATGCCTTAGCTGATATGTATATGGGCACATTATCGGCATAAAAAATAATGCATATGGGT
1 GAAAGGATGCCTTAGCTGATATGTATATGGACACAATATCAACATAAAAAATAATGCATATAGGT
*
623496 GCATTAATGGCAT
66 ACATTAATGGCAT
* *
623509 GAAAGTATGCCTTAGCTGATATGTATATGGATACAATATCAACATAAAAAAATAATGCATATAGG
1 GAAAGGATGCCTTAGCTGATATGTATATGGACACAATATCAACAT-AAAAAATAATGCATATAGG
*
623574 TACATTAATGTCAT
65 TACATTAATGGCAT
623588 GAAAGGATGCC
1 GAAAGGATGCC
623599 AAAGTTGAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 38 0.49
79 40 0.51
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (78 bp):
GAAAGGATGCCTTAGCTGATATGTATATGGACACAATATCAACATAAAAAATAATGCATATAGGT
ACATTAATGGCAT
Found at i:623628 original size:79 final size:79
Alignment explanation
Indices: 623476--623636 Score: 196
Period size: 79 Copynumber: 2.0 Consensus size: 79
623466 TTATCGGCAT
* * * ** * *
623476 AAAAAATAATGCATATGGGTGCATTAATGGCATGAAAGTATGCCTTAGCTGATATGTATATGGAT
1 AAAAAATAATGCATATAGGTACATTAATGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGAT
623541 ACAATATCAACATA
66 ACAATATCAACATA
* * * *
623555 AAAAAATAATGCATATAGGTACATTAATGTCATGAAAGGATGCCAAAGTTGAAATGCATGTGGGT
1 AAAAAATAATGCATATAGGTACATTAATGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGAT
* * *
623620 GCATTATCAATATA
66 ACAATATCAACATA
623634 AAA
1 AAA
623637 GAGGAAATCA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (79 bp):
AAAAAATAATGCATATAGGTACATTAATGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGAT
ACAATATCAACATA
Found at i:623731 original size:60 final size:60
Alignment explanation
Indices: 623638--623786 Score: 253
Period size: 60 Copynumber: 2.5 Consensus size: 60
623628 AATATAAAAG
*
623638 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTTTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * * *
623698 AGGAAATAATACTGAGTGTTTGAATTTCTAGATAAGGGCACTTTGTGTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
623758 AGGAAATCATACTAAGTGTATGAATTTCC
1 AGGAAATCATACTAAGTGTATGAATTTCC
623787 GTATAGGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (60 bp):
AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
Found at i:626147 original size:2 final size:2
Alignment explanation
Indices: 626140--626200 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
626130 GATGTCATAA
626140 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
626181 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
626201 CTTTTATGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:626954 original size:12 final size:12
Alignment explanation
Indices: 626937--626987 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
626927 TTCAAAAAGG
626937 TTTTATATTTAA
1 TTTTATATTTAA
626949 TTTTATA-TTATA
1 TTTTATATTTA-A
*
626961 TTTGAT-TTTAA
1 TTTTATATTTAA
626972 TTTTA-ATATTAA
1 TTTTATAT-TTAA
626984 TTTT
1 TTTT
626988 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:626991 original size:14 final size:14
Alignment explanation
Indices: 626972--627082 Score: 59
Period size: 14 Copynumber: 8.8 Consensus size: 14
626962 TTGATTTTAA
626972 TTTTAATATTAATT
1 TTTTAATATTAATT
626986 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
626996 ATTAAATATTAATT
1 TTTTAATATTAATT
* *
627010 TATTAATATT-ATA
1 TTTTAATATTAATT
*
627023 TTATAGATATTAA--
1 TTTTA-ATATTAATT
627036 -TTTAATA-TAATT
1 TTTTAATATTAATT
627048 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
627058 ATTAAATATTAATT
1 TTTTAATATTAATT
627072 TTTTAATATTA
1 TTTTAATATTA
627083 TATTATAGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 26
0.65 0.12 0.24
Matches are distributed among these distances:
10 11 0.15
11 5 0.07
12 16 0.23
13 11 0.15
14 27 0.38
15 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:627003 original size:24 final size:27
Alignment explanation
Indices: 626970--627118 Score: 90
Period size: 30 Copynumber: 5.2 Consensus size: 27
626960 ATTTGATTTT
* *
626970 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTATTAATATTA
626995 AATTA-AATATTAATTTATTAATATTA
1 AATTATAATATTAATTTATTAATATTA
* *
627021 TATTATAGATATTAATTTAATATAATTTTTTA
1 AATTATA-ATATTAATTT-AT-TAA--TATTA
* *
627053 AATAAATTAAATATTAATTTTTTAATATTA
1 AAT-TA-T-AATATTAATTTATTAATATTA
