Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001002.1 Hibiscus syriacus cultivar Beakdansim tig00002004_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: 75823
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2544 original size:31 final size:31
Alignment explanation
Indices: 2474--2624 Score: 211
Period size: 31 Copynumber: 4.9 Consensus size: 31
2464 GAGTTGAGGG
* *
2474 TTACCTATGT-TCTTCGGAACATATGGACAGAA
1 TTACCTATGTCT-TTCGGGACATATGGACAG-T
2506 TTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGT
2537 TTACCTATGTCTTTCGGGACATATGGACAG-
1 TTACCTATGTCTTTCGGGACATATGGACAGT
*
2567 TTACCTATGTTCTTT-GTGACATATGGACAGT
1 TTACCTATG-TCTTTCGGGACATATGGACAGT
2598 TTACCTATGT-TCTTCGGGACATATGGA
1 TTACCTATGTCT-TTCGGGACATATGGA
2625 TAGATTATTA
Statistics
Matches: 110, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
29 1 0.01
30 26 0.24
31 55 0.50
32 27 0.25
33 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGT
Found at i:2600 original size:61 final size:62
Alignment explanation
Indices: 2474--2631 Score: 241
Period size: 61 Copynumber: 2.5 Consensus size: 62
2464 GAGTTGAGGG
*
2474 TTACCTATGTTCTTCGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAG-ATTACCTATGTCTTTCGGGACATATGGACAGT
*
2537 TTACCTATG-TCTTTCGGGACATATGGACAG-TTACCTATGTTCTTT-GTGACATATGGACAGT
1 TTACCTATGTTC-TTCGGGACATATGGACAGATTACCTATG-TCTTTCGGGACATATGGACAGT
*
2598 TTACCTATGTTCTTCGGGACATATGGATAGATTA
1 TTACCTATGTTCTTCGGGACATATGGACAGATTA
2632 TTATACGAGC
Statistics
Matches: 88, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
61 50 0.57
62 12 0.14
63 26 0.30
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTCTTTCGGGACATATGGACAGT
Found at i:3270 original size:21 final size:21
Alignment explanation
Indices: 3246--3292 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3236 GGTCGGAATT
*
3246 ACTGTAGTAGGGTATCGGTAC
1 ACTGTAGCAGGGTATCGGTAC
3267 ACTGTAGCAGGGTATCGGTAC
1 ACTGTAGCAGGGTATCGGTAC
3288 ACTGT
1 ACTGT
3293 TCACAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGGTAC
Found at i:3743 original size:2 final size:2
Alignment explanation
Indices: 3727--3783 Score: 98
Period size: 2 Copynumber: 28.5 Consensus size: 2
3717 AGTTAATTAC
3727 TA TA -A TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3769 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3784 GCACTTCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5996 original size:24 final size:23
Alignment explanation
Indices: 5966--6023 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
5956 TGCTTTGATT
5966 TAATTTAATTACTAAATTAATATA
1 TAATTTAATTACTAAATTAAT-TA
* * *
5990 TAATTTAA-TATTTATTTAATTA
1 TAATTTAATTACTAAATTAATTA
6012 TAATTGTAATTA
1 TAATT-TAATTA
6024 TTATGTTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 12 0.41
24 10 0.34
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTTAATTACTAAATTAATTA
Found at i:5997 original size:12 final size:11
Alignment explanation
Indices: 5966--6024 Score: 57
Period size: 12 Copynumber: 5.1 Consensus size: 11
5956 TGCTTTGATT
5966 TAATTTAATTA
1 TAATTTAATTA
*
5977 CTAAATTAATATA
1 -TAATTTAAT-TA
5990 TAATTTAA-TA
1 TAATTTAATTA
*
6000 TTTATTTAATTA
1 -TAATTTAATTA
6012 TAATTGTAATTA
1 TAATT-TAATTA
6024 T
1 T
6025 TATGTTAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.05
11 11 0.28
12 24 0.62
13 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TAATTTAATTA
Found at i:7526 original size:2 final size:2
Alignment explanation
Indices: 7519--7565 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
7509 ATGAAGTTCA
7519 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
7561 AT AT A
1 AT AT A
7566 CTGCAATTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9614 original size:14 final size:14
Alignment explanation
Indices: 9595--9674 Score: 86
Period size: 14 Copynumber: 6.3 Consensus size: 14
9585 CGTTCATGAA
9595 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9609 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9623 CG-T---TTATGTT
1 CGTTCGGTTATGTT
9633 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
