Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008946.1 Corchorus capsularis cultivar CVL-1 contig08967, 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: 46691
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3080 original size:21 final size:21
Alignment explanation
Indices: 3047--3086 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3037 ACTTTGTACT
*
3047 AAAAATACTTATATAGTTTATA
1 AAAAAAACTTATATA-TTTATA
3069 AAAAAAAC-TATATATTTA
1 AAAAAAACTTATATATTTA
3087 CAGACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAAAAACTTATATATTTATA
Found at i:3598 original size:20 final size:21
Alignment explanation
Indices: 3573--3616 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
3563 TATGACATAG
3573 TAAAAAAGAAAAGTAAAG-TC
1 TAAAAAAGAAAAGTAAAGTTC
3593 TAAAAAAGAAAAGTAAAGTTC
1 TAAAAAAGAAAAGTAAAGTTC
3614 TAA
1 TAA
3617 GCATTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.18
Consensus pattern (21 bp):
TAAAAAAGAAAAGTAAAGTTC
Found at i:6266 original size:29 final size:29
Alignment explanation
Indices: 6228--6302 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 29
6218 ACAAATTGAG
6228 AGTTCAGGGGGCAAACGTCCAAAAT-TA-A
1 AGTTCAGGGGGCAAACGT-CAAAATCTAGA
*
6256 AGTTTAGGGGGCAAAACGTCAAAATCGTAGA
1 AGTTCAGGGGGC-AAACGTCAAAATC-TAGA
6287 AGTTCAGGGGGGCAAA
1 AGTTCA-GGGGGCAAA
6303 AAGGGCATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 17 0.43
29 6 0.15
30 2 0.05
31 9 0.22
32 6 0.15
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (29 bp):
AGTTCAGGGGGCAAACGTCAAAATCTAGA
Found at i:7010 original size:181 final size:181
Alignment explanation
Indices: 6706--7068 Score: 690
Period size: 181 Copynumber: 2.0 Consensus size: 181
6696 GATTATTTGA
*
6706 TAAAAAAAATCACAGAAAAGCTATACCGCTATCAATTTATAAGAAATGCATAAATTATAAGTTTT
1 TAAAAAAAATCACAGAAAAGCCATACCGCTATCAATTTATAAGAAATGCATAAATTATAAGTTTT
* *
6771 AATGGAGTATCAAAGAAACTATTCGTGTTCTTGGTATGGGTTTAAGATGGTGCTTGGTAACACCA
66 AATGGAGTATCAAAGAAACTATTCGTGTTCTTGGTATGAGTTTAACATGGTGCTTGGTAACACCA
6836 TGAGCAGTATCTTGTCTTGTTAGTATTTGAATAAACTTTTGAGAAATTGCT
131 TGAGCAGTATCTTGTCTTGTTAGTATTTGAATAAACTTTTGAGAAATTGCT
*
6887 TAAAAAAAATCACAGAAAAGCCATACCGCTATTAATTTATAAGAAATGCATAAATTATAAGTTTT
1 TAAAAAAAATCACAGAAAAGCCATACCGCTATCAATTTATAAGAAATGCATAAATTATAAGTTTT
6952 AATGGAGTATCAAAGAAACTATTCGTGTTCTTGGTATGAGTTTAACATGGTGCTTGGTAACACCA
66 AATGGAGTATCAAAGAAACTATTCGTGTTCTTGGTATGAGTTTAACATGGTGCTTGGTAACACCA
7017 TGAGCAGTATCTTGTCTTGTTAGTATTTGAATAAACTTTTGAGAAATTGCT
131 TGAGCAGTATCTTGTCTTGTTAGTATTTGAATAAACTTTTGAGAAATTGCT
7068 T
1 T
7069 GTATAATATT
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 178 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (181 bp):
TAAAAAAAATCACAGAAAAGCCATACCGCTATCAATTTATAAGAAATGCATAAATTATAAGTTTT
AATGGAGTATCAAAGAAACTATTCGTGTTCTTGGTATGAGTTTAACATGGTGCTTGGTAACACCA
TGAGCAGTATCTTGTCTTGTTAGTATTTGAATAAACTTTTGAGAAATTGCT
Found at i:9481 original size:25 final size:27