* *
627083 TATTATAGATATTTAATTTTATATCATA-TA
1 AATTATA-ATA-TTAA-TTTAT-TAATATTA
627113 AATTAT
1 AATTAT
627119 TTTATATATT
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
24 15 0.16
25 5 0.05
26 6 0.06
27 2 0.02
28 14 0.15
29 7 0.07
30 20 0.21
31 4 0.04
32 9 0.09
33 2 0.02
34 11 0.11
35 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
AATTATAATATTAATTTATTAATATTA
Found at i:627043 original size:11 final size:11
Alignment explanation
Indices: 626945--627048 Score: 50
Period size: 12 Copynumber: 8.6 Consensus size: 11
626935 GGTTTTATAT
*
626945 TTAATTTTATA
1 TTAATTTAATA
* *
626956 TTATATTTGATT
1 TTA-ATTTAATA
626968 TTAATTTTAATA
1 TTAA-TTTAATA
626980 TTAATTTTTTAA-A
1 TTAA---TTTAATA
* *
626993 TAAATTAAATA
1 TTAATTTAATA
627004 TTAATTTATTAATA
1 TTAA--T-TTAATA
627018 TTATATTATAGATA
1 TTA-ATT-TA-ATA
627032 TTAATTTAATA
1 TTAATTTAATA
627043 -TAATTT
1 TTAATTT
627049 TTTAAATAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
10 10 0.14
11 11 0.15
12 21 0.28
13 11 0.15
14 20 0.27
15 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:627047 original size:62 final size:62
Alignment explanation
Indices: 626953--627106 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 62
626943 ATTTAATTTT
*
626953 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTATTA
1 ATATTATATTATAGATATTAA-TTTAATA-TAATTTTTTAAATAAATTAAATATTAATTTATTA
*
627015 ATATTATATTATAGATATTAATTTAATATAATTTTTTAAATAAATTAAATATTAATTTTTTA
1 ATATTATATTATAGATATTAATTTAATATAATTTTTTAAATAAATTAAATATTAATTTATTA
*
627077 ATATTATATTATAGATATTTAATTTTATAT
1 ATATTATATTATAGATA-TTAATTTAATAT
627107 CATATAAATT
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
62 60 0.70
63 19 0.22
64 7 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (62 bp):
ATATTATATTATAGATATTAATTTAATATAATTTTTTAAATAAATTAAATATTAATTTATTA
Found at i:627126 original size:21 final size:18
Alignment explanation
Indices: 627097--627147 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
627087 ATAGATATTT
627097 AATTTTATATCA-TATAAA
1 AATTTTATAT-ATTATAAA
*
627115 TTATTTTATATATTATAAA
1 -AATTTTATATATTATAAA
627134 AATTTTATAT-TTAT
1 AATTTTATATATTAT
627148 TTTAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTTATATATTATAAA
Found at i:627158 original size:20 final size:18
Alignment explanation
Indices: 627098--627159 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
627088 TAGATATTTA
627098 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTAT-AATT
**
627117 ATTTTATATATTATAAAA
1 ATTTTATATATTATAATT
*
627135 ATTTTATATTTATTTTAATT
1 ATTTTATA--TATTATAATT
627155 ATTTT
1 ATTTT
627160 GATTTAAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.31
19 12 0.34
20 12 0.34
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTATATATTATAATT
Found at i:627661 original size:31 final size:31
Alignment explanation
Indices: 627624--627683 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
627614 TAGTTGTATG
* *
627624 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
*
627655 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
627684 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:629531 original size:60 final size:60
Alignment explanation
Indices: 629376--629522 Score: 240
Period size: 60 Copynumber: 2.5 Consensus size: 60
629366 AATATAAAAG
*
629376 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTTTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * * *
629436 AGGAAATAATATTGAGTGTTTGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
*
629496 AGGAAATCATACTAAGTGTATAAATTT
1 AGGAAATCATACTAAGTGTATGAATTT
629523 TCGTATAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 77 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (60 bp):
AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
Found at i:629964 original size:81 final size:81
Alignment explanation
Indices: 629818--629966 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
629808 TGTAAAGGCC
* * * ** *
629818 TAACTGTGCATATGACAGAAATGTGTTAATTATGCCAGTTAGATAAACGGTTAAGTACCGTTGAG
1 TAACTGTGCATATGACAGAAAGGTGTCAATTATACCAGTTAGATAAACGGTTAAACACCGATGAG
629883 TAAAAGAATAATGGTT