9647 CG-T---TTACGTT
1 CGTTCGGTTATGTT
*
9657 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
9671 CGTT
1 CGTT
9675 TATGTTCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 16 0.30
11 2 0.04
13 2 0.04
14 34 0.63
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:9623 original size:24 final size:24
Alignment explanation
Indices: 9596--9681 Score: 145
Period size: 24 Copynumber: 3.6 Consensus size: 24
9586 GTTCATGAAC
*
9596 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
9620 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
* *
9644 GTTCGTTTACGTTCATTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
9668 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
9682 ATTCATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.09, C:0.14, G:0.24, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:9668 original size:38 final size:37
Alignment explanation
Indices: 9595--9674 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 37
9585 CGTTCATGAA
*
9595 CGTTCGGTTATGTTCGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTCGGTTA-GTTCGGTTATGTT
9633 CGTTCGGTTATGTTCGTTTAC-GTTCA-TTCGGTTATGTT
1 CGTTCGGTTATGTTCG-TT-CGGTT-AGTTCGGTTATGTT
9671 CGTT
1 CGTT
9675 TATGTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
38 31 0.82
39 5 0.13
40 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (37 bp):
CGTTCGGTTATGTTCGTTCGGTTAGTTCGGTTATGTT
Found at i:9682 original size:24 final size:24
Alignment explanation
Indices: 9596--9694 Score: 144
Period size: 24 Copynumber: 4.1 Consensus size: 24
9586 GTTCATGAAC
* *
9596 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
*
9620 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
*
9644 GTTCGTTTACGTTCATTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
**
9668 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
9692 GTT
1 GTT
9695 TAACTCAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.54
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGGTTAT
Found at i:10210 original size:23 final size:23
Alignment explanation
Indices: 10180--10267 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
10170 TGGGATAATG
*
10180 TCGACCTTGAATTGAGCTCAGAA
1 TCGACCTTGAATCGAGCTCAGAA
*
10203 TCGACCTTGAATTGAGCTCAGAA
1 TCGACCTTGAATCGAGCTCAGAA
* * *
10226 TCGAGCTTGAATCGAGCTTAGAC
1 TCGACCTTGAATCGAGCTCAGAA
* *
10249 TCGAGCTTCAATCGAGCTC
1 TCGACCTTGAATCGAGCTC
10268 GAGTCTCGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
TCGACCTTGAATCGAGCTCAGAA
Found at i:10239 original size:11 final size:11
Alignment explanation
Indices: 10180--10266 Score: 75
Period size: 11 Copynumber: 7.6 Consensus size: 11
10170 TGGGATAATG
*
10180 TCGACCTTGAA
1 TCGAGCTTGAA
* *
10191 TTGAGCTCAGAA
1 TCGAGCT-TGAA
*
10203 TCGACCTTGAA
1 TCGAGCTTGAA
* *
10214 TTGAGCTCAGAA
1 TCGAGCT-TGAA
10226 TCGAGCTTGAA
1 TCGAGCTTGAA
*
10237 TCGAGCTTAGAC
1 TCGAGCTT-GAA
*
10249 TCGAGCTTCAA
1 TCGAGCTTGAA
10260 TCGAGCT
1 TCGAGCT
10267 CGAGTCTCGA
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
11 32 0.54
12 27 0.46
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:10266 original size:46 final size:47
Alignment explanation
Indices: 10180--10291 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 47
10170 TGGGATAATG
* * * *
10180 TCGACCTTGAATTGAGCTCAGAATCGACCTTGAATTGAGCTC-AGAA
1 TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
* * * **
10226 TCGAGCTTGAATCGAGCTTAGACTCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
* *
10273 TCGAGTTTTAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
10292 TTAATTTTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
46 35 0.66
47 18 0.34
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
Found at i:10285 original size:24 final size:24
Alignment explanation
Indices: 10193--10291 Score: 87
Period size: 23 Copynumber: 4.2 Consensus size: 24
10183 ACCTTGAATT
* * * *
10193 GAGCTC-AGAATCGACCTTGAATT
1 GAGCTCGAGACTCGAGCTTCAATC
* *
10216 GAGCTC-AGAATCGAGCTTGAATC
1 GAGCTCGAGACTCGAGCTTCAATC
*
