Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2792861 original size:24 final size:24
Alignment explanation
Indices: 2792816--2792862 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2792806 TTCCAACAGT
*
2792816 TATGCCACTTGAAGTTCAAAAAGA
1 TATGCCACTTGAAGTGCAAAAAGA
* *
2792840 TATGTCACTTGAAGTGCCAAAAG
1 TATGCCACTTGAAGTGCAAAAAG
2792863 TTGTGATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (24 bp):
TATGCCACTTGAAGTGCAAAAAGA
Found at i:2793933 original size:30 final size:31
Alignment explanation
Indices: 2793897--2793956 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2793887 CTTAGCTTTA
**
2793897 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
2793927 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2793957 GGAAGCATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2804043 original size:18 final size:20
Alignment explanation
Indices: 2803997--2804060 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 20
2803987 GTGATGCAAC
2803997 AAAAGCAACAAAAATAGAAAA
1 AAAAG-AACAAAAATAGAAAA
*
2804018 AGAAAGAACAAAAA-A-AACA
1 A-AAAGAACAAAAATAGAAAA
2804037 AAAAGAA-AAGAAA-AGAAAA
1 AAAAGAACAA-AAATAGAAAA
2804056 GAAAA
1 -AAAA
2804061 AGACTCCTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 2 0.05
18 10 0.27
19 7 0.19
20 5 0.14
21 9 0.24
22 4 0.11
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAGAACAAAAATAGAAAA
Found at i:2804046 original size:23 final size:22
Alignment explanation
Indices: 2803997--2804063 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
2803987 GTGATGCAAC
* *
2803997 AAAAGCAACAAAAATAGAAAAAG
1 AAAAG-AACAAAAAAACAAAAAG
2804020 -AAAGAACAAAAAAAACAAAAAG
1 AAAAGAAC-AAAAAAACAAAAAG
* *
2804042 AAAAGAA-AAGAAAAGAAAAAG
1 AAAAGAACAAAAAAACAAAAAG
2804063 A
1 A
2804064 CTCCTACATC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 16 0.42
22 16 0.42
23 6 0.16
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (22 bp):
AAAAGAACAAAAAAACAAAAAG
Found at i:2807085 original size:19 final size:20
Alignment explanation
Indices: 2807048--2807087 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
2807038 GGATAATAAT
2807048 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
2807068 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
2807087 A
1 A
2807088 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:2811366 original size:8 final size:8
Alignment explanation
Indices: 2811345--2811379 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2811335 TTTAAACTTC
*
2811345 TCTTTTTT
1 TCTTCTTT
*
2811353 TTTTCTTT
1 TCTTCTTT
2811361 TCTTCTTT
1 TCTTCTTT
2811369 TCTTCTTT
1 TCTTCTTT
2811377 TCT
1 TCT
2811380 GATTTTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TCTTCTTT
Found at i:2811684 original size:22 final size:22
Alignment explanation
Indices: 2811658--2811706 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
2811648 TAAAGGGGAT
2811658 AATAAT-ATAAGTAATGAAAAT-A
1 AATAATAATAAG-AAT-AAAATGA
2811680 AATAATAATAAGAATAAAATGA
1 AATAATAATAAGAATAAAATGA
2811702 AATAA
1 AATAA
2811707 AGAAAGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (22 bp):
AATAATAATAAGAATAAAATGA
Found at i:2812742 original size:13 final size:13
Alignment explanation
Indices: 2812724--2812756 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2812714 TTCATCTTGT
2812724 AGCTCAAATATTC
1 AGCTCAAATATTC
2812737 AGCTCAAATATTC
1 AGCTCAAATATTC
2812750 AGCTCAA
1 AGCTCAA
2812757 TCCAGCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (13 bp):
AGCTCAAATATTC
Found at i:2824106 original size:51 final size:52
Alignment explanation
Indices: 2824003--2824109 Score: 162
Period size: 56 Copynumber: 2.0 Consensus size: 52
2823993 CATTATGTCA
*
2824003 TTCACGTGCATTCACATTCAAATAGCATGGTATCATTTATTTTCTTTTTAATTCAC
1 TTCACGTGCATTCACATTCAAATAGCATGATATCATTTA---T-TTTTTAATTCAC
2824059 TTCACGTGCATTCACATTCAAATAGCATGATATCATTTA-TTTTTAATTCAC
1 TTCACGTGCATTCACATTCAAATAGCATGATATCATTTATTTTTTAATTCAC
2824110 ACATGGCATT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 12 0.24
56 38 0.76
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (52 bp):