66 TAAAAGAATAATGGTT
* ** *
629899 TAACTGTGCA-ATTGGCAGAAAGGTGTCAATTATACCAGTTAGATAATGGGTTAAACACTGATGA
1 TAACTGTGCATA-TGACAGAAAGGTGTCAATTATACCAGTTAGATAAACGGTTAAACACCGATGA
629963 GTAA
65 GTAA
629967 GAGGATAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.02
81 56 0.98
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (81 bp):
TAACTGTGCATATGACAGAAAGGTGTCAATTATACCAGTTAGATAAACGGTTAAACACCGATGAG
TAAAAGAATAATGGTT
Found at i:630835 original size:21 final size:21
Alignment explanation
Indices: 630810--630884 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
630800 GATATTACTA
630810 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
630831 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
*
630852 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
630873 TCGCAATGCGAT
1 TCGCAATGCGAT
630885 ACTGACTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 47 0.92
22 4 0.08
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:630898 original size:20 final size:19
Alignment explanation
Indices: 630873--631006 Score: 72
Period size: 20 Copynumber: 6.6 Consensus size: 19
630863 TTTTCCCAAT
630873 TCGCAATGCGATACTGACTA
1 TCGCAATGCGATACT-ACTA
* * *
630893 TCGCAACGCGATAATACAAAA
1 TCGCAATGCGATACTAC--TA
*
630914 TCGCAATGCGATACTTACTT
1 TCGCAATGCGATAC-TACTA
* * *
630934 TCGCAACGTGATACTTACTT
1 TCGCAATGCGATAC-TACTA
* *
630954 TCGCAACT-AGATACTGACTT
1 TCGCAA-TGCGATACT-ACTA
* * *
630974 TCGCAACGAGATAATACATAA
1 TCGCAATGCGATACTAC-T-A
630995 TCGCAATGCGAT
1 TCGCAATGCGAT
631007 TTTCAAAGCG
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
19 5 0.06
20 59 0.66
21 23 0.26
22 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (19 bp):
TCGCAATGCGATACTACTA
Found at i:630918 original size:41 final size:40
Alignment explanation
Indices: 630873--631006 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 40
630863 TTTTCCCAAT
* *
630873 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAA
1 TCGCAATGCGATACTGACTTTCGCAACGAGATAATAC-AAA
* * * **
630914 TCGCAATGCGATACTTACTTTCGCAACGTGATACTTAC-TT
1 TCGCAATGCGATACTGACTTTCGCAACGAGATA-ATACAAA
*
630954 TCGCAACT-AGATACTGACTTTCGCAACGAGATAATACATAA
1 TCGCAA-TGCGATACTGACTTTCGCAACGAGATAATACA-AA
630995 TCGCAATGCGAT
1 TCGCAATGCGAT
631007 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
39 3 0.04
40 29 0.39
41 40 0.53
42 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGATACTGACTTTCGCAACGAGATAATACAAA
Found at i:631201 original size:22 final size:22
Alignment explanation
Indices: 631173--631216 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
631163 CACTCTCTCA
631173 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
631195 CCCATCTTCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
631217 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:631472 original size:20 final size:20
Alignment explanation
Indices: 631423--631481 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
631413 TTTATTCTCT
* **
631423 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATTGTCATTTTCG
*
631443 CGTTGCGATTGTCATTTTCG
1 TGTTGCGATTGTCATTTTCG
*
631463 TGTTGCGATTTTCATTTTC
1 TGTTGCGATTGTCATTTTC
631482 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
TGTTGCGATTGTCATTTTCG
Found at i:631673 original size:25 final size:24
Alignment explanation
Indices: 631619--631673 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
631609 TGTTTATTAT
* *
631619 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
631643 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
631669 TGTTT
1 TGTTT
631674 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:632829 original size:17 final size:17
Alignment explanation
Indices: 632807--632849 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
632797 TTCGGGAGCC
632807 ATCACCTCACCCA-AGCT
1 ATCACCTCACCCAGA-CT
632824 ATCACCTCACCCAGACT
1 ATCACCTCACCCAGACT
632841 ATACACCTC
1 AT-CACCTC
632850 CACAACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.30, C:0.47, G:0.05, T:0.19
Consensus pattern (17 bp):
ATCACCTCACCCAGACT
Found at i:633393 original size:20 final size:20
Alignment explanation