10239 GAGCT-TAGACTCGAGCTTCAATC
1 GAGCTCGAGACTCGAGCTTCAATC
* * *
10262 GAGCTCGAGTCTCGAGTTTTAATC
1 GAGCTCGAGACTCGAGCTTCAATC
10286 GAGCTC
1 GAGCTC
10292 TTAATTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
23 46 0.70
24 20 0.30
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (24 bp):
GAGCTCGAGACTCGAGCTTCAATC
Found at i:10512 original size:16 final size:16
Alignment explanation
Indices: 10490--10551 Score: 115
Period size: 16 Copynumber: 3.9 Consensus size: 16
10480 GGTCTCTAAT
10490 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
*
10506 ATTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
10522 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
10538 GTTTATGTTCGTGT
1 GTTTATGTTCGTGT
10552 AACACCCTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.08, C:0.11, G:0.24, T:0.56
Consensus pattern (16 bp):
GTTTATGTTCGTGTTC
Found at i:11202 original size:30 final size:30
Alignment explanation
Indices: 11162--11318 Score: 287
Period size: 30 Copynumber: 5.2 Consensus size: 30
11152 TCCGAATGAC
11162 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
11192 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
11222 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
11252 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
11282 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
11312 CTATCCA
1 CTATCCA
11319 TATGTTCCTT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 122 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:11555 original size:4 final size:4
Alignment explanation
Indices: 11546--11802 Score: 514
Period size: 4 Copynumber: 64.2 Consensus size: 4
11536 ATATAACCAT
11546 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11594 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11642 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11690 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11738 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11786 TACA TACA TACA TACA T
1 TACA TACA TACA TACA T
11803 GTCATCATTT
Statistics
Matches: 253, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 253 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:12735 original size:19 final size:19
Alignment explanation
Indices: 12711--12760 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
12701 TTTAATGGGG
12711 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
12730 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
12749 TGCATCGATGCA
1 TGCATCGATGCA
12761 TCGATGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:17366 original size:30 final size:30
Alignment explanation
Indices: 17208--17364 Score: 287
Period size: 30 Copynumber: 5.2 Consensus size: 30
17198 TCCGAAAAAC
17208 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
17238 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
17268 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
17298 CTATCCAGAGGTCATAAAGACCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
17328 CTATCCATAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
17358 CTATCCA
1 CTATCCA
17365 TATGTTCCTT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 123 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:17609 original size:4 final size:4
Alignment explanation
Indices: 17592--17628 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
17582 ATATAACCAT
*
17592 TACA TACA TCCA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
17629 GTCATCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:19783 original size:19 final size:19
Alignment explanation
Indices: 19760--19802 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19750 TACTTTTTTT
19760 AAAATTAT-GATTTTAAAA
1 AAAATTATAGATTTTAAAA
*
19778 ATAAATTATATATTTTAAAA
1 A-AAATTATAGATTTTAAAA
19798 AAAAT
1 AAAAT
19803 CATTTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTATAGATTTTAAAA
Found at i:23584 original size:27 final size:27
Alignment explanation
Indices: 23546--23607 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
