Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015784.1 Corchorus capsularis cultivar CVL-1 contig15805, 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: 98704
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3929 original size:3 final size:3
Alignment explanation
Indices: 3921--4034 Score: 95
Period size: 3 Copynumber: 37.7 Consensus size: 3
3911 ATTAAACATT
* *
3921 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * *
3969 ACA ACA ACA ACA ACA ACA ACA ATA ATA ATA ATA ATT TTA CTTCA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA
4015 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
4035 TTTTGTTATC
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.02
3 97 0.95
4 2 0.02
5 1 0.01
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:4715 original size:1 final size:1
Alignment explanation
Indices: 4709--4741 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
4699 TCAGAAAACT
4709 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4742 CTATCTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12567 original size:27 final size:27
Alignment explanation
Indices: 12524--12582 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
12514 AATTAGAAGC
*
12524 TCTAATCTCCCCATATGAGGTTACACT
1 TCTAATCTACCCATATGAGGTTACACT
*
12551 TCTAATCTACCCGTATGAGGTTACACT
1 TCTAATCTACCCATATGAGGTTACACT
12578 TCTAA
1 TCTAA
12583 AGCATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (27 bp):
TCTAATCTACCCATATGAGGTTACACT
Found at i:31738 original size:32 final size:30
Alignment explanation
Indices: 31681--31740 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
31671 GACAACTTGT
* * *
31681 CCCATGAATTTTCAAATTTATGACAATTTA
1 CCCATGAACTTTCAAATTGAGGACAATTTA
31711 CCCATTGAACTTTCTAAATTGAGGACAATT
1 CCCA-TGAACTTTC-AAATTGAGGACAATT
31741 ATCCCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (30 bp):
CCCATGAACTTTCAAATTGAGGACAATTTA
Found at i:35700 original size:2 final size:2
Alignment explanation
Indices: 35693--35718 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35683 ACCATCACAA
35693 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
35719 CATTGCTTTT
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:36197 original size:18 final size:17
Alignment explanation
Indices: 36174--36207 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36164 TATTCACTTG
36174 TTTCATCCATTGATTGTT
1 TTTCATCC-TTGATTGTT
*
36192 TTTCATGCTTGATTGT
1 TTTCATCCTTGATTGT
36208 ATGCATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (17 bp):
TTTCATCCTTGATTGTT
Found at i:38747 original size:21 final size:21
Alignment explanation
Indices: 38721--38760 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38711 GGAGCAAGGT
*
38721 TTTTCTTTTTTTCACGCTGGG
1 TTTTCTTTATTTCACGCTGGG
38742 TTTTCTTTATTTCACGCTG
1 TTTTCTTTATTTCACGCTG
38761 ATTTGGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.20, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTTCTTTATTTCACGCTGGG
Found at i:45420 original size:41 final size:41
Alignment explanation
Indices: 45360--45442 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
45350 CCTAAATTTT
* * *
45360 AGGCATGGGGTTGTATCGTTCCTGAAATACAGGCACTGAGA
1 AGGCACGGGGTTGTATCGTTCCTAAAATACAGGCACAGAGA
*
45401 AGGCACGGGGTTGTGTCGTTCCTAAAATACAGGCACAGAGA
1 AGGCACGGGGTTGTATCGTTCCTAAAATACAGGCACAGAGA
45442 A
1 A
45443 CGTCTATGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (41 bp):
AGGCACGGGGTTGTATCGTTCCTAAAATACAGGCACAGAGA
Found at i:45563 original size:9 final size:9
Alignment explanation
Indices: 45549--45573 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
45539 AATTCAAATA
45549 ATATTATTT
1 ATATTATTT
45558 ATATTATTT
1 ATATTATTT
45567 ATATTAT
1 ATATTAT
