Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000039.1 Hibiscus syriacus cultivar Beakdansim tig00000060_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: 120519
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:15583 original size:22 final size:21
Alignment explanation
Indices: 15554--15599 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
15544 ATTATGATGA
15554 AATAAATTTAAAA-GCAAAATT
1 AATAAA-TTAAAATGCAAAATT
*
15575 AATATAATTAAAATGTAAAATT
1 AATA-AATTAAAATGCAAAATT
15597 AAT
1 AAT
15600 TTACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
AATAAATTAAAATGCAAAATT
Found at i:15822 original size:49 final size:49
Alignment explanation
Indices: 15748--15873 Score: 128
Period size: 49 Copynumber: 2.5 Consensus size: 49
15738 TTAGCAGTAA
* * * **
15748 AGCGCGCCCCCTACACCGCGTTATACGATGATTTGACGCCACGTGGGATAT
1 AGCGCG-CCCCTGCAGCGCGCTATACGATGAGCTGACGCCACGTGGG-TAT
* * * * *
15799 AGTGC-CCCCTGTATCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCTGCAGCGCGCTATACGATGAGCTGACGCCACGTGGGTAT
15847 AGCGCTGCCCCTGCAGCGCGCTATACG
1 AGCGC-GCCCCTGCAGCGCGCTATACG
15874 CCACGTAGGG
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
48 7 0.11
49 32 0.52
50 18 0.30
51 4 0.07
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (49 bp):
AGCGCGCCCCTGCAGCGCGCTATACGATGAGCTGACGCCACGTGGGTAT
Found at i:15990 original size:51 final size:49
Alignment explanation
Indices: 15885--16006 Score: 178
Period size: 51 Copynumber: 2.5 Consensus size: 49
15875 CACGTAGGGG
15885 TATAGCGC-GGATCAGGTA-CGCGCTATACCTTTACTCCTAATAATTTTA
1 TATAGCGCGGGA-CAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
*
15933 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGACAGGTACCGCG-CTATACCTTTACTCCT-A-ATAATTTTA
15984 TATAGCGCGGGACAGGTACCGCG
1 TATAGCGCGGGACAGGTACCGCG
16007 TTTTGTATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
48 14 0.21
49 20 0.30
50 2 0.03
51 31 0.46
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (49 bp):
TATAGCGCGGGACAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
Found at i:20108 original size:15 final size:15
Alignment explanation
Indices: 20088--20128 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
20078 TGGAAAGGCG
20088 ATGGCTGCATCATAT
1 ATGGCTGCATCATAT
20103 ATGGCTGCGGCATCATAT
1 ATGGCT---GCATCATAT
20121 ATGGCTGC
1 ATGGCTGC
20129 GGTGGCTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
18 15 0.65
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (15 bp):
ATGGCTGCATCATAT
Found at i:20117 original size:18 final size:18
Alignment explanation
Indices: 20094--20130 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20084 GGCGATGGCT
20094 GCATCATATATGGCTGCG
1 GCATCATATATGGCTGCG
20112 GCATCATATATGGCTGCG
1 GCATCATATATGGCTGCG
20130 G
1 G
20131 TGGCTGCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
GCATCATATATGGCTGCG
Found at i:21809 original size:110 final size:111
Alignment explanation
Indices: 21615--21827 Score: 356
Period size: 110 Copynumber: 1.9 Consensus size: 111
21605 ATTACAAAAA
* * * *
21615 TTAATTCTTAATCTAATAATCATGCATTAAATGAATTAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATTA
*
21680 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTTGAAATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAAATAT
*
21726 TTAATTATTAATATAATAATCATGCATTAAAT-AAATAACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATTA
*
21790 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
21828 AGAGATATAT
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 65 0.68
111 30 0.32
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAAATAT
Found at i:21945 original size:10 final size:10
Alignment explanation
Indices: 21930--21957 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
21920 AATATAATAG
21930 TAAAATATTA
1 TAAAATATTA
21940 TAAAATATTA
1 TAAAATATTA
21950 TAAAATAT
1 TAAAATAT
21958 ACCTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAAATATTA
Found at i:35407 original size:31 final size:31
Alignment explanation
Indices: 35372--35655 Score: 496
Period size: 31 Copynumber: 9.2 Consensus size: 31
35362 GGTCACAATA
*
35372 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
35403 TAAACTATTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
35434 TAAATTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35465 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35496 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
35527 TAAAATGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
