Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013244.1 Corchorus capsularis cultivar CVL-1 contig13265, 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: 40783
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1148 original size:14 final size:14
Alignment explanation
Indices: 1129--1162 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1119 ACAATTTTAG
1129 AACATTTAT-TATAT
1 AACATTTATGT-TAT
1143 AACATTTATGTTAT
1 AACATTTATGTTAT
1157 AACATT
1 AACATT
1163 GAATTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (14 bp):
AACATTTATGTTAT
Found at i:1416 original size:15 final size:15
Alignment explanation
Indices: 1396--1429 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1386 ATAATTAGTC
*
1396 TTAGTCATACTATTT
1 TTAGTCATACTATTA
1411 TTAGTCATACTATTA
1 TTAGTCATACTATTA
1426 TTAG
1 TTAG
1430 GTGTTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (15 bp):
TTAGTCATACTATTA
Found at i:1906 original size:11 final size:11
Alignment explanation
Indices: 1892--1929 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1882 ATTCATAGCA
1892 AATTTATAATT
1 AATTTATAATT
1903 AATTTATAATT
1 AATTTATAATT
1914 -ATTTGATAATT
1 AATTT-ATAATT
*
1925 TATTT
1 AATTT
1930 TATATGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:10927 original size:30 final size:30
Alignment explanation
Indices: 10891--10950 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
10881 AAGAGGCGTA
*
10891 TCCGTCCTTTAAATCCTCATCT-GATTGATC
1 TCCGTCCTCTAAATCCTCAT-TGGATTGATC
* *
10921 TCCGTCCTCTGAGTCCTCATTGGATTGATC
1 TCCGTCCTCTAAATCCTCATTGGATTGATC
10951 CGGGCAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (30 bp):
TCCGTCCTCTAAATCCTCATTGGATTGATC
Found at i:11258 original size:48 final size:48
Alignment explanation
Indices: 11204--11332 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 48
11194 ATAATTAAAT
*
11204 TCTCTGCCATATCTGTAAAACTCCCTGCCTCTGCTTCTATTCTGAAAA
1 TCTCTGCCATTTCTGTAAAACTCCCTGCCTCTGCTTCTATTCTGAAAA
* * * * * *
11252 TCTCTGCCTTTTCTGTAAAACTCTCTTCCTCTGCTTCTATTTTGGAAT
1 TCTCTGCCATTTCTGTAAAACTCCCTGCCTCTGCTTCTATTCTGAAAA
* * *
11300 TCTCT-CCTGTTTCTATAAAACTCCCTGTCTCTG
1 TCTCTGCC-ATTTCTGTAAAACTCCCTGCCTCTG
11333 TTAAAGTGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 2 0.03
48 66 0.97
ACGTcount: A:0.18, C:0.30, G:0.10, T:0.42
Consensus pattern (48 bp):
TCTCTGCCATTTCTGTAAAACTCCCTGCCTCTGCTTCTATTCTGAAAA
Found at i:13245 original size:120 final size:120
Alignment explanation
Indices: 13032--13272 Score: 482
Period size: 120 Copynumber: 2.0 Consensus size: 120
13022 GTTTCCTTGA
13032 AGATTGTCTTTCCATAATTCCATTGATCTTATGGAGGTTAGAGAGAGTTTTCTTACCACGAAGTC
1 AGATTGTCTTTCCATAATTCCATTGATCTTATGGAGGTTAGAGAGAGTTTTCTTACCACGAAGTC
13097 CAACCTACAAGAAAAAAAATGTTTGACAATAGCTTAAACATTAATTTATGGAGTT
66 CAACCTACAAGAAAAAAAATGTTTGACAATAGCTTAAACATTAATTTATGGAGTT
13152 AGATTGTCTTTCCATAATTCCATTGATCTTATGGAGGTTAGAGAGAGTTTTCTTACCACGAAGTC
1 AGATTGTCTTTCCATAATTCCATTGATCTTATGGAGGTTAGAGAGAGTTTTCTTACCACGAAGTC
13217 CAACCTACAAGAAAAAAAATGTTTGACAATAGCTTAAACATTAATTTATGGAGTT
66 CAACCTACAAGAAAAAAAATGTTTGACAATAGCTTAAACATTAATTTATGGAGTT
13272 A
1 A
13273 ACGTGAGTAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (120 bp):
