Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012494.1 Corchorus capsularis cultivar CVL-1 contig12515, 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: 107948
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1013 original size:13 final size:15
Alignment explanation
Indices: 985--1016 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
975 TACATCAACA
985 TGAAAACATAATAAT
1 TGAAAACATAATAAT
1000 TGAAAA-AT-ATAAT
1 TGAAAACATAATAAT
1013 TGAA
1 TGAA
1017 TGTCTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.28
Consensus pattern (15 bp):
TGAAAACATAATAAT
Found at i:5813 original size:3 final size:3
Alignment explanation
Indices: 5799--5852 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
5789 AGTATAGTAT
* *
5799 ATA ATA ACA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5847 ATA ATA
1 ATA ATA
5853 TAGCTTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6537 original size:27 final size:27
Alignment explanation
Indices: 6499--6552 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
6489 GCGCATCTAA
*
6499 TTATGGTTGGTGAGTCTACCAACGGGG
1 TTATGGTGGGTGAGTCTACCAACGGGG
*
6526 TTATGGTGGGTGAGTCTACCAATGGGG
1 TTATGGTGGGTGAGTCTACCAACGGGG
6553 GCAGCTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.39, T:0.30
Consensus pattern (27 bp):
TTATGGTGGGTGAGTCTACCAACGGGG
Found at i:7986 original size:38 final size:38
Alignment explanation
Indices: 7933--8009 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
7923 GATCCCCTTT
7933 ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
* *
7971 ACATTTAATGTTAATCTGCTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
8009 A
1 A
8010 AATCTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (38 bp):
ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
Found at i:13513 original size:34 final size:34
Alignment explanation
Indices: 13470--13689 Score: 186
Period size: 34 Copynumber: 6.5 Consensus size: 34
13460 TTTCCTCAGC
* *
13470 ATGACAACTTCTAGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTAAT
* *
13504 ATGACAACTTCTGGTGTC-A-ATCAT--TTTCAAC
1 ATGACAACTTCTGGTGTCAAGATAATAATTT-AAT
* *
13535 ATGACAACTTTTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTAAT
* * *
13569 ATGACAACTTCTGATGTC-A-ATCAT--TTTCAAC
1 ATGACAACTTCTGGTGTCAAGATAATAATTT-AAT
*
13600 ATGACAACTTCTGGTGTCAAGATAATAATTTCAT
1 ATGACAACTTCTGGTGTCAAGATAATAATTTAAT
* * *
13634 ATGGCAACTTCAGGTGCCAATGTCAAGATAATAATTTCAT
1 ATGACAACTTC---TG---GTGTCAAGATAATAATTTAAT
*
13674 ATGGCAACTTCTGGTG
1 ATGACAACTTCTGGTG
13690 CCAATTAAAT
Statistics
Matches: 150, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
30 6 0.04
31 36 0.24
32 10 0.07
33 10 0.07
34 47 0.31
35 6 0.04
37 4 0.03
40 31 0.21
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (34 bp):
ATGACAACTTCTGGTGTCAAGATAATAATTTAAT
Found at i:13542 original size:31 final size:31
Alignment explanation
Indices: 13437--13619 Score: 172
Period size: 31 Copynumber: 5.6 Consensus size: 31
13427 CAATCTTAGG
*
13437 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAATAATTT--TCAAC
* * *
13470 ATGACAACTTCTAGTGTCAAGATAATAATTT-GAT
1 ATGACAACTTCTGGTGTC-A-ATAAT--TTTCAAC
*
13504 ATGACAACTTCTGGTGTCAATCATTTTCAAC
1 ATGACAACTTCTGGTGTCAATAATTTTCAAC
* * *
13535 ATGACAACTTTTGGTGTCAAGATAATAATTT-GAT
1 ATGACAACTTCTGGTGTC-A-ATAAT--TTTCAAC
* *
13569 ATGACAACTTCTGATGTCAATCATTTTCAAC
1 ATGACAACTTCTGGTGTCAATAATTTTCAAC
13600 ATGACAACTTCTGGTGTCAA