35558 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35589 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35620 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
35651 TAAAC
1 TAAAC
35656 CCTCGACTCT
Statistics
Matches: 243, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 243 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:35495 original size:16 final size:16
Alignment explanation
Indices: 35474--35527 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
35464 ATAAACTGTT
35474 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
35490 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
35505 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
35521 CATATGT
1 CATATGT
35528 AAAATGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 7 0.24
16 14 0.48
17 2 0.07
18 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:35588 original size:16 final size:16
Alignment explanation
Indices: 35567--35651 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
35557 GTAAATTGTT
35567 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
35583 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
35598 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
35614 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
35629 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
35645 CATATGT
1 CATATGT
35652 AAACCCTCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:36162 original size:64 final size:63
Alignment explanation
Indices: 36054--36230 Score: 212
Period size: 64 Copynumber: 2.8 Consensus size: 63
36044 TAATAAAGGT
* * ** * **
36054 ATGCATCGATGCACTATTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTCTT-ATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAATGGG
** *
36118 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACT-CTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
*
36182 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACT-CTTATGCATCGATGCATAAATTGCATTCGATGT
36231 CTTTATTTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 95 0.97
65 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:36251 original size:64 final size:64
Alignment explanation
Indices: 36117--36279 Score: 213
Period size: 64 Copynumber: 2.5 Consensus size: 64
36107 TTATTGCTGG
* * *
36117 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
** *
36181 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
** *
36244 GAGTGCATCGATGCACTACCAATGCATCGATACACC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCACC
36280 TTCAAACAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 79 0.92
65 5 0.06
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:39348 original size:31 final size:31
Alignment explanation
Indices: 39313--39565 Score: 461
Period size: 31 Copynumber: 8.2 Consensus size: 31
39303 GGTCACAATA
39313 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
39344 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
39375 TAAATTATTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39406 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39437 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39468 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
39499 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39530 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
39561 TAAAC
1 TAAAC
39566 CCTCGACTCT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 214 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:40149 original size:64 final size:64
Alignment explanation
Indices: 40028--40170 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
40018 TATTGCTGGG
* * * * **
40028 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATACATCCATGCACTACCA
** *
40092 ATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AGAGTACATCCATGCACTACC
1 ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAGA-TACATCCATGCACTACC
40155 A
64 A
*
40156 ATGCATCGATACACC
1 ATGCATCGATGCACC
40171 TTCAAACAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 58 0.89
65 5 0.08
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATACATCCATGCACTACCA
Found at i:42202 original size:16 final size:15
Alignment explanation
Indices: 42174--42233 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
42164 TAAGTTGGGA
42174 TTAGATTGT-ATTTACT
1 TTAGATT-TAATTTA-T
42190 TTAGATTTAATTTAT
1 TTAGATTTAATTTAT
*
42205 ATTAAATTTAATTTTAT
1 -TTAGATTTAA-TTTAT
*
42222 TTGGATTTAATT
1 TTAGATTTAATT
42234 CCGTTCTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.11
16 29 0.76