Indices: 633368--633409 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
633358 TAGTTTACTT
633368 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
633388 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
633408 TC
1 TC
633410 ACAATGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:633422 original size:19 final size:20
Alignment explanation
Indices: 633379--633423 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
633369 CGCAACACGA
*
633379 AAATGACTATCGCAACGCGG
1 AAATGACTATCACAACGCGG
* *
633399 AAATGGCTATCACAATGC-G
1 AAATGACTATCACAACGCGG
633418 AAATGA
1 AAATGA
633424 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:633465 original size:19 final size:19
Alignment explanation
Indices: 633411--633508 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
633401 ATGGCTATCA
633411 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
* *
633430 CAA--CG--A-CAAAATTG
1 CAATGCGAAATGAAAATCG
633444 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
633463 CAACGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
633482 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
633501 CAATGCGA
1 CAATGCGA
633509 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 53 0.78
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:633488 original size:38 final size:38
Alignment explanation
Indices: 633387--633508 Score: 137
Period size: 38 Copynumber: 3.3 Consensus size: 38
633377 GAAAATGACT
*** *
633387 ATCGCAACGCGGAAATGGCTATCACAATGCGAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAATGCGAAATGAAA
* *
633426 ATCGCAA--CG--A-CAAAATTGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
633459 ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
*
633497 ATCGCAATGCGA
1 ATCGCAACGCGA
633509 TTTGTGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
33 24 0.35
34 1 0.01
35 2 0.03
36 1 0.01
37 2 0.03
38 32 0.46
39 7 0.10
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
Found at i:633552 original size:33 final size:33
Alignment explanation
Indices: 633515--633594 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
633505 GCGATTTGTG
* * *
633515 TTTCGCGTTGCGATTTTGTTGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
633548 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
633581 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
633595 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
Found at i:633560 original size:19 final size:19
Alignment explanation
Indices: 633536--633594 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
633526 GATTTTGTTG
633536 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
633555 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
633569 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
633588 TTGCGAT
1 TTGCGAT
633595 AGCCATTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
16 3 0.09
17 3 0.09
19 18 0.51
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:633572 original size:14 final size:14
Alignment explanation
Indices: 633515--633579 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
633505 GCGATTTGTG
*
633515 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
* *
633529 TTTGTTGTTGCGAT
1 TTTCTCGTTGCGAT
633543 TTTCATTTCGCATTGCGAT
1 TTTC---TCG--TTGCGAT
633562 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
633576 TTTC
1 TTTC
633580 ATTTCGCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
16 3 0.07
17 2 0.05
19 11 0.27
ACGTcount: A:0.09, C:0.18, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:633613 original size:20 final size:19
Alignment explanation
Indices: 633579--633633 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
633569 TTGCGATTTT
*
633579 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
633598 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
633618 CATTTTCGCGTTGCGA
1 CA-TTTCGCGTTGCGA
633634 AAGTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:633644 original size:20 final size:19
Alignment explanation
Indices: 633599--633658 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
633589 TGCGATAGCC
* *
633599 ATTTCCGCGTTGCGATAGT
