Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002245.1 Hibiscus syriacus cultivar Beakdansim tig00004563_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: 87417
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2523 original size:29 final size:29
Alignment explanation
Indices: 2490--2547 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2480 AAAACGTCAT
*
2490 GTTTTTCTAATTCGTACTCATGCTCTCTC
1 GTTTTTATAATTCGTACTCATGCTCTCTC
2519 GTTTTTATAATTCGTACTCATGCTCTCTC
1 GTTTTTATAATTCGTACTCATGCTCTCTC
2548 CTGGTTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.10, T:0.48
Consensus pattern (29 bp):
GTTTTTATAATTCGTACTCATGCTCTCTC
Found at i:2579 original size:3 final size:3
Alignment explanation
Indices: 2571--2598 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2561 ATGCACACTC
2571 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
2599 TTGTTCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:11567 original size:21 final size:21
Alignment explanation
Indices: 11540--11594 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
11530 CAGTTTCCAG
11540 ATTCGCAATGCGATTTT-ACA
1 ATTCGCAATGCGATTTTCACA
* * *
11560 ATTTCGCATTGCAATTTTCCCA
1 A-TTCGCAATGCGATTTTCACA
11582 ATTCGCAATGCGA
1 ATTCGCAATGCGA
11595 ATAAGTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCACA
Found at i:11609 original size:20 final size:21
Alignment explanation
Indices: 11584--11635 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
11574 TTTTCCCAAT
*
11584 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
11604 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
11625 TCGCAATGCGA
1 TCGCAATGCGA
11636 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:11649 original size:20 final size:20
Alignment explanation
Indices: 11624--11713 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
11614 AATTTGGAAA
*
11624 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
11644 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
11665 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
11685 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
11705 TTCGCAACG
1 ATCGCAACG
11714 AGATTCTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 41 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:11718 original size:20 final size:20
Alignment explanation
Indices: 11666--11722 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
11656 TAATACAAAA
*
11666 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
11686 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
11706 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
11723 AAATCGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:11729 original size:20 final size:20
Alignment explanation
Indices: 11601--11731 Score: 84
Period size: 20 Copynumber: 6.5 Consensus size: 20
11591 GCGAATAAGT
*
11601 AAATCGCAATGCGAATT-TGGA
1 AAATCGCAACGCG-ATTCT-GA
* *
11622 AAATCGCAATGCGATACTGA
1 AAATCGCAACGCGATTCTGA
** ** *
11642 CTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCT-GA
*
11663 AAATCGCAACGCGATACTGA
1 AAATCGCAACGCGATTCTGA
***
11683 CTTTCGCAACGCGATTCTGA
1 AAATCGCAACGCGATTCTGA
*** *
11703 CTTTCGCAACGAGATTCTGA
1 AAATCGCAACGCGATTCTGA
11723 AAATCGCAA
1 AAATCGCAA
11732 TCATCTTCAA
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
20 60 0.67
21 30 0.33
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGATTCTGA
Found at i:11980 original size:34 final size:34
Alignment explanation
Indices: 11915--11981 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
11905 GACATTCATT
* * *
11915 TGACTATCACAACGGGGAAATCGCACCGCGAAAA
1 TGACTATCACAACGAGAAAATCGCAACGCGAAAA
* *
11949 TGACTATCGCAACGAGAAAATCGCAATGCGAAA
1 TGACTATCACAACGAGAAAATCGCAACGCGAAA
11982 TAAAAATCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (34 bp):
TGACTATCACAACGAGAAAATCGCAACGCGAAAA
Found at i:13632 original size:42 final size:42
Alignment explanation
Indices: 13586--13678 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
13576 CCTCTTCAAC
* *
13586 GATGACAGTGGCCTCTTGAACG-GTGGGGGAGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGG-GGACTCTTGAGG
*
13628 GATGACAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
13670 GATGACAGG
1 GATGACAGG