TTCACGTGCATTCACATTCAAATAGCATGATATCATTTATTTTTTAATTCAC
Found at i:2826688 original size:30 final size:31
Alignment explanation
Indices: 2826652--2826711 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2826642 CTTAGCTTTA
**
2826652 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
2826682 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2826712 GGAAGCATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2829723 original size:24 final size:24
Alignment explanation
Indices: 2829678--2829724 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2829668 TTCCAACAGT
*
2829678 TATGCCACTTGAAGTTCAAAAAGA
1 TATGCCACTTGAAGTGCAAAAAGA
* *
2829702 TATGTCACTTGAAGTGCCAAAAG
1 TATGCCACTTGAAGTGCAAAAAG
2829725 TTGTGATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (24 bp):
TATGCCACTTGAAGTGCAAAAAGA
Found at i:2830794 original size:30 final size:31
Alignment explanation
Indices: 2830758--2830817 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2830748 CTTAGCTTTA
**
2830758 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
2830788 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2830818 GGAAGCATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2848855 original size:250 final size:253
Alignment explanation
Indices: 2848412--2848916 Score: 971
Period size: 250 Copynumber: 2.0 Consensus size: 253
2848402 TGTAAGATAC
2848412 TATCCTCACAACCATCCCTTTGTTTCATCAGCCATAACCCATAGACATATCAATCATCTTCCGCT
1 TATCCTCACAACCATCCCTTTGTTTCATCAGCCATAACCCATAGACATATCAATCATCTTCCGCT
2848477 TCCATCTCTCATTTAAACAGCCCACCTATTTACCCATACATTTACCACCCTTAACCATATCTTTT
66 TCCA-CTCTCATTTAAACAGCCCACCTATTTACCCATACATTTACCACCCTTAACCATATCTTTT
2848542 GAGTCATTCATTTGTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCAATTGTTAAGGTACA
130 GAGTCATTCATTTGTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCAATTGTTAAGGTACA
2848607 AATGCCTTACATCACACTTGAAGTGCCAAGAGTTTGGATCACTG-A-TCCAAGTAAATT
195 AATGCCTTACATCACACTTGAAGTGCCAAGAGTTTGGATCACTGAACTCCAAGTAAATT
2848664 TATCCTCACAACCATCCCTTTGTTTCATCAGCCATAACCCATAGACATATCAATCATCTTCCGCT
1 TATCCTCACAACCATCCCTTTGTTTCATCAGCCATAACCCATAGACATATCAATCATCTTCCGCT
2848729 TCCA-TCTCATTTAAACAGCCCACCTATTTACCCATACATTTACCACCCTTAACCATATCTTTTG
66 TCCACTCTCATTTAAACAGCCCACCTATTTACCCATACATTTACCACCCTTAACCATATCTTTTG
2848793 AGTCATTCATTTGTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCAATTGTTAAGGTACAA
131 AGTCATTCATTTGTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCAATTGTTAAGGTACAA
2848858 ATGCCTTACATCACACTTGAAGTGCCAAGAGTTTGGATCACTGATACTCCAAGTAAATT
196 ATGCCTTACATCACACTTGAAGTGCCAAGAGTTTGGATCACTGA-ACTCCAAGTAAATT
2848917 GCACATATTG
Statistics
Matches: 250, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
250 168 0.67
252 70 0.28
253 12 0.05
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (253 bp):
TATCCTCACAACCATCCCTTTGTTTCATCAGCCATAACCCATAGACATATCAATCATCTTCCGCT
TCCACTCTCATTTAAACAGCCCACCTATTTACCCATACATTTACCACCCTTAACCATATCTTTTG
AGTCATTCATTTGTGCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCAATTGTTAAGGTACAA
ATGCCTTACATCACACTTGAAGTGCCAAGAGTTTGGATCACTGAACTCCAAGTAAATT
Found at i:2849760 original size:19 final size:20
Alignment explanation
Indices: 2849718--2849760 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2849708 GAAACCCCTT
*
2849718 TGAAAACACATGATTTTCAA
1 TGAAAACACATAATTTTCAA
*
2849738 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTCAA
2849757 TGAA
1 TGAA
2849761 GGTAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTCAA
Found at i:2850705 original size:17 final size:17
Alignment explanation
Indices: 2850685--2850728 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2850675 TCTTTTAATG
*
2850685 GAATACATCCTTTGGCC
1 GAATTCATCCTTTGGCC
2850702 GAATTCATCCTTTGGCC
1 GAATTCATCCTTTGGCC
*
2850719 AAATTCATCC
1 GAATTCATCC
2850729 CACCTTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (17 bp):
GAATTCATCCTTTGGCC
Found at i:2850847 original size:10 final size:10
Alignment explanation
Indices: 2850832--2850860 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2850822 TTTGGCTTCT
2850832 TGCATGAATA
1 TGCATGAATA
2850842 TGCATGAATA
