Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011194.1 Corchorus capsularis cultivar CVL-1 contig11215, 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: 88228
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1962 original size:1 final size:1
Alignment explanation
Indices: 1956--1982 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1946 TACTAGCGTC
1956 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1983 GACAACAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2870 original size:212 final size:211
Alignment explanation
Indices: 2504--2903 Score: 755
Period size: 212 Copynumber: 1.9 Consensus size: 211
2494 TTTGTGGATC
2504 TTTCCTTGGAGGTCTGTGATGTAAGCGGAGGGATCAAGTCAAAACCCCCTGGTTTGGACCTGTAT
1 TTTCCTTGGAGGTCTGTGATGTAAGCGGAGGGATCAAGTCAAAACCCCCTGGTTTGGACCTGTAT
2569 TCATAATCCAAATAGGAACCAAGTACCCTAAGTTTATATAAGGAGTCGAAATCACTTATATACTT
66 TCATAATCCAAATAGGAACCAAGTACCCTAAGTTTATATAAGGAGTCGAAATCACTTATATACTT
*
2634 GATGTATTGTTTTCTCTTCCAAATTAATAAGAACTCTCCCTCCCTACCCGTGGACGTACGTAGAT
131 GATGTATTGTTTTCTCTTCCAAATTAATAAAAACTCTCCCTCCCTACCCGTGGACGTACGTAGAT
2699 CATATCGAACCACATT
196 CATATCGAACCACATT
*
2715 TTTCCTTGGAGGTCTGTGATGTAAGCGGAGGGATCAAGTCAAAACCCACGTGGTTTGGACCTGTA
1 TTTCCTTGGAGGTCTGTGATGTAAGCGGAGGGATCAAGTCAAAACCC-CCTGGTTTGGACCTGTA
*
2780 TTCATAATCCAAATAGGAACCAAGTACCCTAAGTTTATATAAGGAGTCGAAATCACTTGTATACT
65 TTCATAATCCAAATAGGAACCAAGTACCCTAAGTTTATATAAGGAGTCGAAATCACTTATATACT
*
2845 TGATGTATTGTTTTCTCTTCCAAATTAATAAAAACTCTCCCTCCCTACCTGTGGACGTA
130 TGATGTATTGTTTTCTCTTCCAAATTAATAAAAACTCTCCCTCCCTACCCGTGGACGTA
2904 GATCATATTG
Statistics
Matches: 184, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
211 47 0.26
212 137 0.74
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (211 bp):
TTTCCTTGGAGGTCTGTGATGTAAGCGGAGGGATCAAGTCAAAACCCCCTGGTTTGGACCTGTAT
TCATAATCCAAATAGGAACCAAGTACCCTAAGTTTATATAAGGAGTCGAAATCACTTATATACTT
GATGTATTGTTTTCTCTTCCAAATTAATAAAAACTCTCCCTCCCTACCCGTGGACGTACGTAGAT
CATATCGAACCACATT
Found at i:6522 original size:20 final size:20
Alignment explanation
Indices: 6497--6538 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6487 AGTTTGATAA
6497 TGTAAAGAAGTAGGAAAAGT
1 TGTAAAGAAGTAGGAAAAGT
*
6517 TGTAAAGGAGTAGGAAAAGT
1 TGTAAAGAAGTAGGAAAAGT
6537 TG
1 TG
6539 AGTAGCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (20 bp):
TGTAAAGAAGTAGGAAAAGT
Found at i:6928 original size:37 final size:37
Alignment explanation
Indices: 6878--6968 Score: 146
Period size: 37 Copynumber: 2.4 Consensus size: 37
6868 CATATGAAAT
*
6878 ACCCACTTAACATATCAATAATTAAAGGGGATTAAAA
1 ACCCACTTAACATATCAATAATTAAAGGGAATTAAAA
*
6915 ACCCACTTAACATATCAATAATTAAAGGGAATTGAAA
1 ACCCACTTAACATATCAATAATTAAAGGGAATTAAAA
6952 ACCCACTTGTAACATAT
1 ACCCAC-T-TAACATAT
6969 TAAAAACCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 41 0.82
38 1 0.02
