Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006582.1 Hibiscus syriacus cultivar Beakdansim tig00016134_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: 120232
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10963 original size:2 final size:2
Alignment explanation
Indices: 10956--11003 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
10946 AATGATCTTG
* * *
10956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10998 TA TA TA
1 TA TA TA
11004 CTTCTTTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13778 original size:27 final size:28
Alignment explanation
Indices: 13734--13786 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
13724 TATGACTATT
*
13734 ATTCTAAATTTATCTCTAAATTATGAAC
1 ATTCTAAATTTATCTCTAAACTATGAAC
13762 ATTCT-AATTTCAT-TCTAAACTATGA
1 ATTCTAAATTT-ATCTCTAAACTATGA
13787 CCCTCATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (28 bp):
ATTCTAAATTTATCTCTAAACTATGAAC
Found at i:13819 original size:58 final size:56
Alignment explanation
Indices: 13655--13832 Score: 153
Period size: 58 Copynumber: 3.0 Consensus size: 56
13645 TGTACCACAA
* * *
13655 ATTCTCAAACTATGACTTTC-TTCTTAAATTAGTCTTCAAATTTTTAAATATTCTATTTC
1 ATTCT-AAACTATGACTATCATTC-TAAATTAGTC-TCAAA-TTTTGAACATTCTATTTC
* * * *
13714 ATCCCCAAACTATGACTATTATTCTAAATTTA-TCTCTAAATTATGAACATTCTAATTTC
1 AT-TCTAAACTATGACTATCATTCTAAA-TTAGTCTC-AAATTTTGAACATTCT-ATTTC
** * *
13773 ATTCTAAACTATGACCCTCATTCTAAATTGGTCTCAAACTTTTGAACATTTCGATTTC
1 ATTCTAAACTATGACTATCATTCTAAATTAGTCTCAAA-TTTTGAACA-TTCTATTTC
13831 AT
1 AT
13833 CCCCAATCTA
Statistics
Matches: 96, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
57 5 0.05
58 51 0.53
59 33 0.34
60 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (56 bp):
ATTCTAAACTATGACTATCATTCTAAATTAGTCTCAAATTTTGAACATTCTATTTC
Found at i:16382 original size:20 final size:20
Alignment explanation
Indices: 16343--16382 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16333 TGCCACATGT
*
16343 CATGTCATACAAGATGATGG
1 CATGTCATACAAGATAATGG
* *
16363 CATGTCATCCAAGGTAATGG
1 CATGTCATACAAGATAATGG
16383 TTTTCTGTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
CATGTCATACAAGATAATGG
Found at i:16525 original size:26 final size:28
Alignment explanation
Indices: 16463--16525 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 28
16453 CGAGTATTGC
16463 TGAGCTCGACTCGACTCGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCGAAAACTCTG--A
16493 TGAAGCTCGACTCGACTCGAAAACTC-G-
1 TG-AGCTCGACTCGACTCGAAAACTCTGA
16520 TGAGCT
1 TGAGCT
16526 TAAAATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
30 3 0.09
31 23 0.72
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:19833 original size:28 final size:29
Alignment explanation
Indices: 19776--19842 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
19766 TCATATTTTA
* * *
19776 TTAGTCCCTTACTACATAAGCTGTTGA-T
1 TTAGTCCCTTACTACATAAACTGATCATT
*
19804 TTAGTCCCTTGC-ACACTAAACTGATCATT
1 TTAGTCCCTTACTACA-TAAACTGATCATT
19833 TTAGTCCCTT
1 TTAGTCCCTT
19843 TTAATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.58
29 11 0.33
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (29 bp):
TTAGTCCCTTACTACATAAACTGATCATT
Found at i:20121 original size:15 final size:15
Alignment explanation
Indices: 20097--20127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20087 GTGAAAGGGA
20097 TGGGACTTATAAAAT
1 TGGGACTTATAAAAT
*
20112 TGGGATTTATAAAAT
1 TGGGACTTATAAAAT
20127 T
1 T
20128 TTAGGAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (15 bp):
TGGGACTTATAAAAT
Found at i:25197 original size:13 final size:13
Alignment explanation
Indices: 25179--25203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25169 TTAGCTACTT
25179 TTTTACATTTACC
1 TTTTACATTTACC
25192 TTTTACATTTAC
1 TTTTACATTTAC
25204 GTTTACAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTACATTTACC
Found at i:33431 original size:38 final size:37
Alignment explanation
Indices: 33381--33459 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 37
33371 TAAGTTATAT
33381 AACACGTCCACATTAAATGGTTGTATTTTCAGCAGCA
1 AACACGTCCACATTAAATGGTTGTATTTTCAGCAGCA
*
33418 AACACGGTCCACATTAAATGGTTGTATTTTCAGCCGCA
1 AACAC-GTCCACATTAAATGGTTGTATTTTCAGCAGCA
33456 AACA
1 AACA
33460 TAGTAATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 5 0.12
38 35 0.88
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (37 bp):