1 TGCATGAATA
2850852 TGCATGAAT
1 TGCATGAAT
2850861 GGATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (10 bp):
TGCATGAATA
Found at i:2853984 original size:17 final size:17
Alignment explanation
Indices: 2853964--2854007 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2853954 TCTTTTAATG
*
2853964 GAATACATCCTTTGGCC
1 GAATTCATCCTTTGGCC
2853981 GAATTCATCCTTTGGCC
1 GAATTCATCCTTTGGCC
2853998 GAATTCATCC
1 GAATTCATCC
2854008 CACCTTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.32
Consensus pattern (17 bp):
GAATTCATCCTTTGGCC
Found at i:2855010 original size:11 final size:11
Alignment explanation
Indices: 2854994--2855022 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2854984 TCCATGTGTT
2854994 TGAGCTGAAGA
1 TGAGCTGAAGA
2855005 TGAGCTGAAGA
1 TGAGCTGAAGA
2855016 TGAGCTG
1 TGAGCTG
2855023 GCCATAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (11 bp):
TGAGCTGAAGA
Found at i:2857500 original size:17 final size:17
Alignment explanation
Indices: 2857478--2857510 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2857468 ATCGGCTAAA
2857478 AGAAATGGTTATGGTAT
1 AGAAATGGTTATGGTAT
2857495 AGAAATGGTTATGGTA
1 AGAAATGGTTATGGTA
2857511 GATGTAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (17 bp):
AGAAATGGTTATGGTAT
Found at i:2857749 original size:30 final size:30
Alignment explanation
Indices: 2857715--2857772 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2857705 TGTGAGTGTA
2857715 CTTTGCAACTTT-TTATTCTCTTTTCTTTTG
1 CTTTG-AACTTTCTTATTCTCTTTTCTTTTG
* * *
2857745 CTTTGAATTTTCTTCTTTTCTTTTCTTT
1 CTTTGAACTTTCTTATTCTCTTTTCTTT
2857773 CTTTTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (30 bp):
CTTTGAACTTTCTTATTCTCTTTTCTTTTG
Found at i:2858044 original size:15 final size:16
Alignment explanation
Indices: 2858024--2858057 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2858014 TATATTGGAA
*
2858024 ATAAGAAAT-GAATGG
1 ATAAGAAATAAAATGG
2858039 ATAAGAAATAAAATGG
1 ATAAGAAATAAAATGG
2858055 ATA
1 ATA
2858058 GAGATGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (16 bp):
ATAAGAAATAAAATGG
Found at i:2868549 original size:15 final size:15
Alignment explanation
Indices: 2868513--2868542 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2868503 GTGCTTCAAC
2868513 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
2868527 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
2868542 T
1 T
2868543 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:2868625 original size:11 final size:11
Alignment explanation
Indices: 2868609--2868633 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2868599 TTGTTTTTCT
2868609 TTCACTTGCAC
1 TTCACTTGCAC
2868620 TTCACTTGCAC
1 TTCACTTGCAC
2868631 TTC
1 TTC
2868634 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:2881396 original size:23 final size:23
Alignment explanation
Indices: 2881366--2881410 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2881356 TTTCTTTTCT
2881366 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
* *
2881389 TTTTGAGTGCTTTGATTTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
2881411 TACTGGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.13, G:0.16, T:0.60
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:2889461 original size:22 final size:25
Alignment explanation
Indices: 2889412--2889465 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
2889402 CTTTTCTTTT
2889412 TTTCTTCCTCTTTGAGTGCTTTAAA
1 TTTCTTCCTCTTTGAGTGCTTTAAA
* *
2889437 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTAAA
2889460 TTTCTT
1 TTTCTT
2889466 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTAAA
Found at i:2891779 original size:17 final size:17
Alignment explanation
Indices: 2891721--2891780 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
2891711 GAGTTGTAAG
*
2891721 TTATCTTCACTTTC-TTA
1 TTAT-TTCATTTTCTTTA
*
2891738 CTATTTCA-TTTCTTTA
1 TTATTTCATTTTCTTTA
* * *
2891754 TTCTTTCATTTTTTTTC
1 TTATTTCATTTTCTTTA
2891771 TTATTTCATT
1 TTATTTCATT
2891781 ACCATATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 13 0.37
17 18 0.51