39 8 0.16
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (37 bp):
ACCCACTTAACATATCAATAATTAAAGGGAATTAAAA
Found at i:6971 original size:59 final size:57
Alignment explanation
Indices: 6908--7028 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 57
6898 ATTAAAGGGG
*
6908 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTGAAAACCCACTTGTAACAT
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCAC-T-TAACAT
*
6967 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCTACTTAACAT
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCACTTAACAT
7024 ATTAA
1 ATTAA
7029 TAATTAAAGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 11 0.18
58 1 0.02
59 48 0.80
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (57 bp):
ATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCACTTAACAT
Found at i:6986 original size:20 final size:22
Alignment explanation
Indices: 6949--6988 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6939 AAGGGAATTG
6949 AAAACCCACTTGTAACATATTA
1 AAAACCCACTTGTAACATATTA
6971 AAAACCCAC-T-TAACATAT
1 AAAACCCACTTGTAACATAT
6989 CAATAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAACCCACTTGTAACATATTA
Found at i:7019 original size:37 final size:37
Alignment explanation
Indices: 6967--7041 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
6957 CTTGTAACAT
6967 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
* *
7004 ATTAAAAACCTACTTAACATATTAATAATTAAAGGGA
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
7041 A
1 A
7042 CCTCAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (37 bp):
ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
Found at i:7021 original size:96 final size:96
Alignment explanation
Indices: 6857--7041 Score: 316
Period size: 96 Copynumber: 1.9 Consensus size: 96
6847 GTCTTTAAAG
* *
6857 CCCACTTATAACATATGAAATACCCACTTAACATATCAATAATTAAAGGGGATTAAAAACCCACT
1 CCCACTTATAACATATGAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCACT
6922 TAACATATCAATAATTAAAGGGAATTGAAAA
66 TAACATATCAATAATTAAAGGGAATTGAAAA
* * *
6953 CCCACTTGTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCTACT
1 CCCACTTATAACATATGAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCACT
*
7018 TAACATATTAATAATTAAAGGGAA
66 TAACATATCAATAATTAAAGGGAA
7042 CCTCAAATTA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (96 bp):
CCCACTTATAACATATGAAAAACCCACTTAACATATCAATAATTAAAGGGAATTAAAAACCCACT
TAACATATCAATAATTAAAGGGAATTGAAAA
Found at i:8951 original size:345 final size:345
Alignment explanation
Indices: 8320--9009 Score: 1380
Period size: 345 Copynumber: 2.0 Consensus size: 345
8310 AATACTACCA
8320 TTGCTAGGAGAAATTAATCCTAAGCTTGTAGTGTTTCATGATATCTCACATATATAATGGAGAAG
1 TTGCTAGGAGAAATTAATCCTAAGCTTGTAGTGTTTCATGATATCTCACATATATAATGGAGAAG
8385 CAGAATCAGATTAACGATCATTCTATATAATTACCGCCTTCATTGCTGTTCTTTACCAAATTCTC