1 ATGACAACTTCTGGTGTCAA
13620 GATAATAATT
Statistics
Matches: 122, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.05
31 38 0.31
32 9 0.07
33 23 0.19
34 35 0.29
35 9 0.07
37 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (31 bp):
ATGACAACTTCTGGTGTCAATAATTTTCAAC
Found at i:13557 original size:65 final size:65
Alignment explanation
Indices: 13437--13654 Score: 337
Period size: 65 Copynumber: 3.3 Consensus size: 65
13427 CAATCTTAGG
* * *
13437 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTAGTGTCAAGATAATAATTTG
1 ATGACAACTTCTGGTGTCAATCATTT--TCAACATGACAACTTCTGGTGTCAAGATAATAATTTG
13502 AT
64 AT
*
13504 ATGACAACTTCTGGTGTCAATCATTTTCAACATGACAACTTTTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAATCATTTTCAACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
* *
13569 ATGACAACTTCTGATGTCAATCATTTTCAACATGACAACTTCTGGTGTCAAGATAATAATTTCAT
1 ATGACAACTTCTGGTGTCAATCATTTTCAACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
* * *
13634 ATGGCAACTTCAGGTGCCAAT
1 ATGACAACTTCTGGTGTCAAT
13655 GTCAAGATAA
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
65 115 0.82
67 25 0.18
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (65 bp):
ATGACAACTTCTGGTGTCAATCATTTTCAACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
Found at i:13669 original size:40 final size:40
Alignment explanation
Indices: 13614--13694 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
13604 CAACTTCTGG
13614 TGTCAAGATAATAATTTCATATGGCAACTTCAGGTGCCAA
1 TGTCAAGATAATAATTTCATATGGCAACTTCAGGTGCCAA
*
13654 TGTCAAGATAATAATTTCATATGGCAACTTCTGGTGCCAA
1 TGTCAAGATAATAATTTCATATGGCAACTTCAGGTGCCAA
13694 T
1 T
13695 TAAATTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (40 bp):
TGTCAAGATAATAATTTCATATGGCAACTTCAGGTGCCAA
Found at i:14023 original size:38 final size:38
Alignment explanation
Indices: 13967--14039 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
13957 CCCTTTACAT
13967 TTAATGCTAATCTACTTTACTTGCAAGCAAAGTAACAC
1 TTAATGCTAATCTACTTTACTTGCAAGCAAAGTAACAC
*
14005 TTAATGCTAATCTGCTTTACTTGCAAGCAAAGTAA
1 TTAATGCTAATCTACTTTACTTGCAAGCAAAGTAA
14040 AATCTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (38 bp):
TTAATGCTAATCTACTTTACTTGCAAGCAAAGTAACAC
Found at i:19098 original size:109 final size:109
Alignment explanation
Indices: 18945--19240 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
18935 TAAATTAAAA
* *
18945 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAATAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
19009 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
19056 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATTGAGTTTTTAGTAGA
1 TGGTAAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
19121 ATAAAATTGTATATTAGGAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
19165 TGGTAAAAATAAAATAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAATAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
19230 GTAGAATAAAA
61 GTAGAATAAAA
19241 CTATAATAGT
Statistics
Matches: 169, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
109 118 0.70
110 13 0.08
111 11 0.07
114 27 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:36107 original size:158 final size:159
Alignment explanation
Indices: 35818--36134 Score: 539
Period size: 158 Copynumber: 2.0 Consensus size: 159
35808 GCTTGACATT
* *
35818 GTAAAATGGCATTTTACAGTTTCTTTTAACAAGATTCTGCAAATTGCCTCTTTGTTTGTATAATC
