Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001186.1 Hibiscus syriacus cultivar Beakdansim tig00002353_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: 110824
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4628 original size:16 final size:16
Alignment explanation
Indices: 4607--4658 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
4597 ATTTTTTTGG
4607 AATTCGGTTAACGATT
1 AATTCGGTTAACGATT
4623 AATTCGGTT--CGA--
1 AATTCGGTTAACGATT
4635 AA-TCGGTTAACGATT
1 AATTCGGTTAACGATT
4650 AATTCGGTT
1 AATTCGGTT
4659 CGAAATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 6 0.19
12 2 0.06
13 3 0.10
14 3 0.10
15 2 0.06
16 15 0.48
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (16 bp):
AATTCGGTTAACGATT
Found at i:4641 original size:27 final size:27
Alignment explanation
Indices: 4610--4671 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
4600 TTTTTGGAAT
4610 TCGGTTAACGATTAATTCGGTTCGAAA
1 TCGGTTAACGATTAATTCGGTTCGAAA
4637 TCGGTTAACGATTAATTCGGTTCGAAA
1 TCGGTTAACGATTAATTCGGTTCGAAA
*
4664 TCGCTTAA
1 TCGGTTAA
4672 TTAACCGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (27 bp):
TCGGTTAACGATTAATTCGGTTCGAAA
Found at i:4816 original size:17 final size:17
Alignment explanation
Indices: 4794--4832 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4784 TGAATCAAAT
4794 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
4811 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
4828 -AATTA
1 TAATTA
4833 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:4832 original size:26 final size:25
Alignment explanation
Indices: 4803--4858 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
4793 TTAATTAGAT
4803 ATTATT-TATAATTAGATATTATTTAA
1 ATTATTGTA-AATTA-ATATTATTTAA
* *
4829 ATTAATTGTAAATTATTATTATTTTA
1 ATT-ATTGTAAATTAATATTATTTAA
4855 ATTA
1 ATTA
4859 AAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 1 0.04
26 15 0.58
27 8 0.31
28 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTATTGTAAATTAATATTATTTAA
Found at i:17437 original size:16 final size:15
Alignment explanation
Indices: 17418--17490 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 15
17408 ATTTTTCTGA
17418 TAATTATGTTTTAGTT
1 TAATTAT-TTTTAGTT
17434 TAATTATTTATT-GTT
1 TAATTATTT-TTAGTT
*
17449 ATAATTAATTTTTTG-T
1 -TAATT-ATTTTTAGTT
* *
17465 TGATTAATGTTTTAATT
1 TAATT-AT-TTTTAGTT
17482 TAATTATTT
1 TAATTATTT
17491 AATAATGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
15 14 0.30
16 23 0.49
17 10 0.21
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (15 bp):
TAATTATTTTTAGTT
Found at i:19439 original size:18 final size:18
Alignment explanation
Indices: 19399--19452 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
19389 TTAACCGGTT
* *
19399 CCGACTCGACTCGTTGA-
1 CCGACCCGACCCGTTGAC
*
19416 CCGACCCGATCCGTTGAC
1 CCGACCCGACCCGTTGAC
*
19434 CCGACCTGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
19452 C
1 C
19453 GTGGACCGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.17, C:0.43, G:0.22, T:0.19
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:19550 original size:29 final size:29