23536 GAATGTCGTC
*
23546 GTTGCAATACAGATTTCCAACATCATT
1 GTTGCCATACAGATTTCCAACATCATT
23573 GTTGCCATACAGATTTCCAACATCATT
1 GTTGCCATACAGATTTCCAACATCATT
23600 GTTGCCAT
1 GTTGCCAT
23608 TAACTTATAC
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:0.24, G:0.13, T:0.34
Consensus pattern (27 bp):
GTTGCCATACAGATTTCCAACATCATT
Found at i:26744 original size:3 final size:3
Alignment explanation
Indices: 26738--26787 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
26728 GCTGTCATCA
* * * *
26738 TCG TCG TCG TTG TCG TCA TCG TCG TCG TTG TCA TCG TCG TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
26786 TC
1 TC
26788 ATCCTGAGCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.04, C:0.30, G:0.28, T:0.38
Consensus pattern (3 bp):
TCG
Found at i:26756 original size:18 final size:18
Alignment explanation
Indices: 26730--26790 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
26720 GACTCCTTGC
*
26730 TGTCATCATCGTCGTCGT
1 TGTCGTCATCGTCGTCGT
26748 TGTCGTCATCGTCGTCG-
1 TGTCGTCATCGTCGTCGT
26765 T-T-GTCATCGTCGTCGT
1 TGTCGTCATCGTCGTCGT
*
26781 CGTCGTCATC
1 TGTCGTCATC
26791 CTGAGCAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 13 0.34
16 1 0.03
17 2 0.05
18 22 0.58
ACGTcount: A:0.08, C:0.30, G:0.25, T:0.38
Consensus pattern (18 bp):
TGTCGTCATCGTCGTCGT
Found at i:26759 original size:12 final size:12
Alignment explanation
Indices: 26731--26787 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
26721 ACTCCTTGCT
*
26731 GTCATCATCGTC
1 GTCATCGTCGTC
* *
26743 GTCGTTGTCGTC
1 GTCATCGTCGTC
* * *
26755 ATCGTCGTCGTT
1 GTCATCGTCGTC
26767 GTCATCGTCGTC
1 GTCATCGTCGTC
*
26779 GTCGTCGTC
1 GTCATCGTC
26788 ATCCTGAGCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.07, C:0.30, G:0.26, T:0.37
Consensus pattern (12 bp):
GTCATCGTCGTC
Found at i:28889 original size:17 final size:18
Alignment explanation
Indices: 28846--28886 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28836 TAATTATATT
28846 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
28863 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
28881 ATTAAA
1 AGTAAA
28887 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:28947 original size:10 final size:10
Alignment explanation
Indices: 28928--28958 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28918 CTTAAACAAA
*
28928 GAGAGTATTT
1 GAGAGAATTT
28938 GAGAGAATTT
1 GAGAGAATTT
28948 GAGAGAATTT
1 GAGAGAATTT
28958 G
1 G
28959 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:30297 original size:75 final size:75
Alignment explanation
Indices: 30195--30356 Score: 249
Period size: 75 Copynumber: 2.2 Consensus size: 75
30185 AGACGTTACC
*
30195 TATTATGTTAAACTACTTACCAGTTTGTTTGAA-GGTTACTAATAATGTAAACGGTAAAATAAAA
1 TATTATGTTAAAATACTTACCAGTTTGTTT-AATGGTTACTAATAATGTAAACGGTAAAATAAAA
30259 T-AGGTGCTACA
65 TAAGG-GCTACA
*
30270 TATTATGTTAAAATA-TCTACCGGTTTGTTTAATGGTTACTAATAATGTAAACGGTAAAATAAAA
1 TATTATGTTAAAATACT-TACCAGTTTGTTTAATGGTTACTAATAATGTAAACGGTAAAATAAAA
*
30334 TAAGGGCTACC
65 TAAGGGCTACA
30345 TATTATGTTAAA
1 TATTATGTTAAA
30357 TAGGTGCTCT
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
74 3 0.04
75 75 0.93
76 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (75 bp):
TATTATGTTAAAATACTTACCAGTTTGTTTAATGGTTACTAATAATGTAAACGGTAAAATAAAAT
AAGGGCTACA
Found at i:30515 original size:75 final size:75
Alignment explanation
Indices: 30392--30554 Score: 254
Period size: 75 Copynumber: 2.2 Consensus size: 75
30382 CAAGCGCTAG
* * *
30392 CTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAA
1 CTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAA
*
30457 TAGGTGATAC
66 TAGGCGATAC
* *
30467 CTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATAAAA
1 CTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAA
* *
30532 TTGGCGCTAC
66 TAGGCGATAC
30542 CTATTACGTTAAA
1 CTATTACGTTAAA
30555 TAAGCGCTAC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (75 bp):
CTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAA
TAGGCGATAC
Found at i:30543 original size:198 final size:194