1 GTAAAATAGCATTTTACAGTTTCTTTTAACAAGATTCTGCAAATTGCCTCTTTGTTTATATAATC
* *
35883 TACTCGAAACTTAGATGTATCATCTCTTACTGTAGTGTTATGTTAGAGTGGTAGATAACTGATGG
66 TACTCGAAACTTAGATGTAGCATCTCTTACTGTAGTGTTATGTTAGAGTGATAGATAACTGATGG
35948 ATAGTCCACTAAGAGTTTTGGGAGCTTAA
131 ATAGTCCACTAAGAGTTTTGGGAGCTTAA
* *
35977 GTAAAATAGCATTTTACAGTTTCTTTTAACTAGATTCTGCGAATTGCCTCTTT-TTTATATAATC
1 GTAAAATAGCATTTTACAGTTTCTTTTAACAAGATTCTGCAAATTGCCTCTTTGTTTATATAATC
* *
36041 TACTCGAAACTTAGTTGTAGCATCTCTTACTGTAGTGTTATG-TACGAGTGATAGATATCTGATG
66 TACTCGAAACTTAGATGTAGCATCTCTTACTGTAGTGTTATGTTA-GAGTGATAGATAACTGATG
36105 GATAGTCCACTAAGAGTTTTGGGAGCTTAA
130 GATAGTCCACTAAGAGTTTTGGGAGCTTAA
36135 CTTAGCTGTC
Statistics
Matches: 149, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
157 2 0.01
158 97 0.65
159 50 0.34
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (159 bp):
GTAAAATAGCATTTTACAGTTTCTTTTAACAAGATTCTGCAAATTGCCTCTTTGTTTATATAATC
TACTCGAAACTTAGATGTAGCATCTCTTACTGTAGTGTTATGTTAGAGTGATAGATAACTGATGG
ATAGTCCACTAAGAGTTTTGGGAGCTTAA
Found at i:37459 original size:2 final size:2
Alignment explanation
Indices: 37452--37485 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
37442 CCTGAAATAG
37452 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
37486 TTTCATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44692 original size:32 final size:32
Alignment explanation
Indices: 44651--44726 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 32
44641 AATTTTTTTT
*
44651 TTTTTTTGCAATTATAAAGGCAGTTTACTTTA
1 TTTTTTTGCAATTACAAAGGCAGTTTACTTTA
*
44683 TTTTTTTGCAATTACAAAGGCAGTTTATTTTA
1 TTTTTTTGCAATTACAAAGGCAGTTTACTTTA
44715 TTTTATTTGCAA
1 TTTT-TTTGCAA
44727 GAACTATGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 34 0.83
33 7 0.17
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTTTTTGCAATTACAAAGGCAGTTTACTTTA
Found at i:57350 original size:3 final size:3
Alignment explanation
Indices: 57342--57367 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57332 TGCGGCGACC
57342 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
57368 ATGGCCGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:60472 original size:27 final size:27
Alignment explanation
Indices: 60430--60487 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
60420 CAAATTCAAG
* * *
60430 TATTTCTGCTGGTACTTCTATTGGTCA
1 TATTTCTGCCGATACTTCTATTGATCA
*
60457 TATTTCTGCCGATACTTCTGTTGATCA
1 TATTTCTGCCGATACTTCTATTGATCA
60484 TATT
1 TATT
60488 CCATCTTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (27 bp):
TATTTCTGCCGATACTTCTATTGATCA
Found at i:63449 original size:26 final size:25
Alignment explanation
Indices: 63404--63495 Score: 130
Period size: 25 Copynumber: 3.6 Consensus size: 25
63394 TAGCCAATGT
*
63404 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
63429 GTTTGCTAAAATGCAAGCACAGGCTC
1 GTTTGCT-AAACGCAAGCACAGGCTC
* *
63455 ATTTGCTAAACGTAAGCACAGGCTC
1 GTTTGCTAAACGCAAGCACAGGCTC
*
63480 GTTTGCCAAACGCAAG
1 GTTTGCTAAACGCAAG
63496 AACATGAGCG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
25 35 0.60
26 23 0.40
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (25 bp):
GTTTGCTAAACGCAAGCACAGGCTC
Found at i:85056 original size:19 final size:18
Alignment explanation
Indices: 85032--85068 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
85022 ATTTTGTTCG
85032 TTTCATCATTTTCTTTCTT
1 TTTCAT-ATTTTCTTTCTT
*
85051 TTTCATTTTTTCTTTCTT
1 TTTCATATTTTCTTTCTT