13679 TGAGTCGGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.22, C:0.16, G:0.42, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:13643 original size:21 final size:21
Alignment explanation
Indices: 13616--13678 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
13606 CGGTGGGGGA
13616 GGACTCTTGAGGGATGACAGG
1 GGACTCTTGAGGGATGACAGG
* ** *
13637 GGCCTCTTGAACGATTG-GAGG
1 GGACTCTTGAGGGA-TGACAGG
13658 GGACTCTTGAGGGATGACAGG
1 GGACTCTTGAGGGATGACAGG
13679 TGAGTCGGGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.21
Consensus pattern (21 bp):
GGACTCTTGAGGGATGACAGG
Found at i:14065 original size:20 final size:20
Alignment explanation
Indices: 14042--14134 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
14032 AAACTTACTT
14042 TCGCAACGCAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* *
14062 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCAAAAATGACTA
** *
14082 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCAAAAATGACTA
* * **
14102 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCAAAAATGACTA
14121 TCGCAACGACAAAA
1 TCGCAACG-CAAAA
14135 TCGCAATGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.23
20 46 0.74
21 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:14066 original size:40 final size:40
Alignment explanation
Indices: 14022--14134 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 40
14012 TAGTTTACTT
* * *
14022 TCGCAACACGAAACTTACTTTCGCAACGCAAAAATGACTA
1 TCGCAACACGAAAATGACTATCGCAACGCAAAAATGACTA
* * ** *
14062 TCGCAACGCGAAAATGGCTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCAAAAATGACTA
** **
14102 TCGCAATGCG-AAATGAAAATCGCAACGACAAAA
1 TCGCAACACGAAAATGACTATCGCAACG-CAAAA
14135 TCGCAATGCG
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
39 14 0.24
40 44 0.76
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACGCAAAAATGACTA
Found at i:14123 original size:19 final size:19
Alignment explanation
Indices: 14101--14161 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
14091 GGAAATGGCT
14101 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
14120 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
14134 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
14153 ATCGCAATG
1 ATCGCAATG
14162 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:14136 original size:14 final size:14
Alignment explanation
Indices: 14117--14175 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
14107 ATGCGAAATG
14117 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
14131 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
14150 AAAATCGCAATGAC
1 AAAATCGCAACGAC
14164 AAAATCGCAACG
1 AAAATCGCAACG
14176 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:14191 original size:33 final size:33
Alignment explanation
Indices: 14101--14180 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
14091 GGAAATGGCT
14101 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
14134 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
14167 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
14181 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:14209 original size:19 final size:19
Alignment explanation
Indices: 14187--14270 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
14177 GAAACACAAA
14187 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
14206 TCGCGTTGC-AATTT--TT
1 TCGCATTGCGATTTTCATT
14222 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
14239 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
14258 TCCGCATTGCGAT
1 T-CGCATTGCGAT
14271 AGTCATTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
14 4 0.08
15 4 0.08
16 5 0.09
17 5 0.09
18 4 0.08
19 20 0.38
20 11 0.21
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:14289 original size:20 final size:20
Alignment explanation
Indices: 14235--14278 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
14225 TTGCGATTTT
14235 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
14254 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
14274 CATTT
1 CATTT
14279 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:14851 original size:18 final size:18
Alignment explanation
Indices: 14828--14875 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
