Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007012.1 Hibiscus syriacus cultivar Beakdansim tig00018103_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: 70335
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:359 original size:29 final size:31
Alignment explanation
Indices: 308--382 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
298 AAAAATTAAA
*
308 AGTTTAGGTACTAAAATTGAGT-AATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
338 AGTTTAGGTACTAAAA-GGAGTAAATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
368 AGTTT-GGTACATAAA
1 AGTTTAGGTAC-TAAA
383 GGCACGGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 9 0.21
30 33 0.79
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (31 bp):
AGTTTAGGTACTAAAATGGAGTAAATTTGAT
Found at i:636 original size:39 final size:40
Alignment explanation
Indices: 593--731 Score: 228
Period size: 39 Copynumber: 3.5 Consensus size: 40
583 TATCTAATTG
*
593 ACATTCAAACATAA-CACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACAATAATAACACTGGGAATCATT
632 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAAT--CACAATAATAACACTGGGAATCATT
*
674 ACATTGAAACATAATCAC-ACAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACAATAATAACACTGGGAATCATT
713 ACATTGAAACATAATCACA
1 ACATTGAAACATAATCACA
732 CAAATCCATT
Statistics
Matches: 94, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
39 51 0.54
40 3 0.03
42 40 0.43
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (40 bp):
ACATTGAAACATAATCACAATAATAACACTGGGAATCATT
Found at i:665 original size:42 final size:42
Alignment explanation
Indices: 606--734 Score: 237
Period size: 42 Copynumber: 3.1 Consensus size: 42
596 TTCAAACATA
606 ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
1 ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
648 ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
1 ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
690 ACAC---AATAACACTGGGAATCATTACATTGAAACATAATC
1 ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
729 ACACAA
1 ACACAA
735 ATCCATTAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
39 39 0.46
42 46 0.54
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.22
Consensus pattern (42 bp):
ACACAATAATAACACTGGGAATCATTACATTGAAACATAATC
Found at i:3188 original size:24 final size:23
Alignment explanation
Indices: 3159--3212 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
3149 TCAATTATAA
*
3159 TTACAAATATCTTAAAGTGTAAAT
1 TTACAAATATCTTAAAGAGT-AAT
3183 TTACAAATATCTTAAAGAGTAAT
1 TTACAAATATCTTAAAGAGTAAT
*
3206 TAACAAA
1 TTACAAA
3213 GGAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
TTACAAATATCTTAAAGAGTAAT
Found at i:7884 original size:30 final size:30
Alignment explanation
Indices: 7850--7935 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
7840 GCTAAAATAT
*
7850 AACTTTTAAAAATTATATTTTTAGTCCTTA
1 AACTTTTAAAAATTATATTTTTAGTCATTA
* * * *
7880 AACTTTTTAAAGTT-TATACTTTAGTCATTT
1 AACTTTTAAAAATTATAT-TTTTAGTCATTA
* *
7910 AACTTTCAAAAATTAGA-TTTTAGTCA
1 AACTTTTAAAAATTATATTTTTAGTCA
7936 CTAGCCAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 11 0.25
30 32 0.73
31 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (30 bp):
AACTTTTAAAAATTATATTTTTAGTCATTA
Found at i:7935 original size:29 final size:29
Alignment explanation
Indices: 7849--7935 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
7839 AGCTAAAATA
*
7849 TAACTTTTAAAAATTATATTTTTAGTCCTT
1 TAACTTTTAAAAATTATA-TTTTAGTCATT
* ** *
7879 AAACTTTTTAAAGTTTATACTTTAGTCATT
1 TAAC-TTTTAAAAATTATATTTTAGTCATT
* *
7909 TAACTTTCAAAAATTAGATTTTAGTCA
1 TAACTTTTAAAAATTATATTTTAGTCA
7936 CTAGCCAAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 18 0.40