45574 ATAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATATTATTT
Found at i:46352 original size:33 final size:32
Alignment explanation
Indices: 46310--46371 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
46300 GGGACGACAT
46310 GCCATGGCTAGGCCGTCCC-CCTGGGGCGGCTGA
1 GCCATGGCTAGGCCG-CCCTCCT-GGGCGGCTGA
46343 GCCATGGCTAGGCCGCCCTCCTGGGCGGC
1 GCCATGGCTAGGCCGCCCTCCTGGGCGGC
46372 ACTACGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.08, C:0.39, G:0.39, T:0.15
Consensus pattern (32 bp):
GCCATGGCTAGGCCGCCCTCCTGGGCGGCTGA
Found at i:46382 original size:32 final size:32
Alignment explanation
Indices: 46310--46437 Score: 100
Period size: 32 Copynumber: 3.9 Consensus size: 32
46300 GGGACGACAT
46310 GCCATGGCTAGGCCGTCCCCCTGGGGCGGCTGA
1 GCCATGGCTAGGCCG-CCCCCTGGGGCGGCTGA
46343 GCCATGGCTAGGCCGCCCTCCT-GGGCGGCACT-A
1 GCCATGGCTAGGCCGCCC-CCTGGGGCGG--CTGA
* * * * * **
46376 -CGATGGCCAGGCTGCCCCCCCTAGGGCAGCTCT
1 GCCATGGCTAGGC--CGCCCCCTGGGGCGGCTGA
* *
46409 GCCATGGATAGACCGCCCCCTGGGGCGGC
1 GCCATGGCTAGGCCGCCCCCTGGGGCGGC
46438 ACCGGTACTA
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
32 34 0.45
33 22 0.29
34 19 0.25
ACGTcount: A:0.12, C:0.39, G:0.35, T:0.14
Consensus pattern (32 bp):
GCCATGGCTAGGCCGCCCCCTGGGGCGGCTGA
Found at i:46543 original size:33 final size:33
Alignment explanation
Indices: 46485--46606 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
46475 GTCTTGCTGC
* *
46485 CCTAGTGGGGCGGCT-AGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
* *
46517 CCTAGTGGGGCGGCTCCGCCGTGGCAGAGCCGC
1 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
46550 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
46583 CCTAGTGGGGAGGCTCCG-CGTGGC
1 CCTAGTGGGGAGGCTCCGCCGTGGC
46607 TAAGGGCAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
32 21 0.25
33 64 0.75
ACGTcount: A:0.11, C:0.31, G:0.43, T:0.15
Consensus pattern (33 bp):
CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
Found at i:51315 original size:40 final size:41
Alignment explanation
Indices: 51217--51315 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 41
51207 GGTAAGAGAT
* *
51217 TAATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAAAAG
1 TAATCAGTAAAATCGGTAATTAAAGAGTCAAAGTAAAAAAG
*
51258 TAATCAGTAAAAT-GGTAATT-AAGAGT-AAGAGTATAAGAAG
1 TAATCAGTAAAATCGGTAATTAAAGAGTCAA-AGTA-AAAAAG
51298 TAATCAGT-AAATCGGTAA
1 TAATCAGTAAAATCGGTAA
51316 AGAGTAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.04
39 14 0.27
40 24 0.46
41 12 0.23
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (41 bp):
TAATCAGTAAAATCGGTAATTAAAGAGTCAAAGTAAAAAAG
Found at i:51332 original size:16 final size:17
Alignment explanation
Indices: 51306--51369 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 17
51296 AGTAATCAGT
51306 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAGAGTAA
*
51323 AAAT-GGTAAAAAGTAGGGA
1 AAATCGGTAAAGAGTA---A
* *
51342 GTAATCAGTAAAGAGTAA
1 -AAATCGGTAAAGAGTAA
51360 AAAT-GGTAAA
1 AAATCGGTAAA
51370 ATGATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
16 15 0.42
17 7 0.19
18 1 0.03
19 1 0.03
20 3 0.08
21 9 0.25
ACGTcount: A:0.53, C:0.03, G:0.25, T:0.19
Consensus pattern (17 bp):
AAATCGGTAAAGAGTAA
Found at i:51495 original size:14 final size:14
Alignment explanation
Indices: 51457--51501 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
51447 GGATAAAATA
51457 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
51471 AGGAAAAAGTAAAG
1 AGTAATCAGTAAAG
51485 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
51498 AGTA
1 AGTA
51502 GAAATGGCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:51543 original size:14 final size:13
Alignment explanation
Indices: 51521--51561 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
51511 AAAAGTAGTA