17 5 0.13
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (15 bp):
TTAGATTTAATTTAT
Found at i:42203 original size:11 final size:11
Alignment explanation
Indices: 42183--42233 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
42173 ATTAGATTGT
*
42183 ATTTACTTTAG
1 ATTTAATTTAG
*
42194 ATTTAATTTAT
1 ATTTAATTTAG
*
42205 ATTAAATTTA-
1 ATTTAATTTAG
* *
42215 ATTTTATTTGG
1 ATTTAATTTAG
42226 ATTTAATT
1 ATTTAATT
42234 CCGTTCTATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
10 7 0.22
11 25 0.78
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (11 bp):
ATTTAATTTAG
Found at i:50586 original size:2 final size:2
Alignment explanation
Indices: 50579--50683 Score: 92
Period size: 2 Copynumber: 51.0 Consensus size: 2
50569 ATTTTCATCA
* *
50579 AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AGT TT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
50620 -T ACC AT CAT GAT CAT CAT CAT -T AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT -AT -AT -AT -AT -AT AT AT AT AT AT AT AT AT AT AT AT
50662 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
50684 TTCAAAATAA
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
1 4 0.05
2 70 0.80
3 14 0.16
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50723 original size:27 final size:27
Alignment explanation
Indices: 50691--50744 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
50681 TATTTCAAAA
50691 TAATTATATTTTTCATTTTCATTATTT
1 TAATTATATTTTTCATTTTCATTATTT
50718 TAATTATATTTTTCATTTTCATTATTT
1 TAATTATATTTTTCATTTTCATTATTT
50745 ATTATTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TAATTATATTTTTCATTTTCATTATTT
Found at i:51411 original size:14 final size:15
Alignment explanation
Indices: 51360--51411 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
51350 CTTTGGTATT
51360 ATTTAAATTTTTGTC
1 ATTTAAATTTTTGTC
*
51375 ATTTAAA-TTTTGTT
1 ATTTAAATTTTTGTC
*
51389 ATTTTAATTTTTG-C
1 ATTTAAATTTTTGTC
*
51403 CTTTAAATT
1 ATTTAAATT
51412 AGCAGTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTTAAATTTTTGTC
Found at i:51927 original size:139 final size:138
Alignment explanation
Indices: 51766--52030 Score: 350
Period size: 138 Copynumber: 1.9 Consensus size: 138
51756 GACAAATTCC
* * *
51766 ATAATTGATTAAAATTAATTAGGATTACTATTACAGCCTTCACTTTAGGCCTAATTTCAAACTTA
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAA-TTA
* ** * * *
51831 GTCCTTAAAATTAGGGGAATTTTTAATTTGGTCATCATTTTTGCTCGATGTTCCATTTTAATTAT
65 GTCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAATTAT
51896 TCGAATCAA
130 TCGAATCAA
* * * * * *
51905 ATAATTGGTTAAAATTAATTAGGAATAATATTAGAGCCTCCATTTTAGGCTTAATTTTATATTAG
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAATTAG
* * * *
51970 TCCTTTAATTTATAGGAATGCTTAATTTGGTCCTCACTTATGCTCGAGGTTCCATTTTAAT
66 TCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAAT
52031 CAAACAAAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
138 55 0.51
139 52 0.49
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (138 bp):
ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAATTAG
TCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAATTATT
CGAATCAA
Found at i:54280 original size:2 final size:2
Alignment explanation
Indices: 54273--54324 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
54263 TATAAAGTAA
54273 AT AT AT AT A- 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
54314 AT AT AT AT AT A
1 AT AT AT AT AT A
54325 GTTTGAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55353 original size:32 final size:33
Alignment explanation
Indices: 55275--55379 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
55265 CTAAATCTGA
*
55275 ACCCGACCTGAATATCACACATAAAAAACCCCG
1 ACCCGACCTGAATATCACACTTAAAAAACCCCG
* *
55308 ACCC-AACTCGAATATCACACTTACAAAA-CCCG
1 ACCCGACCT-GAATATCACACTTAAAAAACCCCG
*
55340 ACCCGACCTGAATATCAAACTTATAAAAACCCCG
1 ACCCGACCTGAATATCACACTTA-AAAAACCCCG
55374 ACCCGA
1 ACCCGA
55380 TTTTTTTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
32 24 0.39
33 28 0.45
34 10 0.16
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (33 bp):
ACCCGACCTGAATATCACACTTAAAAAACCCCG
Found at i:55428 original size:34 final size:33
Alignment explanation
Indices: 55370--55441 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 33
55360 TTATAAAAAC
*
55370 CCCGACCCGATTTTTTTTTAAAAAAAAATCCGA
1 CCCGACCCGATTTTTTTTTAAAAAAAAATCAGA
55403 CCCGATCCCAGATTTTTTTTT-AAAAAAAATCAGA
1 CCCGA-CCC-GATTTTTTTTTAAAAAAAAATCAGA
55437 CCCGA
1 CCCGA
55442 ATACCAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