14818 CGGGTCGATC
14828 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
14846 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
14864 AGGTGATGGCTC
1 AGGTGATGGCTC
14876 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:15230 original size:20 final size:20
Alignment explanation
Indices: 15205--15270 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
15195 TATTATATCA
15205 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
*
15225 TTGCGAAAGTAAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
15245 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
15265 TTGCGA
1 TTGCGA
15271 TTTTGTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCG
Found at i:15374 original size:21 final size:20
Alignment explanation
Indices: 15322--15383 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
15312 ATTTACTTAT
15322 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
15343 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
*
15364 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
15384 CTGATTTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.79
22 4 0.12
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:15559 original size:3 final size:3
Alignment explanation
Indices: 15551--15575 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
15541 TAACATGATT
15551 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
15576 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26187 original size:30 final size:29
Alignment explanation
Indices: 26153--26213 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
26143 TTTATTTTAA
* *
26153 ATAATT-TATCTTTAAATTTTTAACTAATTT
1 ATAATTATAT-TTTAAATTCTTAA-GAATTT
*
26183 ATAATTATATTTTGAATTCTTAAGAATTT
1 ATAATTATATTTTAAATTCTTAAGAATTT
26212 AT
1 AT
26214 CTTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.26
30 17 0.63
31 3 0.11
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (29 bp):
ATAATTATATTTTAAATTCTTAAGAATTT
Found at i:26194 original size:23 final size:23
Alignment explanation
Indices: 26147--26195 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26137 TTACCCTTTA
**
26147 TTTTAAATAATTTATCTTTAAAT
1 TTTTAAATAATTTATAATTAAAT
* *
26170 TTTTAACTAATTTATAATTATAT
1 TTTTAAATAATTTATAATTAAAT
26193 TTT
1 TTT
26196 GAATTCTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTAAATAATTTATAATTAAAT
Found at i:26483 original size:2 final size:2
Alignment explanation
Indices: 26478--26565 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
26468 ACACACACAC
26478 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
26520 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
26562 AT AT
1 AT AT
26566 TAAGAGAGAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30929 original size:17 final size:17
Alignment explanation
Indices: 30907--30940 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30897 TAAATTAAAT
30907 ATAACATAATACAAAAA
1 ATAACATAATACAAAAA
*
30924 ATAACATAATATAAAAA
1 ATAACATAATACAAAAA
30941 CCAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAACATAATACAAAAA
Found at i:31036 original size:51 final size:50
Alignment explanation
Indices: 30934--31039 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 50
30924 ATAACATAAT
* * * *
30934 ATAAAAACCAAATATATAAATATAATATTCAATTAAAATATAAAATTAAAC
1 ATAAAAACCAAATATAAAAATATAACATTCAATTAAAAGACAAAA-TAAAC
* *
30985 ATAAAAACTAAATATAAAAAATATAACCTTCAATTAAAAGACATAAA-AAAC
1 ATAAAAACCAAATAT-AAAAATATAACATTCAATTAAAAGACA-AAATAAAC
31036 ATAA
1 ATAA
31040 GATAAAATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 22 0.47
52 22 0.47
53 3 0.06
ACGTcount: A:0.64, C:0.09, G:0.01, T:0.25
Consensus pattern (50 bp):
ATAAAAACCAAATATAAAAATATAACATTCAATTAAAAGACAAAATAAAC
Found at i:33283 original size:15 final size:15
Alignment explanation
Indices: 33263--33313 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
33253 TAGGATTTTA
33263 ATTTTTATTATTAAG
1 ATTTTTATTATTAAG
33278 ATTTTTAGTT-TT-A-
1 ATTTTTA-TTATTAAG
33291 ATTATTTATTATTAAG
1 ATT-TTTATTATTAAG
33307 ATTTTTA
1 ATTTTTA
33314 GTTTACTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 14 0.45
16 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
ATTTTTATTATTAAG
Found at i:33302 original size:29 final size:28