30 15 0.33
31 12 0.27
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (29 bp):
TAACTTTTAAAAATTATATTTTAGTCATT
Found at i:9410 original size:60 final size:59
Alignment explanation
Indices: 9346--9472 Score: 159
Period size: 59 Copynumber: 2.1 Consensus size: 59
9336 ATTGGCCTCT
** * *
9346 AAACTTTTAAACAGAT-CATTTTCATCCTTAAACTATGACTATT-ATTCTAAATTAGTTCCC
1 AAACTTTTAAA-A-ATCCATTCACATCCCTAAACTATG-CTATTCATTCTAAATTAGTCCCC
* *
9406 AAACTTTTAAAATTCCATTCACATCCCTAAACTATGCTCTTCATTCTAAATTAGTCCCC
1 AAACTTTTAAAAATCCATTCACATCCCTAAACTATGCTATTCATTCTAAATTAGTCCCC
9465 AAACTTTT
1 AAACTTTT
9473 TGAACATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.08
59 43 0.73
60 11 0.19
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
AAACTTTTAAAAATCCATTCACATCCCTAAACTATGCTATTCATTCTAAATTAGTCCCC
Found at i:13617 original size:24 final size:24
Alignment explanation
Indices: 13575--13624 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
13565 AATGCAATGC
* * *
13575 GAAGAACATGTTACTGGACGGATT
1 GAAGAACAAGTTACAGGACAGATT
*
13599 GAAGAACAAGTTGCAGGACAGATT
1 GAAGAACAAGTTACAGGACAGATT
13623 GA
1 GA
13625 TTTCGATCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (24 bp):
GAAGAACAAGTTACAGGACAGATT
Found at i:15530 original size:37 final size:37
Alignment explanation
Indices: 15479--15554 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
15469 ATAAAAATTC
15479 AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
1 AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
* *
15516 AAGGTTTTGTCATGAAACTCAGAATACTCGAGTGCTG
1 AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
15553 AA
1 AA
15555 AAGTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (37 bp):
AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
Found at i:19596 original size:20 final size:20
Alignment explanation
Indices: 19573--19617 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19563 AATTAGCGTT
* *
19573 GCGAAAATGAAATTTGCAAC
1 GCGAAAATCAAATTCGCAAC
*
19593 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
19613 GCGAA
1 GCGAA
19618 TAGTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:19597 original size:49 final size:49
Alignment explanation
Indices: 19498--19597 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
19488 GCGAATAGTT
* * ****
19498 AATTACCTATATAGGTAATTAGCGTTGTGAAAATGAAATTCGGTTTGCG
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCG
*
19547 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATGAAATTTGCAACGCG
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCG
19596 AA
1 AA
19598 AGTCAAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (49 bp):
AATTACCTAAATAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCG
Found at i:19673 original size:76 final size:76
Alignment explanation
Indices: 19547--19700 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 76
19537 TCGGTTTGCG
* *
19547 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATGAAATTTGCAACGCGAAAGTCAAATTCGCAA
1 AATTACCTAAACAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCGAAAGTCAAATTCGCAA
19612 CGCGAATAGTT
66 CGCGAATAGTT
* *
19623 AATTACCTATACAGGTGATTAGCGTTGCGAAAATGAAATTCGCAACGCGAAAGTCAAATTCGCAA
1 AATTACCTAAACAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCGAAAGTCAAATTCGCAA
19688 CGCGAATAGTT
66 CGCGAATAGTT
19699 AA
1 AA
19701 ATCGCAACGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (76 bp):
AATTACCTAAACAGGTAATTAGCGTTGCGAAAATGAAATTCGCAACGCGAAAGTCAAATTCGCAA
CGCGAATAGTT
Found at i:19674 original size:20 final size:19
Alignment explanation
Indices: 19649--19773 Score: 70
Period size: 20 Copynumber: 6.3 Consensus size: 19
19639 GATTAGCGTT
19649 GCGAAAATGAAATTCGCAAC