Alignment explanation
Indices: 19480--19618 Score: 142
Period size: 29 Copynumber: 4.8 Consensus size: 29
19470 GATCGGGTGA
* *
19480 TATTTTAGGAA-TAAATTCG-AAATGGGTGC
1 TATTTTGGGAATTTAATTCGAAAAT--GTGC
*
19509 TATTTTGGGAA-TTAATTCGAAATGTGTGC
1 TATTTTGGGAATTTAATTCGAAA-ATGTGC
* *
19538 TATTTGGGGAATTTAATTC-AAAAAGTGC
1 TATTTTGGGAATTTAATTCGAAAATGTGC
* *
19566 TATATTGGGAATTTAATTTGAAAATGTGC
1 TATTTTGGGAATTTAATTCGAAAATGTGC
* *
19595 TATTTTGAGAATTTAATTTGAAAA
1 TATTTTGGGAATTTAATTCGAAAA
19619 AGGTGATATT
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.21
29 64 0.68
30 9 0.10
31 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (29 bp):
TATTTTGGGAATTTAATTCGAAAATGTGC
Found at i:19574 original size:57 final size:57
Alignment explanation
Indices: 19505--19612 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
19495 TTCGAAATGG
* * *
19505 GTGCTATTTTGGGAA-TTAATTCGAAATGTGTGCTATTTGGGGAATTTAATTCAAAAA
1 GTGCTATATTGGGAATTTAATTCGAAA-ATGTGCTATTTGGAGAATTTAATTCAAAAA
* *
19562 GTGCTATATTGGGAATTTAATTTGAAAATGTGCTATTTTGAGAATTTAATT
1 GTGCTATATTGGGAATTTAATTCGAAAATGTGCTATTTGGAGAATTTAATT
19613 TGAAAAAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
57 35 0.78
58 10 0.22
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (57 bp):
GTGCTATATTGGGAATTTAATTCGAAAATGTGCTATTTGGAGAATTTAATTCAAAAA
Found at i:20408 original size:15 final size:15
Alignment explanation
Indices: 20388--20420 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20378 TGATACGTGA
20388 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
20403 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
20418 TTC
1 TTC
20421 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:29143 original size:186 final size:185
Alignment explanation
Indices: 28824--29214 Score: 669
Period size: 186 Copynumber: 2.1 Consensus size: 185
28814 AACCGAAATT
* * * *
28824 AAATTTTAAATATATTATATATAACATATGTGTTCAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCAAAACCATTTAAAATCCAATTAATAA
*
28889 TTTAAGATCCAATAATTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
*
28954 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTT-AATTAAA
29010 AAATATTAAATATATTATATATAACATATGGGCTCAGCCAAAACCATTTAAAA-CCTAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCAAAACCATTTAAAATCC-AATTAATA
*
29074 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATT
29139 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
* *
29195 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
29215 AATTAGAAAA
Statistics
Matches: 195, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
184 8 0.04
185 19 0.10
186 168 0.86
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCAAAACCATTTAAAATCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
Found at i:37487 original size:18 final size:19
Alignment explanation
Indices: 37457--37502 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
37447 CTCTTTAATT
*
37457 TATTTTAAT-TTTTTTATA
1 TATTTTTATATTTTTTATA
*
37475 T-TTTTTATA-TTTTTATC
1 TATTTTTATATTTTTTATA
37492 TATTTTTATAT
1 TATTTTTATAT