51521 AAAAGTAATCAGAT
1 AAAAGTAATCAG-T
*
51535 AATAGTAATCAGT
1 AAAAGTAATCAGT
51548 AAAAGGTAATCAGT
1 AAAA-GTAATCAGT
51562 CAGAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.24
Consensus pattern (13 bp):
AAAAGTAATCAGT
Found at i:51576 original size:28 final size:29
Alignment explanation
Indices: 51511--51577 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
51501 AGAAATGGCA
*
51511 AAAAGTAGTAAAAAGTAATCAGATAATAGT
1 AAAA-TAGTAAAAAGTAATCAGATAAGAGT
* *
51541 --AATCAGTAAAAGGTAATCAG-TCAGAGT
1 AAAAT-AGTAAAAAGTAATCAGATAAGAGT
51568 AAAATAGTAA
1 AAAATAGTAA
51578 TCAGTAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 6 0.19
28 22 0.71
29 3 0.10
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (29 bp):
AAAATAGTAAAAAGTAATCAGATAAGAGT
Found at i:54144 original size:12 final size:12
Alignment explanation
Indices: 54127--54157 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54117 GAGAAGAAGA
54127 AGAAGGAGGAGG
1 AGAAGGAGGAGG
54139 AGAAGGAGGAGG
1 AGAAGGAGGAGG
*
54151 AGGAGGA
1 AGAAGGA
54158 TAGAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (12 bp):
AGAAGGAGGAGG
Found at i:54743 original size:16 final size:16
Alignment explanation
Indices: 54698--54815 Score: 150
Period size: 16 Copynumber: 7.4 Consensus size: 16
54688 GTTTTCTCGA
54698 GTCATTCGGGTTTCGG
1 GTCATTCGGGTTTCGG
*
54714 GTGA-TCTGGG-TTCGG
1 GTCATTC-GGGTTTCGG
*
54729 GTTATTCGGGTTTCGG
1 GTCATTCGGGTTTCGG
*
54745 GTCATTCGGGTCTCGG
1 GTCATTCGGGTTTCGG
*
54761 GTCATACGGGTTTCGG
1 GTCATTCGGGTTTCGG
* *
54777 GTCATTCCGGTCTCGG
1 GTCATTCGGGTTTCGG
*
54793 GTCATTCGGGTTCCGG
1 GTCATTCGGGTTTCGG
54809 GTCATTC
1 GTCATTC
54816 AGGTCTTGGG
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
15 13 0.15
16 74 0.85
ACGTcount: A:0.08, C:0.21, G:0.36, T:0.35
Consensus pattern (16 bp):
GTCATTCGGGTTTCGG
Found at i:54771 original size:32 final size:32
Alignment explanation
Indices: 54692--54827 Score: 177
Period size: 32 Copynumber: 4.3 Consensus size: 32
54682 CAGACAGTTT
* *
54692 TCTCGAGTCATTCGGGTTTCGGGTGA-TCTGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATTC-GGG
*
54724 T-TCGGGTTATTCGGGTTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATTCGGG
* *
54755 TCTCGGGTCATACGGGTTTCGGGTCATTCCGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATTCGGG
* *
54787 TCTCGGGTCATTCGGGTTCCGGGTCATTCAGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATTCGGG
*
54819 TCTTGGGTC
1 TCTCGGGTC
54828 TACCGGGTCT
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 25 0.27
32 67 0.73
ACGTcount: A:0.08, C:0.21, G:0.36, T:0.35
Consensus pattern (32 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATTCGGG
Found at i:54826 original size:16 final size:16
Alignment explanation
Indices: 54692--54842 Score: 148
Period size: 16 Copynumber: 9.5 Consensus size: 16
54682 CAGACAGTTT
*
54692 TCTCGAGTCATTCGGG
1 TCTCGGGTCATTCGGG
* *
54708 TTTCGGGTGA-TCTGGG
1 TCTCGGGTCATTC-GGG
*
54724 T-TCGGGTTATTCGGG
1 TCTCGGGTCATTCGGG
*
54739 TTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
*
54755 TCTCGGGTCATACGGG
1 TCTCGGGTCATTCGGG
* *
54771 TTTCGGGTCATTCCGG
1 TCTCGGGTCATTCGGG
54787 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
*
54803 T-TCCGGGTCATTCAGG
1 TCT-CGGGTCATTCGGG
* *
54819 TCTTGGGTC-TACCGGG
1 TCTCGGGTCAT-TCGGG
54835 TCTCGGGT
1 TCTCGGGT
54843 TGGGCGGGTT
Statistics
Matches: 112, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
15 15 0.13
16 96 0.86
17 1 0.01
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:55681 original size:16 final size:16
Alignment explanation
Indices: 55660--55791 Score: 133
Period size: 16 Copynumber: 8.2 Consensus size: 16
55650 GGTTAACTTC
*
55660 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
