Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007878.1 Corchorus capsularis cultivar CVL-1 contig07899, 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: 84010
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4031 original size:9 final size:9
Alignment explanation
Indices: 4011--4043 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
4001 AGTTATATCG
4011 AAAAATATAA
1 AAAAATA-AA
4021 AAAAATAAA
1 AAAAATAAA
4030 AAAAATAAA
1 AAAAATAAA
4039 AAAAA
1 AAAAA
4044 ATTCGACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:4044 original size:10 final size:10
Alignment explanation
Indices: 4011--4045 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
4001 AGTTATATCG
*
4011 AAAAATATAA
1 AAAAATAAAA
4021 AAAAAT-AAA
1 AAAAATAAAA
4030 AAAAATAAAA
1 AAAAATAAAA
4040 AAAAAT
1 AAAAAT
4046 TCGACCAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:5521 original size:33 final size:32
Alignment explanation
Indices: 5424--5528 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
5414 TTGAAAAGAG
*
5424 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
5457 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
5490 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
5523 TGTTTT
1 TGTTTT
5529 GGATGTTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:5542 original size:33 final size:34
Alignment explanation
Indices: 5477--5563 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 34
5467 GTTGTTTGCA
* * **
5477 ATGACACTAAATCTGTTTT-AAGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTTGGAGTGTTAATTGTG
*
5510 ATGATACTAAATCTGTTTTGGA-TGTTAATTGTG
1 ATGAAACTAAATCTGTTTTGGAGTGTTAATTGTG
5543 ATGAAAAC-AAATCTGTTTTGG
1 ATG-AAACTAAATCTGTTTTGG
5564 TTGATCATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 43 0.91
34 4 0.09
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (34 bp):
ATGAAACTAAATCTGTTTTGGAGTGTTAATTGTG
Found at i:5591 original size:33 final size:33
Alignment explanation
Indices: 5554--5692 Score: 230
Period size: 33 Copynumber: 4.3 Consensus size: 33
5544 TGAAAACAAA
5554 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
5587 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
5620 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * *
5653 TTTGTTTTGGTTG---ATGGCATTGAAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
5683 TCTGTTTTGG
1 TCTGTTTTGG
5693 GTGAAAAGAA
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
30 24 0.24
33 78 0.76
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:6087 original size:30 final size:30
Alignment explanation
Indices: 6035--6093 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
6025 CAAGGGGGAG
*
6035 GGAATGATGCGCCCAAGGCTTATCATGGAA
1 GGAATGATGCGCCCAAGACTTATCATGGAA
* *
6065 GGAATTATGCG-CCAATGACTTATTATGGA
1 GGAATGATGCGCCCAA-GACTTATCATGGA
6094 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (30 bp):
GGAATGATGCGCCCAAGACTTATCATGGAA
Found at i:14101 original size:15 final size:15
Alignment explanation
Indices: 14058--14103 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
14048 GACAATATTT
14058 AAATTTAAAGAAAAA
1 AAATTTAAAGAAAAA
** * *
14073 AAAAATGAACAAAAA
1 AAATTTAAAGAAAAA
14088 AAATTTAAAGAAAAA
1 AAATTTAAAGAAAAA
14103 A
1 A
14104 GCCAAGCCCA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (15 bp):
AAATTTAAAGAAAAA
Found at i:23640 original size:6 final size:7
Alignment explanation
Indices: 23605--23639 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
23595 ACTAGTTCTG
23605 TGAAAAC
1 TGAAAAC
23612 TGAAAAC
1 TGAAAAC
23619 TGAAAAC
1 TGAAAAC
23626 TGAAAAC
1 TGAAAAC
23633 T-AAAAC
1 TGAAAAC
23639 T
1 T
23640 ATGTTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.17
Consensus pattern (7 bp):
TGAAAAC
Found at i:23881 original size:2 final size:2
Alignment explanation
Indices: 23874--23899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23864 TCTGTTGTGC
23874 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
23900 TTTAAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26713 original size:103 final size:103
Alignment explanation
Indices: 26538--26787 Score: 312
Period size: 108 Copynumber: 2.4 Consensus size: 103
26528 GGGTTAAATT
* * *
26538 GGGCTAAATTTAGTG-AATTAGTTATATT-TTTTATTTCTAAAACTCTATAACAATATTATTAAT
1 GGGCTAAATTTAGTGAAATTAATT-TTTTATTTTATTTCTAAAACCCTATAACAATATTATTAAT
* *
26601 TATGGAATTTATCCTTAAAAT-AAA-AAAA-TTAATTTG
65 TATGAAATTTACCCTTAAAATAAAATAAAATTTAATTTG
* *
26637 GGGTTAAATTTAGTGAAATTAATTTTTGTATTTTATTTCTATAACCCTATAACAATAAATTATTA
1 GGGCTAAATTTAGTGAAATTAATTTTT-TATTTTATTTCTAAAACCCTATAACAAT--ATTATTA
*
26702 ATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTG
63 ATTATGAAATTTACCCTTAAAAT-AAAATAAAA-TTTAATTTG
* * *
26745 GGGCTAAACTTAGTGAAATTAATTTTATATTTTAATTCTAAAA
1 GGGCTAAATTTAGTGAAATTAATTTTTTATTTTATTTCTAAAA
26788 TTCTATAATA