Alignment explanation
Indices: 9453--9512 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
9443 GTAATAACGC
*
9453 ATAATTATTT-GATG-AGTTTTCATGA
1 ATAATTATTTGGACGAAGTTTTCATGA
* *
9478 ATAATTTTTTTGGCCGAAGTTTTCATGA
1 ATAA-TTATTTGGACGAAGTTTTCATGA
9506 ATAATTA
1 ATAATTA
9513 ATGATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 4 0.14
26 5 0.18
27 4 0.14
28 15 0.54
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (27 bp):
ATAATTATTTGGACGAAGTTTTCATGA
Found at i:9817 original size:13 final size:13
Alignment explanation
Indices: 9799--9823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9789 TCCCAGGAAA
9799 TAATTAAAAATAT
1 TAATTAAAAATAT
9812 TAATTAAAAATA
1 TAATTAAAAATA
9824 AATATTATAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAAATAT
Found at i:9834 original size:19 final size:19
Alignment explanation
Indices: 9812--9851 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9802 TTAAAAATAT
9812 TAATTAAAAATAAATATTA
1 TAATTAAAAATAAATATTA
* *
9831 TAATTAAAAATTATTATTA
1 TAATTAAAAATAAATATTA
9850 TA
1 TA
9852 TTATAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTAAAAATAAATATTA
Found at i:12317 original size:37 final size:37
Alignment explanation
Indices: 12275--12345 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
12265 ACATGATTAT
* *
12275 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
12312 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
12346 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:14866 original size:37 final size:37
Alignment explanation
Indices: 14824--14894 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
14814 ACATGATTAT
* *
14824 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
14861 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
14895 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:17248 original size:160 final size:155
Alignment explanation
Indices: 17074--17384 Score: 480
Period size: 156 Copynumber: 2.0 Consensus size: 155
17064 GCTTTATTGC
*
17074 TTTTTTGTCTCCCTTTTAATAATTTAAATTTTGCATTTGATTTTCTTTGTCTCAAAAAAAAAAAA
1 TTTTTTGTCTCCCTTTTAATAATTTAAATTTTGCATTTGATTTTCTTTATCTC----AAAAAAAA
** * *
17139 AAGTTGATGTCTATTCTGTTAGGCTTTAATCTTATTAAAGAATAAAAATGTT-TCCCTTAGCCTT
62 AAGTTGATGTCTATTCTGTTAAACTTTAATCTTATTAAAAAATAAAAATGTTCT-CCTTA-ACTT
17203 AGAGCTTTGAAATAGACAAATATATATTGTT
125 AGAGCTTTGAAATAGACAAATATATATTGTT
*
17234 TTTTTTGTCTCCCTTTTAATAATTTAAATTTTGCATTTGATTTTCTTTATCTCAAAAGAAAAAGT
1 TTTTTTGTCTCCCTTTTAATAATTTAAATTTTGCATTTGATTTTCTTTATCTCAAAAAAAAAAGT
* * *
17299 TGATGTCTATTTTGTTAAACTTTAATCTTATTAAAAAATAAAAATGTTCTCCTTAACTTTGGGCT
66 TGATGTCTATTCTGTTAAACTTTAATCTTATTAAAAAATAAAAATGTTCTCCTTAACTTAGAGCT
17364 TTGAAATAGACAAATATATAT
131 TTGAAATAGACAAATATATAT
17385 AAATATAGAT
Statistics
Matches: 141, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
155 28 0.20
156 60 0.43
157 1 0.01
160 52 0.37