AGATTGTCTTTCCATAATTCCATTGATCTTATGGAGGTTAGAGAGAGTTTTCTTACCACGAAGTC
CAACCTACAAGAAAAAAAATGTTTGACAATAGCTTAAACATTAATTTATGGAGTT
Found at i:23084 original size:16 final size:17
Alignment explanation
Indices: 23063--23095 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23053 AAACAAAATT
*
23063 TTTAT-AATTTAAATAA
1 TTTATAAATATAAATAA
23079 TTTATAAATATAAATAA
1 TTTATAAATATAAATAA
23096 AATGAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAAATATAAATAA
Found at i:23831 original size:29 final size:31
Alignment explanation
Indices: 23771--23834 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
23761 AACTTTATGT
*
23771 TTTCCGATTGTACCCTTATTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
23802 TTTCCAATTGTACCCTT-TTTT-AAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
23831 TTTC
1 TTTC
23835 TAAATTGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 16 0.50
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:23841 original size:30 final size:31
Alignment explanation
Indices: 23777--23841 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 31
23767 ATGTTTTCCG
*
23777 ATTGTACCCTTATTTTAAAAACATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
23808 ATTGTACCCTT-TTTT-AAAACATATTTCTAA
1 ATTGTACCCTTATTTTAAAAACATATTTC-AA
23838 ATTG
1 ATTG
23842 CAATTACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 12 0.38
30 9 0.28
31 11 0.34
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.45
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:24297 original size:22 final size:22
Alignment explanation
Indices: 24196--24582 Score: 89
Period size: 22 Copynumber: 17.4 Consensus size: 22
24186 GCAAGGAATG
*
24196 TCATAGTGTGGTTAACAAAATT
1 TCATAGTGTGGTTATCAAAATT
** *
24218 TCATTAG-GACGTTAAT-AATATT
1 TCA-TAGTGTGGTT-ATCAAAATT
* * *
24240 TCATGGGGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
*
24262 TTATAGTGTGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
*
24284 TCATA-TGAAT-GTTATAAAAGTCTCAATT
1 TCATAGTG--TGGTTAT-CAA-----AATT
* *
24312 TCATA-AG-GAG-TACCAAAATT
1 TCATAGTGTG-GTTATCAAAATT
* ** *
24332 TGATAG-AAGGTTATC-AAATC
1 TCATAGTGTGGTTATCAAAATT
* ** *
24352 TCATAGAGTAATTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
24374 TCATAGAGATCAGATTATCAAAATT
1 TCATAGTG-T--GGTTATCAAAATT
* *
24399 T-ATAG-GAAGATTATCAAAATT
1 TCATAGTG-TGGTTATCAAAATT
* *
24420 TCATAGTGTTTGTTATCAAAACT
1 TCATAGTG-TGGTTATCAAAATT
* * *
24443 TGAAAGTGAGGTTATC-AAATT
1 TCATAGTGTGGTTATCAAAATT
* * * *
24464 TATATAATGTGATTATCAGAATT
1 T-CATAGTGTGGTTATCAAAATT
* * * *
24487 TCATAGAGGGGTCAACAAAATT
1 TCATAGTGTGGTTATCAAAATT
* ** *
24509 TTATAAAGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
** * * *
24531 TCATAAAGAGGTTATTAAATTT
1 TCATAGTGTGGTTATCAAAATT
* * *
24553 TCAAAATGTGATTA-CAAAAATT
1 TCATAGTGTGGTTATC-AAAATT
24575 TCATAGTG
1 TCATAGTG
24583 GTATTTTTGG
Statistics
Matches: 269, Mismatches: 69, Indels: 54
0.69 0.18 0.14
Matches are distributed among these distances:
20 18 0.07
21 34 0.13
22 154 0.57
23 32 0.12
24 4 0.01
25 14 0.05
26 2 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:24409 original size:21 final size:24
Alignment explanation
Indices: 24342--24425 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 24