Statistics
Matches: 128, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
99 16 0.12
100 8 0.06
101 24 0.19
103 27 0.21
105 3 0.02
106 4 0.03
107 14 0.11
108 32 0.25
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (103 bp):
GGGCTAAATTTAGTGAAATTAATTTTTTATTTTATTTCTAAAACCCTATAACAATATTATTAATT
ATGAAATTTACCCTTAAAATAAAATAAAATTTAATTTG
Found at i:26803 original size:108 final size:102
Alignment explanation
Indices: 26538--26795 Score: 324
Period size: 101 Copynumber: 2.5 Consensus size: 102
26528 GGGTTAAATT
* * *
26538 GGGCTAAATTTAGTG-AATTAGTTATATTTTTTATTTCTAAAACTCTATAACAAT--ATTATTAA
1 GGGCTAAATTTAGTGAAATTAATTTTATATTTTATTTCTAAAACTCTATAACAATAAATTATTAA
* *
26600 TTATGGAATTTATCCTTAAAATAAAAAAATTAATTTG
66 TTATGAAATTTACCCTTAAAATAAAAAAATTAATTTG
* * * *
26637 GGGTTAAATTTAGTGAAATTAATTTTTGTATTTTATTTCTATAACCCTATAACAATAAATTATTA
1 GGGCTAAATTTAGTGAAATTAA-TTTTATATTTTATTTCTAAAACTCTATAACAATAAATTATTA
*
26702 ATTTTGAAATTTACCCTTAAAATAAAAATAAAATTTTAATTTG
65 ATTATGAAATTTACCCTTAAAAT--AAA-AAAA--TTAATTTG
* * *
26745 GGGCTAAACTTAGTGAAATTAATTTTATATTTTAATTCTAAAATTCTATAA
1 GGGCTAAATTTAGTGAAATTAATTTTATATTTTATTTCTAAAACTCTATAA
26796 TAAATAAAAA
Statistics
Matches: 133, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
99 14 0.11
100 5 0.04
101 28 0.21
103 27 0.20
105 3 0.02
106 4 0.03
107 24 0.18
108 28 0.21
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (102 bp):
GGGCTAAATTTAGTGAAATTAATTTTATATTTTATTTCTAAAACTCTATAACAATAAATTATTAA
TTATGAAATTTACCCTTAAAATAAAAAAATTAATTTG
Found at i:26857 original size:2 final size:2
Alignment explanation
Indices: 26850--26880 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26840 GGTAAGAAGA
26850 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26881 TATTTTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:26884 original size:10 final size:11
Alignment explanation
Indices: 26851--26884 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
26841 GTAAGAAGAA
26851 TATATATATAT
1 TATATATATAT
26862 ATATATATATAT
1 -TATATATATAT
26874 TATATAT-TAT
1 TATATATATAT
26884 T
1 T
26885 TTTAACTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATAT
Found at i:30415 original size:31 final size:31
Alignment explanation
Indices: 30347--30650 Score: 253
Period size: 30 Copynumber: 9.6 Consensus size: 31
30337 AGTCTCCAAA
* *
30347 TGACACCAGAAGTTGTC-ATGATAAATCT-CCAT
1 TGACACCAGAAGTTGTCAATGAT--CT-TACAAT
* * *
30379 TGACACCAAAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* *
30410 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* * *
30441 TGACACCATAAGTTGTC-ATGGTCTTACAAA
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
*
30471 TGACACCAGAAGTTGTC-ATGATGTTACAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
*
30501 TGACACCAGAAGTTGTCAATAATCTTACAGATTTTACAAT
1 TGACACCAGAAGTTGTC---AA---T---GATCTTACAAT
* *
30541 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
* *
30571 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
1 TGACACCAGAAGTTGTCAATGATCTTACAAT
** * *
30601 TGACACTTGAAGATGTC-ATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCAATGATCTTA--CAAT
30633 TGACACCAGAAGTTGTCA
1 TGACACCAGAAGTTGTCA
30651 TATACACCAT
Statistics
Matches: 232, Mismatches: 25, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
30 117 0.50
31 46 0.20
32 34 0.15
33 5 0.02
34 1 0.00
36 1 0.00
37 1 0.00
40 27 0.12
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (31 bp):
TGACACCAGAAGTTGTCAATGATCTTACAAT
Found at i:30618 original size:100 final size:100
Alignment explanation
Indices: 30434--30618 Score: 271
Period size: 100 Copynumber: 1.9 Consensus size: 100
30424 GTCAATAATC
* *
30434 TTACAAATGACACCATAAGTTGTCATGGTCTTACAAATGACACCAGAAGTTGTCATGATGTTACA
1 TTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATGTTACA
*
30499 ATTGACACCAGAAGTTGTCAATAATCTTACAGATT
66 ATTGACACCAGAAGATGTCAATAATCTTACAGATT
* * * * * *
30534 TTACAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCA
1 TTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATGTTACA
**
30599 ATTGACACTTGAAGATGTCA
66 ATTGACACCAGAAGATGTCA
30619 TGATTTTATT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 74 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (100 bp):
TTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATGTTACA
ATTGACACCAGAAGATGTCAATAATCTTACAGATT
Found at i:32699 original size:39 final size:39
Alignment explanation
Indices: 32642--32722 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
32632 TTTATCGAGG
32642 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
1 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
*
32681 AAACCAAGTTGCCTTGATATGGCACAAAATAAAGAGAGC
1 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
32720 AAA
1 AAA
32723 ATACTGAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (39 bp):
AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