AACACGTCCACATTAAATGGTTGTATTTTCAGCAGCA
Found at i:35650 original size:20 final size:20
Alignment explanation
Indices: 35625--35666 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
35615 TTTGATCAGG
35625 TTTTTACTTT-TATAATTTTA
1 TTTTTA-TTTGTATAATTTTA
*
35645 TTTTTATTTGTATTATTTTA
1 TTTTTATTTGTATAATTTTA
35665 TT
1 TT
35667 GTATTTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATTTGTATAATTTTA
Found at i:35747 original size:15 final size:15
Alignment explanation
Indices: 35729--35810 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
35719 TTCTGGAAAA
*
35729 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
35744 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
35759 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
35774 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
35789 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
35803 TGAATTAC
1 TGAATTAC
35811 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:35772 original size:45 final size:44
Alignment explanation
Indices: 35721--35810 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 44
35711 AATTGGTTTT
* **
35721 CTGGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTA
1 CTGGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTA
35766 CTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTA
1 CTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTA
35810 C
1 C
35811 ATTTCTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.33
45 28 0.67
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (44 bp):
CTGGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTA
Found at i:35808 original size:29 final size:30
Alignment explanation
Indices: 35729--35810 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
35719 TTCTGGAAAA
***
35729 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
35759 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
35789 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
35811 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:35816 original size:20 final size:20
Alignment explanation
Indices: 35793--35842 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
35783 GGAATTTGAA
35793 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
35813 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
35833 TTCTGGAAAA
1 TTCTGGAAAA
35843 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:36075 original size:29 final size:26
Alignment explanation
Indices: 36042--36103 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
36032 TTACTAAAAT
36042 ATTATTGAAATATATAAATAATATTATTC
1 ATTATT-AAATATATAAA-AAT-TTATTC
36071 ATTATTAAATATATAAAAATTTATT-
1 ATTATTAAATATATAAAAATTTATTC
36096 ATATATTA
1 AT-TATTA
36104 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.06
26 10 0.31
27 3 0.09
28 11 0.34
29 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTATTAAATATATAAAAATTTATTC
Found at i:36094 original size:26 final size:27
Alignment explanation
Indices: 36041--36184 Score: 100
Period size: 29 Copynumber: 5.1 Consensus size: 27
36031 TTTACTAAAA
36041 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAATAATATTAT
36069 TCATTATTAAATATATAAA-AATTTATTAT
1 T-ATTATTAAATATATAAATAA--TATTAT
36098 ATATTATTAAA-ATA-AAATAAATATCT-T
1 -TATTATTAAATATATAAAT-AATAT-TAT
** * *
36125 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* *
36155 ATAATATTAAAAATAT-AATAATATTAT
1 -TATTATTAAATATATAAATAATATTAT
36182 TAT
1 TAT
36185 AAATATTAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
26 2 0.02
27 26 0.28
28 20 0.21
29 30 0.32
30 14 0.15
31 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:36104 original size:29 final size:29
Alignment explanation
Indices: 36040--36202 Score: 99
Period size: 29 Copynumber: 5.6 Consensus size: 29
36030 CTTTACTAAA
36040 ATATTATTGAAATATATAAATAA--TATTAT
1 ATATTATT-AAATATATAAA-AATTTATTAT
36069 -TCATTATTAAATATATAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAATTTATTAT
*
36098 ATATTATTAAA-ATA-AAATAA-ATATCT-T
1 ATATTATTAAATATATAAA-AATTTAT-TAT
*** *
36125 ATATTATTATAATATA-ATTGATTATTTTAT
1 ATATTATTA-AATATATAAAAATT-TATTAT
* * *
36155 ATAATATTAAAAATATAATAATATTATTAT
1 ATATTATTAAATATATAAAAAT-TTATTAT
*
36185 AAATATTAATAAATATAT
1 --ATATTATTAAATATAT
36203 TTTAAATATT
Statistics
Matches: 105, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
27 18 0.17
28 21 0.20
29 31 0.30
30 21 0.20
31 1 0.01