85069 CCTCCCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATATTTTCTTTCTT
Found at i:86242 original size:138 final size:134
Alignment explanation
Indices: 85951--86322 Score: 561
Period size: 138 Copynumber: 2.8 Consensus size: 134
85941 AGGTTAGATT
* * * * *
85951 TTTTGAATGTTGTGTTTGATTTTCTGACATACCTTGAATTGTGTGTGGAAGAGATAGGGTTTTAA
1 TTTTGAATGTTGTGTTTGATTTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGGTTTTAA
* *
86016 TCTACGGTCACATTTGAATATG--CCTTT-AATCCAACCGTTTGAAATAGGGTTAGATTTTCTGA
66 TCAACGGTCACATTTGAATATGAACATTTAAATCCAACCGTTTGAAATAGGGTTAGATTTTCTGA
*
86078 AAGT
131 AAGG
* *
86082 TTTTGAATGTTGTTTTTGATTTTCTGACATGCCTTGGATAGTGTGCGTAAGAGATAAGGTTTTAA
1 TTTTGAATGTTGTGTTTGATTTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGGTTTTAA
*
86147 TCAACGGTCACATTTGAATATGAACATTTAAATCCAACCGTTGGATTGAAATATGGTTAGATTTT
66 TCAACGGTCACATTTGAATATGAACATTTAAATCCAACCG-T---TTGAAATAGGGTTAGATTTT
86212 CTGAAAGG
127 CTGAAAGG
*
86220 TTTTGAATGTTGTGTTTGATTTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGATTTTAA
1 TTTTGAATGTTGTGTTTGATTTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGGTTTTAA
* *
86285 TCAATGGTCACATTTGAATATGAACGTTTAAATCCAAC
66 TCAACGGTCACATTTGAATATGAACATTTAAATCCAAC
86323 GGCTACATTT
Statistics
Matches: 218, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
131 79 0.36
133 4 0.02
134 10 0.05
135 1 0.00
138 124 0.57
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (134 bp):
TTTTGAATGTTGTGTTTGATTTTCTGACATGCCTTGGATAGTGTGCGGAAGAGATAAGGTTTTAA
TCAACGGTCACATTTGAATATGAACATTTAAATCCAACCGTTTGAAATAGGGTTAGATTTTCTGA
AAGG
Found at i:88006 original size:36 final size:36
Alignment explanation
Indices: 87966--88034 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
87956 TGAATATATA
* *
87966 AATTAATATTACATGTA-TATACTAATTATTATTATT
1 AATTAATATTACAAGTATTAT-CTAAATATTATTATT
88002 AATTAATATTACAAGTATTATCTAAATATTATT
1 AATTAATATTACAAGTATTATCTAAATATTATT
88035 TTTATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
AATTAATATTACAAGTATTATCTAAATATTATTATT
Found at i:88065 original size:21 final size:20
Alignment explanation
Indices: 88024--88070 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
88014 AAGTATTATC
*
88024 TAAAT-ATT-ATTTTTATTA
1 TAAATAATTAATTTTTATAA
*
88042 TAATTAATTAATTTTTATGAA
1 TAAATAATTAATTTTTAT-AA
88063 TAAATAAT
1 TAAATAAT
88071 ATGATTAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 3 0.13
20 8 0.35
21 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAATAATTAATTTTTATAA
Found at i:89463 original size:107 final size:107
Alignment explanation
Indices: 89263--89475 Score: 401
Period size: 107 Copynumber: 2.0 Consensus size: 107
89253 TTAGTCATCA
89263 ATGCAAATAACAAAAAAACCAAGCATGCAATGACCAAAATACCCCTCCCAATTTGGTCTTGGATC
1 ATGCAAATAACAAAAAAACCAAGCATGCAATGACCAAAATACCCCTCCCAATTTGGTCTTGGATC
89328 ATTATGCTCAGATCTTTTGATTGGTTTTTTTAGTAATTTCAT
66 ATTATGCTCAGATCTTTTGATTGGTTTTTTTAGTAATTTCAT
* *
89370 ATGCAAATAACAAAAAAACCAAGTATGCAATGACCAAAATACCCCTCCCAATTTTGTCTTGGATC
1 ATGCAAATAACAAAAAAACCAAGCATGCAATGACCAAAATACCCCTCCCAATTTGGTCTTGGATC
89435 ATTATGCT-AGATCTTTTGATTGGTTTTTTTAGTAATTTCAT
66 ATTATGCTCAGATCTTTTGATTGGTTTTTTTAGTAATTTCAT
89476 TTCTTCCTAT
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
106 33 0.32
107 71 0.68
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (107 bp):
ATGCAAATAACAAAAAAACCAAGCATGCAATGACCAAAATACCCCTCCCAATTTGGTCTTGGATC
ATTATGCTCAGATCTTTTGATTGGTTTTTTTAGTAATTTCAT
Found at i:89567 original size:26 final size:26