Found at i:32796 original size:33 final size:33
Alignment explanation
Indices: 32733--32796 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
32723 ATACTGAATA
* **
32733 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
* *
32766 ATATTGCCCCTGTAGTGGCACAAACCCATGA
1 ATATTGCCCCTGAAGAGGCACAAACCCATGA
32797 AAAGATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCACAAACCCATGAGC
Found at i:40855 original size:6 final size:6
Alignment explanation
Indices: 40836--40865 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40826 TGCATTTTTA
*
40836 CTATAT CTACAT CTATAT CTATAT CTATAT
1 CTATAT CTATAT CTATAT CTATAT CTATAT
40866 ATTAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (6 bp):
CTATAT
Found at i:44108 original size:22 final size:22
Alignment explanation
Indices: 44072--44115 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44062 AATTTCAGGA
*
44072 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
44094 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
44116 GCGCAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:44129 original size:52 final size:52
Alignment explanation
Indices: 44067--44167 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
44057 ACAAGAATTT
*
44067 CAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCG
1 CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTTGCG
*
44119 CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACGGAAGTTGTT
1 CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTT
44168 CCGGAAAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (52 bp):
CAGGACAACTTCGGCCCAGAACTTGTACAACTTCGGGACAGAAGTTGTTGCG
Found at i:58397 original size:42 final size:42
Alignment explanation
Indices: 58338--58424 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
58328 AAAGGGTCGA
58338 ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGACCCGGGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGACCCGGGCG
* * *
58380 ATGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGACCCGGGCG
58422 ATG
1 ATG
58425 TCCCATGAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.09, C:0.26, G:0.45, T:0.20
Consensus pattern (42 bp):
ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGACCCGGGCG
Found at i:63838 original size:10 final size:10
Alignment explanation
Indices: 63823--63859 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
63813 TTTCTGGTCG
63823 ATTTTTTTTT
1 ATTTTTTTTT
*
63833 ATTTTTTTTG
1 ATTTTTTTTT
63843 ATTTTTTTTAT
1 ATTTTTTTT-T
63854 ATTTTT
1 ATTTTT
63860 CGATATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:63839 original size:9 final size:9
Alignment explanation
Indices: 63825--63859 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
63815 TCTGGTCGAT
63825 TTTTTTTTA
1 TTTTTTTTA
63834 TTTTTTTTGA
1 TTTTTTTT-A
63844 TTTTTTTTA
1 TTTTTTTTA
*
63853 TATTTTT
1 TTTTTTT
63860 CGATATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:64915 original size:30 final size:30
Alignment explanation
Indices: 64879--64944 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
64869 AAAGGGTCGA
64879 ATGGCCGGTTGTGGCCGAATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCGAATGGCCCGTGCG
* * *
64909 ATGGCCGGTTGTGGCTGGATGGCTCGTGCG
1 ATGGCCGGTTGTGGCCGAATGGCCCGTGCG
64939 ATGGCC
1 ATGGCC
64945 CGTGCGATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.09, C:0.24, G:0.44, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGAATGGCCCGTGCG
Found at i:72860 original size:19 final size:18
Alignment explanation
Indices: 72823--72862 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
72813 TTCTTGAAAT
*
72823 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
72841 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
72860 AAT
1 AAT
72863 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:81726 original size:6 final size:6
Alignment explanation
Indices: 81717--81749 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
81707 AAAAGCAAGC
81717 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
81750 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:81761 original size:12 final size:13
Alignment explanation
Indices: 81746--81790 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
81736 AATCTAAATC
81746 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
81758 TAAAGCAAATTAA
1 TAAAGCAGATTAA
81771 TAAAGCAGATTAA
1 TAAAGCAGATTAA
81784 TAAAGCA
1 TAAAGCA
81791 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:81797 original size:25 final size:25
Alignment explanation
Indices: 81746--81798 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
81736 AATCTAAATC
*
81746 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
81771 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
81796 TAA
1 TAA
81799 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.