55676 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
* *
55692 TCGGGTCACTCGGATT
1 TCGGGTCATTCGGGTT
*
55708 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
55724 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
55740 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
55756 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* * *
55772 GCGGGTCATCCGGGTC
1 TCGGGTCATTCGGGTT
55788 TCGG
1 TCGG
55792 TCGGGCGGGT
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
15 4 0.04
16 86 0.92
17 3 0.03
ACGTcount: A:0.09, C:0.22, G:0.38, T:0.31
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:55696 original size:32 final size:32
Alignment explanation
Indices: 55658--55791 Score: 173
Period size: 32 Copynumber: 4.2 Consensus size: 32
55648 CGGGTTAACT
* * *
55658 TCTCGGGTTAT-TCGGGTTTCGGGTCATACGGG
1 TCTCGGGTCATCT-GGGTTACGGGTCATTCGGG
*
55690 TCTCGGGTCA-CTCGGATTACGGGTCATTCGGG
1 TCTCGGGTCATCT-GGGTTACGGGTCATTCGGG
*
55722 TTTCGGGTCATCTGGGTTACGGGTCATTCGGG
1 TCTCGGGTCATCTGGGTTACGGGTCATTCGGG
* *
55754 TCTCGGGTCATCTGGGTTGCGGGTCATCCGGG
1 TCTCGGGTCATCTGGGTTACGGGTCATTCGGG
55786 TCTCGG
1 TCTCGG
55792 TCGGGCGGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
32 89 0.98
33 2 0.02
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.31
Consensus pattern (32 bp):
TCTCGGGTCATCTGGGTTACGGGTCATTCGGG
Found at i:55719 original size:48 final size:47
Alignment explanation
Indices: 55658--55791 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 47
55648 CGGGTTAACT
*
55658 TCTCGGGTTATTCGGGTTTCGGGTCATACGGGTCTCGGGTCACTCGGA
1 TCTCGGGTCATTCGGGTTTCGGGTCAT-CGGGTCTCGGGTCACTCGGA
* *
55706 T-TACGGGTCATTCGGGTTTCGGGTCATCTGGGT-TACGGGTCATTCGGG
1 TCT-CGGGTCATTCGGGTTTCGGGTCATC-GGGTCT-CGGGTCACTCGGA
*
55754 TCTCGGGTCA-TCTGGGTTGCGGGTCATCCGGGTCTCGG
1 TCTCGGGTCATTC-GGGTTTCGGGTCAT-CGGGTCTCGG
55792 TCGGGCGGGT
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
47 5 0.07
48 67 0.89
49 3 0.04
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.31
Consensus pattern (47 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATCGGGTCTCGGGTCACTCGGA
Found at i:56119 original size:21 final size:22
Alignment explanation
Indices: 56095--56137 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
56085 ATTATGGGGA
56095 TTACTAAATACCGCCC-CCTTT
1 TTACTAAATACCGCCCTCCTTT
**
56116 TTACTAGGTACCGCCCTCCTTT
1 TTACTAAATACCGCCCTCCTTT
56138 GGACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (22 bp):
TTACTAAATACCGCCCTCCTTT
Found at i:56494 original size:13 final size:13
Alignment explanation
Indices: 56476--56500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56466 AGAGAGGACC
56476 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
56489 TTTTTCTTCTTT
1 TTTTTCTTCTTT
56501 AAAGGCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:63098 original size:8 final size:8
Alignment explanation
Indices: 63085--63115 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
63075 AACATAGAGG
63085 TCTGAGTC
1 TCTGAGTC
63093 TCTGAGTC
1 TCTGAGTC
63101 TCTGAGTC
1 TCTGAGTC
63109 TCTGAGT
1 TCTGAGT
63116 GGAGTGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.39
Consensus pattern (8 bp):
TCTGAGTC
Found at i:71021 original size:20 final size:20
Alignment explanation
Indices: 70996--71040 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
70986 ATTTAAACTA
*
70996 TTTTATTTAGAATTATTATT
1 TTTTATTCAGAATTATTATT
**
71016 TTTTATTCATTATTATTATT
1 TTTTATTCAGAATTATTATT
71036 TTTTA
1 TTTTA
71041 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATTCAGAATTATTATT
Found at i:76026 original size:13 final size:13
Alignment explanation
Indices: 76008--76043 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
75998 AAAAACCCTA
76008 AACCTTATAATCT
1 AACCTTATAATCT
76021 AACCTTATAATCT