1 GCGAAAATGAAA-TCGCAAC
* *
19669 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATGAAA-TCGCAAC
* *
19689 GCGAATAGTTAAATCGCAAC
1 GCGAA-AATGAAATCGCAAC
** * * *
19709 GATAATATGTAATTCTCAAC
1 GCGAAAATG-AAATCGCAAC
* *
19729 GCGAATAGGTAAATCGCAAC
1 GCGAAAATG-AAATCGCAAC
** *
19749 GATAATATGTAAATCGCAAC
1 GCGAAAATG-AAATCGCAAC
19769 GCGAA
1 GCGAA
19774 TTCTCCAAAT
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
19 1 0.01
20 76 0.92
21 6 0.07
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (19 bp):
GCGAAAATGAAATCGCAAC
Found at i:19706 original size:40 final size:41
Alignment explanation
Indices: 19678--19774 Score: 162
Period size: 40 Copynumber: 2.4 Consensus size: 41
19668 CGCGAAAGTC
*
19678 AAATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
19719 -AATTCTCAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
19759 AAA-TCGCAACGCGAAT
1 AAATTCGCAACGCGAAT
19775 TCTCCAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23
Consensus pattern (41 bp):
AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:20115 original size:20 final size:20
Alignment explanation
Indices: 20077--20125 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20067 TGGAGAATTC
20077 GCGTTGCGATTTATATATTA
1 GCGTTGCGATTTATATATTA
* *
20097 TCGTTGCGATTTA-ACTATTC
1 GCGTTGCGATTTATA-TATTA
20117 GCGTTGCGA
1 GCGTTGCGA
20126 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
GCGTTGCGATTTATATATTA
Found at i:20139 original size:21 final size:21
Alignment explanation
Indices: 20115--20191 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 21
20105 ATTTAACTAT
20115 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
* **
20136 TCGCGTTGCGATTTTGGAACC
1 TCGCGTTGCGAATTTGGAAAA
* * **
20157 T-GTGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
20176 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
20192 TTGGTCATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.04
20 24 0.53
21 19 0.42
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:21755 original size:43 final size:42
Alignment explanation
Indices: 21682--21769 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
21672 ACCCTAAACT
21682 CGACCCGACCCGACCCGAACAGTACATTAAAAAAAATCCGACC
1 CGACCCGACCCGACCCGAACAGTACATT-AAAAAAATCCGACC
* ***
21725 CGACCCGACCCGAGCCCGAA-ATTTTTTTAAAAAAATCCGACC
1 CGACCCGACCCGA-CCCGAACAGTACATTAAAAAAATCCGACC
21767 CGA
1 CGA
21770 TCGGGTCGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 17 0.43
43 17 0.43
44 6 0.15
ACGTcount: A:0.36, C:0.35, G:0.15, T:0.14
Consensus pattern (42 bp):
CGACCCGACCCGACCCGAACAGTACATTAAAAAAATCCGACC
Found at i:23404 original size:18 final size:18
Alignment explanation
Indices: 23381--23419 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23371 CTCTTGAAAA
23381 TTTAAAATTATCATATAT
1 TTTAAAATTATCATATAT
* * *
23399 TTTAAATTTTTTATATAT
1 TTTAAAATTATCATATAT
23417 TTT
1 TTT
23420 TCTATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATCATATAT
Found at i:24022 original size:17 final size:18
Alignment explanation
Indices: 24000--24036 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
23990 TAATAATGTA
24000 ATCTCCTTT-AAAAAATT
1 ATCTCCTTTAAAAAAATT
24017 ATCTCCTTTAAAAAAATT
1 ATCTCCTTTAAAAAAATT
24035 AT
1 AT
24037 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (18 bp):
ATCTCCTTTAAAAAAATT
Found at i:27029 original size:30 final size:30
Alignment explanation
Indices: 26964--27034 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
26954 TTGATTGAAT
*
26964 CGAATTAATTCAGTTAATTCGATCGATTAC
1 CGAATTAATTCAGTTAATTCGATCGATCAC
* * * *
26994 TGAATTAATTCAGTTAATTTGGTCGGTCAC
1 CGAATTAATTCAGTTAATTCGATCGATCAC
27024 CGAATTAATTC
1 CGAATTAATTC