Alignment explanation
Indices: 33258--33317 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
33248 TAAATTAGGA
33258 TTTTAATTTTTATTATTAAGATTTTTAG
1 TTTTAATTTTTATTATTAAGATTTTTAG
33286 TTTTAATTATTTATTATTAAGATTTTTAG
1 TTTTAATT-TTTATTATTAAGATTTTTAG
33315 TTT
1 TTT
33318 ACTATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (28 bp):
TTTTAATTTTTATTATTAAGATTTTTAG
Found at i:35902 original size:15 final size:15
Alignment explanation
Indices: 35882--35919 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
35872 AATGGATTCA
35882 TCAAAATTCAAAGGT
1 TCAAAATTCAAAGGT
35897 TCAAAATTCAAAGGT
1 TCAAAATTCAAAGGT
35912 TCAAAATT
1 TCAAAATT
35920 TATACATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (15 bp):
TCAAAATTCAAAGGT
Found at i:37136 original size:21 final size:21
Alignment explanation
Indices: 37106--37150 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37096 AGACGAGCTA
* *
37106 TGACTTTGAAGTAAGGCGCCT
1 TGACTATGAAGTAAAGCGCCT
*
37127 TGACTATGAAGTAAAGCTCCT
1 TGACTATGAAGTAAAGCGCCT
37148 TGA
1 TGA
37151 TTTTTAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (21 bp):
TGACTATGAAGTAAAGCGCCT
Found at i:41236 original size:11 final size:11
Alignment explanation
Indices: 41220--41251 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
41210 TAAAGAGAAC
41220 TAAACTAAATA
1 TAAACTAAATA
41231 TAAACTAAATA
1 TAAACTAAATA
41242 TAAACTAAAT
1 TAAACTAAAT
41252 GCCATGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAACTAAATA
Found at i:45043 original size:37 final size:37
Alignment explanation
Indices: 44993--45069 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
44983 GAGATCAGTT
44993 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
1 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
45030 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
1 GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
45067 GTC
1 GTC
45070 AAACACAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCGTTTCAACTCAGTAAATGCGCCGAGACATAACTC
Found at i:51784 original size:23 final size:23
Alignment explanation
Indices: 51758--51831 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
51748 AAGTGCCACA
* *
51758 TAGATTTGTCCCGAAGGATCGCG
1 TAGAATTGTCCCGAAGGACCGCG
* * *
51781 TAGAATTGTCTCGAAGGACCACA
1 TAGAATTGTCCCGAAGGACCGCG
* *
51804 TAGAATTATCCCGAAAGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
51827 TAGAA
1 TAGAA
51832 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Found at i:51998 original size:57 final size:58
Alignment explanation
Indices: 51903--52020 Score: 150
Period size: 57 Copynumber: 2.0 Consensus size: 58
51893 ACCATATAAA
* * *
51903 TATTTCACATAGCATTATTCAATTTATTATTTTCTCACATAGA-ACATATACTCATAG
1 TATTTCACATAGCATTATTCAAATGATCATTTTCTCACATAGACACATATACTCATAG
* * *
51960 TATTTCACCTAGCATTATTCAAATGATCATTTAT-TCACATAGAGCACATTTACTTATAG
1 TATTTCACATAGCATTATTCAAATGATCATTT-TCTCACATAGA-CACATATACTCATAG
52019 TA
1 TA
52021 ACGAAATCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 37 0.71
58 1 0.02
59 14 0.27
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.41
Consensus pattern (58 bp):
TATTTCACATAGCATTATTCAAATGATCATTTTCTCACATAGACACATATACTCATAG
Found at i:52691 original size:43 final size:43
Alignment explanation
Indices: 52630--52720 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
52620 TTGACCCAAT
52630 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
1 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
52673 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
1 ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
52716 ACTCA
1 ACTCA
52721 AAAACTCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (43 bp):
ACTCACCTAAATCTCATACTTCTAACTCCATTTATGCCCTTAA
Found at i:56779 original size:3 final size:3
Alignment explanation
Indices: 56771--56838 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
56761 TTAAAGTTAT
56771 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56819 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
56839 TTGCAAATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57231 original size:19 final size:20
Alignment explanation
Indices: 57207--57253 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
57197 GGCATGAAGG