1 ATTTTCGCGTTGCGAAAGT
633618 CATTTTCGCGTTGCGAAAGT
1 -ATTTTCGCGTTGCGAAAGT
*
633638 ATGTTTCGTGTTGCGAAAGT
1 AT-TTTCGCGTTGCGAAAGT
633658 A
1 A
633659 AACTATTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (19 bp):
ATTTTCGCGTTGCGAAAGT
Found at i:634077 original size:42 final size:42
Alignment explanation
Indices: 634001--634089 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
633991 GACTCACCTG
* * *
634001 TCATCCCTCAAGAGTCCCCTCCAATCGTTTAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* *
634043 TCATCCCTCAAGAGTCTCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTC-CCCTCCAACCGTTCAAGAGGCCACTA
634085 TCATC
1 TCATC
634090 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:635683 original size:19 final size:19
Alignment explanation
Indices: 635659--635794 Score: 178
Period size: 19 Copynumber: 7.4 Consensus size: 19
635649 GCAATGAGAG
635659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* * *
635678 AATCGCAACGACAAAATCG-C
1 AATCGCAATG-CGAAAT-GAA
635698 AA-CGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635716 AATCGCAA--CGAAATG-A
1 AATCGCAATGCGAAATGAA
635732 AA-CGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635750 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
635768 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
635787 AATCGCAA
1 AATCGCAA
635795 CGAGAGAATC
Statistics
Matches: 102, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.05
16 3 0.03
17 15 0.15
18 28 0.27
19 43 0.42
20 7 0.07
21 1 0.01
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:635787 original size:71 final size:71
Alignment explanation
Indices: 635646--635816 Score: 238
Period size: 71 Copynumber: 2.4 Consensus size: 71
635636 GAAACAGACT
* * * *
635646 ATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCAATGCGAA
1 ATCGCAACGAAAGAAACGCAATGCGAAATGAAAATCGCAACGACAAAATCGAAACGCAATGCGAA
635711 ATGAAA
66 ATGAAA
* *
635717 ATCGCAACGAAATGAAACGCAATGCGAAATGAAAATCGCAATG-CGAAAT-GAAATCGCAATGCG
1 ATCGCAACGAAA-GAAACGCAATGCGAAATGAAAATCGCAACGACAAAATCGAAA-CGCAATGCG
635780 AAATGAAA
64 AAATGAAA
* *
635788 ATCGCAACGAGAGAATCGCAATGCGAAAT
1 ATCGCAACGAAAGAAACGCAATGCGAAAT
635817 TCGCCTCGCA
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
70 19 0.21
71 43 0.48
72 28 0.31
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (71 bp):
ATCGCAACGAAAGAAACGCAATGCGAAATGAAAATCGCAACGACAAAATCGAAACGCAATGCGAA
ATGAAA
Found at i:635859 original size:33 final size:33
Alignment explanation
Indices: 635822--635892 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
635812 GAAATTCGCC
*
635822 TCGCAACGCGATTCGATCGTTGCGATTTTCATT
1 TCGCAACGCGATTCGATCATTGCGATTTTCATT
** **
635855 TCGCATTGCGATTCTCTCATTGCGATTTTCATT
1 TCGCAACGCGATTCGATCATTGCGATTTTCATT
635888 TCGCA
1 TCGCA
635893 TTGCGATGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (33 bp):
TCGCAACGCGATTCGATCATTGCGATTTTCATT
Found at i:635865 original size:19 final size:19
Alignment explanation
Indices: 635841--635899 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
635831 GATTCGATCG
635841 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
635860 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
635874 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
635893 TTGCGAT
1 TTGCGAT
635900 GGTCAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:636392 original size:20 final size:20
Alignment explanation
Indices: 636367--636440 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
636357 GCGATTTTCA
636367 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
636387 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
636407 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
636427 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
636441 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:636698 original size:20 final size:20
Alignment explanation
Indices: 636670--636720 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
636660 TTTTGATTGC
*
636670 CTTTTGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
636690 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
636710 CTTTCGCAACG