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (155 bp):
TTTTTTGTCTCCCTTTTAATAATTTAAATTTTGCATTTGATTTTCTTTATCTCAAAAAAAAAAGT
TGATGTCTATTCTGTTAAACTTTAATCTTATTAAAAAATAAAAATGTTCTCCTTAACTTAGAGCT
TTGAAATAGACAAATATATATTGTT
Found at i:23260 original size:21 final size:22
Alignment explanation
Indices: 23211--23267 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
23201 TCACTCACTT
* *
23211 TTTACTGAATTACTGATTACTAT
1 TTTACTG-ATTACTCATTACTAC
*
23234 TTTACTGATTACTCTTTACT-C
1 TTTACTGATTACTCATTACTAC
23255 TTTACTGATTACT
1 TTTACTGATTACT
23268 AGTTATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.42
22 11 0.35
23 7 0.23
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTACTGATTACTCATTACTAC
Found at i:23344 original size:42 final size:43
Alignment explanation
Indices: 23211--23351 Score: 119
Period size: 42 Copynumber: 3.3 Consensus size: 43
23201 TCACTCACTT
* **
23211 TTTACTGAATTACTGATTACTATTTTACTGATTACTC-TTTACTC
1 TTTACTG-ATTACTGATTAATATTTTACTCTTTACTCATTTAC-C
* * * *
23255 TTTACTGATTACT-AGTTATTATTTTATTCTTTACTGA-TTGCC
1 TTTACTGATTACTGA-TTAATATTTTACTCTTTACTCATTTACC
* ** *
23297 ATTACTTTTTACTGATTAATATTTTACTCTTTAC-CATTTTCC
1 TTTACTGATTACTGATTAATATTTTACTCTTTACTCATTTACC
*
23339 TTTACTAATTACT
1 TTTACTGATTACT
23352 CTTTATCCTT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 43 0.56
43 26 0.34
44 7 0.09
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.53
Consensus pattern (43 bp):
TTTACTGATTACTGATTAATATTTTACTCTTTACTCATTTACC
Found at i:23350 original size:27 final size:27
Alignment explanation
Indices: 23320--23459 Score: 89
Period size: 27 Copynumber: 5.3 Consensus size: 27
23310 GATTAATATT
23320 TTACTCTTTACCATTTTCCTTTACTAA
1 TTACTCTTTACCATTTTCCTTTACTAA
* * *
23347 TTACTCTTTATCC-TTTACCATTTTGCTGA
1 TTACTCTTTA-CCATTTTCC--TTTACTAA
* * *
23376 TTGCTCTTTA-C-TGATT--ATT-CT--
1 TTACTCTTTACCAT-TTTCCTTTACTAA
* *
23397 TTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTACCATTTTCCTTTACTAA
* * *
23424 TTACTTTTTACCATTTTTCTTTAATAA
1 TTACTCTTTACCATTTTCCTTTACTAA
23451 TTACTCTTT
1 TTACTCTTT
23460 TACTTTTTAC
Statistics
Matches: 88, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
21 9 0.10
22 3 0.03
23 3 0.03
24 4 0.05
25 2 0.02
27 49 0.56
28 3 0.03
29 15 0.17
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (27 bp):
TTACTCTTTACCATTTTCCTTTACTAA
Found at i:23467 original size:27 final size:28
Alignment explanation
Indices: 23397--23462 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
23387 TGATTATTCT
* *
23397 TTACTC-TTTACCATTTTTCTTTACTGA
1 TTACTCTTTTACCATTTTTCTTTAATAA
23424 TTACT-TTTTACCATTTTTCTTTAATAA
1 TTACTCTTTTACCATTTTTCTTTAATAA
23451 TTACTCTTTTAC
1 TTACTCTTTTAC
23463 TTTTTACTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 29 0.83
28 6 0.17
ACGTcount: A:0.21, C:0.20, G:0.02, T:0.58
Consensus pattern (28 bp):
TTACTCTTTTACCATTTTTCTTTAATAA
Found at i:23469 original size:7 final size:7
Alignment explanation