57207 ACCGAACATCGCCCAATG-T
1 ACCGAACATCGCCCAATGTT
57226 ACCGAACATCGCCCAATGTT
1 ACCGAACATCGCCCAATGTT
57246 A-CGAACAT
1 ACCGAACAT
57254 AGCCTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (20 bp):
ACCGAACATCGCCCAATGTT
Found at i:61402 original size:35 final size:35
Alignment explanation
Indices: 61356--61434 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
61346 TCTTCGATGA
*
61356 GAGGGAGAGTTACAGAGAGAGAATAGAGAGTAATC
1 GAGGGAGAGTTACAGAGAGAGAAGAGAGAGTAATC
*
61391 GAGGGAGAGTTACAGAGAGAGAAGAGAGAGTAATG
1 GAGGGAGAGTTACAGAGAGAGAAGAGAGAGTAATC
61426 GAGGGAGAG
1 GAGGGAGAG
61435 GGAAGGGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.04, G:0.43, T:0.11
Consensus pattern (35 bp):
GAGGGAGAGTTACAGAGAGAGAAGAGAGAGTAATC
Found at i:63402 original size:29 final size:30
Alignment explanation
Indices: 63348--63424 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
63338 TAAAAAATAA
* * *
63348 TTTACATAAAATAAATTACTTGAAAATTAT
1 TTTACGTAAAATGAATTACCTGAAAATTAT
*
63378 TTTACGTAAAATGAATTACCT-AAAATTGT
1 TTTACGTAAAATGAATTACCTGAAAATTAT
*
63407 TTTAGGTAAAATGAATTA
1 TTTACGTAAAATGAATTA
63425 TATTTAATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACCTGAAAATTAT
Found at i:63827 original size:25 final size:26
Alignment explanation
Indices: 63756--63858 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 26
63746 TATTACTCAT
63756 TATTAATAATTTAATAATATTATATTTA
1 TATTAATAATTT-ATAATA-TATATTTA
** **
63784 TAAAAATAATAGATAATAT-TATTTA
1 TATTAATAATTTATAATATATATTTA
* *
63809 TATTAATAATTTATTATATATTATTAA
1 TATTAATAATTTATAATATA-TATTTA
63836 TA-TAATATATTGCTATAATATAT
1 TATTAATA-ATT--TATAATATAT
63859 CTGAGTATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
25 20 0.34
26 6 0.10
27 16 0.27
28 9 0.15
29 8 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (26 bp):
TATTAATAATTTATAATATATATTTA
Found at i:63829 original size:27 final size:25
Alignment explanation
Indices: 63756--63856 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 25
63746 TATTACTCAT
63756 TATTAATAATTTAATAATATTATATTTA
1 TATTAATAATTT-ATAATA-T-TATTTA
** **
63784 TAAAAATAATAGATAATATTATTTA
1 TATTAATAATTTATAATATTATTTA
*
63809 TATTAATAATTTATTATATATTATTAA
1 TATTAATAATTTA-TA-ATATTATTTA
63836 TA-TAATATATTGCTATAATAT
1 TATTAATA-ATT--TATAATAT
63857 ATCTGAGTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
25 15 0.25
26 8 0.14
27 24 0.41
28 10 0.17
29 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (25 bp):
TATTAATAATTTATAATATTATTTA
Found at i:63844 original size:18 final size:18
Alignment explanation
Indices: 63756--63845 Score: 60
Period size: 18 Copynumber: 5.1 Consensus size: 18
63746 TATTACTCAT
*
63756 TATTAATAATTTAATA-A
1 TATTAATAATATAATATA
* *
63773 TATT-ATATTTATAA-AAA
1 TATTAATA-ATATAATATA
* * *
63790 TAATAGATAATATTATTTA
1 TATTA-ATAATATAATATA
* *
63809 TATTAATAATTTATTATA
1 TATTAATAATATAATATA
*
63827 TATTATTAATATAATATA
1 TATTAATAATATAATATA
63845 T
1 T
63846 TGCTATAATA
Statistics
Matches: 53, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
16 4 0.08
17 12 0.23
18 29 0.55
19 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
TATTAATAATATAATATA
Found at i:63889 original size:14 final size:14
Alignment explanation
Indices: 63872--63921 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
63862 AGTATATATT
63872 AATATAATATTAAA
1 AATATAATATTAAA
* **
63886 AATATAATGTTATT
1 AATATAATATTAAA
63900 AATATAATATTAAA
1 AATATAATATTAAA
63914 AATATAAT
1 AATATAAT
63922 GTTATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AATATAATATTAAA
Found at i:63901 original size:17 final size:17
Alignment explanation
Indices: 63879--63936 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
63869 ATTAATATAA
63879 TATTAAAAATATAATGT
1 TATTAAAAATATAATGT
63896 TATT---AATATAA---
1 TATTAAAAATATAATGT
63907 TATTAAAAATATAATGT
1 TATTAAAAATATAATGT
*
63924 TATTAAAATTATA
1 TATTAAAAATATA
63937 TTATATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
11 4 0.12
14 14 0.41
17 16 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TATTAAAAATATAATGT
Found at i:63903 original size:28 final size:28
Alignment explanation
Indices: 63868--63939 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
63858 TCTGAGTATA
63868 TATTAATATAATATTAAAAATATAATGT