33 5 0.14
34 20 0.56
35 11 0.31
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (33 bp):
CCCGACCCGATTTTTTTTTAAAAAAAAATCAGA
Found at i:56745 original size:16 final size:16
Alignment explanation
Indices: 56713--56752 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
56703 TTTACTTCAG
56713 AATGATT-AAACGTTA
1 AATGATTCAAACGTTA
*
56728 AATGATTCAAATGTTA
1 AATGATTCAAACGTTA
56744 AATGATTCA
1 AATGATTCA
56753 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (16 bp):
AATGATTCAAACGTTA
Found at i:67700 original size:21 final size:21
Alignment explanation
Indices: 67583--67700 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
67573 ACGCGAAATA
**
67583 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
67603 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
67623 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
67644 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
67665 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
*
67686 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
67701 ACACATAAAT
Statistics
Matches: 71, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 44 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:67713 original size:20 final size:20
Alignment explanation
Indices: 67688--67837 Score: 124
Period size: 20 Copynumber: 7.5 Consensus size: 20
67678 GATTTTCCAG
67688 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTAAC-CATA
* *
67708 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* ** *
67728 AATCGCAACGTGTATTCGTA
1 AATCGCAACGCGTAACCATA
* *
67748 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
67768 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
67788 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* *
67808 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTAA-CCATA
67828 AATCGCAACG
1 AATCGCAACG
67838 AGAATCTGTA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
19 2 0.02
20 112 0.97
21 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTAACCATA
Found at i:67888 original size:20 final size:20
Alignment explanation
Indices: 67706--67896 Score: 224
Period size: 20 Copynumber: 9.6 Consensus size: 20
67696 CGCGAACACA
*
67706 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
67726 TAAATCGCAACGTGTATTCG
1 TAAATCGCAACGAGTATCCG
*
67746 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
67766 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
67786 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
67806 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
67826 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
67846 TAAATCGCAACGA-TAATTCG
1 TAAATCGCAACGAGT-ATCCG
* *
67866 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
67886 TAAATCACAAC
1 TAAATCGCAAC
67897 ACTGAAATTT
Statistics
Matches: 149, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 148 0.99
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:68625 original size:24 final size:24
Alignment explanation
Indices: 68586--68632 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
68576 AAATTTGGTC
68586 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
68610 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
68633 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:68824 original size:12 final size:12
Alignment explanation
Indices: 68807--68831 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68797 ATATAATCCT
68807 GAAGAAGAAAAA
1 GAAGAAGAAAAA
68819 GAAGAAGAAAAA
1 GAAGAAGAAAAA
68831 G
1 G
68832 TCCCCGAAGT
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:71154 original size:33 final size:33
Alignment explanation
Indices: 71112--71362 Score: 179
Period size: 33 Copynumber: 7.2 Consensus size: 33
71102 CGGAAATTAC
*
71112 AATCGCAACAAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
71145 AATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
71179 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
71218 AATGCGGCAAC--GAAAATCGCAATGCGAAATGAA
1 AAT-C-GCAACAAGAAAATCGCAATGCGAAATGAA
* *
71251 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
71284 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* * *
71323 AATGCGGAA-ATGAAAATCGAAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
71356 AATCGCA
1 AATCGCA
71363 TTGCGATTCT
Statistics
Matches: 172, Mismatches: 24, Indels: 45
0.71 0.10 0.19
Matches are distributed among these distances:
31 5 0.03
32 6 0.03
33 63 0.37
34 42 0.24
35 2 0.01
36 1 0.01
37 1 0.01
38 16 0.09
39 25 0.15
40 7 0.04