Indices: 23451--23558 Score: 63
Period size: 7 Copynumber: 14.7 Consensus size: 7
23441 TCTTTAATAA
23451 TTACTCTT
1 TTACT-TT
23459 TTACTTT
1 TTACTTT
**
23466 TTACTGA
1 TTACTTT
*
23473 TTACCCTT
1 TTA-CTTT
23481 TTACTTT
1 TTACTTT
**
23488 TTACTGA
1 TTACTTT
23495 TTACTATT
1 TTACT-TT
* *
23503 TTTCTCT
1 TTACTTT
**
23510 TTACTAA
1 TTACTTT
*
23517 TTACCATT
1 TTA-CTTT
23525 TTACTTT
1 TTACTTT
**
23532 TTACTGG
1 TTACTTT
23539 TTACCTTT
1 TTA-CTTT
23547 TTACTTT
1 TTACTTT
23554 TTACT
1 TTACT
23559 GATTACCATT
Statistics
Matches: 73, Mismatches: 23, Indels: 9
0.70 0.22 0.09
Matches are distributed among these distances:
7 51 0.70
8 22 0.30
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.58
Consensus pattern (7 bp):
TTACTTT
Found at i:23475 original size:22 final size:22
Alignment explanation
Indices: 23457--24040 Score: 499
Period size: 22 Copynumber: 26.8 Consensus size: 22
23447 ATAATTACTC
*
23457 TTTTACTTTTTACTGATTACCC
1 TTTTACTTTTTACTGATTACCA
*
23479 TTTTACTTTTTACTGATTACTA
1 TTTTACTTTTTACTGATTACCA
* * *
23501 TTTTTCTCTTTACTAATTACCA
1 TTTTACTTTTTACTGATTACCA
* *
23523 TTTTACTTTTTACTGGTTACCT
1 TTTTACTTTTTACTGATTACCA
23545 TTTTACTTTTTACTGATTACCA
1 TTTTACTTTTTACTGATTACCA
*
23567 --TTACTTCTTACTGATTA-C-
1 TTTTACTTTTTACTGATTACCA
* *
23585 TATTACTCTTTAAC-GATTACCA
1 TTTTACT-TTTTACTGATTACCA
* * *
23607 TTTTACTCTTTT-CTAAATATCA
1 TTTTACT-TTTTACTGATTACCA
* *
23629 TTTTACCCTTTTACTGATTACCT
1 TTTTA-CTTTTTACTGATTACCA
*
23652 TTTTACTTTTTACTGATTACCT
1 TTTTACTTTTTACTGATTACCA
* *
23674 TTTTGC-TTTTACTGATTACTA
1 TTTTACTTTTTACTGATTACCA
* *
23695 TTTTACTCTTTACTCATTACCA
1 TTTTACTTTTTACTGATTACCA
* * *
23717 TTTTACTTCTTACTAATTACCT
1 TTTTACTTTTTACTGATTACCA
* *
23739 TTTTACTCTTTAATGATTACCA
1 TTTTACTTTTTACTGATTACCA
* *
23761 TTTTATTCTTTTACTGATTACCT
1 TTTTACT-TTTTACTGATTACCA
* * **
23784 TTTTACTTTTTGCTAATTATTA
1 TTTTACTTTTTACTGATTACCA
** ** **
23806 TTCGACGCTTTACTGATTGTCA
1 TTTTACTTTTTACTGATTACCA
* *
23828 TTTTACTCTTTACTGATTGCC-
1 TTTTACTTTTTACTGATTACCA
* *
23849 TTTTACTTCTTACTGATTACCT
1 TTTTACTTTTTACTGATTACCA
* *
23871 TTTTACTCTTTAATGATTACCA
1 TTTTACTTTTTACTGATTACCA
* *
23893 TTTTATTCTTTTACTGATTACCT
1 TTTTACT-TTTTACTGATTACCA
* * **
23916 TTTTACTTTTTGCTAATTATTA
1 TTTTACTTTTTACTGATTACCA
** ** *
23938 TTCGACGCTTTACTGATTGCCA
1 TTTTACTTTTTACTGATTACCA
*
23960 TTTTA-TTCTTTACTGATTGCC-
1 TTTTACTT-TTTACTGATTACCA
*
23981 TTTTACTCTTTACTGATTACCA
1 TTTTACTTTTTACTGATTACCA
*
24003 TTTTATTCTTTTACTGATTACC-
1 TTTTACT-TTTTACTGATTACCA
*
24025 -TTTACTTCTTACTGAT
1 TTTTACTTTTTACTGAT
24041 CACTATTATT
Statistics
Matches: 445, Mismatches: 101, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.00
20 35 0.08
21 64 0.14
22 284 0.64
23 61 0.14
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTTACTTTTTACTGATTACCA
Found at i:23774 original size:132 final size:132
Alignment explanation
Indices: 23431--24024 Score: 617