27035 GGTCGAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (30 bp):
CGAATTAATTCAGTTAATTCGATCGATCAC
Found at i:27113 original size:9 final size:9
Alignment explanation
Indices: 27099--27133 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
27089 GAAAGCGGTT
27099 AATTAACCG
1 AATTAACCG
*
27108 AATTAATCG
1 AATTAACCG
27117 AATTAACCG
1 AATTAACCG
27126 AATTAACC
1 AATTAACC
27134 TTTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:27270 original size:17 final size:17
Alignment explanation
Indices: 27248--27286 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
27238 TGAATCAGAT
27248 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
27265 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
27282 -AATTA
1 TAATTA
27287 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:28414 original size:29 final size:29
Alignment explanation
Indices: 28372--28429 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28362 GTACTATAAC
28372 ATGCGAAACAATTTATTTTAATTCAAATA
1 ATGCGAAACAATTTATTTTAATTCAAATA
28401 ATGCGAAACAATTTATTTTAATTCAAATA
1 ATGCGAAACAATTTATTTTAATTCAAATA
28430 TATTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (29 bp):
ATGCGAAACAATTTATTTTAATTCAAATA
Found at i:28501 original size:12 final size:11
Alignment explanation
Indices: 28483--28532 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
28473 ATGAACATAT
28483 TATTTTTTTTG
1 TATTTTTTTTG
* *
28494 TAATTTTTCTG
1 TATTTTTTTTG
28505 -A--TTTTTTG
1 TATTTTTTTTG
28513 TATTTTTTTTTG
1 TA-TTTTTTTTG
28525 TATTTTTT
1 TATTTTTT
28533 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 1 0.03
11 15 0.47
12 9 0.28
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (11 bp):
TATTTTTTTTG
Found at i:28541 original size:19 final size:19
Alignment explanation
Indices: 28487--28541 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
28477 ACATATTATT
* *
28487 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTATTTTTTTTGA
28506 TTTTTTGTATTTTTTTTTGTA
1 TTTTTTGTA-TTTTTTTTG-A
28527 TTTTTTG-ATTTTTTT
1 TTTTTTGTATTTTTTT
28542 AAATTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.50
20 8 0.25
21 8 0.25
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (19 bp):
TTTTTTGTATTTTTTTTGA
Found at i:28634 original size:20 final size:21
Alignment explanation
Indices: 28609--28654 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
28599 AACATACTAA
28609 TTTTTTTGTAATTATTCTG-T
1 TTTTTTTGTAATTATTCTGAT
* *
28629 TTTTTTTGTATTTTTTCTGAT
1 TTTTTTTGTAATTATTCTGAT
28650 TTTTT
1 TTTTT
28655 AAAATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.76
Consensus pattern (21 bp):
TTTTTTTGTAATTATTCTGAT
Found at i:30749 original size:29 final size:29
Alignment explanation
Indices: 30707--30805 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
30697 CCCGAAGGAC
30707 CTATCCAGAGGTCACACAGACCCCGGTAA
1 CTATCCAGAGGTCACACAGACCCCGGTAA
* * * *
30736 CTATCCAGAGGTCATAAAGAACCTCGG-CA
1 CTATCCAGAGGTCACACAG-ACCCCGGTAA
30765 -TATCCAGAGGTCACACAGACCCCGGTAA
1 CTATCCAGAGGTCACACAGACCCCGGTAA
* *
30793 CTGTCCATAGGTC
1 CTATCCAGAGGTC
30806 CCAAAGAACC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 6 0.11
28 17 0.30
29 28 0.49
30 6 0.11
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.17
Consensus pattern (29 bp):
CTATCCAGAGGTCACACAGACCCCGGTAA
Found at i:30772 original size:57 final size:57
Alignment explanation
Indices: 30708--30816 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
30698 CCGAAGGACC
*
30708 TATCCAGAGGTCACACAGACCCCGGTAACTATCCAGAGGTCATAAAGAACCTCGGCA
1 TATCCAGAGGTCACACAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTCGGCA
* * *
30765 TATCCAGAGGTCACACAGACCCCGGTAACTGTCCATAGGTCCCAAAGAACCT
1 TATCCAGAGGTCACACAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCT
30817 AGGTAAATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (57 bp):
TATCCAGAGGTCACACAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTCGGCA
Found at i:30829 original size:31 final size:31
Alignment explanation
Indices: 30791--30885 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
30781 AGACCCCGGT
* *
30791 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * **
30822 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
30853 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
30884 AA
1 AA
30886 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 47 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:31644 original size:64 final size:65
Alignment explanation
Indices: 31531--31696 Score: 196
Period size: 64 Copynumber: 2.6 Consensus size: 65
31521 TCTTTCAATG
* * *
31531 AAGGTATGCATCGATGCACT-ACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTA
1 AAGGCATGCATCGATGCACTCA-TTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
31594 A
65 A
** * * *
31595 TGGGGATGCATCGATACACTCATTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTA
1 AAGGCATGCATCGATGCACTCATTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTA
31659 A
65 A
*
31660 AAGTCATGCATCGATGCACTGCA-TGTGCATCGATGCA
1 AAGGCATGCATCGATGCACT-CATTGTGCATCGATGCA
31697 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 5 0.06
64 42 0.49
65 36 0.42
66 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGCATGCATCGATGCACTCATTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA
Found at i:33636 original size:23 final size:22
Alignment explanation
Indices: 33610--33720 Score: 67
Period size: 23 Copynumber: 5.2 Consensus size: 22
33600 ACACAATAAT
33610 AACACTAGGAATCATTACATTGA
1 AACACT-GGAATCATTACATTGA
* * *
33633 AACA-T--AATCA-CACAATAA
1 AACACTGGAATCATTACATTGA
33651 TAACACTGAGAATCATTACATTGA
1 -AACACTG-GAATCATTACATTGA
* * *
33675 AACA-T--AATCA-CACAATAA
1 AACACTGGAATCATTACATTGA
33693 TAACACTGGGAATCATTACATTGA
1 -AACACT-GGAATCATTACATTGA
33717 AACA
1 AACA
33721 TAATCACACA
Statistics
Matches: 64, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
18 10 0.16
19 18 0.28
20 2 0.03
22 2 0.03
23 22 0.34
24 10 0.16
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (22 bp):
AACACTGGAATCATTACATTGA
Found at i:33643 original size:42 final size:41
Alignment explanation
Indices: 33584--33731 Score: 260
Period size: 42 Copynumber: 3.5 Consensus size: 41
33574 TCTTAAATTG
*
33584 ACATTCAAACATAATCACACAATAATAACACTAGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACT-GGAATCATT
33626 ACATTGAAACATAATCACACAATAATAACACTGAGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTG-GAATCATT
33668 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACT-GGAATCATT
33710 ACATTGAAACATAATCACACAA
1 ACATTGAAACATAATCACACAA
33732 ATCCATTAAT
Statistics
Matches: 103, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
41 1 0.01
42 101 0.98
43 1 0.01
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (41 bp):
ACATTGAAACATAATCACACAATAATAACACTGGAATCATT
Found at i:33655 original size:19 final size:19
Alignment explanation
Indices: 33591--33697 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 19
33581 TTGACATTCA
33591 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
33610 AACACTAGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
33633 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
33652 AACACTGAGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
33675 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
33694 AACA
1 AACA
33698 CTGGGAATCA
Statistics
Matches: 64, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
18 10 0.16