41 4 0.02
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:71189 original size:53 final size:53
Alignment explanation
Indices: 71126--71362 Score: 406
Period size: 53 Copynumber: 4.5 Consensus size: 53
71116 GCAACAAGAG
* *
71126 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
* *
71179 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGCAACGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
71232 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
71284 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
71337 AATCGAAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
71363 TTGCGATTCT
Statistics
Matches: 175, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
52 50 0.29
53 124 0.71
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:71230 original size:22 final size:20
Alignment explanation
Indices: 71202--71367 Score: 76
Period size: 19 Copynumber: 9.0 Consensus size: 20
71192 AATGAAAATC
71202 GCAACGAGAGAATCGCAATGCG
1 GCAACGA-A-AATCGCAATGCG
71224 GCAACGAAAATCGCAATGC-
1 GCAACGAAAATCGCAATGCG
* *
71243 GAAATGAAAATCGCAA--C-
1 GCAACGAAAATCGCAATGCG
*
71260 G--A-GAGAATCGCAATGC-
1 GCAACGAAAATCGCAATGCG
* *
71276 GAAATGAAAATCGCAATGC-
1 GCAACGAAAATCGCAATGCG
* *
71295 GAAATGAAAATCGCAA--C-
1 GCAACGAAAATCGCAATGCG
*
71312 G--A-GAGAATCGCAATGCG
1 GCAACGAAAATCGCAATGCG
* * *
71329 GAAATGAAAATCGAAATGC-
1 GCAACGAAAATCGCAATGCG
* * *
71348 GAAATGAAAATCGCATTGCG
1 GCAACGAAAATCGCAATGCG
71368 ATTCTCTCGT
Statistics
Matches: 123, Mismatches: 9, Indels: 26
0.78 0.06 0.16
Matches are distributed among these distances:
14 20 0.16
15 2 0.02
16 3 0.02
17 5 0.04
18 1 0.01
19 61 0.50
20 23 0.19
21 1 0.01
22 7 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (20 bp):
GCAACGAAAATCGCAATGCG
Found at i:71312 original size:105 final size:106
Alignment explanation
Indices: 71126--71362 Score: 406
Period size: 105 Copynumber: 2.2 Consensus size: 106
71116 GCAACAAGAG
*
71126 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
71191 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGCAACGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAACGAA
*
71232 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
*
71295 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
65 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAACGAA
*
71337 AATCGAAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
71363 TTGCGATTCT
Statistics
Matches: 125, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
105 84 0.67
106 40 0.32
107 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAACGAA
Found at i:71402 original size:53 final size:52
Alignment explanation
Indices: 71345--71454 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 52
71335 AAAATCGAAA
71345 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCAT
** ** **
71398 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
71450 TGCGA
1 TGCGA
71455 TTCTCTCGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 10 0.20
53 41 0.80
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (52 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:71417 original size:19 final size:19
Alignment explanation
Indices: 71377--71497 Score: 145
Period size: 19 Copynumber: 6.8 Consensus size: 19
71367 GATTCTCTCG
71377 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
71397 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
71416 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
71430 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
71449 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
71463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
71482 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
71498 AACATAATGC
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
14 12 0.14
16 14 0.16
17 14 0.16
19 32 0.37
20 15 0.17
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:71435 original size:14 final size:14
Alignment explanation
Indices: 71416--71470 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
71406 TCATTTCGCA
71416 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
71430 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
71447 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
71463 TTGCGATT
1 TTGCGATT
71471 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:71439 original size:33 final size:33
Alignment explanation
Indices: 71397--71489 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
71387 CATTTCCGCA
71397 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