66 CAGAATCAGATTAACGATCATTCTATATAATTACCGCCTTCATTGCTGTTCTTTACCAAATTCTC
8450 ATCTTCTTCATGGTTCTACAGTCTACACTGCTGATGAACTCATTAGAAGGCGGTGAATTGAAGAA
131 ATCTTCTTCATGGTTCTACAGTCTACACTGCTGATGAACTCATTAGAAGGCGGTGAATTGAAGAA
8515 CTATATATACTTAACATTCGATTGGGCTTGGTTTAGTGCTTCTATACCGCAAATGACGGTAAAAA
196 CTATATATACTTAACATTCGATTGGGCTTGGTTTAGTGCTTCTATACCGCAAATGACGGTAAAAA
8580 GATTATCTGTAAAAGCGATAAACGTAACGCGACCAAATTGATTAAGGCTTAGTTTGGGATTGAGG
261 GATTATCTGTAAAAGCGATAAACGTAACGCGACCAAATTGATTAAGGCTTAGTTTGGGATTGAGG
8645 TTGTTGTTTGAAAAAGTTTG
326 TTGTTGTTTGAAAAAGTTTG
8665 TTGCTAGGAGAAATTAATCCTAAGCTTGTAGTGTTTCATGATATCTCACATATATAATGGAGAAG
1 TTGCTAGGAGAAATTAATCCTAAGCTTGTAGTGTTTCATGATATCTCACATATATAATGGAGAAG
8730 CAGAATCAGATTAACGATCATTCTATATAATTACCGCCTTCATTGCTGTTCTTTACCAAATTCTC
66 CAGAATCAGATTAACGATCATTCTATATAATTACCGCCTTCATTGCTGTTCTTTACCAAATTCTC
8795 ATCTTCTTCATGGTTCTACAGTCTACACTGCTGATGAACTCATTAGAAGGCGGTGAATTGAAGAA
131 ATCTTCTTCATGGTTCTACAGTCTACACTGCTGATGAACTCATTAGAAGGCGGTGAATTGAAGAA
8860 CTATATATACTTAACATTCGATTGGGCTTGGTTTAGTGCTTCTATACCGCAAATGACGGTAAAAA
196 CTATATATACTTAACATTCGATTGGGCTTGGTTTAGTGCTTCTATACCGCAAATGACGGTAAAAA
8925 GATTATCTGTAAAAGCGATAAACGTAACGCGACCAAATTGATTAAGGCTTAGTTTGGGATTGAGG
261 GATTATCTGTAAAAGCGATAAACGTAACGCGACCAAATTGATTAAGGCTTAGTTTGGGATTGAGG
8990 TTGTTGTTTGAAAAAGTTTG
326 TTGTTGTTTGAAAAAGTTTG
9010 GTTTGCAGAG
Statistics
Matches: 345, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
345 345 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (345 bp):
TTGCTAGGAGAAATTAATCCTAAGCTTGTAGTGTTTCATGATATCTCACATATATAATGGAGAAG
CAGAATCAGATTAACGATCATTCTATATAATTACCGCCTTCATTGCTGTTCTTTACCAAATTCTC
ATCTTCTTCATGGTTCTACAGTCTACACTGCTGATGAACTCATTAGAAGGCGGTGAATTGAAGAA
CTATATATACTTAACATTCGATTGGGCTTGGTTTAGTGCTTCTATACCGCAAATGACGGTAAAAA
GATTATCTGTAAAAGCGATAAACGTAACGCGACCAAATTGATTAAGGCTTAGTTTGGGATTGAGG
TTGTTGTTTGAAAAAGTTTG
Found at i:9082 original size:29 final size:30
Alignment explanation
Indices: 9028--9099 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
9018 AGTTTTTTTA
**
9028 CCAAACTATAACATTTTATAAACTTATTTC
1 CCAAACTATAACACATTATAAACTTATTTC
*
9058 CCAATCTATAACACATT-TAAACTTATTTC
1 CCAAACTATAACACATTATAAACTTATTTC
9087 CCAAACTATAACA
1 CCAAACTATAACA
9100 AATCATGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.35
Consensus pattern (30 bp):
CCAAACTATAACACATTATAAACTTATTTC
Found at i:9668 original size:23 final size:22
Alignment explanation
Indices: 9638--9684 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
9628 CCATTCTTAC
*
9638 AATTTAATAGTTTCTTGGTGCA
1 AATTTAATAGTTTCTAGGTGCA
* *
9660 AATTATAATGGTTTCTAGTTGCA
1 AATT-TAATAGTTTCTAGGTGCA
9683 AA
1 AA
9685 GTATTACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (22 bp):
AATTTAATAGTTTCTAGGTGCA
Found at i:10739 original size:2 final size:2
Alignment explanation