32 13 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATTATTAAATATATAAAAATTTATTAT
Found at i:36163 original size:15 final size:16
Alignment explanation
Indices: 36125--36201 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 16
36115 TAAATATCTT
36125 ATATTATTATAATATA
1 ATATTATTATAATATA
*
36141 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
36158 ATATTA--AAAATATA
1 ATATTATTATAATATA
* *
36172 ATAATATTATTATA-A
1 ATATTATTATAATATA
*
36187 ATATTAATA-AATATA
1 ATATTATTATAATATA
36202 TTTTAAATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
14 13 0.28
15 13 0.28
16 6 0.13
17 8 0.17
18 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:36196 original size:21 final size:21
Alignment explanation
Indices: 36158--36212 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
36148 ATTTTATATA
*
36158 ATATTAAAAATA-TAAT-AAT
1 ATATTATAAATATTAATAAAT
36177 ATTATTATAAATATTAATAAAT
1 A-TATTATAAATATTAATAAAT
*
36199 ATATTTTAAATATT
1 ATATTATAAATATT
36213 TTAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 10 0.32
21 16 0.52
22 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:36460 original size:42 final size:42
Alignment explanation
Indices: 36401--36515 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
36391 ATGAATTACA
* *
36401 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
36443 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
36485 TTCCGAAAAACGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
36516 TGAAATTCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:38691 original size:16 final size:17
Alignment explanation
Indices: 38650--38683 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38640 ATATTATCCG
*
38650 ATCCG-AAATTTTGGAT
1 ATCCGAAAATTTGGGAT
38666 ATCCGAAAATTTGGGAT
1 ATCCGAAAATTTGGGAT
38683 A
1 A
38684 CCTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (17 bp):
ATCCGAAAATTTGGGAT
Found at i:52521 original size:21 final size:21
Alignment explanation
Indices: 52495--52535 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
52485 TAGCGATTGC
52495 GATCGCGTTTTCGACCGGGTT
1 GATCGCGTTTTCGACCGGGTT
52516 GATCGCGTTTTCGACCGGGT
1 GATCGCGTTTTCGACCGGGT
52536 CGATTGCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.34, T:0.32
Consensus pattern (21 bp):
GATCGCGTTTTCGACCGGGTT
Found at i:53920 original size:57 final size:58
Alignment explanation
Indices: 53841--53950 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
53831 TTATGACTTT
*
53841 CATTTTAAATTAGTCCTCAAAC-TTTTAAACATTTCA-ATTTCATCCCCAAACTATGTTG
1 CATTCTAAATTAGTCCTCAAACTTTTTAAACA-TTCATATTTCAT-CCCAAACTATGTTG
* *
53899 CATTCTAAATTGGTCC-CAAACTTTTTGAACATTCATATTTCATCCCAAACTA
1 CATTCTAAATTAGTCCTCAAACTTTTTAAACATTCATATTTCATCCCAAACTA
53951 AACATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
57 18 0.38
58 29 0.62
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (58 bp):
CATTCTAAATTAGTCCTCAAACTTTTTAAACATTCATATTTCATCCCAAACTATGTTG
Found at i:55587 original size:17 final size:17
Alignment explanation
Indices: 55565--55603 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
55555 TGAATCAAAT
55565 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
55582 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
55599 -AATTA
1 TAATTA
55604 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:57053 original size:23 final size:23
Alignment explanation
Indices: 56996--57057 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
56986 CAAACGACTG
* *
56996 AAAACGTGACATAAAGACAGAGA
1 AAAACGTGTCATAAAGACAGAAA
* *
57019 TAAACGTATCATAAAGACA-AAA
1 AAAACGTGTCATAAAGACAGAAA
57041 AAAATCGTGTCATAAAG
1 AAAA-CGTGTCATAAAG
57058 GTAAAATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAACGTGTCATAAAGACAGAAA
Found at i:57352 original size:29 final size:31
Alignment explanation
Indices: 57319--57376 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
57309 TTTAATTATT
*
57319 TTATTTAAAAGTAAA-ATAATT-TATTTTAA
1 TTATTTAAAAGTAAATAAAATTATATTTTAA
57348 TTATTTAAAAGTAAATAAAATTATATTTT
1 TTATTTAAAAGTAAATAAAATTATATTTT
57377 TAATAACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.58
30 5 0.19
31 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
TTATTTAAAAGTAAATAAAATTATATTTTAA
Found at i:57496 original size:17 final size:17
Alignment explanation
Indices: 57462--57517 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
57452 TAATAGTGAG
* *