1 CTTTCGCAACG
636721 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:637491 original size:24 final size:24
Alignment explanation
Indices: 637464--637517 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
637454 GTATTCGAAA
*
637464 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
* *
637488 TTTGATATTGGTCAATACTTGGAT
1 TTTGATATTGGTCAATACTCGGAC
637512 TTTGAT
1 TTTGAT
637518 GATGTTTCAG
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:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:637709 original size:12 final size:12
Alignment explanation
Indices: 637692--637716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
637682 ATATAATCCT
637692 GAAGAAGAAAAA
1 GAAGAAGAAAAA
637704 GAAGAAGAAAAA
1 GAAGAAGAAAAA
637716 G
1 G
637717 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:640003 original size:19 final size:18
Alignment explanation
Indices: 639979--640075 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
639969 TCATTTGACC
639979 ATCGCAATGCGAAATGAGA
1 ATCGCAA-GCGAAATGAGA
639998 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAGA
*
640012 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAGA
*
640031 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAGA
*
640045 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAGA
640064 ATCGCAACGCGA
1 ATCGCAA-GCGA
640076 TTTTAGTATC
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
14 18 0.29
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 28 0.45
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAGA
Found at i:640013 original size:14 final size:14
Alignment explanation
Indices: 639994--640051 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
639984 AATGCGAAAT
639994 GAGAATCGCAACGA
1 GAGAATCGCAACGA
640008 GAGAATCGCAATGCGAAA
1 GAGAATCGCAA--CG--A
*
640026 TGAAAATCGCAACGA
1 -GAGAATCGCAACGA
*
640041 GGGAATCGCAA
1 GAGAATCGCAA
640052 AGCGAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.43, C:0.19, G:0.28, T:0.10
Consensus pattern (14 bp):
GAGAATCGCAACGA
Found at i:640021 original size:33 final size:33
Alignment explanation
Indices: 639979--640072 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
639969 TCATTTGACC
*
639979 ATCGCAATGCGAAATGAGAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
640012 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
640045 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
640073 CGATTTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:640096 original size:19 final size:19
Alignment explanation
Indices: 640072--640149 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
640062 AAATCGCAAC
640072 GCGATTTTAGTATCGCGTT
1 GCGATTTTAGTATCGCGTT
* *
640091 GTGA-TTTAGTTTCGCGTT
1 GCGATTTTAGTATCGCGTT
640109 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTATCGCGTT
*
640123 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTATCGCGTT
640142 GCGATTTT
1 GCGATTTT
640150 CATTTCGCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 17 0.35
19 18 0.37
ACGTcount: A:0.12, C:0.15, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTATCGCGTT
Found at i:640100 original size:18 final size:18
Alignment explanation
Indices: 640072--640115 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
640062 AAATCGCAAC
640072 GCGATTTTAGTATCGCGTT
1 GCGA-TTTAGTATCGCGTT
* *
640091 GTGATTTAGTTTCGCGTT
1 GCGATTTAGTATCGCGTT
640109 GCGATTT
1 GCGATTT
640116 TGTCGTTGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (18 bp):
GCGATTTAGTATCGCGTT
Found at i:640176 original size:52 final size:52
Alignment explanation
Indices: 640084--640198 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
640074 GATTTTAGTA
* * * *
640084 TCGCGTTGTGA-TTTAGTTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAGTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
640135 TCGCGTTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTT-AGTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
640187 TCGCATTGCGAT
1 TCGCGTTGCGAT
640199 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 10 0.18
52 46 0.81
53 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (52 bp):
TCGCGTTGCGATTTTAGTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:640206 original size:19 final size:19
Alignment explanation
Indices: 640121--640198 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
640111 GATTTTGTCG
*
640121 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
640140 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
640159 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
640173 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
640192 TTGCGAT
1 TTGCGAT
640199 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 7 0.14
19 31 0.61
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:640324 original size:14 final size:14
Alignment explanation
Indices: 640305--640341 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
640295 CATCAATTAA
640305 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
640319 ACAAATCATCTTTT
1 ACAAATCAACTTTT
640333 ACAAATCAA
1 ACAAATCAA
640342 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:641738 original size:21 final size:21
Alignment explanation
Indices: 641709--641789 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
641699 GAATGGTGGG
*
641709 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
641730 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
641751 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
641772 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
641790 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:641771 original size:42 final size:41
Alignment explanation
Indices: 641694--641812 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 41
641684 GTGAATCGGG
* * * *
641694 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
641736 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
641778 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
641813 CAGGCGAGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.06
42 55 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:642254 original size:94 final size:94
Alignment explanation
Indices: 642093--642307 Score: 385
Period size: 94 Copynumber: 2.3 Consensus size: 94
642083 GAATAGTTTC
*
642093 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
* *
642158 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGATAAAGAACACACAGTTTAGCAG
*
642187 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAATCAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
642252 ACAGTGATAAAGAACACACAGTTTAGCAG
66 ACAGTGATAAAGAACACACAGTTTAGCAG
*
642281 AATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
642308 AAGCAATCTA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 116 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGATAAAGAACACACAGTTTAGCAG
Found at i:644103 original size:20 final size:19
Alignment explanation
Indices: 644010--644133 Score: 132
Period size: 19 Copynumber: 6.7 Consensus size: 19
644000 AAAATCGCAA
**
644010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
644029 TGCGATTTTCAGTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
644048 TGCGA--TT-A--TCTCGT
1 TGCGATTTTCATTTCGCGT
644062 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
644081 TGCGATTTTCATTCTCTCGT
1 TGCGATTTTCATT-TCGCGT
**
644101 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
644121 TGCGATTTTCATT
1 TGCGATTTTCATT
644134 CTCGAAACTA
Statistics
Matches: 87, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 3 0.03
19 40 0.46
20 31 0.36
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:644113 original size:39 final size:40
Alignment explanation
Indices: 644056--644136 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
644046 GTTGCGATTA
**
644056 TCTCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATTC
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTCATTC
644095 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTCATTC
1 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTCATTC
644135 TC
1 TC
644137 GAAACTATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTCATTC
Found at i:644704 original size:20 final size:20
Alignment explanation