37503 CTCGTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTATATTTTTTATA
Found at i:37488 original size:10 final size:10
Alignment explanation
Indices: 37450--37498 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
37440 TGATTGTCTC
37450 TTTA-ATTTAT
1 TTTATATTT-T
37460 TTTA-ATTTT
1 TTTATATTTT
37469 TTTATA-TTT
1 TTTATATTTT
37478 TTTATATTTT
1 TTTATATTTT
* *
37488 TATCTATTTT
1 TTTATATTTT
37498 T
1 T
37499 ATATCTCGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 14 0.40
10 21 0.60
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATATTTT
Found at i:37499 original size:10 final size:10
Alignment explanation
Indices: 37464--37502 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
37454 ATTTATTTTA
*
37464 ATTTTTTTAT
1 ATTTTTATAT
37474 ATTTTT-TAT
1 ATTTTTATAT
*
37483 ATTTTTATCT
1 ATTTTTATAT
37493 ATTTTTATAT
1 ATTTTTATAT
37503 CTCGTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:37855 original size:53 final size:53
Alignment explanation
Indices: 37785--37890 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
37775 AATACCGTGT
37785 TAGTTGAGTTTATGAGTGTCCTTTTATCATTCGAACTTTATTTAAAAAAATTC
1 TAGTTGAGTTTATGAGTGTCCTTTTATCATTCGAACTTTATTTAAAAAAATTC
*
37838 TAGTTGAGTTTATGAGTGTCCTTTTATCATTCTAACTTTATTTAAAAAAATTC
1 TAGTTGAGTTTATGAGTGTCCTTTTATCATTCGAACTTTATTTAAAAAAATTC
37891 AAGTCTAATC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (53 bp):
TAGTTGAGTTTATGAGTGTCCTTTTATCATTCGAACTTTATTTAAAAAAATTC
Found at i:51014 original size:17 final size:17
Alignment explanation
Indices: 50989--51028 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
50979 TTCTGGGTAG
*
50989 AAATTTATCTTCTTCAC
1 AAATGTATCTTCTTCAC
51006 AAATGTATCTTCTTCAC
1 AAATGTATCTTCTTCAC
51023 AAATGT
1 AAATGT
51029 GAGAGGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (17 bp):
AAATGTATCTTCTTCAC
Found at i:58286 original size:370 final size:370
Alignment explanation
Indices: 57802--58541 Score: 1381
Period size: 370 Copynumber: 2.0 Consensus size: 370
57792 AAAGTCTACA
57802 TGATTCGTATGATCAACTCATCATCAACTTGACAAATAGTAATGTCACCACTCTAGTCTTCGATG
1 TGATTCGTATGATCAACTCATCATCAACTTGACAAATAGTAATGTCACCACTCTAGTCTTCGATG
* *
57867 ACATTGTAGCTGCTGTTCTCCAAGAAGAAAATCGGCGCAAGAACAAGGAAGACATACAAGTAAAT
66 ACATTGCAGCTGCTGTTCTCCAAGAAGAAAATCGGCGCAAGAACAAGGAAGACAGACAAGTAAAT
* *
57932 CTGCAACAAGCAGAAGCGTTGACAACGATGAGAGGGAGATCAACAAAACGTGGCCAAAGCAACAG
131 CTGCAACAAGCAGAAGCGTTGACAACGATGAAAGGGAGATCAACAAAACGTGACCAAAGCAACAG
57997 TCACAAACATGGTAGATCGAAGTCGAGGAGCAAGAAAAATTTAAAGTGCTACAACTTTGGAAAGA
196 TCACAAACATGGTAGATCGAAGTCGAGGAGCAAGAAAAATTTAAAGTGCTACAACTTTGGAAAGA
58062 ATGGTCACTTGAAGAAGGATTGTTGGGGTCTAAATAAAAACTCCAATCCACAAGGCAATACCGCA
261 ATGGTCACTTGAAGAAGGATTGTTGGGGTCTAAATAAAAACTCCAATCCACAAGGCAATACCGCA
*
58127 AACACTTCAGATGATGGAGATATTATATGTTGTGAAGCGTCAACC
326 AACACTTCAGATGATGGAGATATTATATGCTGTGAAGCGTCAACC
58172 TGATTCGTATGATCAACTCATCATCAACTTGACAAATAGTAATGTCACCACTCTAGTCTTCGATG
1 TGATTCGTATGATCAACTCATCATCAACTTGACAAATAGTAATGTCACCACTCTAGTCTTCGATG
*
58237 ACGTTGCAGCTGCTGTTCTCCAAGAAGAAAATCGGCGCAAGAACAAGGAAGACAGACAAGTAAAT
66 ACATTGCAGCTGCTGTTCTCCAAGAAGAAAATCGGCGCAAGAACAAGGAAGACAGACAAGTAAAT