Indices: 10732--10765 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10722 AGTGGGCGTT
10732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10766 GACACACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13369 original size:30 final size:29
Alignment explanation
Indices: 13304--13370 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
13294 TGACATGATT
* * **
13304 TGTTATAGCTTGGGAAATAAGTTTAAATG
1 TGTTATAGATTCGGAAATAAGTTTAAAAA
13333 TGTTATAGATTCGGAAATAAGTTTATAAAA
1 TGTTATAGATTCGGAAATAAGTTTA-AAAA
13363 TGTTATAG
1 TGTTATAG
13371 TTTGGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (29 bp):
TGTTATAGATTCGGAAATAAGTTTAAAAA
Found at i:14077 original size:15 final size:14
Alignment explanation
Indices: 14057--14108 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
14047 CTATAAAAAT
14057 AAATAATTAAATTAA
1 AAATAA-TAAATTAA
*
14072 AAATAATAAATGTAT
1 AAATAATAAAT-TAA
* *
14087 AATTAATAATTTAA
1 AAATAATAAATTAA
14101 TAAATAAT
1 -AAATAAT
14109 TGAAAATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAATAAATTAA
Found at i:25971 original size:4 final size:4
Alignment explanation
Indices: 25936--25984 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
25926 ATTCTTTTTC
* *
25936 TTAA ATAA TAAA TTAA TT-A TT-A TT-A TTAAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA
25982 TTA
1 TTA
25985 TAATACTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 9 0.23
4 27 0.69
5 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:33094 original size:8 final size:9
Alignment explanation
Indices: 33076--33104 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
33066 GGTTGTCAGA
33076 TTTTTCTTT
1 TTTTTCTTT
33085 TTTTTCTTT
1 TTTTTCTTT
33094 TTTTTCTTT
1 TTTTTCTTT
33103 TT
1 TT
33105 GCTTGGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:43523 original size:183 final size:176
Alignment explanation
Indices: 43180--43530 Score: 517
Period size: 183 Copynumber: 1.9 Consensus size: 176
43170 CATAATATGA
43180 CTTCTGCCATTCAAGCTTCATATTTTCGATGAATTCATCAGACCTTGCTCTCAATAGAGACGATG
1 CTTCTGCCATTCAAGCTTCATATTTTCGATGAATTCATCAGACCTTGCTCTCAATAGAGACGATG
* * * *
43245 TTATATGGTTAGAATCACATCGTTCTACTCCATTGGCCAGGGCTGTTGTTTCATCTTGCGGCGCT
66 TTAAATGGTTAGAATCACATCGTTCTACTCCATTGGCCAGGGCCGTTGTTCCATCTTCCGGCGCT
*
43310 TCATGCTCCACCTCCGGCGTAATGGACTCTTGTTTTGAGGCGAATTC
131 TCA-GCTCCAACTCCGGCGTAATGGACTCTTGTTTTGAGGCGAATTC
*
43357 CTTCTGCCATTCAAGCTTCATATTTTCGATGAATTCATCAGATCTTGCTCTCAATAGAGACCGAG
1 CTTCTGCCATTCAAGCTTCATATTTTCGATGAATTCATCAGACCTTGCTCTCAATAGAGA-C--G
* *
43422 ACAATGTTAAATGGTTAGAATCACATCGTTCTACTCCATTGGGCC-GTGCCGTTGTTCCGTCTTC
63 ---ATGTTAAATGGTTAGAATCACATCGTTCTACTCCATT-GGCCAGGGCCGTTGTTCCATCTTC
*
43486 CGGCGCTTCA-CTATCAACTGCCGGCGTAATGGACTCTTGTTTTGA
124 CGGCGCTTCAGCT-CCAACT-CCGGCGTAATGGACTCTTGTTTTGA
43531 CGAGATAACA
Statistics
Matches: 156, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