Alignment explanation
Indices: 30194--30845 Score: 689
Period size: 198 Copynumber: 3.3 Consensus size: 194
30184 TAGACGTTAC
* * *
30194 CTATTATGTTAAACTA-CTTACCAGTTTGTTTGAAGGTTACTAATAATGTAAACGGTAAAATAAA
1 CTATTACGTTAAACTAGC-TACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAA
* * *
30258 ATAGGTGCTACATATTATGTTAAAATATCTACCGGTTTGTTTAATGGTTACTAATAATGTAAACG
65 ATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAACG
* *
30323 GTAAAATAAAATAAGGGCTACCTATTATGTTAAATAGGTGCTCTATCTATTACGTTAAACAAGCG
130 GTAAAATAAAAT-AGGGCTACCTATTATGTTAAATA-G-GCGCTACCTATTACGTTAAACAAGCG
30388 CTA
192 CTA
*
30391 GCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAA
1 -CTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAA
* * *
30456 ATAGGTGATACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAATGTAAACG
65 ATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAACG
* * * *
30521 GTAAAATAAAATTGGCGCTACCTATTACGTTAAATAAGCGCTACCTATTACGTTAAACTAA---T
130 GTAAAATAAAATAGG-GCTACCTATTATGTTAAATAGGCGCTACCTATTACGTTAAAC-AAGCGC
30583 TA
193 TA
* * * * * * * ** *
30585 CTGATT-TGTTTAAA--GGTTACTAATAATG--TAAACGGTAAAATAA-AATAGTTGCTAC-ATA
1 CT-ATTACG-TTAAACTAGCTACCAGT-TTGTTTAAA-GGT-TAATAATAAT-G-T-AAACGGTA
** * * * * * *
30643 TTATGTTAACTAAGCGCTACATATTACGTTAAAATA-CTTACCAGCTTATTTAAAGGTTACTAAT
58 --AAATAAAATAGGTGCTACATATTACGTTAAAATATC-TACCAGTTTGTTTAAAGGTTACTAAT
* *
30707 AATGTAAACGATAAAATAAAATAGGTACTACCTATTATGTTAAATAGGCGCTACCTATTACGTTA
120 AATGTAAACGGTAAAATAAAATAGG-GCTACCTATTATGTTAAATAGGCGCTACCTATTACGTTA
*
30772 AATAAGCGCTA
184 AACAAGCGCTA
* *
30783 CCTATTACGTTAAACTAGCTATCAGTTTGTTTAAAGGTTAATAATAATATAAACGGTAAAATA
1 -CTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATA
30846 TATACAACTT
Statistics
Matches: 368, Mismatches: 61, Indels: 52
0.77 0.13 0.11
Matches are distributed among these distances:
191 4 0.01
192 11 0.03
193 11 0.03
194 13 0.04
195 5 0.01
196 131 0.36
197 6 0.02
198 161 0.44
199 11 0.03
200 11 0.03
201 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (194 bp):
CTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAA
TAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAACGG
TAAAATAAAATAGGGCTACCTATTATGTTAAATAGGCGCTACCTATTACGTTAAACAAGCGCTA
Found at i:30566 original size:98 final size:98
Alignment explanation
Indices: 30464--30773 Score: 437
Period size: 98 Copynumber: 3.2 Consensus size: 98
30454 AAATAGGTGA
*
30464 TACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAATGTAAACGGTAAAATA
1 TACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATA
* * *
30529 AAATTGGCGCTACCTATTACGTTAAATAAGCGC
66 AAATAGGTGCTACCTATTATGTTAAATAAGCGC
* *
30562 TACCTATTACGTTAAACTAAT-TA-CTGATTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAA
1 TACCTATTACGTTAAAAT-ATCTACCAG-TTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAA
* * *
30625 TAAAATAGTTGCTACATATTATGTTAACTAAGCGC
64 TAAAATAGGTGCTACCTATTATGTTAAATAAGCGC
* * * *
30660 TACATATTACGTTAAAATA-CTTACCAGCTTATTTAAAGGTTACTAATAATGTAAACGATAAAAT
1 TACCTATTACGTTAAAATATC-TACCAGTTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAAT
* *
30724 AAAATAGGTACTACCTATTATGTTAAATAGGCGC
65 AAAATAGGTGCTACCTATTATGTTAAATAAGCGC
30758 TACCTATTACGTTAAA
1 TACCTATTACGTTAAA
30774 TAAGCGCTAC
Statistics
Matches: 186, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
97 3 0.02
98 179 0.96
99 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (98 bp):
TACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAATGTAAACGGTAAAATA
AAATAGGTGCTACCTATTATGTTAAATAAGCGC
Found at i:30754 original size:23 final size:23
Alignment explanation
Indices: 30725--30796 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
30715 CGATAAAATA
** *
30725 AAATAGGTACTACCTATTATGTT
1 AAATAGGCGCTACCTATTACGTT
30748 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
*
30771 AAATAAGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
30794 AAA
1 AAA
30797 CTAGCTATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTACGTT
Found at i:31548 original size:108 final size:108
Alignment explanation