*
58302 CTGCAACAAGCAGAAGCGTTGACAACGATGAAAGGGAGATCAACAGAACGTGACCAAAGCAACAG
131 CTGCAACAAGCAGAAGCGTTGACAACGATGAAAGGGAGATCAACAAAACGTGACCAAAGCAACAG
* *
58367 TCACAAACATGGTAGATCGAAGTCGAGGAGCAAGAAGAATTTAAAGTTCTACAACTTTGGAAAGA
196 TCACAAACATGGTAGATCGAAGTCGAGGAGCAAGAAAAATTTAAAGTGCTACAACTTTGGAAAGA
58432 ATGGTCACTTGAAGAAGGATTGTTGGGGTCTAAATAAAAACTCCAATCCACAAGGCAATACCGCA
261 ATGGTCACTTGAAGAAGGATTGTTGGGGTCTAAATAAAAACTCCAATCCACAAGGCAATACCGCA
* *
58497 GACACTTCAGATGATGGAGATGTTATATGCTGTGAAGCGTCAACC
326 AACACTTCAGATGATGGAGATATTATATGCTGTGAAGCGTCAACC
58542 ACCGTAGAAG
Statistics
Matches: 359, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
370 359 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (370 bp):
TGATTCGTATGATCAACTCATCATCAACTTGACAAATAGTAATGTCACCACTCTAGTCTTCGATG
ACATTGCAGCTGCTGTTCTCCAAGAAGAAAATCGGCGCAAGAACAAGGAAGACAGACAAGTAAAT
CTGCAACAAGCAGAAGCGTTGACAACGATGAAAGGGAGATCAACAAAACGTGACCAAAGCAACAG
TCACAAACATGGTAGATCGAAGTCGAGGAGCAAGAAAAATTTAAAGTGCTACAACTTTGGAAAGA
ATGGTCACTTGAAGAAGGATTGTTGGGGTCTAAATAAAAACTCCAATCCACAAGGCAATACCGCA
AACACTTCAGATGATGGAGATATTATATGCTGTGAAGCGTCAACC
Found at i:61726 original size:16 final size:16
Alignment explanation
Indices: 61705--61743 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
61695 AATTTAATAT
61705 GCATGCACCGAAAGTA
1 GCATGCACCGAAAGTA
61721 GCATGCACCGAAAGTA
1 GCATGCACCGAAAGTA
61737 GCATGCA
1 GCATGCA
61744 AATGTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.26, T:0.13
Consensus pattern (16 bp):
GCATGCACCGAAAGTA
Found at i:64695 original size:30 final size:32
Alignment explanation
Indices: 64659--64724 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
64649 TAAAGTCTTA
64659 ATCACTTATGTTA-T-ATATTA-TAACATTTTG
1 ATCACTTATGTTATTAAT-TTACTAACATTTTG
64689 ATCACTTATGTTATTAATTTACTAACATTTTG
1 ATCACTTATGTTATTAATTTACTAACATTTTG
64721 ATCA
1 ATCA
64725 TTGAGACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 13 0.39
31 4 0.12
32 16 0.48
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (32 bp):
ATCACTTATGTTATTAATTTACTAACATTTTG
Found at i:64720 original size:32 final size:30
Alignment explanation
Indices: 64659--64724 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 30
64649 TAAAGTCTTA
64659 ATCACTTATGTTATATATTATAACATTTTG
1 ATCACTTATGTTATATATTATAACATTTTG
64689 ATCACTTATGTTAT-TAATTTACTAACATTTTG
1 ATCACTTATGTTATAT-A-TTA-TAACATTTTG
64721 ATCA
1 ATCA
64725 TTGAGACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 1 0.03
30 15 0.45
31 3 0.09
32 14 0.42
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (30 bp):
ATCACTTATGTTATATATTATAACATTTTG
Found at i:64829 original size:21 final size:21
Alignment explanation
Indices: 64800--64840 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64790 ACCCATAAAT
*
64800 TTTATATAAAATATTAATTTC
1 TTTAGATAAAATATTAATTTC
*
64821 TTTAGATAAAATTTTAATTT
1 TTTAGATAAAATATTAATTT
64841 AATCCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTAGATAAAATATTAATTTC
Found at i:64999 original size:2 final size:2
Alignment explanation
Indices: 64992--65023 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