71430 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
71463 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
71490 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:71607 original size:14 final size:14
Alignment explanation
Indices: 71588--71624 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
71578 CATCAATTAC
71588 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
71602 ACAAATCATCTTTT
1 ACAAATCAACTTTT
71616 ACAAATCAA
1 ACAAATCAA
71625 TTAAACAATC
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:73588 original size:19 final size:19
Alignment explanation
Indices: 73546--73718 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
73536 TAGTTTACTT
* *
73546 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
73566 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
73585 TCGCAACGAGAAACAAAAA
1 TCGCAACGCGAAATGAAAA
**
73604 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
73623 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
73642 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
73656 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
73675 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
73689 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
73708 TCGCAATGCGA
1 TCGCAACGCGA
73719 TTTTGGTTTC
Statistics
Matches: 129, Mismatches: 14, Indels: 21
0.79 0.09 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.09
17 11 0.09
19 79 0.61
20 12 0.09
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:73659 original size:14 final size:14
Alignment explanation
Indices: 73640--73696 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
73630 GCGAAATGAA
*
73640 AATCGCAACGACAG
1 AATCGCAACGAAAG
73654 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
73671 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
73687 AATCGCAACG
1 AATCGCAACG
73697 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:73667 original size:33 final size:33
Alignment explanation
Indices: 73621--73713 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
73611 GCGAAACCAA
*
73621 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
73654 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
73687 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
73714 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:73749 original size:14 final size:14
Alignment explanation
Indices: 73730--73756 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
73720 TTTGGTTTCG
73730 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
73744 CGTTGCGATTTTG
1 CGTTGCGATTTTG
73757 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:73756 original size:33 final size:33
Alignment explanation
Indices: 73714--73808 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
73704 AAAATCGCAA
73714 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
73747 TGCGATTTTGGTTTCGCGTTGCGATTATT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
**
73780 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
73809 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:73768 original size:19 final size:19
Alignment explanation
Indices: 73714--73842 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
73704 AAAATCGCAA
73714 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
73733 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
73747 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
73766 TGCGATTAT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
73780 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
73799 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
73818 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
73838 TGCGA
1 TGCGA
73843 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 48 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.15, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:74023 original size:93 final size:93
Alignment explanation
Indices: 73887--74541 Score: 1276
Period size: 93 Copynumber: 7.1 Consensus size: 93
73877 ATGGATTGCA
73887 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
73951 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
73979 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
74044 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74072 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
74137 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74165 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