24332 TGATAGAAGG
* *
24342 TTATC-AAATCTCATAGAG-TA-A
1 TTATCAAAATTTCATAGAGACAGA
*
24363 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAGAGA-CAGA
24388 TTATCAAAATTT-ATAG-GA-AGA
1 TTATCAAAATTTCATAGAGACAGA
24409 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
24426 TGTTTGTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
21 20 0.36
22 16 0.29
23 2 0.04
24 5 0.09
25 12 0.22
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (24 bp):
TTATCAAAATTTCATAGAGACAGA
Found at i:24552 original size:21 final size:22
Alignment explanation
Indices: 24450--24555 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
24440 ACTTGAAAGT
24450 GAGGTTATC-AAATTT-ATATAA
1 GAGGTTATCAAAATTTCATA-AA
* * * *
24471 TGTGATTATCAGAATTTCATAGA
1 -GAGGTTATCAAAATTTCATAAA
* * * *
24494 GGGGTCAACAAAATTTTATAAA
1 GAGGTTATCAAAATTTCATAAA
24516 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
* *
24538 GAGGTTATTAAATTTTCA
1 GAGGTTATCAAAATTTCA
24556 AAATGTGATT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
22 56 0.86
23 6 0.09
24 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAA
Found at i:24711 original size:22 final size:22
Alignment explanation
Indices: 24684--24954 Score: 138
Period size: 22 Copynumber: 12.4 Consensus size: 22
24674 GGAGGATACC
*
24684 AAATTTCATATGAATGTTATCA
1 AAATTTCATAGGAATGTTATCA
** *
24706 AAATTTCATAGTTA-GTTTTCA
1 AAATTTCATAGGAATGTTATCA
* **
24727 AAATTTCATAAGAGGGTTATCA
1 AAATTTCATAGGAATGTTATCA
** *
24749 AAATTTCATA-GTTTGTAGATCA
1 AAATTTCATAGGAATGT-TATCA
24771 AAATTTCATAGGGAATGAGGTTATCA
1 AAATTTCATA-GGAAT---GTTATCA
** * *
24797 AAAAATCATAGGGAGGTTATCA
1 AAATTTCATAGGAATGTTATCA
*
24819 AAA-TT--T--GTA-GTTATCA
1 AAATTTCATAGGAATGTTATCA
*
24835 AGATTTCATAAGGAA-GTTATCA
1 AAATTTCAT-AGGAATGTTATCA
* * *
24857 AAATTTTATAGGGAGGTTTATCA
1 AAATTTCATAGGAATG-TTATCA
*
24880 AAATTTTATAGGAA-GATTTATCA
1 AAATTTCATAGGAATG--TTATCA
24903 AAATTTCATAGCG-A-GATTATCA
1 AAATTTCATAG-GAATG-TTATCA
*
24925 CAATTTCATAGTG--TGATTATCA
1 AAATTTCATAG-GAATG-TTATCA
24947 AAATTTCA
1 AAATTTCA
24955 GAATATGATT
Statistics
Matches: 198, Mismatches: 33, Indels: 36
0.74 0.12 0.13
Matches are distributed among these distances:
16 9 0.05
17 4 0.02
19 2 0.01
21 24 0.12
22 101 0.51
23 38 0.19
24 3 0.02
25 3 0.02
26 12 0.06
27 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAATGTTATCA
Found at i:24746 original size:43 final size:44
Alignment explanation
Indices: 24684--24780 Score: 133
Period size: 43 Copynumber: 2.2 Consensus size: 44
24674 GGAGGATACC
* * **
24684 AAATTTCATATGAATGTTATCAAAATTTCATAGTTAGT-TTTCA
1 AAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGTAGATCA
* *
24727 AAATTTCATAAGAGGGTTATCAAAATTTCATAGTTTGTAGATCA
1 AAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGTAGATCA
24771 AAATTTCATA
1 AAATTTCATA
24781 GGGAATGAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 34 0.72
44 13 0.28
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (44 bp):
AAATTTCATAAGAAGGTTATCAAAATTTCATAGTTAGTAGATCA
Found at i:24879 original size:23 final size:23
Alignment explanation
Indices: 24829--25110 Score: 117
Period size: 22 Copynumber: 12.7 Consensus size: 23
24819 AAATTTGTAG
* * *
24829 TTATCAAGATTTCATAAGGAAG-