64982 CTCAAAACGA
64992 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
65024 CATTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66234 original size:24 final size:24
Alignment explanation
Indices: 66207--66258 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
66197 TATATCAAAA
66207 ATCAAAACATAAA-TCAGGTCAAGT
1 ATCAAAACA-AAATTCAGGTCAAGT
* *
66231 ATCATATCAAAATTCAGGTCAAGT
1 ATCAAAACAAAATTCAGGTCAAGT
66255 ATCA
1 ATCA
66259 GATCAGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATTCAGGTCAAGT
Found at i:66263 original size:24 final size:24
Alignment explanation
Indices: 66220--66318 Score: 119
Period size: 24 Copynumber: 4.1 Consensus size: 24
66210 AAAACATAAA
* *
66220 TCAGGTCAAGTATCATATCAAAAT
1 TCAGGTCAAGTATCAGATCAGAAT
66244 TCAGGTCAAGTATCAGATCAGAAT
1 TCAGGTCAAGTATCAGATCAGAAT
* * *
66268 CCATGTC-AGATATCATATCAGAAT
1 TCAGGTCAAG-TATCAGATCAGAAT
* *
66292 CCATGTCAAGTATCAGATCAGAAT
1 TCAGGTCAAGTATCAGATCAGAAT
66316 TCA
1 TCA
66319 AATCGAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
TCAGGTCAAGTATCAGATCAGAAT
Found at i:66276 original size:12 final size:12
Alignment explanation
Indices: 66261--66299 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
66251 AAGTATCAGA
66261 TCAGAATCCATG
1 TCAGAATCCATG
*
66273 TCAGATAT-CATA
1 TCAGA-ATCCATG
66285 TCAGAATCCATG
1 TCAGAATCCATG
66297 TCA
1 TCA
66300 AGTATCAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (12 bp):
TCAGAATCCATG
Found at i:66331 original size:48 final size:48
Alignment explanation
Indices: 66231--66338 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
66221 CAGGTCAAGT
* ** *
66231 ATCATATCAAAATTCAGGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAGAA
* * *
66279 ATCATATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAA
1 ATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAG-AA
66327 ATCATAT-AAAAT
1 ATCATATCAAAAT
66339 ATTCATGTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
47 5 0.10
48 46 0.90
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.27
Consensus pattern (48 bp):
ATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:74325 original size:14 final size:14
Alignment explanation
Indices: 74306--74332 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
74296 AAGTTATGTA
74306 ATTATATTTTAGTG
1 ATTATATTTTAGTG
74320 ATTATATTTTAGT
1 ATTATATTTTAGT
74333 CATGTAATTA
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
ATTATATTTTAGTG
Found at i:85480 original size:7 final size:7
Alignment explanation
Indices: 85468--85496 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
85458 AAGAGATCCC
85468 GGGGAGG
1 GGGGAGG
85475 GGGGAGG
1 GGGGAGG
85482 GGGGAGG
1 GGGGAGG
85489 GGGGAGG
1 GGGGAGG
85496 G
1 G
85497 AGTGTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (7 bp):
GGGGAGG
Found at i:85914 original size:2 final size:2
Alignment explanation
Indices: 85907--85958 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
85897 TGCTTACTTG
85907 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
85949 AT AT AT AT AT
1 AT AT AT AT AT