74230 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74258 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
74323 TAGCAGAATTGGCAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74351 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
74416 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74444 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
74509 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
74537 TTACT
1 TTACT
74542 AAGCAATCTA
Statistics
Matches: 557, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 553 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:83036 original size:2 final size:2
Alignment explanation
Indices: 83029--83058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
83019 ATTTTCATCA
83029 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
83059 TATTTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83118 original size:6 final size:6
Alignment explanation
Indices: 83081--83115 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
83071 TATTATTACC
*
83081 ATCATG ATCATG ATCATG ATCATG ATCATT ATCAT
1 ATCATG ATCATG ATCATG ATCATG ATCATG ATCAT
83116 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (6 bp):
ATCATG
Found at i:83290 original size:3 final size:3
Alignment explanation
Indices: 83276--83338 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
83266 TACTACTATC
83276 ATT A-T ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
83322 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
83339 CATCATTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:83846 original size:15 final size:15
Alignment explanation
Indices: 83826--83867 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
83816 CTTTGGTATT
83826 ATTTAAATTTTTGTC
1 ATTTAAATTTTTGTC
*
83841 ATTTAAA-TTTTGTT
1 ATTTAAATTTTTGTC
*
83855 ATTTTAATTTTTG
1 ATTTAAATTTTTG
83868 CCTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (15 bp):
ATTTAAATTTTTGTC
Found at i:84392 original size:139 final size:138
Alignment explanation
Indices: 84232--84496 Score: 341
Period size: 138 Copynumber: 1.9 Consensus size: 138
84222 GACAAATTCC
* * *
84232 ATAATTGATTAAAATTAATTAGGATTACTATTACAGCCTTCACTTTAGGCCTAATTTCAAACTTA
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAA-TTA
* ** * * * *
84297 GTCCTTAAAATTAGGGGAATTTTTAATTTGGTCATCATTTTTGCTCGATGTTCCATTTTAATTAT
65 GTCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCAAGGTTCCATTTTAATTAT
84362 TCGAATCAA
130 TCGAATCAA
* * * * * *
84371 ATAATTGGTTAAAATTAATTAGGAATAATATTAGAGCCTCCATTTTAGGCTTAATTTTATATTAG
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAATTAG
* * * *
84436 TCCTTTAATTTATAGGAATGCTTAATTTGGTCCTCACTTATGCTCAAGGTTCCATTTTAAT
66 TCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCAAGGTTCCATTTTAAT
84497 CAAACAAAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
138 54 0.51
139 52 0.49
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (138 bp):
ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAATTAG
TCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCAAGGTTCCATTTTAATTATT
CGAATCAA
Found at i:87775 original size:32 final size:33
Alignment explanation
Indices: 87697--87801 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
87687 CTAAATCTGA
*
87697 ACCCGACCTGAATATCACACATAAAAAACCCCG
1 ACCCGACCTGAATATCACACTTAAAAAACCCCG
* *
87730 ACCC-AACTCGAATATCACACTTACAAAA-CCCG
1 ACCCGACCT-GAATATCACACTTAAAAAACCCCG
*
87762 ACCCGACCTGAATATCAAACTTATAAAAACCCCG
1 ACCCGACCTGAATATCACACTTA-AAAAACCCCG
87796 ACCCGA
1 ACCCGA
87802 TTTTTTTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
32 24 0.39
33 28 0.45
34 10 0.16
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (33 bp):
ACCCGACCTGAATATCACACTTAAAAAACCCCG
Found at i:87851 original size:34 final size:33
Alignment explanation
Indices: 87792--87863 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
87782 TTATAAAAAC
*
87792 CCCGACCCGATTTTTTTTAAAAAAAAAATCCGA
1 CCCGACCCGATTTTTTTTAAAAAAAAAATCAGA
**
87825 CCCGATCCCAGATTTTTTTT-TTAAAAAAATCAGA
1 CCCGA-CCC-GATTTTTTTTAAAAAAAAAATCAGA
87859 CCCGA
1 CCCGA
87864 ATACCAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 5 0.15
34 19 0.56
35 10 0.29
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (33 bp):
CCCGACCCGATTTTTTTTAAAAAAAAAATCAGA
Found at i:89172 original size:16 final size:16
Alignment explanation
Indices: 89140--89179 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
89130 TTTACTTCAG
89140 AATGATT-AAACGTTA
1 AATGATTCAAACGTTA
*
89155 AATGATTCAAATGTTA
1 AATGATTCAAACGTTA
89171 AATGATTCA
1 AATGATTCA