57462 TTATTATAAATATTTTT
1 TTATTATAATTATATTT
*
57479 TTATTATAATTCTATTT
1 TTATTATAATTATATTT
57496 TTATT-T--TTATATTT
1 TTATTATAATTATATTT
57510 TTATTATA
1 TTATTATA
57518 GTTTAAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 12 0.36
15 1 0.03
16 1 0.03
17 19 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATAATTATATTT
Found at i:57583 original size:2 final size:2
Alignment explanation
Indices: 57572--57618 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
57562 TAAGTTTATT
57572 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57613 TA TA TA
1 TA TA TA
57619 AAGATAAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59071 original size:155 final size:156
Alignment explanation
Indices: 58789--59101 Score: 619
Period size: 155 Copynumber: 2.0 Consensus size: 156
58779 TTAGATGTCG
58789 TTTGAATTCTATAAATTAAATCAATAATAGTCAATTGTAATTGAAAGATGAAATTTTCAGAATTA
1 TTTGAATTCTATAAATTAAATCAATAATAGTCAATTGTAATTGAAAGATGAAATTTTCAGAATTA
58854 TGTCTGGTTGAATATTAGATGTATCTAAATAATATTTTAGCTCTATTCAGTGTTATATAAAAAAG
66 TGTCTGGTTGAATATTAGATGTATCTAAATAATATTTTAGCTCTATTCAGTGTTATATAAAAAAG
58919 GTGTTATATTGCATTAG-TACAGAGC
131 GTGTTATATTGCATTAGTTACAGAGC
58944 TTTGAATTCTATAAATTAAATCAATAATAGTCAATTGTAATTGAAAGATGAAATTTTCAGAATTA
1 TTTGAATTCTATAAATTAAATCAATAATAGTCAATTGTAATTGAAAGATGAAATTTTCAGAATTA
59009 TGTCTGGTTGAATATTAGATGTATCTAAATAATATTTTAGCTCTATTCAGTGTTATATAAAAAAG
66 TGTCTGGTTGAATATTAGATGTATCTAAATAATATTTTAGCTCTATTCAGTGTTATATAAAAAAG
59074 GTGTTATATTGCATTAGTTACAGAGC
131 GTGTTATATTGCATTAGTTACAGAGC
59100 TT
1 TT
59102 ATGTCGAGAC
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 147 0.94
156 10 0.06
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (156 bp):
TTTGAATTCTATAAATTAAATCAATAATAGTCAATTGTAATTGAAAGATGAAATTTTCAGAATTA
TGTCTGGTTGAATATTAGATGTATCTAAATAATATTTTAGCTCTATTCAGTGTTATATAAAAAAG
GTGTTATATTGCATTAGTTACAGAGC
Found at i:59505 original size:26 final size:26
Alignment explanation
Indices: 59451--59515 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
59441 CTAAAGTATA
* **
59451 AATAATAATTAATCACATAATGTAAT
1 AATATTAATTAATCACATAAAATAAT
*
59477 AATTATTAATTAAT-ACATAAAATATT
1 AA-TATTAATTAATCACATAAAATAAT
59503 AATATTAAATTAA
1 AATATT-AATTAA
59516 CTTAATTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 19 0.58
27 10 0.30
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (26 bp):
AATATTAATTAATCACATAAAATAAT
Found at i:60725 original size:19 final size:20
Alignment explanation
Indices: 60701--60756 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 20
60691 CTTCTATTTG
*
60701 TAATATTATTTAATAATA-A
1 TAATATTATATAATAATATA
60720 TAATATTATGATATATAATATA
1 TAATATTAT-ATA-ATAATATA
60742 TAATATTATATAATA
1 TAATATTATATAATA
60757 TAAACATCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 9 0.27
20 5 0.15
21 9 0.27
22 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATATTATATAATAATATA
Found at i:61114 original size:41 final size:41
Alignment explanation
Indices: 61068--61206 Score: 120
Period size: 41 Copynumber: 3.3 Consensus size: 41
61058 AAATCTGTTC
61068 CACTACTCTTCTGTGGAGAGCGAATTTTGGTTGGATTACTT
1 CACTACTCTTCTGTGGAGAGCGAATTTTGGTTGGATTACTT
* * * * * * * *
61109 CACTACTCTT-TCGTGAAGGTTGCAAACTTT-GCTGAAAAATCCGTT
1 CACTACTCTTCT-GTGGA-G-AGCGAATTTTGGTTG--GATTAC-TT
*
61154 CCACTACTCTTCTGTGGAGAGCGAATTTTGGTTGGATTATTT
1 -CACTACTCTTCTGTGGAGAGCGAATTTTGGTTGGATTACTT
61196 CACTACTCTTC
1 CACTACTCTTC
61207 CGTGAAGGCT
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
40 1 0.01
41 25 0.35
42 6 0.08
43 9 0.12
44 10 0.14
45 6 0.08
46 14 0.19
47 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (41 bp):
CACTACTCTTCTGTGGAGAGCGAATTTTGGTTGGATTACTT
Found at i:61120 original size:87 final size:87
Alignment explanation
Indices: 61015--61214 Score: 319
Period size: 87 Copynumber: 2.3 Consensus size: 87
61005 CTTAATTTGC
* * * * * * *
61015 ATTACTCCATTACTCTTTCATGAAGGTTTCATATTTTGCTGAAAAATCTGTTCCACTACTCTTCT
1 ATTACTTCACTACTCTTTCGTGAAGGTTGCAAACTTTGCTGAAAAATCCGTTCCACTACTCTTCT
61080 GTGGAGAGCGAATTTTGGTTGG
66 GTGGAGAGCGAATTTTGGTTGG
61102 ATTACTTCACTACTCTTTCGTGAAGGTTGCAAACTTTGCTGAAAAATCCGTTCCACTACTCTTCT
1 ATTACTTCACTACTCTTTCGTGAAGGTTGCAAACTTTGCTGAAAAATCCGTTCCACTACTCTTCT
61167 GTGGAGAGCGAATTTTGGTTGG
66 GTGGAGAGCGAATTTTGGTTGG
* *
61189 ATTATTTCACTACTCTTCCGTGAAGG
1 ATTACTTCACTACTCTTTCGTGAAGG