85959 GTAGTGCACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86853 original size:20 final size:17
Alignment explanation
Indices: 86801--86853 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
86791 TTTCTTGATG
*
86801 TAAAATAATCAATATTA
1 TAAAATATTCAATATTA
* *
86818 TAAAATATTTATTATTA
1 TAAAATATTCAATATTA
86835 TAAATAAATATTCAATATT
1 T--A-AAATATTCAATATT
86854 CTTTAAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 15 0.54
19 1 0.04
20 12 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATTCAATATTA
Found at i:87486 original size:25 final size:26
Alignment explanation
Indices: 87436--87487 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
87426 AATTGAATTC
*
87436 AGTTAATTTATAATGAATTTTATAAT
1 AGTTAATCTATAATGAATTTTATAAT
*
87462 AGTTAATCTA-AATTAATTATT-TAAT
1 AGTTAATCTATAATGAATT-TTATAAT
87487 A
1 A
87488 AGTCTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
AGTTAATCTATAATGAATTTTATAAT
Found at i:91704 original size:60 final size:60
Alignment explanation
Indices: 91591--91769 Score: 166
Period size: 60 Copynumber: 3.0 Consensus size: 60
91581 TTGTATGTTC
* ** * * * * *
91591 TCAAGCTATGATCTCT-ATTTTAAATTGGTCTCTAGACTTTTAAATATTTTAATTTTATCA
1 TCAAACTATGATCT-TAATTTTAAATTAATCTTTAAACTTTTAAACATTCTAATTTCATCA
* * * *
91651 TCAAACTATTATAC-TCATTTTAAATTAATCTTTAAACTTTTGAACATTCTAATTTCATCC
1 TCAAACTATGAT-CTTAATTTTAAATTAATCTTTAAACTTTTAAACATTCTAATTTCATCA
* * * *
91711 TCCAACTATGATCTTAATTCTAAATTAATCCTTAAACTTCTAAATC-TTCTAATTTCATC
1 TCAAACTATGATCTTAATTTTAAATTAATCTTTAAACTTTTAAA-CATTCTAATTTCATC
91770 TTTAAATTCA
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
59 2 0.02
60 93 0.96
61 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (60 bp):
TCAAACTATGATCTTAATTTTAAATTAATCTTTAAACTTTTAAACATTCTAATTTCATCA
Found at i:95134 original size:141 final size:141
Alignment explanation
Indices: 94879--95147 Score: 414
Period size: 141 Copynumber: 1.9 Consensus size: 141
94869 AGCCCACCTT
* *
94879 CGAGGTCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTGCACTTGACGCCATACGATTTAG
1 CGAGGTCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACACTTGAAGCCATACGATTTAG
** * *
94944 AGATTCCAAATCCGAGTCGCAACGATTTGAACGTTGAAATTTGCGATATACAAAACAAAGATGAC
66 AGATTCCAAATCCGAGTCGCAACGATTCAAACGATGAAATTTGCAATATACAAAACAAAGATGAC
95009 GACTCCATCTG
131 GACTCCATCTG
* **
95020 CGAGGTCAATAACAGAGATGCTGCAGGTTTGGATCTAAGCCTATGCTTGAAGCCATACGATTTAG
1 CGAGGTCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACACTTGAAGCCATACGATTTAG
* * *
95085 AGATTCCAAATCTGAGTCGCAATGATTCAAATGATGACAA-TTGCAATATACAAAACAAAGATG
66 AGATTCCAAATCCGAGTCGCAACGATTCAAACGATGA-AATTTGCAATATACAAAACAAAGATG
95148 CCGGCCTGCA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
141 113 0.98
142 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (141 bp):
CGAGGTCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACACTTGAAGCCATACGATTTAG
AGATTCCAAATCCGAGTCGCAACGATTCAAACGATGAAATTTGCAATATACAAAACAAAGATGAC
GACTCCATCTG
Found at i:96613 original size:22 final size:23
Alignment explanation
Indices: 96576--96622 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