89180 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (16 bp):
AATGATTCAAACGTTA
Found at i:90195 original size:10 final size:10
Alignment explanation
Indices: 90180--90204 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
90170 TGATAATTTG
90180 TATTATCTTA
1 TATTATCTTA
90190 TATTATCTTA
1 TATTATCTTA
90200 TATTA
1 TATTA
90205 AATTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTATCTTA
Found at i:95152 original size:44 final size:44
Alignment explanation
Indices: 95086--95212 Score: 168
Period size: 44 Copynumber: 2.9 Consensus size: 44
95076 AAAATCATAC
* * * * * *
95086 ATGTTAGGGTATTGTGATCCGAATTTCGTTTAAATTTATGTTAT
1 ATGTTAGAGTTTTGTGACCCGAATTTCGTTTGAATTCATATTAT
*
95130 ATGTTAGAGTTTTGTGACCCGAATTTCGTTTGAATTCGTATTAT
1 ATGTTAGAGTTTTGTGACCCGAATTTCGTTTGAATTCATATTAT
*
95174 ATGTT--AGTTTTGTGACCCAAATTTCGTTTGAATTCATAT
1 ATGTTAGAGTTTTGTGACCCGAATTTCGTTTGAATTCATAT
95213 AGTATGATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 32 0.43
44 42 0.57
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.46
Consensus pattern (44 bp):
ATGTTAGAGTTTTGTGACCCGAATTTCGTTTGAATTCATATTAT
Found at i:99298 original size:20 final size:20
Alignment explanation
Indices: 99258--99299 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
99248 TTCGCGTTGC
* **
99258 ATTTCGCGTTGTGATTTTCT
1 ATTTCGCGTTGCGATAGTCT
99278 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
99298 AT
1 AT
99300 AATGTCGTTG
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:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:99865 original size:34 final size:32
Alignment explanation
Indices: 99820--99929 Score: 105
Period size: 34 Copynumber: 3.3 Consensus size: 32
99810 ATTGGGTTCT
*
99820 GGTCGGGTTTTTTTAAGTTTGATATTCGGATC
1 GGTCGGGTTTTTTTAAGTATGATATTCGGATC
* * * * *
99852 GGTTTGGTTTTTTTTTAAGCATAATATTCGGGTC
1 GG-TCGG-GTTTTTTTAAGTATGATATTCGGATC
*
99886 GGTCGGGTTTTTTTAAGTGTGATATTCAGG-TC
1 GGTCGGGTTTTTTTAAGTATGATATTC-GGATC
99918 GGGTTCGGGTTT
1 -GG-TCGGGTTT
99930 AGGGTGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
32 21 0.34
33 10 0.16
34 31 0.50
ACGTcount: A:0.15, C:0.09, G:0.30, T:0.46
Consensus pattern (32 bp):
GGTCGGGTTTTTTTAAGTATGATATTCGGATC
Found at i:102247 original size:3 final size:3
Alignment explanation
Indices: 102239--102290 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
102229 ATATTCAAAC
102239 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
102286 A-A ATA
1 ATA ATA
102291 TAGCTTCTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:107672 original size:6 final size:6
Alignment explanation
Indices: 107662--107709 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
107652 TAGCATTCGT
* * * *
107662 GGACCT GGACCC GGACCC GGACCA GGACCC GGAGCC GGACCA GGACCC
1 GGACCC GGACCC GGACCC GGACCC GGACCC GGACCC GGACCC GGACCC
107710 ATTTGCCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.21, C:0.42, G:0.35, T:0.02
Consensus pattern (6 bp):
GGACCC
Found at i:107689 original size:18 final size:18
Alignment explanation
Indices: 107662--107709 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
107652 TAGCATTCGT
*
107662 GGACCTGGACCCGGACCC
1 GGACCAGGACCCGGACCC
*
107680 GGACCAGGACCCGGAGCC
1 GGACCAGGACCCGGACCC
107698 GGACCAGGACCC
1 GGACCAGGACCC
107710 ATTTGCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.42, G:0.35, T:0.02
Consensus pattern (18 bp):
GGACCAGGACCCGGACCC
Found at i:109264 original size:2 final size:2
Alignment explanation
Indices: 109257--109318 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
109247 ATTGATTTTA
109257 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
109299 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
109319 TGTCTCCTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110634 original size:17 final size:17
Alignment explanation
Indices: 110599--110637 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
110589 GGAAATTATA
110599 TAAT-TATATTAGTTAC
1 TAATGTATATTAGTTAC
110615 TAATGTATAGTTAGTT-C
1 TAATGTATA-TTAGTTAC
110632 TAATGT
1 TAATGT
110638 GTGTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (17 bp):
TAATGTATATTAGTTAC
Found at i:112838 original size:13 final size:13
Alignment explanation
Indices: 112820--112856 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
112810 CTTCAATTAT
112820 GATGATTGAATAA
1 GATGATTGAATAA
112833 GATGATTGAATAA
1 GATGATTGAATAA
112846 GATGATTGAAT
1 GATGATTGAAT
112857 GTTAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.32
Consensus pattern (13 bp):
GATGATTGAATAA
Done.