1 AACCTTATAATCT
76034 AACCTT-TAAT
1 AACCTTATAAT
76044 ATCTCTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (13 bp):
AACCTTATAATCT
Found at i:76476 original size:3 final size:3
Alignment explanation
Indices: 76470--76507 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
76460 TTATTTTACG
76470 ATT ATT ATT -TT -TT ATT CATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
76508 CTTTTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:83309 original size:3 final size:3
Alignment explanation
Indices: 83301--83330 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
83291 AAAGATTGAT
83301 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
83331 AGATTGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:84831 original size:108 final size:109
Alignment explanation
Indices: 84607--84880 Score: 419
Period size: 108 Copynumber: 2.5 Consensus size: 109
84597 ACTATTATAG
* * *
84607 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTTTAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
84672 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
84721 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* * *
84786 TT-CTAAAAAGTTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
84829 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
84881 TAATTTTTTT
Statistics
Matches: 153, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
107 7 0.05
108 82 0.54
109 38 0.25
110 3 0.02
111 2 0.01
114 21 0.14
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:89990 original size:15 final size:15
Alignment explanation
Indices: 89970--90002 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
89960 CTTTGTTTTT
89970 AAAAACAAAAACAAA
1 AAAAACAAAAACAAA
*
89985 AAAAACAAAAGCAAA
1 AAAAACAAAAACAAA
90000 AAA
1 AAA
90003 TCATTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAACAAA
Found at i:92734 original size:24 final size:26
Alignment explanation
Indices: 92706--92754 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
92696 AACACTTCGT
92706 ACAGCAGG-AAGAA-AAGGAAAACTC
1 ACAGCAGGAAAGAACAAGGAAAACTC
92730 ACAGCAGGAAAAGAACAAGGAAAAC
1 ACAGCAGG-AAAGAACAAGGAAAAC
92755 CCAGCTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.57, C:0.16, G:0.24, T:0.02
Consensus pattern (26 bp):
ACAGCAGGAAAGAACAAGGAAAACTC
Found at i:98700 original size:135 final size:136
Alignment explanation
Indices: 98318--98702 Score: 614
Period size: 137 Copynumber: 2.8 Consensus size: 136
98308 ACACAATTCG
* * ** *
98318 TGGAACAGATAAGGATTCAAA-CAACGATCACATTTTTATCTCACTTTTAACCCAACGGTTAGAT
1 TGGAAGAGATAAGGATTCAAATTAACG-TCACATTTGAATCTCACTTTTAATCCAACGGTTAGAT
*
98382 TGAGATAAGGTTAGATTTTCTGAAATTATTGACTATTGTGTTAGATTTTCTGACATATCTTGGAT
65 TGAGATAAGGTTAGATTCTCTGAAATTATTGACTATTGTGTTAGATTTTCTGACATATCTTGGAT
98447 ATTGTGT
130 ATTGTGT
*
98454 TGGAAGAGATAAGGATTCAAATTTACGGTCACATTTGAATCTCACTTTTAATCCAACGGTT-GTA
1 TGGAAGAGATAAGGATTCAAATTAAC-GTCACATTTGAATCTCACTTTTAATCCAACGGTTAG-A
* * *
98518 TTAAGATAAGGTTAGATTCTTTGAAATTATTGACTATTGTGTTAGATTTTCTTACATATCTTGGA
64 TTGAGATAAGGTTAGATTCTCTGAAATTATTGACTATTGTGTTAGATTTTCTGACATATCTTGGA
98583 TATTGTGT
129 TATTGTGT
*
98591 TGGAAGAGATAAGGATTCAAATTAACG-CACATTTGAATCTCACTTTTAATTCAACGGTTAGATT
1 TGGAAGAGATAAGGATTCAAATTAACGTCACATTTGAATCTCACTTTTAATCCAACGGTTAGATT
*
98655 GAGATAAGGCTAGATTCTCTGAAATTATTGACTATTGTGTTAGATTTT
66 GAGATAAGGTTAGATTCTCTGAAATTATTGACTATTGTGTTAGATTTT
98703 TG
Statistics
Matches: 230, Mismatches: 15, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
135 79 0.34
136 23 0.10
137 127 0.55
138 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (136 bp):
TGGAAGAGATAAGGATTCAAATTAACGTCACATTTGAATCTCACTTTTAATCCAACGGTTAGATT
GAGATAAGGTTAGATTCTCTGAAATTATTGACTATTGTGTTAGATTTTCTGACATATCTTGGATA
TTGTGT
Done.