Indices: 31389--31595 Score: 317
Period size: 108 Copynumber: 1.9 Consensus size: 108
31379 GCTCAATATG
*
31389 CTTAAACTTTTAGTAACATTTTAGGCGCTACCTAATATGATGATAATATTAATAACAAAATAAAT
1 CTTAAACTTTGAGTAACATTTTAGGCGCTACCTAATATGATGATAATATTAATAACAAAATAAAT
* *
31454 AATTAACTTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAA
66 AATTAACCTA-TTTGTTATCGTCAGATTTCTAAGGCCCCATCAA
* * * * *
31498 CTTAAACTTTGA-TAATATTTTAGGCGCTACCTAATATGTTGATAATATTAATGACAAATTAAGT
1 CTTAAACTTTGAGTAACATTTTAGGCGCTACCTAATATGATGATAATATTAATAACAAAATAAAT
*
31562 AATTAACCTATTTGTTATCGTCAGATTTTTAAGG
66 AATTAACCTATTTGTTATCGTCAGATTTCTAAGG
31596 TATATTAGCT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 22 0.25
108 56 0.63
109 11 0.12
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (108 bp):
CTTAAACTTTGAGTAACATTTTAGGCGCTACCTAATATGATGATAATATTAATAACAAAATAAAT
AATTAACCTATTTGTTATCGTCAGATTTCTAAGGCCCCATCAA
Found at i:32240 original size:85 final size:85
Alignment explanation
Indices: 32136--32309 Score: 303
Period size: 85 Copynumber: 2.0 Consensus size: 85
32126 TAAATGTTTA
*
32136 TATATCATTGCAGATATGATATTAGAACTCAAAATCTTAAGAGATAACATCAATTTCTTAATCAT
1 TATATCATTGCAAATATGATATTAGAACTCAAAATCTTAAGAGATAACATCAATTTCTTAATCAT
*
32201 TAAAGTCTCTTGGTTTGTGC
66 TAAAGTCTCTTGGTTCGTGC
* *
32221 TATATCATTGCAAATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
1 TATATCATTGCAAATATGATATTAGAACTCAAAATCTTAAGAGATAACATCAATTTCTTAATCAT
*
32286 TAAAGTTTCTTGGTTCGTGC
66 TAAAGTCTCTTGGTTCGTGC
32306 TATA
1 TATA
32310 ACAACAAGTA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (85 bp):
TATATCATTGCAAATATGATATTAGAACTCAAAATCTTAAGAGATAACATCAATTTCTTAATCAT
TAAAGTCTCTTGGTTCGTGC
Found at i:32378 original size:26 final size:24
Alignment explanation
Indices: 32341--32409 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
32331 AGTTTGCACA
32341 ATTTTA-AATTTATATTTATTTATAT
1 ATTTTAGAATTTATATTTA-TTAT-T
*
32366 ATTTTAGAATTTAAAATCTTATTATT
1 ATTTTAGAATTT-ATAT-TTATTATT
* *
32392 GTTTAAGAATTTATATTT
1 ATTTTAGAATTTATATTT
32410 TAATATTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.05
25 9 0.24
26 16 0.43
27 7 0.19
28 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTTAGAATTTATATTTATTATT
Found at i:32445 original size:48 final size:48
Alignment explanation
Indices: 32393--32489 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 48
32383 CTTATTATTG
* *
32393 TTTAAGAATT-TATATTTTAATA-TTCAGAATTTAAGATTTA-ATTTAAAA
1 TTTAA-AATTATATATTTTAATATTTAAGAA-TTAA-ATTTACAGTTAAAA
* *
32441 TTTAAAGTTATATATTTTAGTATTTAAGAATTAAATTTACAGTTAAAA
1 TTTAAAATTATATATTTTAATATTTAAGAATTAAATTTACAGTTAAAA
32489 T
1 T
32490 AATTAGATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
47 8 0.19
48 28 0.67
49 6 0.14
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTAAAATTATATATTTTAATATTTAAGAATTAAATTTACAGTTAAAA
Found at i:39456 original size:2 final size:2
Alignment explanation
Indices: 39449--39485 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39439 GATTAGATTA
39449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39486 AGTAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39666 original size:2 final size:2
Alignment explanation
Indices: 39659--39691 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39649 AGGTAAAAGG
39659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39692 ACTATGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47669 original size:43 final size:43
Alignment explanation
Indices: 47608--47823 Score: 324
Period size: 43 Copynumber: 5.0 Consensus size: 43
47598 TGCCATGCCC
*
47608 CAGGTCCGGTCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
*
47651 CAGGTCCGGTCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
*
47694 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAATGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
* * **
47737 CAGGTCCGGGCCTGCTATTAATTCTCCCACCAAACTCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
* * * * *
47780 CAGGTCGGGGCCTGCTATTAATTCTACCACCAAACGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
47823 C