61215 CTGAGAATGA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 104 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (87 bp):
ATTACTTCACTACTCTTTCGTGAAGGTTGCAAACTTTGCTGAAAAATCCGTTCCACTACTCTTCT
GTGGAGAGCGAATTTTGGTTGG
Found at i:61400 original size:40 final size:40
Alignment explanation
Indices: 61355--61552 Score: 148
Period size: 40 Copynumber: 5.0 Consensus size: 40
61345 ATACTGACAG
**
61355 ATGACCCAAAAGATTTGTAAATTACCTGAAGGCTTTACAA
1 ATGACCCAAAAGATTTACAAATTACCTGAAGGCTTTACAA
** * * *
61395 ATGACCCGGAGGCTTTACAAATTACCTGGAGGCTTTACAA
1 ATGACCCAAAAGATTTACAAATTACCTGAAGGCTTTACAA
* * * * *
61435 ATGACCCGAAGGCTTTACAAATGACCCAGATA--CTTTACAA
1 ATGACCCAAAAGATTTACAAATTA-CCTGA-AGGCTTTACAA
** * * * * * *
61475 ATGACCCGGAGGCTTTACAAATGACCCGGAGACTTTACAA
1 ATGACCCAAAAGATTTACAAATTACCTGAAGGCTTTACAA
* * * *
61515 ATGACCCAGAGGATTTACAAATGACCCGAAGGCTTTAC
1 ATGACCCAAAAGATTTACAAATTACCTGAAGGCTTTAC
61553 TTTTCTTGAA
Statistics
Matches: 136, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 128 0.94
41 3 0.02
42 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
ATGACCCAAAAGATTTACAAATTACCTGAAGGCTTTACAA
Found at i:61407 original size:20 final size:20
Alignment explanation
Indices: 61384--61552 Score: 248
Period size: 20 Copynumber: 8.4 Consensus size: 20
61374 AATTACCTGA
61384 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCGG
* *
61404 AGGCTTTACAAATTACCTGG
1 AGGCTTTACAAATGACCCGG
*
61424 AGGCTTTACAAATGACCCGA
1 AGGCTTTACAAATGACCCGG
*
61444 AGGCTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCGG
**
61464 ATACTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCGG
61484 AGGCTTTACAAATGACCCGG
1 AGGCTTTACAAATGACCCGG
* *
61504 AGACTTTACAAATGACCCAG
1 AGGCTTTACAAATGACCCGG
* *
61524 AGGATTTACAAATGACCCGA
1 AGGCTTTACAAATGACCCGG
61544 AGGCTTTAC
1 AGGCTTTAC
61553 TTTTCTTGAA
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 130 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
AGGCTTTACAAATGACCCGG
Found at i:69727 original size:23 final size:23
Alignment explanation
Indices: 69685--69728 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
69675 TCGGGTTTGG
**
69685 TTGTAATCGGGCCTGGATTTGCT
1 TTGTAATCGGGCCTCCATTTGCT
69708 TTGTAATCGGGCCTCCATTTG
1 TTGTAATCGGGCCTCCATTTG
69729 TAAATGGGCT
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:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (23 bp):
TTGTAATCGGGCCTCCATTTGCT
Found at i:69730 original size:18 final size:17
Alignment explanation
Indices: 69707--69750 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
69697 CTGGATTTGC
69707 TTTGTAATCGGGCCTCCA
1 TTTGTAAT-GGGCCTCCA
*
69725 TTTGTAAATGGGCTTCCA
1 TTTGT-AATGGGCCTCCA
*
69743 TTCGTAAT
1 TTTGTAAT
69751 ATTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (17 bp):
TTTGTAATGGGCCTCCA
Found at i:71025 original size:32 final size:32
Alignment explanation
Indices: 70933--71030 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
70923 AAGAACCCAT
* *
70933 GTAA-ACTGTCTATATGTTCCTTAGAACATAG
1 GTAATACTGTCCATATGTTCCGTAGAACATAG
* *
70964 GT-ATACTTTCCATATG-TCTCG-AAAGACATAG
1 GTAATACTGTCCATATGTTC-CGTAGA-ACATAG
*
70995 GTAATTCTGTCCATATGTTCCGTAGAACATAG
1 GTAATACTGTCCATATGTTCCGTAGAACATAG
71027 GTAA
1 GTAA
71031 ACCTCGACTC
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
30 5 0.09
31 21 0.39
32 24 0.44
33 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (32 bp):
GTAATACTGTCCATATGTTCCGTAGAACATAG
Found at i:72141 original size:29 final size:29
Alignment explanation
Indices: 72095--72153 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
72085 GCATCGGTAC
72095 ACTCATGGCATTCAATGTTTTCATTTTTA
1 ACTCATGGCATTCAATGTTTTCATTTTTA
**
72124 ACTCATGGCATTTGATGTTTTCATTTTTA
1 ACTCATGGCATTCAATGTTTTCATTTTTA
72153 A
1 A
72154 GGGGTGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (29 bp):
ACTCATGGCATTCAATGTTTTCATTTTTA
Found at i:73650 original size:64 final size:64
Alignment explanation
Indices: 73582--73759 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 64
73572 GGGACACTTA
*
73582 GTGCATCGGTGCACT-AAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
1 GTGCATCGATGCACTGAAGG-TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
* *** * *
73646 GTGCATCGATGCATTGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTG-AAAATATTCC-G
1 GTGCATCGATGCACTGAAGGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATA-GCCTG
* * * *
73709 CGTGCATCGATGCA-TGGAGAGTGCATTGGTGCATGAAATGCATTCGATGTT