1 TTATCAAAATTTCATAGGGAGGA
* *
24851 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGA
* *
24874 TTATCAAAATTTTATA-GGAAGA
1 TTATCAAAATTTCATAGGGAGGA
*
24896 TTTATCAAAATTTCATAGCGA-GA
1 -TTATCAAAATTTCATAGGGAGGA
* * *
24919 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGA
* ** *
24941 TTATCAAAATTTCAGA-ATATGA
1 TTATCAAAATTTCATAGGGAGGA
*
24963 TTA-CTAACAA-TTCATATGGAGG-
1 TTATC-AA-AATTTCATAGGGAGGA
* * * ** *
24985 TTTTTAAATTTTCATAACGTGG-
1 TTATCAAAATTTCATAGGGAGGA
* * * *
25007 TTATCAATATATCATATGAAGG-
1 TTATCAAAATTTCATAGGGAGGA
*
25029 TTATCAAAATTTCACT-GGGAAG-
1 TTATCAAAATTTCA-TAGGGAGGA
**
25051 TTATCAAAATTTCATATTGAGG-
1 TTATCAAAATTTCATAGGGAGGA
* * *
25073 TCT-TCAAAATTCCTTAAGGAGG-
1 T-TATCAAAATTTCATAGGGAGGA
*
25095 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
25111 AGAAGGTTAA
Statistics
Matches: 198, Mismatches: 48, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
21 4 0.02
22 153 0.77
23 39 0.20
24 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGA
Found at i:24923 original size:45 final size:45
Alignment explanation
Indices: 24829--24954 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
24819 AAATTTGTAG
* * * *
24829 TTATCAAGATTTCATAAGGAAG-TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCAT-AGGAAGATTATCAAAATTTCATAGCGAGGA
*
24874 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-GA
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGA
* *
24919 TTATCACAATTTCATAGTG-TGATTATCAAAATTTCA
1 TTATCAAAATTTCATAG-GAAGATTATCAAAATTTCA
24955 GAATATGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
44 20 0.29
45 31 0.44
46 19 0.27
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGA
Found at i:25102 original size:22 final size:22
Alignment explanation
Indices: 25077--25120 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25067 TTGAGGTCTT
* *
25077 CAAAATTCCTTAAGGAGGTTAA
1 CAAAATTCCATAAGAAGGTTAA
*
25099 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTCCATAAGAAGGTTAA
25121 AAGAAATTTA
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:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (22 bp):
CAAAATTCCATAAGAAGGTTAA
Found at i:33014 original size:3 final size:3
Alignment explanation
Indices: 33006--33034 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32996 TGATTTGCAT
33006 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
33035 GTAAAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:33921 original size:12 final size:12
Alignment explanation
Indices: 33904--33929 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33894 GAAGTCAATT
33904 TTAATGTTTTGA
1 TTAATGTTTTGA
33916 TTAATGTTTTGA
1 TTAATGTTTTGA
33928 TT
1 TT
33930 CTAAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTAATGTTTTGA
Found at i:36243 original size:12 final size:12
Alignment explanation
Indices: 36228--36259 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
36218 GAATCATTAA
36228 AATCATCAAAAT
1 AATCATCAAAAT
36240 AATCATCAAAAT
1 AATCATCAAAAT
*
36252 AAACATCA
1 AATCATCA
36260 TCATCGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (12 bp):
AATCATCAAAAT
Found at i:36259 original size:15 final size:14
Alignment explanation