1 C
47824 TGTAAAACAA
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 164 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
Found at i:51836 original size:18 final size:19
Alignment explanation
Indices: 51801--51837 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
51791 ACGAGAATGT
51801 AAGATTATTAGTGAGAATAA
1 AAGATTATTAG-GAGAATAA
51821 AAGATTATTA-GAGAATA
1 AAGATTATTAGGAGAATA
51838 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (19 bp):
AAGATTATTAGGAGAATAA
Found at i:54369 original size:18 final size:19
Alignment explanation
Indices: 54327--54369 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
54317 ACCAAGATTA
* *
54327 AATTTAATTCTTAATTTTT
1 AATTTAAGTCTTAATTTTC
54346 AA-TTAAGTCTTAA-TTTC
1 AATTTAAGTCTTAATTTTC
54363 AATTTAA
1 AATTTAA
54370 TATAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTAAGTCTTAATTTTC
Found at i:54430 original size:2 final size:2
Alignment explanation
Indices: 54423--54451 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54413 CCCGATTTAT
54423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54452 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54549 original size:39 final size:39
Alignment explanation
Indices: 54483--54597 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
54473 ACTTTTATTT
* *
54483 ATAA-TTCTCAAATTATTTCA-TTCTAACATTCTAAATTC
1 ATAATTTCTTAAATTATTTCACAT-TAACATTCTAAATTC
*
54521 ATAATTTCTTAAATT-TTTCCACCA-TAACATTTTAAATTC
1 ATAATTTCTTAAATTATTT-CA-CATTAACATTCTAAATTC
*
54560 TTAATTTCTTAAATTATTTCACATTAACATTCTAAATT
1 ATAATTTCTTAAATTATTTCACATTAACATTCTAAATT
54598 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
38 9 0.14
39 54 0.82
40 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (39 bp):
ATAATTTCTTAAATTATTTCACATTAACATTCTAAATTC
Found at i:58492 original size:44 final size:44
Alignment explanation
Indices: 58429--58522 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
58419 TACACCAATA
* * * * *
58429 ACAGTACATAAAACTTAAAAGCATCCCCTGGCATAAAATCCTTT
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
58473 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
58517 ACAGTA
1 ACAGTA
58523 GAATAGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.21
Consensus pattern (44 bp):
ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
Found at i:69121 original size:128 final size:126
Alignment explanation
Indices: 68960--69208 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 126
68950 CTCGACGAAC
68960 AGTAGTGAGCACAACTAATGATGAGCACCGCTGAACACTATTAATTTAATTTATAAAAATTTAAA
1 AGTAGTGAGCACAACTAATGATGAGCACCGCTGAACACTATTAATTTAATTTATAAAAATTTAAA
* *
69025 ATTATAAGTTACTCAACACATAATCATAGATTAGTTAAAAGTTACAAAATAAATTATTTATTT
66 ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTT--AAAATAAAATATTTATTT
* * * *
69088 AGTAGTGATCACAACTAATGATGAGTACCGCTGAACACTATTAGTTTAATTTCTAAAAATTTAAA
1 AGTAGTGAGCACAACTAATGATGAGCACCGCTGAACACTATTAATTTAATTTATAAAAATTTAAA
* *
69153 ATTATAAGTTACTCAATATATAATCATAAATTAGTTAAAAGTTAAAATAAAATATT
66 ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTTAAAATAAAATATT
69209 AATTACATTA
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
126 12 0.11
128 101 0.89
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (126 bp):
AGTAGTGAGCACAACTAATGATGAGCACCGCTGAACACTATTAATTTAATTTATAAAAATTTAAA
ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTTAAAATAAAATATTTATTT
Found at i:69352 original size:14 final size:14
Alignment explanation
Indices: 69304--69346 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
69294 AAATTATGAA
69304 AAATAATTTA--TT
1 AAATAATTTATTTT
69316 -AATAATTTATTTT
1 AAATAATTTATTTT
69329 AAATAATTTATCTTT
1 AAATAATTTAT-TTT
69344 AAA
1 AAA
69347 ATTTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
13 2 0.07
14 10 0.37
15 6 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATAATTTATTTT
Found at i:69358 original size:23 final size:23
Alignment explanation
Indices: 69324--69377 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
69314 TTAATAATTT
*
69324 ATTTTAAATAATTTAT-CTTTAAA