1 -GTGCATCGATGCACTGAAG-GTGCATCGATGCATAAAATGCATTCGATGTT
73760 CAATTAAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 9 0.09
64 87 0.90
65 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCACTGAAGGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
Found at i:75369 original size:44 final size:42
Alignment explanation
Indices: 75255--75372 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
75245 AAAACCCGAC
* * *
75255 GGATGCATCGGTGCATGGTCTTATGCATCGATGCATATTCAAG
1 GGATGCATCGGTGCATTGT-TAATGCATCGATACATATTCAAG
* * *
75298 GCATGCATCGGTGCATCATGGTGATGCATCGATACATATTCAAAG
1 GGATGCATCGGTGCAT--TGTTAATGCATCGATACATATTC-AAG
*
75343 GGATGCATCGATGCATTGTTAAATGCATCG
1 GGATGCATCGGTGCATTGTT-AATGCATCG
75373 GTGCATGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.29
44 26 0.42
45 18 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
GGATGCATCGGTGCATTGTTAATGCATCGATACATATTCAAG
Found at i:80852 original size:64 final size:64
Alignment explanation
Indices: 80784--80961 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 64
80774 GGGACACTTA
*
80784 GTGCATCGGTGCACT-AAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
1 GTGCATCGATGCACTGAAGG-TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
* *** * *
80848 GTGCATCGATGCATTGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTG-AAAATATTCC-G
1 GTGCATCGATGCACTGAAGGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATA-GCCTG
* * * *
80911 CGTGCATCGATGCA-TGGAGAGTGCATTGGTGCATGAAATGCATTCGATGTT
1 -GTGCATCGATGCACTGAAG-GTGCATCGATGCATAAAATGCATTCGATGTT
80962 CAATTAAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 9 0.09
64 87 0.90
65 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCACTGAAGGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
Found at i:83315 original size:63 final size:62
Alignment explanation
Indices: 83204--83321 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 62
83194 GGCAACTGTC
* *
83204 CATAGGTCCCGAAGAACCTAGGTAAATTGTCCATATATTCCTTAGAACATAGGTATAATGTT
1 CATAGGTCCCGAAGAACATAGGTAAATTGTCCATATATTCCGTAGAACATAGGTATAATGTT
* * * *
83266 CATATGTCCCGAA-AGACATAGGTAATTTTGTCCATTTGTTCCGTAGAACATAGGTA
1 CATAGGTCCCGAAGA-ACATAGGTAA-ATTGTCCATATATTCCGTAGAACATAGGTA
83322 AACCCTCGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 1 0.02
62 21 0.44
63 26 0.54
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (62 bp):
CATAGGTCCCGAAGAACATAGGTAAATTGTCCATATATTCCGTAGAACATAGGTATAATGTT
Found at i:83322 original size:32 final size:32
Alignment explanation
Indices: 83200--83322 Score: 108
Period size: 31 Copynumber: 3.9 Consensus size: 32
83190 GCTCGGCAAC
* * * *
83200 TGTCCATAGGTCCCGAAGAACCTAGGTAA-AT
1 TGTCCATATGTTCCGTAGAACATAGGTAATAT
* * *
83231 TGTCCATATATTCCTTAGAACATAGGT-ATAA
1 TGTCCATATGTTCCGTAGAACATAGGTAATAT
* * * *
83262 TGTTCATATGTCCCG-AAAGACATAGGTAATTT
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATAT
*
83294 TGTCCATTTGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTTCCGTAGAACATAGGTAA
83323 ACCCTCGACT
Statistics
Matches: 70, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
30 3 0.04
31 41 0.59
32 24 0.34
33 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATAT
Found at i:84699 original size:20 final size:20
Alignment explanation
Indices: 84674--84714 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
84664 TCAAGAATTA
84674 TACCAACTTTGCAACATGTT
1 TACCAACTTTGCAACATGTT
84694 TACCAACTTTGCAACATGTT
1 TACCAACTTTGCAACATGTT
84714 T
1 T
84715 TAATTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
TACCAACTTTGCAACATGTT
Found at i:85333 original size:19 final size:19
Alignment explanation
Indices: 85306--85363 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
85296 GCACTACATA
85306 TTATTATTTTTTTGTTATT
1 TTATTATTTTTTTGTTATT
*
85325 TTATGA-TTTTTTGTT-TT
1 TTATTATTTTTTTGTTATT
85342 TT-TTACTTTCTTTTGTTATT
1 TTATTA-TTT-TTTTGTTATT
85362 TT
1 TT
85364 TTTCTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 11 0.33
19 12 0.36
20 4 0.12
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (19 bp):
TTATTATTTTTTTGTTATT
Found at i:85355 original size:20 final size:20
Alignment explanation
Indices: 85333--85370 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
85323 TTTTATGATT
85333 TTTTGTT-TTTTTTACTTTC
1 TTTTGTTATTTTTTACTTTC
*
85352 TTTTGTTATTTTTTTCTTT
1 TTTTGTTATTTTTTACTTT
85371 TACTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTGTTATTTTTTACTTTC
Found at i:85382 original size:26 final size:28
Alignment explanation
Indices: 85338--85400 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
85328 TGATTTTTTG
85338 TTTT-TTTTACTTTCTTTTGTTAT-TT-
1 TTTTCTTTTACTTTCTTTTGTTATATTA
85363 TTTTCTTTTACTTTAC-TTTGTTATATTA
1 TTTTCTTTTACTTT-CTTTTGTTATATTA
85391 TTTTCTTTTA
1 TTTTCTTTTA
85401 TTCTATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.12
26 17 0.50
27 3 0.09
28 10 0.29
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.75
Consensus pattern (28 bp):
TTTTCTTTTACTTTCTTTTGTTATATTA
Found at i:85392 original size:31 final size:30
Alignment explanation
Indices: 85316--85394 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
85306 TTATTATTTT
* * *
85316 TTTGTTATTTTATGATTTTTTGTTTTTTTTAC
1 TTTGTTATATTAT--TTTTTTCTTTTCTTTAC
* * *
85348 TTTCTTTTGTTATTTTTTTCTTTTACTTTAC
1 TTTGTTATATTATTTTTTTCTTTT-CTTTAC
85379 TTTGTTATATTATTTT
1 TTTGTTATATTATTTT
85395 CTTTTATTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 10 0.26
31 18 0.47
32 10 0.26
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (30 bp):
TTTGTTATATTATTTTTTTCTTTTCTTTAC
Found at i:86679 original size:21 final size:21
Alignment explanation
Indices: 86654--86697 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
86644 GAAATGTTAA
* *
86654 AAAAATATTAATGTTTTAGGT
1 AAAAATAATAATATTTTAGGT
*
86675 AAAAATAATAATATTTTTGGT
1 AAAAATAATAATATTTTAGGT
86696 AA
1 AA
86698 TTTTTTTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGGT
Found at i:95338 original size:30 final size:30
Alignment explanation
Indices: 95304--95390 Score: 165
Period size: 30 Copynumber: 2.9 Consensus size: 30
95294 TTTATGTATG
*
95304 TTTTTGTGGTATTCGAACAAATTAACTATA
1 TTTTTGTCGTATTCGAACAAATTAACTATA
95334 TTTTTGTCGTATTCGAACAAATTAACTATA
1 TTTTTGTCGTATTCGAACAAATTAACTATA
95364 TTTTTGTCGTATTCGAACAAATTAACT
1 TTTTTGTCGTATTCGAACAAATTAACT
95391 CTAAAGTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTTTGTCGTATTCGAACAAATTAACTATA
Found at i:95536 original size:16 final size:16
Alignment explanation
Indices: 95515--95545 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
95505 ATTTATTATA
95515 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
95531 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
95546 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:95960 original size:22 final size:22
Alignment explanation
Indices: 95932--96273 Score: 515
Period size: 22 Copynumber: 15.5 Consensus size: 22
95922 ATTTTAAAAT
*
95932 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
*
95954 TTTATTTTAAAATACGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
95976 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
95997 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
96020 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
96042 TTTATTTTAAAATATGGATCGA
1 TTTATTTTAAAATATGGATTGA
*
96064 TTTATTTTAAAATATGGATCGA
1 TTTATTTTAAAATATGGATTGA
*
96086 TTTATTTTAAAATATGGACTGA
1 TTTATTTTAAAATATGGATTGA
* *
96108 TTTATTTTAAAATATAGATCGA
1 TTTATTTTAAAATATGGATTGA
*
96130 TTTATTTTAAAATATTGATTGA
1 TTTATTTTAAAATATGGATTGA
*
96152 TTTATTTTAAAATATTGATTGA
1 TTTATTTTAAAATATGGATTGA
**
96174 TTTATTTTAAAATATAAATTGA
1 TTTATTTTAAAATATGGATTGA
*
96196 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
*
96218 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
**
96240 TTTATTTTAAAATATAAATTGA
1 TTTATTTTAAAATATGGATTGA
96262 TTTATTTTAAAA
1 TTTATTTTAAAA
96274 AATTTATTAT
Statistics
Matches: 299, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
21 1 0.00
22 297 0.99
23 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:98851 original size:23 final size:22
Alignment explanation
Indices: 98817--98859 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
98807 AATATTTTTA
98817 TTTTTTTAAAATAATAAATTAGG
1 TTTTTTTAAAATAA-AAATTAGG
98840 TTTTTATT-AAATAAAAATTA
1 TTTTT-TTAAAATAAAAATTA
98860 AGAGACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 11 0.58
24 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTTTTAAAATAAAAATTAGG
Found at i:99965 original size:16 final size:16
Alignment explanation
Indices: 99940--99981 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
99930 AGATCTAACA
* *
99940 TTGGGTCCTTCCCATC
1 TTGGGCCCTTACCATC
99956 TTGGGCCCTTACCATC
1 TTGGGCCCTTACCATC
99972 TTGGGCCCTT
1 TTGGGCCCTT