19 22 0.34
20 2 0.03
22 2 0.03
23 18 0.28
24 10 0.16
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (19 bp):
AACATAATCACACAATAAT
Found at i:36509 original size:24 final size:23
Alignment explanation
Indices: 36480--36533 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
36470 TCAATTATAA
*
36480 TTACAAATATCTTAAAGTGTAAAT
1 TTACAAATATCTTAAAGAGT-AAT
36504 TTACAAATATCTTAAAGAGTAAT
1 TTACAAATATCTTAAAGAGTAAT
*
36527 TAACAAA
1 TTACAAA
36534 GAAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
TTACAAATATCTTAAAGAGTAAT
Found at i:39418 original size:19 final size:18
Alignment explanation
Indices: 39382--39418 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
39372 AAGCTCAACC
*
39382 TTTTGCAACGATTGTCAA
1 TTTTGCAACGAGTGTCAA
39400 TTTTGCAACGACGTGTCAA
1 TTTTGCAACGA-GTGTCAA
39419 CATTTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
TTTTGCAACGAGTGTCAA
Found at i:53276 original size:24 final size:24
Alignment explanation
Indices: 53249--53364 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
53239 TTCGATTTGA
*
53249 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
53273 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
53297 ATTCTGATATAATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
53321 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
*
53344 ATTTCTGATATGATTCTTGAC
1 A-TTCTGATATGATACTTGAC
53365 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:53302 original size:12 final size:12
Alignment explanation
Indices: 53265--53303 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53255 ATCTGATACT
53265 TGACATGGATTC
1 TGACATGGATTC
*
53277 TGATAT-GATATC
1 TGACATGGAT-TC
53289 TGACATGGATTC
1 TGACATGGATTC
53301 TGA
1 TGA
53304 TATAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:56587 original size:20 final size:21
Alignment explanation
Indices: 56544--56587 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
56534 CCATAATAAT
* *
56544 TTCAACTTCCCTAAATCTTCA
1 TTCAACTTCCATAAATATTCA
*
56565 TTCAA-TTCCATAAATATTTA
1 TTCAACTTCCATAAATATTCA
56585 TTC
1 TTC
56588 TCATCACCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (21 bp):
TTCAACTTCCATAAATATTCA
Found at i:59763 original size:60 final size:60
Alignment explanation
Indices: 59634--59763 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 60
59624 GTCGGGTGAC
* * * * *
59634 CATTTTCTAACTTTTGATAGTCGAGGGACTCAACAAAGCAACACTTTATAGTCGGAGGAT
1 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAATCGGAGGAG
** * * *
59694 CATTTTGTAACTTTTAATAGTCGAGGGACTCAATGAAGCATCAC-CTATAATTGGGGGAG
1 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAATCGGAGGAG
59753 CATTTGTGTAA
1 CATTT-TGTAA
59764 TTTACCCTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 15 0.25
60 44 0.75
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAATCGGAGGAG
Found at i:60837 original size:39 final size:39
Alignment explanation
Indices: 60793--60868 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
60783 TCCTTAAACT
*
60793 TTTGAACATTCAAATTTTATCCCTAAACTATGAATCTCA
1 TTTGAACATTCAAATTTCATCCCTAAACTATGAATCTCA
60832 TTTGAACATTCAAATTTCATCCCTAAACTATGAATCT
1 TTTGAACATTCAAATTTCATCCCTAAACTATGAATCT
60869 AATTCTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (39 bp):
TTTGAACATTCAAATTTCATCCCTAAACTATGAATCTCA
Found at i:63388 original size:20 final size:19
Alignment explanation
Indices: 63354--63391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
63344 TTTGTTATGT
*
63354 TAGGGGCGAACTAAAATTA
1 TAGGGGCGAAATAAAATTA
63373 TAGGGAGCGAAATAAAATT
1 TAGGG-GCGAAATAAAATT
63392 TCAATAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.08, G:0.26, T:0.21
Consensus pattern (19 bp):
TAGGGGCGAAATAAAATTA
Done.