96566 AACCCTAAAT
96576 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
96599 AAGCCC-ATAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
96621 AA
1 AA
96623 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:98877 original size:53 final size:53
Alignment explanation
Indices: 98796--99062 Score: 263
Period size: 53 Copynumber: 5.0 Consensus size: 53
98786 TAAGAAAAAA
** *
98796 TAGCAACATCAC---GAGAACGTTGCATAGGTTTAAAACTAGGATTTAAGCAT
1 TAGCAACATCACGAGGAGAACGTTGCATAGGTTTAACGCTGGGATTTAAGCAT
* * * *
98846 TAGCAACATCATGAGGAGAATGTTGCGTAGGTTTAATGCTGGGATTTAAGCAT
1 TAGCAACATCACGAGGAGAACGTTGCATAGGTTTAACGCTGGGATTTAAGCAT
* **** * * * ***
98899 TTGCAACATCACGAGGAGAACGTTGCATTAGCAACATCAC-GAGAAGAACATTGCAT
1 TAGCAACATCACGAGGAGAACGTTGCA-TAGGTTTAACGCTGGGATTTA-A--GCAT
* *
98955 TAGCAACATCACGAGGAGAACATTGCATAGGATTAACGCTGGGATTTAAGCAT
1 TAGCAACATCACGAGGAGAACGTTGCATAGGTTTAACGCTGGGATTTAAGCAT
* * *
99008 TTGCAACATCACGAGGAGAACGTTGCGTAGGTTTAATGCTGGGATTTAAGCAT
1 TAGCAACATCACGAGGAGAACGTTGCATAGGTTTAACGCTGGGATTTAAGCAT
99061 TA
1 TA
99063 ACACCGCCAC
Statistics
Matches: 171, Mismatches: 38, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
50 11 0.06
53 113 0.66
54 6 0.04
55 8 0.05
56 33 0.19
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (53 bp):
TAGCAACATCACGAGGAGAACGTTGCATAGGTTTAACGCTGGGATTTAAGCAT
Found at i:98935 original size:28 final size:28
Alignment explanation
Indices: 98895--98982 Score: 149
Period size: 28 Copynumber: 3.1 Consensus size: 28
98885 TGGGATTTAA
* *
98895 GCATTTGCAACATCACGAGGAGAACGTT
1 GCATTAGCAACATCACGAGGAGAACATT
*
98923 GCATTAGCAACATCACGAGAAGAACATT
1 GCATTAGCAACATCACGAGGAGAACATT
98951 GCATTAGCAACATCACGAGGAGAACATT
1 GCATTAGCAACATCACGAGGAGAACATT
98979 GCAT
1 GCAT
98983 AGGATTAACG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (28 bp):
GCATTAGCAACATCACGAGGAGAACATT
Found at i:99086 original size:53 final size:53
Alignment explanation
Indices: 98808--99111 Score: 202
Period size: 53 Copynumber: 5.7 Consensus size: 53
98798 GCAACATCAC
* ** * * * *
98808 GAGAACGTTGCATAGGTTTAAAACTAGGATTTAAGCATTAGCAACATCATGAG
1 GAGAACGTTGCATAGGATTAATGCTGGGATTTAAGCATTAACAACACCACGAG
* * * ** *
98861 GAGAATGTTGCGTAGGTTTAATGCTGGGATTTAAGCATTTGCAACATCACGAG
1 GAGAACGTTGCATAGGATTAATGCTGGGATTTAAGCATTAACAACACCACGAG
* * * *** * *
98914 GAGAACGTTGCATTAGCA--ACAT-CACGAGAAGAACATTGCATTAGCAACATCACGAG
1 GAGAACGTTGCA-TAGGATTA-ATGC-TGGGATTTA-A--GCATTAACAACACCACGAG
* * ** *
98970 GAGAACATTGCATAGGATTAACGCTGGGATTTAAGCATTTGCAACATCACGAG
1 GAGAACGTTGCATAGGATTAATGCTGGGATTTAAGCATTAACAACACCACGAG
* * * * *
99023 GAGAACGTTGCGTAGGTTTAATGCTGGGATTTAAGCATTAACACCGCCACGTG
1 GAGAACGTTGCATAGGATTAATGCTGGGATTTAAGCATTAACAACACCACGAG
* * *
99076 GAGCAA-GTTGCACAAGGCTTAATGCTGGGGTTTAAG
1 GAG-AACGTTGCA-TAGGATTAATGCTGGGATTTAAG
99112 TTAAGAACAA
Statistics
Matches: 200, Mismatches: 40, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
52 2 0.01
53 131 0.65
54 26 0.13
55 5 0.03
56 34 0.17
57 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (53 bp):
GAGAACGTTGCATAGGATTAATGCTGGGATTTAAGCATTAACAACACCACGAG
Done.