99982 GGCCATTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.36, G:0.21, T:0.36
Consensus pattern (16 bp):
TTGGGCCCTTACCATC
Found at i:107027 original size:17 final size:19
Alignment explanation
Indices: 107005--107043 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
106995 GAAAAAAGAT
*
107005 AAACGA-AAACAACG-ACC
1 AAACGACAAAAAACGTACC
107022 AAACGACAAAAAACGTACC
1 AAACGACAAAAAACGTACC
107041 AAA
1 AAA
107044 AGGTAAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.62, C:0.26, G:0.10, T:0.03
Consensus pattern (19 bp):
AAACGACAAAAAACGTACC
Found at i:107585 original size:48 final size:48
Alignment explanation
Indices: 107503--107613 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 48
107493 CATAGTATAA
* * * * * *
107503 AAGAAAAAAGAGCAACATTGATGTTGGTGTTGCCTTCTACAACCAAAG
1 AAGAAAAAGGAACAACACTGAGGTTGATGCTGCCTTCTACAACCAAAG
*
107551 AAGAAAAGGGAACAACACTGAGGTTGATGCTGCCTTCTACAACCAAAG
1 AAGAAAAAGGAACAACACTGAGGTTGATGCTGCCTTCTACAACCAAAG
107599 AAGAAAAAGGAACAA
1 AAGAAAAAGGAACAA
107614 GTAGCTAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (48 bp):
AAGAAAAAGGAACAACACTGAGGTTGATGCTGCCTTCTACAACCAAAG
Found at i:108160 original size:127 final size:128
Alignment explanation
Indices: 107960--108217 Score: 421
Period size: 127 Copynumber: 2.0 Consensus size: 128
107950 ATATTCTTCC
* *
107960 ACATGAATCCATATATTGACATAAACAACAAAATAAATACAAAATGCTTGTTATAGATACAAGAA
1 ACATGAATCCATATATTGACATAAACAACAAAATAAATAAAAAATGCTTGTTACAGATACAAGAA
*
108025 CCCACAAAATGACTTGAATTTAAAAGTTACAAAATATTTAAACATATCG-TTTGACTCGACAT
66 CCCACAAAATGACTTGAATTTAAAAATTACAAAATATTTAAACATATCGTTTTGACTCGACAT
* * **
108087 ACATGAATCTATATATTGACATAAACAACAAAATAAATAAAAAATGTTTGTTTACAGATATGAGA
1 ACATGAATCCATATATTGACATAAACAACAAAATAAATAAAAAATGCTTG-TTACAGATACAAGA
*
108152 ACCC-CAAAATGACTTGAATTTAAAAATTATAAAATATTTAAACATATCGTTTTGACTCGACAT
65 ACCCACAAAATGACTTGAATTTAAAAATTACAAAATATTTAAACATATCGTTTTGACTCGACAT
108215 ACA
1 ACA
108218 CGAGTTCATT
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
127 90 0.74
128 31 0.26
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (128 bp):
ACATGAATCCATATATTGACATAAACAACAAAATAAATAAAAAATGCTTGTTACAGATACAAGAA
CCCACAAAATGACTTGAATTTAAAAATTACAAAATATTTAAACATATCGTTTTGACTCGACAT
Found at i:109024 original size:21 final size:17
Alignment explanation
Indices: 109000--109048 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
108990 GAATATGAAT
109000 TATCGATACCCCTATGGGAAG
1 TATCGATACCCC-AT--G-AG
109021 TATCGATACTCCCATGAG
1 TATCGATAC-CCCATGAG
109039 TATCGATACC
1 TATCGATACC
109049 AAAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 1 0.04
21 11 0.41
22 3 0.11
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (17 bp):
TATCGATACCCCATGAG
Found at i:114237 original size:18 final size:18
Alignment explanation
Indices: 114214--114252 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
114204 TGCATATTGA
114214 CTCAGCCAAAGAAATTCC
1 CTCAGCCAAAGAAATTCC
114232 CTCAGCCAAAGAAATTCC
1 CTCAGCCAAAGAAATTCC
114250 CTC
1 CTC
114253 TCATATTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.18
Consensus pattern (18 bp):
CTCAGCCAAAGAAATTCC
Found at i:118929 original size:18 final size:18
Alignment explanation
Indices: 118902--119026 Score: 169
Period size: 18 Copynumber: 6.9 Consensus size: 18
118892 CATTGAATCA
*
118902 GTATATGTATATGTATAT
1 GTATACGTATATGTATAT
*
118920 GTATACGTATACGTATAT
1 GTATACGTATATGTATAT
* *
118938 GTATACGTATACGTATAC
1 GTATACGTATATGTATAT
*
118956 GTATACGTATATGTATAC
1 GTATACGTATATGTATAT
*
118974 GTATACGTATACGTATAT
1 GTATACGTATATGTATAT
118992 GTATACGTATATGTATAT
1 GTATACGTATATGTATAT
* * *
119010 ATGTATGTATATGTATA
1 GTATACGTATATGTATA
119027 CCTTGACCAC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 97 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.42
Consensus pattern (18 bp):
GTATACGTATATGTATAT
Found at i:119026 original size:6 final size:6
Alignment explanation
Indices: 118902--119008 Score: 151
Period size: 6 Copynumber: 17.8 Consensus size: 6
118892 CATTGAATCA
* * * *
118902 GTATAT GTATAT GTATAT GTATAC GTATAC GTATAT GTATAC GTATAC
1 GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC
* *
118950 GTATAC GTATAC GTATAT GTATAC GTATAC GTATAC GTATAT GTATAC
1 GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC GTATAC
*
118998 GTATAT GTATA
1 GTATAC GTATA
119009 TATGTATGTA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (6 bp):
GTATAC
Done.