Indices: 36225--36262 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
36215 AAAGAATCAT
36225 TAAAATCATCAAAA
1 TAAAATCATCAAAA
36239 T--AATCATCAAAA
1 TAAAATCATCAAAA
36251 TAAACATCATCA
1 TAAA-ATCATCA
36263 TCGTCATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.57
14 2 0.10
15 7 0.33
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATCATCAAAA
Found at i:38432 original size:2 final size:2
Alignment explanation
Indices: 38425--38457 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38415 ATTTACAAAA
38425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38458 AAAACTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39499 original size:21 final size:22
Alignment explanation
Indices: 39473--39517 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
39463 AAAATTTGGA
*
39473 TTGCTAAACACCGTCCC-CTTT
1 TTGCTAAACACCGCCCCTCTTT
*
39494 TTGCTAAATACCGCCCCTCTTT
1 TTGCTAAACACCGCCCCTCTTT
39516 TT
1 TT
39518 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCTCTTT
Found at i:39647 original size:24 final size:25
Alignment explanation
Indices: 39587--39645 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
39577 TTCAAACCCT
*
39587 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
39612 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
39636 AAA-TTCATTT
1 AAACTTCATTT
39646 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:39675 original size:15 final size:15
Alignment explanation
Indices: 39655--39687 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39645 TTCCTTCATT
39655 TTAATCATAAACTAA
1 TTAATCATAAACTAA
39670 TTAATCATAAACTAA
1 TTAATCATAAACTAA
39685 TTA
1 TTA
39688 GATACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:39685 original size:26 final size:26
Alignment explanation
Indices: 39656--39711 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
39646 TCCTTCATTT
*
39656 TAATCATAAACTAATT-AATCATAAAC
1 TAATCAGAAACTAATTAAAT-ATAAAC
* *
39682 TAATTAGATACTAATTAAATATAAAC
1 TAATCAGAAACTAATTAAATATAAAC
39708 TAAT
1 TAAT
39712 AAATTAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (26 bp):
TAATCAGAAACTAATTAAATATAAAC
Found at i:39711 original size:15 final size:14
Alignment explanation
Indices: 39655--39711 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
39645 TTCCTTCATT
39655 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
39670 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
*
39685 TT-AGAT--ACTAA
1 TTAATATAAACTAA
39696 TTAAATATAAACTAA
1 TT-AATATAAACTAA
39711 T
1 T
39712 AAATTAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 7 0.19
13 5 0.14
14 1 0.03
15 23 0.64
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.35
Consensus pattern (14 bp):
TTAATATAAACTAA
Found at i:39847 original size:33 final size:33
Alignment explanation
Indices: 39808--39883 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
39798 TGCCCTTGGT
39808 TAGCCGCCCAAGCTGGGCGGTCCTTG-CCATGGC
1 TAGCCGCCCAAGCTGGGCGG-CCTTGACCATGGC
39841 TAGCCGCCCAAGCTGGGCGGCCTTGACCATGGC
1 TAGCCGCCCAAGCTGGGCGGCCTTGACCATGGC
*
39874 TAGCCACCCA
1 TAGCCGCCCA
39884 GTTTAGGCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.16, C:0.38, G:0.30, T:0.16
Consensus pattern (33 bp):
TAGCCGCCCAAGCTGGGCGGCCTTGACCATGGC
Done.