Indices: 644677--644770 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
644667 CGATAGTCAG
644677 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
644697 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
644717 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
644738 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
644758 ATTCGCATTGCGA
1 ATTCGCATTGCGA
644771 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:644727 original size:41 final size:40
Alignment explanation
Indices: 644677--644770 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
644667 CGATAGTCAG
* * *
644677 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
644717 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
644758 ATTCGCATTGCGA
1 ATTCGCATTGCGA
644771 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:644811 original size:20 final size:21
Alignment explanation
Indices: 644654--644814 Score: 111
Period size: 20 Copynumber: 7.9 Consensus size: 21
644644 ATGGCGCTAT
644654 GTAAATCGCATTGCGA--TA-
1 GTAAATCGCATTGCGATTTAC
*
644672 GTCAGATTCGCATTGCGATTTAC
1 GT-A-AATCGCATTGCGATTTAC
* * *
644695 GT-ATTTGCATTGCGATTTTC
1 GTAAATCGCATTGCGATTTAC
* *
644715 CTAATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* *
644736 -TTAATCGCGTTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* * *
644756 GT-ATTCGCATTGCGAATTAT
1 GTAAATCGCATTGCGATTTAC
* * ** *
644776 GAAAATCACAACGCGA-ATAC
1 GTAAATCGCATTGCGATTTAC
644796 GTAAATCGCATTGCGATTT
1 GTAAATCGCATTGCGATTT
644815 TGTATTATCG
Statistics
Matches: 109, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 75 0.69
21 27 0.25
22 2 0.02
23 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
GTAAATCGCATTGCGATTTAC
Found at i:644845 original size:20 final size:19
Alignment explanation
Indices: 644820--644870 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
644810 GATTTTGTAT
*
644820 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGT-AA
*
644840 TATCGCATTGCGATAGTAA
1 TATCGCGTTGCGATAGTAA
644859 TAATCGCGTTGC
1 T-ATCGCGTTGC
644871 AAATCTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (19 bp):
TATCGCGTTGCGATAGTAA
Found at i:645783 original size:23 final size:23
Alignment explanation
Indices: 645746--645800 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
645736 TGGTGTGGAG
*
645746 GAGAAAG-AAGAAGAAAAGTGAA
1 GAGAAAGAAAGAAGAAAAGTAAA
*
645768 GAGAAAGAAAGAAGAAAATTAAA
1 GAGAAAGAAAGAAGAAAAGTAAA
645791 GAGAAAGAAA
1 GAGAAAGAAA
645801 AAAAGAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.05
Consensus pattern (23 bp):
GAGAAAGAAAGAAGAAAAGTAAA
Found at i:645807 original size:27 final size:26
Alignment explanation
Indices: 645749--645836 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 26
645739 TGTGGAGGAG
* * *
645749 AAAGAAGAAGA-AAAGTGAAGAGAAAG
1 AAAGAAGAAAATAAAGAGAA-AGAAAA
645775 AAAGAAGAAAATTAAAGAGAAAGAAAA
1 AAAGAAGAAAA-TAAAGAGAAAGAAAA
*
645802 AAAGAAGAAAAT-AAGAAAAATGAAAAA
1 AAAGAAGAAAATAAAGAGAAA-G-AAAA
645829 AAAGAAGA
1 AAAGAAGA
645837 GCATGTCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.13
26 12 0.22
27 28 0.52
28 7 0.13
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.06
Consensus pattern (26 bp):
AAAGAAGAAAATAAAGAGAAAGAAAA
Found at i:645818 original size:23 final size:24
Alignment explanation
Indices: 645753--645819 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 24
645743 GAGGAGAAAG
*
645753 AAGAAGAAAAGT--GAAGAGAAAGA
1 AAGAAGAAAAGTAAGAA-AGAAAAA
*
645776 AAGAAGAAAATTAAAGAGAAAGAAAAA
1 AAGAAGAAAAGT--A-AGAAAGAAAAA
645803 AAGAAGAAAA-TAAGAAA
1 AAGAAGAAAAGTAAGAAA
645820 AATGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 16 0.43
24 1 0.03
26 1 0.03
27 16 0.43
28 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (24 bp):
AAGAAGAAAAGTAAGAAAGAAAAA
Found at i:646309 original size:6 final size:6
Alignment explanation
Indices: 646298--646330 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
646288 GATTTCATTC
*
646298 AGAGGG AGAGGG ATAGGG AGAGGG AGAGGG AGA
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGA
646331 CAGGGAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (6 bp):
AGAGGG
Done.