177 59 0.38
178 1 0.01
180 1 0.01
181 2 0.01
182 4 0.03
183 85 0.54
184 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (176 bp):
CTTCTGCCATTCAAGCTTCATATTTTCGATGAATTCATCAGACCTTGCTCTCAATAGAGACGATG
TTAAATGGTTAGAATCACATCGTTCTACTCCATTGGCCAGGGCCGTTGTTCCATCTTCCGGCGCT
TCAGCTCCAACTCCGGCGTAATGGACTCTTGTTTTGAGGCGAATTC
Found at i:43827 original size:32 final size:32
Alignment explanation
Indices: 43791--43891 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 32
43781 ATAAACCGTT
43791 GGGAAATTGACCCAAATCAATTAGGATTTGGA
1 GGGAAATTGACCCAAATCAATTAGGATTTGGA
* *
43823 GGGAAATTGATTGACCCAAAGT-ATATTAGAATTCGGA
1 GGG-AA---ATTGACCCAAA-TCA-ATTAGGATTTGGA
*
43860 GGGAAATTGACCCAATTCAATTAGGATTTGGA
1 GGGAAATTGACCCAAATCAATTAGGATTTGGA
43892 AAATTAGTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
32 15 0.26
33 13 0.23
36 14 0.25
37 15 0.26
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (32 bp):
GGGAAATTGACCCAAATCAATTAGGATTTGGA
Found at i:43861 original size:37 final size:36
Alignment explanation
Indices: 43796--43869 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
43786 CCGTTGGGAA
* *
43796 ATTGACCCAAATCAATTAGGATTTGGAGGGAAATTG
1 ATTGACCCAAATCAATTAGAATTCGGAGGGAAATTG
43832 ATTGACCCAAAGT-ATATTAGAATTCGGAGGGAAATTG
1 ATTGACCCAAA-TCA-ATTAGAATTCGGAGGGAAATTG
43869 A
1 A
43870 CCCAATTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (36 bp):
ATTGACCCAAATCAATTAGAATTCGGAGGGAAATTG
Found at i:59781 original size:16 final size:17
Alignment explanation
Indices: 59760--59791 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
59750 TTTGATCAGA
59760 ATAGTTTG-ATTTTTCT
1 ATAGTTTGAATTTTTCT
59776 ATAGTTTGAATTTTTC
1 ATAGTTTGAATTTTTC
59792 AGTTTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
ATAGTTTGAATTTTTCT
Found at i:77073 original size:32 final size:33
Alignment explanation
Indices: 77032--77096 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
77022 AATCTAAGAG
* *
77032 CATGCAATTTGAAAAGGTGGGAATA-CATTAAT
1 CATGCAATTTAAAAAGGTGGGAACACCATTAAT
77064 CATGCAATTTAAAAAGGTGGGAACACCATTAAT
1 CATGCAATTTAAAAAGGTGGGAACACCATTAAT
77097 TGAAGTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (33 bp):
CATGCAATTTAAAAAGGTGGGAACACCATTAAT
Found at i:78668 original size:24 final size:26
Alignment explanation
Indices: 78612--78678 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 26
78602 ACCTGACCGG
78612 CGCCAGGGGGAAGCTGGCCAGCAGCAC
1 CGCCAGGGGGAAGCTGGCCAGCAG-AC
*
78639 CACCAGGGGGAAGCTGGCCAGC-G-C
1 CGCCAGGGGGAAGCTGGCCAGCAGAC
78663 CGCCAGGGGGAAGCTG
1 CGCCAGGGGGAAGCTG
78679 AGCGCCGCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 16 0.42
26 1 0.03
27 21 0.55
ACGTcount: A:0.21, C:0.31, G:0.43, T:0.04
Consensus pattern (26 bp):
CGCCAGGGGGAAGCTGGCCAGCAGAC
Found at i:78684 original size:21 final size:23