Alignment explanation
Indices: 89538--89591 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
89528 TAGTAATTTC
89538 ATTTC-TCTCTATTATTGTTTTGTATA
1 ATTTCTTC-CTATTATTGTTTTGTATA
89564 ATTTCTTCCTATTATTGTTTTGTATA
1 ATTTCTTCCTATTATTGTTTTGTATA
89590 AT
1 AT
89592 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (26 bp):
ATTTCTTCCTATTATTGTTTTGTATA
Found at i:93052 original size:25 final size:26
Alignment explanation
Indices: 93024--93074 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
93014 ATTACAATTA
93024 GTTTCATTATCA-TTTTTTTAGTGCT
1 GTTTCATTATCATTTTTTTTAGTGCT
93049 GTTTCATTATCATTTTTTTTAGTGCT
1 GTTTCATTATCATTTTTTTTAGTGCT
93075 ACAAGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.61
Consensus pattern (26 bp):
GTTTCATTATCATTTTTTTTAGTGCT
Found at i:93600 original size:107 final size:106
Alignment explanation
Indices: 93467--93670 Score: 309
Period size: 107 Copynumber: 1.9 Consensus size: 106
93457 GGGGCTAACT
93467 TTAGTGAATTAATTATATATTGTATTTCTAAAACCCTATAACAATAAATCATTAATTTTAAAATT
1 TTAGTGAATTAATTATATATTGTATTTCTAAAACCCTATAACAATAAATCATTAATTTTAAAATT
* *
93532 TACCCTTGACATAAAATTAAAATTTTAGTTTGTGGCCAAAC
66 TACCCTTAACATAAAATTAAAATTTTAATTTGTGGCCAAAC
* * * * * * **
93573 TTAGTGAAATTAGTTTTATATTTTATTTCTAAAATCCTATAACAATAAGTTATTAATTTTGGAAT
1 TTAGTG-AATTAATTATATATTGTATTTCTAAAACCCTATAACAATAAATCATTAATTTTAAAAT
93638 TTACCCTTAACATAAAATTAAAATTTTAATTTG
65 TTACCCTTAACATAAAATTAAAATTTTAATTTG
93671 GGGCTTTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 6 0.07
107 81 0.93
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (106 bp):
TTAGTGAATTAATTATATATTGTATTTCTAAAACCCTATAACAATAAATCATTAATTTTAAAATT
TACCCTTAACATAAAATTAAAATTTTAATTTGTGGCCAAAC
Found at i:94883 original size:31 final size:31
Alignment explanation
Indices: 94845--94909 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
94835 TTGGGTTATC
94845 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
94876 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
94907 AGT
1 AGT
94910 TAGTTCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:99047 original size:19 final size:18
Alignment explanation
Indices: 99020--99056 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
99010 CCATGTGTCA
99020 TTTTTGTACACGTGGCAT
1 TTTTTGTACACGTGGCAT
99038 TTTTTGGTACACGTGGCAT
1 TTTTT-GTACACGTGGCAT
99057 GCCACGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.43
Consensus pattern (18 bp):
TTTTTGTACACGTGGCAT
Found at i:102706 original size:16 final size:16
Alignment explanation
Indices: 102685--102719 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
102675 CACTACACTC
*
102685 TTTTTTT-TTTTTTAA
1 TTTTTTTATTATTTAA
102700 TTTTTTTATTATTTAA
1 TTTTTTTATTATTTAA
102716 TTTT
1 TTTT
102720 CCAAGAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTATTATTTAA
Found at i:106963 original size:43 final size:45
Alignment explanation
Indices: 106915--107001 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 45
106905 AGATATCAGG
*
106915 CATTGTTATTAATTTAGT-AATCCAGAGAAATTT-GTTACTATGT
1 CATTGTTATTAATTTAGTAAATCCAGAGAAATTTCCTTACTATGT
* *
106958 CATTGTTATTAATTTAGTAAATCTAGGGAAATTTCCTTACTATG
1 CATTGTTATTAATTTAGTAAATCCAGAGAAATTTCCTTACTATG
107002 CTCCTATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 18 0.46
44 13 0.33
45 8 0.21
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (45 bp):
CATTGTTATTAATTTAGTAAATCCAGAGAAATTTCCTTACTATGT
Done.