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTTTCTTTA
Found at i:2895560 original size:36 final size:35
Alignment explanation
Indices: 2895514--2895625 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 35
2895504 TAAGATACTA
*
2895514 CCTA-AACATCACCTTCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
2895549 CCTATAACATCACCATCTTCCATTACAATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
2895584 CCTATATCCTAACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
*
2895619 TCTATAA
1 CCTATAA
2895626 AACCACCAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 43 0.68
36 20 0.32
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:2904369 original size:19 final size:19
Alignment explanation
Indices: 2904345--2904382 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2904335 AGGAGCTAGC
2904345 ATGTAGCTGAACTTAGCTG
1 ATGTAGCTGAACTTAGCTG
2904364 ATGTAGCTGAACTTAGCTG
1 ATGTAGCTGAACTTAGCTG
2904383 GAGGAGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
ATGTAGCTGAACTTAGCTG
Found at i:2913584 original size:11 final size:11
Alignment explanation
Indices: 2913568--2913623 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
2913558 ATTGGAGTGC
2913568 AAAAAGAAAAG
1 AAAAAGAAAAG
2913579 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
2913590 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
2913604 AAAAAGAAAAG
1 AAAAAGAAAAG
2913615 AAAAAGAAA
1 AAAAAGAAA
2913624 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:2914467 original size:11 final size:13
Alignment explanation
Indices: 2914435--2914464 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2914425 TGGCCAAAGA
2914435 TGAAAAGGTATGT
1 TGAAAAGGTATGT
2914448 TGAAAAGGTATG-
1 TGAAAAGGTATGT
2914460 TGAAA
1 TGAAA
2914465 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:2920151 original size:19 final size:20
Alignment explanation
Indices: 2920105--2920153 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2920095 TAATGAAGGG
2920105 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
2920125 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
2920144 AATAAAATAA
1 AATAAAATAA
2920154 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:2924740 original size:19 final size:20
Alignment explanation
Indices: 2924694--2924742 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2924684 TAATAAAGGG
2924694 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
2924714 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
2924733 AATAAAATAA
1 AATAAAATAA
2924743 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:2930195 original size:11 final size:11
Alignment explanation
Indices: 2930179--2930223 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2930169 TTTCAATTCA
2930179 TTTATCTT-TT
1 TTTATCTTATT
*
2930189 CTTTATCTTGTT
1 -TTTATCTTATT
*
2930201 TTAATCTTATT
1 TTTATCTTATT
2930212 TTTATCTTATT
1 TTTATCTTATT
2930223 T
1 T
2930224 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:2932920 original size:11 final size:11
Alignment explanation
Indices: 2932904--2932948 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2932894 TTTCAATTCA
2932904 TTTATCTT-TT
1 TTTATCTTATT
*
2932914 CTTTATCTTGTT
1 -TTTATCTTATT
*
2932926 TTAATCTTATT
1 TTTATCTTATT
2932937 TTTATCTTATT
1 TTTATCTTATT
2932948 T
1 T
2932949 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:2936597 original size:20 final size:20
Alignment explanation
Indices: 2936560--2936600 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2936550 GAATAATAAT
2936560 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
2936580 ATAAG-AATGAAAATGAAATA
1 ATAAGTAATGAAAA-GAAATA
2936600 A
1 A
2936601 AGAAAGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:2938449 original size:23 final size:23
Alignment explanation
Indices: 2938423--2938467 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2938413 AATTCCAGCA
2938423 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
2938446 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
2938468 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Done.