1 ATTTTAATTAATTTATACTTT-AA
*
69347 ATTTTAATTAATTTATACTTTTA
1 ATTTTAATTAATTTATACTTTAA
69370 ATTTTAAT
1 ATTTTAAT
69378 CTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTAATTAATTTATACTTTAA
Found at i:70021 original size:22 final size:25
Alignment explanation
Indices: 69964--70027 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
69954 ATAAAAATAG
69964 AATATTTTACATTAAGTTAATAGTAA
1 AATATTTTA-ATTAAGTTAATAGTAA
69990 AATATATTTAA-TAAGTTAATA-TAA
1 AATAT-TTTAATTAAGTTAATAGTAA
70014 AA-ATTTTAAGTTAA
1 AATATTTTAA-TTAA
70028 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.14
23 2 0.06
24 8 0.23
25 10 0.29
26 6 0.17
27 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
AATATTTTAATTAAGTTAATAGTAA
Found at i:70118 original size:7 final size:8
Alignment explanation
Indices: 70091--70122 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
70081 AATTATATAA
70091 AAAATTCT
1 AAAATTCT
70099 AAAATTCT
1 AAAATTCT
70107 AAAATT-T
1 AAAATTCT
70114 AAAATTCT
1 AAAATTCT
70122 A
1 A
70123 TAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTCT
Found at i:70118 original size:15 final size:16
Alignment explanation
Indices: 70091--70122 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
70081 AATTATATAA
70091 AAAATTCTAAAATTCT
1 AAAATTCTAAAATTCT
70107 AAAATT-TAAAATTCT
1 AAAATTCTAAAATTCT
70122 A
1 A
70123 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTCTAAAATTCT
Found at i:71098 original size:20 final size:20
Alignment explanation
Indices: 71073--71126 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
71063 AAATTTGAAG
71073 GTGCATCGATGCATTAAGGA
1 GTGCATCGATGCATTAAGGA
71093 GTGCATCGATGCATTAAGGA
1 GTGCATCGATGCATTAAGGA
71113 GTGCATCGATGCAT
1 GTGCATCGATGCAT
71127 GGAATTTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCATTAAGGA
Found at i:73989 original size:22 final size:23
Alignment explanation
Indices: 73948--73994 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
73938 CGCATTGATG
*
73948 CACTGTTCATTGGTACTGTTCAT
1 CACTGTTCATCGGTACTGTTCAT
*
73971 CACTGTTCA-CGGTATTGTTCAT
1 CACTGTTCATCGGTACTGTTCAT
73993 CA
1 CA
73995 TTATTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (23 bp):
CACTGTTCATCGGTACTGTTCAT
Found at i:74001 original size:22 final size:22
Alignment explanation
Indices: 73959--74001 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
73949 ACTGTTCATT
*
73959 GGTACTGTTCATCACTGTTCAC
1 GGTACTGTTCATCACTATTCAC
* *
73981 GGTATTGTTCATCATTATTCA
1 GGTACTGTTCATCACTATTCA
74002 TAAAAAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (22 bp):
GGTACTGTTCATCACTATTCAC
Found at i:75145 original size:22 final size:22
Alignment explanation
Indices: 75120--75171 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
75110 ATACTCTGCA
75120 ACTGTTCACGGTACTG-TTCATC
1 ACTGTTCACGGTA-TGTTTCATC
75142 ACTGTTCACGGTATGTTTCATC
1 ACTGTTCACGGTATGTTTCATC
*
75164 ACTATTCA
1 ACTGTTCA
75172 TAAAAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (22 bp):
ACTGTTCACGGTATGTTTCATC
Found at i:75463 original size:25 final size:25
Alignment explanation
Indices: 75405--75466 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
75395 ATAAGTCTAG
* *
75405 ATTCAATATTTTGATACATGATCAC
1 ATTCAATATTATGATACATGATCAA
*
75430 ATTCTATATTATGATACATGA-CATGA
1 ATTCAATATTATGATACATGATCA--A
75456 ATTC-ATATTAT
1 ATTCAATATTAT
75467 ATGCATTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.06
25 26 0.81
26 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCAATATTATGATACATGATCAA
Found at i:75543 original size:31 final size:29
Alignment explanation
Indices: 75506--75575 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
75496 AAGTTATGAG
*
75506 CTATGTGATAAGGTATGGAAAATGATATGGT
1 CTATGTGATAAGGTATGG-AAATGATA-AGT
*
75537 CTATGTGAAAAGGTATGGAAATGATAAGT
1 CTATGTGATAAGGTATGGAAATGATAAGT
*
75566 CTACGTGATA
1 CTATGTGATA
75576 TAACTATGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 10 0.29
30 8 0.23
31 17 0.49
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (29 bp):
CTATGTGATAAGGTATGGAAATGATAAGT
Done.