Alignment explanation
Indices: 78612--78686 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 23
78602 ACCTGACCGG
78612 CGCCAGGGGGAAGCTGGCCAGCAGCAC
1 CGCCAGGGGGAAGCTGG-CAGC-G--C
*
78639 CACCAGGGGGAAGCTGGCCAGCGC
1 CGCCAGGGGGAAGCTGG-CAGCGC
78663 CGCCAGGGGGAAGCT-G-AGCGC
1 CGCCAGGGGGAAGCTGGCAGCGC
78684 CGC
1 CGC
78687 TGCCAGTCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.17
23 1 0.02
24 15 0.33
26 1 0.02
27 21 0.46
ACGTcount: A:0.20, C:0.33, G:0.43, T:0.04
Consensus pattern (23 bp):
CGCCAGGGGGAAGCTGGCAGCGC
Found at i:86202 original size:16 final size:17
Alignment explanation
Indices: 86181--86214 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
86171 TATATGGAAC
86181 CGTAATCGCAACC-GAA
1 CGTAATCGCAACCAGAA
*
86197 CGTAATCGGAACCAGAA
1 CGTAATCGCAACCAGAA
86214 C
1 C
86215 CGTCCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (17 bp):
CGTAATCGCAACCAGAA
Found at i:88226 original size:197 final size:196
Alignment explanation
Indices: 87733--88228 Score: 562
Period size: 197 Copynumber: 2.6 Consensus size: 196
87723 ACTGTTAGGG
*
87733 TAAA-TTTTGAACTCCATAAGCGGGATAAGAAGTTGACACATACCCTATTTCATAATTAATTAAA
1 TAAATTTTTG-ACTCCATAAGCGGGTTAAGAAGTTGACACATACCCTATTTCATAATTAATTAAA
* * * *
87797 TATAAAATATTAATACATATTCCCTAAGAGG-AC----CAA-----AAACCTCGTACGTGCAGTC
65 TAT-TAATATTAATACATATTCCCTAAG-GGAACATGTCAACCCTTAAACCCCGCAAGTGCAGTC
* * *
87852 TGCTAAACTCCACTTACGGTATAATTTATAATTTTTTTATATGATTAATATACAAAATACACCGT
128 TGCTAAACTCCACTGACGGTATAATTCATAATTTTTTTATATGATTAATATAC-AAATACACCGC
* *
87917 CAGTG
192 CAATA
* * *
87922 TAAATTTTGGACTCCATAAGTGGCTTAA-AAGGTTGACACATACCCTATTTCATAATTAATT-AA
1 TAAATTTTTGACTCCATAAGCGGGTTAAGAA-GTTGACACATACCCTATTTCATAATTAATTAAA
* *
87985 -A-TAATATTAATACAATATTCCATAAGGGAATACATGTAAACCCTTAAACCCCGCAAGTGCAGT
65 TATTAATATTAATAC-ATATTCCCTAAGGG-A-ACATGTCAACCCTTAAACCCCGCAAGTGCAGT
* * *
88048 CTGCTAAACTCCACTGACGGTGT-ATTGCATAATTTTTCTTATATGATTATTATAC-AATACACT
127 CTGCTAAACTCCACTGACGGTATAATT-CATAATTTTT-TTATATGATTAATATACAAATACACC
88111 GCCAATA
190 GCCAATA
* *
88118 TAAATTTTTGACTCCATAAGCGGGTTAAGAAGTTAACACATACTCC-GTTTC-TAATTAATTAAA
1 TAAATTTTTGACTCCATAAGCGGGTTAAGAAGTTGACACATAC-CCTATTTCATAATTAATTAAA
88181 TATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAA
65 TA-TTAATATTAATACATATTCCCTAAGGGA-ACATGTCAACCCTTAA
Statistics
Matches: 258, Mismatches: 26, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
185 13 0.05
186 11 0.04
187 1 0.00
188 6 0.02
189 49 0.19
190 4 0.02
192 2 0.01
195 9 0.03
196 56 0.22
197 66 0.26
198 29 0.11
199 12 0.05
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (196 bp):
TAAATTTTTGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCTATTTCATAATTAATTAAAT
ATTAATATTAATACATATTCCCTAAGGGAACATGTCAACCCTTAAACCCCGCAAGTGCAGTCTGC
TAAACTCCACTGACGGTATAATTCATAATTTTTTTATATGATTAATATACAAATACACCGCCAAT
A
Done.