Period size: 132 Copynumber: 4.5 Consensus size: 132
23421 TGATTACTTT
* * * * *
23431 TTACCATTTT--TCTTTAATAATTACTCTTTTACTTTTTACTGATTACCCTTTTACTTTTTACTG
1 TTACCATTTTACTCTTTACTGATTAC-CTTTTACTTCTTACTGATTACCATTTTACTCTTTACTG
* * * ** * **
23494 ATTACTA-TTT-TTCTCTTTACTAATTACCATTTTACTTTTTACTGGTTACCTT-TT-TACTTTT
65 ATTACCATTTTATTCT-TTTACTGATTACCTTTTTACTTTTTACTAATTA--TTATTCGACGCTT
23555 TACTGA
127 TACTGA
* *
23561 TTACCA--TTACT-TCTTACTGATTA-CTATTAC-TCTTTAAC-GATTACCATTTTACTCTTTTC
1 TTACCATTTTACTCT-TTACTGATTACCTTTTACTTC-TT-ACTGATTACCATTTTACTCTTTAC
* * * ** * * *
23620 TAAATATCATTTTACCCTTTTACTGATTACCTTTTTACTTTTTACTGATTACCTT-TTTG-C-TT
63 TGATTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTACTAATTA--TTATTCGACGCT
23682 TTACTGA
126 TTACTGA
* * * * *
23689 TTACTATTTTACTCTTTACTCATTACCATTTTACTTCTTACTAATTACCTTTTTACTCTTTAATG
1 TTACCATTTTACTCTTTACTGATTACC-TTTTACTTCTTACTGATTACCATTTTACTCTTTACTG
*
23754 ATTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTGCTAATTATTATTCGACGCTTTAC
65 ATTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTACTAATTATTATTCGACGCTTTAC
23819 TGA
130 TGA
** * * *
23822 TTGTCATTTTACTCTTTACTGATTGCCTTTTACTTCTTACTGATTACCTTTTTACTCTTTAATGA
1 TTACCATTTTACTCTTTACTGATTACCTTTTACTTCTTACTGATTACCATTTTACTCTTTACTGA
*
23887 TTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTGCTAATTATTATTCGACGCTTTACT
66 TTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTACTAATTATTATTCGACGCTTTACT
23952 GA
131 GA
* * * *
23954 TTGCCATTTTATTCTTTACTGATTGCCTTTTAC-TCTTTACTGATTACCATTTTATTCTTTTACT
1 TTACCATTTTACTCTTTACTGATTACCTTTTACTTC-TTACTGATTACCATTTTACTC-TTTACT
24018 GATTACC
64 GATTACC
24025 TTTACTTCTT
Statistics
Matches: 400, Mismatches: 44, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
127 1 0.00
128 47 0.12
129 43 0.11
130 33 0.08
131 9 0.02
132 223 0.56
133 44 0.11
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (132 bp):
TTACCATTTTACTCTTTACTGATTACCTTTTACTTCTTACTGATTACCATTTTACTCTTTACTGA
TTACCATTTTATTCTTTTACTGATTACCTTTTTACTTTTTACTAATTATTATTCGACGCTTTACT
GA
Found at i:24184 original size:26 final size:27
Alignment explanation
Indices: 24089--24181 Score: 113
Period size: 27 Copynumber: 3.5 Consensus size: 27
24079 CTAAATACTG
*
24089 TTTCCTACTCTTTTTACTTATGACTCT
1 TTTCTTACTCTTTTTACTTATGACTCT
*
24116 TTTCTTACTC-TTTTACTGAATG--T-T
1 TTTCTTACTCTTTTTACT-TATGACTCT
*
24140 GTTCTCTACTCTTTTTACTTATGACTCT
1 TTTCT-TACTCTTTTTACTTATGACTCT
24168 TTTCTTACTCTTTT
1 TTTCTTACTCTTTT
24182 ACTGATTACT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 5 0.09
25 9 0.16
26 14 0.25
27 22 0.40
28 5 0.09
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (27 bp):
TTTCTTACTCTTTTTACTTATGACTCT
Found at i:27074 original size:23 final size:23
Alignment explanation
Indices: 27043--27106 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
27033 TCCATTATTA
27043 TTTTCTTTTTCCTCCTCACTT-T
1 TTTTCTTTTTCCTCCTCACTTCT
* ** *
27065 TCTTTCTTTTTTCTTTTCTCTTCT