1 TATTAATATAATATTAAAAATATAATGT
63896 TATTAATATAATATTAAAAATATAATGT
1 TATTAATATAATATTAAAAATATAATGT
* *
63924 TATTAAAATTATATTA
1 TATTAATATAATATTA
63940 TATGTATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
TATTAATATAATATTAAAAATATAATGT
Found at i:67214 original size:23 final size:23
Alignment explanation
Indices: 67174--67228 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
67164 ACATATACCA
* * *
67174 AAAGATAGATGAAAGTGTGTCAT
1 AAAGATAAAAGAAAGTGTGTCAC
*
67197 AAAGATAAAAGAACGTGTGTCAC
1 AAAGATAAAAGAAAGTGTGTCAC
67220 AAAGATAAA
1 AAAGATAAA
67229 GTTACTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (23 bp):
AAAGATAAAAGAAAGTGTGTCAC
Found at i:73224 original size:2 final size:2
Alignment explanation
Indices: 73219--73248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73209 AAATTACAAT
73219 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
73249 AAGAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74025 original size:37 final size:37
Alignment explanation
Indices: 73975--74050 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
73965 GTAAGTTAAG
*
73975 TTAGATCTGTTTATCATCTTCCATGGATCTTCTGAGA
1 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
74012 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
1 TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
74049 TT
1 TT
74051 TGAGCTCATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (37 bp):
TTAGATCTGTTTATCATCTTCCATAGATCTTCTGAGA
Found at i:76318 original size:35 final size:35
Alignment explanation
Indices: 76257--76328 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
76247 AATTTCAAAT
**
76257 TAATTTAATTTTATTCTAAATCTTAAATTCTAAAA
1 TAATTTAATTACATTCTAAATCTTAAATTCTAAAA
*
76292 TAATTTAATTACATTTTAAAAT-TTAAATTCTAAAA
1 TAATTTAATTACATTCT-AAATCTTAAATTCTAAAA
76327 TA
1 TA
76329 CTTCAATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (35 bp):
TAATTTAATTACATTCTAAATCTTAAATTCTAAAA
Found at i:77537 original size:35 final size:35
Alignment explanation
Indices: 77392--77538 Score: 179
Period size: 35 Copynumber: 4.2 Consensus size: 35
77382 ATTCCTCCTT
* * * * *
77392 AAATTGAAATATTTTAGAATTT-GGGTTTTATATTG
1 AAATTGAATTACTTTGGAATTTAGGG-TTTAGAATG
* * *
77427 TAATTAAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
77462 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
* * *
77497 AAATTGAATTGCTTTGGAATTTGGGGTTTAAAATG
1 AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
77532 AAATTGA
1 AAATTGA
77539 GGAATGTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
35 96 0.97
36 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAATTACTTTGGAATTTAGGGTTTAGAATG
Found at i:78288 original size:9 final size:9
Alignment explanation
Indices: 78276--78301 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
78266 TAATATTTTA
78276 TATTTAATT
1 TATTTAATT
78285 TATTTAATT
1 TATTTAATT
78294 TATTTAAT
1 TATTTAAT
78302 ATGTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:78297 original size:25 final size:25
Alignment explanation
Indices: 78269--78323 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
78259 ATATTTTTAA
*
78269 TATTTTATAT-TTAATTTATTTAATT
1 TATTTTATATGTT-ACTTATTTAATT
*
78294 TATTTAATATGTTACTTATTTAATT
1 TATTTTATATGTTACTTATTTAATT
78319 T-TTTT
1 TATTTT
78324 GCAGATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 3 0.12
25 21 0.81
26 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTTTATATGTTACTTATTTAATT
Found at i:82198 original size:27 final size:25
Alignment explanation
Indices: 82148--82198 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
82138 TTGATATGCA
82148 TCATTAATATAAAAATTTAGTAAAC
1 TCATTAATATAAAAATTTAGTAAAC
* *
82173 TCATTAATGATATTAAATTTATTAAA
1 TCATTAAT-ATA-AAAATTTAGTAAA
82199 ATGATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 3 0.14
27 11 0.50
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (25 bp):
TCATTAATATAAAAATTTAGTAAAC
Found at i:86810 original size:2 final size:2
Alignment explanation
Indices: 86803--86843 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
86793 TTAATAAGTA
*
86803 AT AT AT AT AG AT -T 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
86844 TTCCTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.