1 T-TTTCTTTTTCCTCCTCACTTCT
*
27089 TTTTCTTTTTCTTCCTCA
1 TTTTCTTTTTCCTCCTCA
27107 GCATCAAACC
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTCTTTTTCCTCCTCACTTCT
Found at i:27088 original size:17 final size:16
Alignment explanation
Indices: 27061--27102 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
27051 TTCCTCCTCA
27061 CTTTTCT-TTCTTTTTT
1 CTTTTCTCTTC-TTTTT
27077 CTTTTCTCTTCTTTTT
1 CTTTTCTCTTCTTTTT
27093 CTTTT-TCTTC
1 CTTTTCTCTTC
27103 CTCAGCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.20
16 17 0.68
17 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
CTTTTCTCTTCTTTTT
Found at i:28499 original size:25 final size:26
Alignment explanation
Indices: 28422--28496 Score: 116
Period size: 25 Copynumber: 2.9 Consensus size: 26
28412 AAAATTTGAC
28422 TAAAAATGACCAAAATGCCCCTGAATG
1 TAAAAATGACCAAAATGCCCCT-AATG
**
28449 TGCAAATGACCAAAATG-CCCTAATG
1 TAAAAATGACCAAAATGCCCCTAATG
28474 TAAAAATGACCAAAATGCCCCTA
1 TAAAAATGACCAAAATGCCCCTA
28497 TGTGACCCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 19 0.44
26 9 0.21
27 15 0.35
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (26 bp):
TAAAAATGACCAAAATGCCCCTAATG
Found at i:35172 original size:69 final size:69
Alignment explanation
Indices: 35096--35233 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
35086 ATTTTGAAGC
35096 TAAATCATTGGATCAACCAATTGACATAGTTGACTCGTCTATTCCACTGGTGCAGTCATCTGTGA
1 TAAATCATTGGATCAACCAATTGACATAGTTGACTCGTCTATTCCACTGGTGCAGTCATCTGTGA
35161 ATAA
66 ATAA
*
35165 TAAATCATTGGATCAACCAATTGACATAGTTGACTTGTCTATTCCACTGGTGCAGTCATCTGTGA
1 TAAATCATTGGATCAACCAATTGACATAGTTGACTCGTCTATTCCACTGGTGCAGTCATCTGTGA
35230 ATAA
66 ATAA
35234 AGTAACATTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (69 bp):
TAAATCATTGGATCAACCAATTGACATAGTTGACTCGTCTATTCCACTGGTGCAGTCATCTGTGA
ATAA
Found at i:39817 original size:31 final size:31
Alignment explanation
Indices: 39725--39895 Score: 193
Period size: 31 Copynumber: 5.5 Consensus size: 31
39715 TCCTTTTGTG
**
39725 CACGTGGCATATCACGTGTCA-TTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
39755 CACGTGTCATGCCACATGTCA-TTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
39785 CACGTGGCATGCCACGTGTCACTTTTTAGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * * *
39816 CACGTGACGTGACATGTGTCACTTGTTTGATA
1 CACGTGGCATGCCACGTGTCACTT-TTTGGTA
* * **
39848 CACTTGGCGTGCCATATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
39879 CACGTGGCATGCCACGT
1 CACGTGGCATGCCACGT
39896 CGGATACCGT
Statistics
Matches: 117, Mismatches: 22, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
30 45 0.38
31 47 0.40
32 25 0.21
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:46661 original size:3 final size:3
Alignment explanation
Indices: 46653--46691 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
46643 GTACTTTCCC
46653 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Done.