Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010613.1 Corchorus capsularis cultivar CVL-1 contig10634, 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: 12646
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Found at i:4638 original size:28 final size:28
Alignment explanation
Indices: 4603--4679 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
4593 AAAATGGACT
*
4603 AAAAATGACCAAAATGCCCCTTTAATGC
1 AAAAATGACCAAAATGCCCCTATAATGC
* *
4631 AAAAATGACCAAAATGCCCCTATGATGT
1 AAAAATGACCAAAATGCCCCTATAATGC
4659 AAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
4680 GGATGACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTATAATGC
Found at i:7668 original size:21 final size:21
Alignment explanation
Indices: 7642--7701 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
7632 TATGAAACTC
*
7642 AAACCCCAAATATTAATGGTT
1 AAACCCCAAATATTAATGGTG
* ** *
7663 AAACCCCAAAGCATCCATTGTG
1 AAACCCCAAA-TATTAATGGTG
7685 AAACCCCAAATATTAAT
1 AAACCCCAAATATTAAT
7702 AGTCAAACTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.23
Consensus pattern (21 bp):
AAACCCCAAATATTAATGGTG
Found at i:7868 original size:87 final size:86
Alignment explanation
Indices: 7685--8219 Score: 423
Period size: 88 Copynumber: 6.1 Consensus size: 86
7675 ATCCATTGTG
** * ** * * *
7685 AAACCCCAAATATTAATAGTCAAACTACAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGC
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCATG-ATTGGC
* * *
7750 AAACCAATACTATTAATGGAATC
65 AAACC-CTACTAGTAATGGGATC
* * * * * **
7773 GAAGCCCAAATCATAATGGTCAAACCCCAAATCATGTACGGTGAACTT-TAAAGCATGATTCCCT
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCATGATTGGC-
*
7837 AAACCCCTACTAGTAATAGGATC
65 AAA-CCCTACTAGTAATGGGATC
* *
7860 AAACCCCAAAGCGTTA-GGTCAAA-CCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGC
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCATGATT-GGC
**
7923 AAA-CCTAGGGATGTAATGGGATC
65 AAACCCTA-CTA-GTAATGGGATC
* * * *** * * * *
7946 AAACCACAAATCTTAGTGGTCAAACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAATAGGC
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCAT-GATTGGC
*
8011 AAACTCATACTAGTAATGGGATC
65 AAAC-CCTACTAGTAATGGGATC
*
8034 AAACCCCAAA-CGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAACATGATTAGGC
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCATGATT-GGC
* * * *
8098 AAACCCAGGGATGTAATTAATAGGATC
65 AAACCC---TA-CT-AGTAATGGGATC
* * * *** * * * * *
8125 AAACCCCAAATCTTAGTGATCAAACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAATAGAC
1 AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCAT-GATTGGC
*
8190 AAACCAGTACTAGTAATGGGATC
65 AAACC-CTACTAGTAATGGGATC
8213 AAACCCC
1 AAACCCC
8220 CAAAGCATCC
Statistics
Matches: 349, Mismatches: 78, Indels: 40
0.75 0.17 0.09
Matches are distributed among these distances:
84 4 0.01
85 22 0.06
86 49 0.14
87 89 0.26
88 109 0.31
89 5 0.01
90 5 0.01
91 20 0.06
92 44 0.13
93 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (86 bp):
AAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAGCATGATTGGCA
AACCCTACTAGTAATGGGATC
Found at i:7968 original size:173 final size:173
Alignment explanation
Indices: 7698--8219 Score: 552
Period size: 179 Copynumber: 3.0 Consensus size: 173
7688 CCCCAAATAT
* * * * * **
7698 TAATAGTCAAACTACAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGCAAACCAATA-CTA
1 TAATGGTCAAAC-CCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAACC--TAGGGA
* * * * * * * *
7762 T-TAATGGAATCGAAGCCCAAATCATAATGGTCAAACCCCAAATCATGTACGGT-GAACTTTAAA
63 TGTAATGGGATC-AAACCCAAATCTTAGTGGTCAAACCACAAATCATGTACGGTCAAAATGTAAA
* * *
7825 GCAT-GATTCCCTAAACCCCTACTAGTAATAGGATCAAACCCCAAAGCG
127 GCATCAATACCC-AAACCCATACTAGTAATAGGATCAAACCCCAAA-CG
*
7873 TTA-GGTCAAACCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAACCTAGGGATGT
1 TAATGGTCAAACCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAACCTAGGGATGT
* * *
7937 AATGGGATCAAACCACAAATCTTAGTGGTCAAACTAGAAATCATGTATGGTCAAAATGTAAAGCA
66 AATGGGATCAAACC-CAAATCTTAGTGGTCAAACCACAAATCATGTACGGTCAAAATGTAAAGCA
** * *
8002 TCAATAGGCAAACTCATACTAGTAATGGGATCAAACCCCAAACG
130 TCAATACCCAAACCCATACTAGTAATAGGATCAAACCCCAAACG
* *
8046 TAATGGTCAAACCCCAAATCATGTATGGTGAAATTGTAAAACATGATTAGGCAAACCCAGGGATG
1 TAATGGTCAAA-CCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAACCTAGGGATG
* * * * *
8111 TAATTAATAGGATCAAACCCCAAATCTTAGTGATCAAACTAGAAATCATGTATGGTCAAAATGTA
65 ----TAATGGGATCAAA-CCCAAATCTTAGTGGTCAAACCACAAATCATGTACGGTCAAAATGTA
** *
8176 AAGCATCAATAGACAAA-CCAGTACTAGTAATGGGATCAAACCCC
125 AAGCATCAATACCCAAACCCA-TACTAGTAATAGGATCAAACCCC
8220 CAAAGCATCC
Statistics
Matches: 301, Mismatches: 33, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
171 2 0.01
172 6 0.02
173 83 0.28
174 55 0.18
175 56 0.19
178 2 0.01
179 95 0.32
180 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (173 bp):
TAATGGTCAAACCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAACCTAGGGATGT
AATGGGATCAAACCCAAATCTTAGTGGTCAAACCACAAATCATGTACGGTCAAAATGTAAAGCAT
CAATACCCAAACCCATACTAGTAATAGGATCAAACCCCAAACG
Found at i:7977 original size:21 final size:22
Alignment explanation
Indices: 7944--7991 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
7934 TGTAATGGGA
7944 TCAAACCACAAATC-T-TAGTGG
1 TCAAACCACAAATCATGTA-TGG
* *
7965 TCAAACTAGAAATCATGTATGG
1 TCAAACCACAAATCATGTATGG
7987 TCAAA
1 TCAAA
7992 ATGTAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 9 0.39
23 2 0.09
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (22 bp):
TCAAACCACAAATCATGTATGG
Found at i:8101 original size:175 final size:175
Alignment explanation
Indices: 7844--8225 Score: 608
Period size: 179 Copynumber: 2.2 Consensus size: 175
7834 CCTAAACCCC
* *
7844 TACTAGTAATAGGATCAAACCCCAAAGCGTTAGGTCAAACCCAAATCATGTATGGTGAAATTGTA
1 TACTAGTAATGGGATCAAACCCCAAAGCGTAAGGTCAAACCCAAATCATGTATGGTGAAATTGTA
* * * *
7909 AAGCATGATTAGGCAAACCTAGGGATG-TAATGGGATCAAACCACAAATCTTAGTGGTCAAACTA
66 AAACATGATTAGGCAAACCCAGGGATGATAATAGGATCAAACCACAAATCTTAGTGATCAAACTA
*
7973 GAAATCATGTATGGTCAAAATGTAAAGCATCAATAGGCAAACTCA-
131 GAAATCATGTATGGTCAAAATGTAAAGCATCAATAGACAAAC-CAG
8018 TACTAGTAATGGGATCAAACCCCAAA-CGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTG
1 TACTAGTAATGGGATCAAACCCCAAAGCGTAA-GGTCAAA-CCCAAATCATGTATGGTGAAATTG
*
8082 TAAAACATGATTAGGCAAACCCAGGGATGTAATTAATAGGATCAAACCCCAAATCTTAGTGATCA
64 TAAAACATGATTAGGCAAACCCAGGGATG--A-TAATAGGATCAAACCACAAATCTTAGTGATCA
8147 AACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAATAGACAAACCAG
126 AACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAATAGACAAACCAG
8197 TACTAGTAATGGGATCAAACCCCCAAAGC
1 TACTAGTAATGGGATCAAA-CCCCAAAGC
8226 ATCCATTGTG
Statistics
Matches: 191, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
173 4 0.02
174 32 0.17
175 51 0.27
178 2 0.01
179 94 0.49
180 7 0.04
181 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (175 bp):
TACTAGTAATGGGATCAAACCCCAAAGCGTAAGGTCAAACCCAAATCATGTATGGTGAAATTGTA
AAACATGATTAGGCAAACCCAGGGATGATAATAGGATCAAACCACAAATCTTAGTGATCAAACTA
GAAATCATGTATGGTCAAAATGTAAAGCATCAATAGACAAACCAG
Found at i:8256 original size:111 final size:111
Alignment explanation
Indices: 8125--8326 Score: 332
Period size: 111 Copynumber: 1.8 Consensus size: 111
8115 TAATAGGATC
* *
8125 AAACCCCAAATCTTAGTGATCAAACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAATAGAC
1 AAACCCCAAATCTTAATGATCAAACTACAAATCATGTATGGTCAAAATGTAAAGCATCAATAGAC
*
8190 AAACCAGTACTAGTAATGGGATCAAACCCCCAAAGCATCCATTGTG
66 AAACCAGTACTAGTAATGGAATCAAACCCCCAAAGCATCCATTGTG
* * * *
8236 AAACCTCAAATCTTAATGATCAAGCTACAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGC
1 AAACCCCAAATCTTAATGATCAAACTACAAATCATGTATGGTCAAAATGTAAAGCATCAATAGAC
*
8301 AAACTAGTACTAGTAATGGAATCAAA
66 AAACCAGTACTAGTAATGGAATCAAA
8327 GCCCAAGTCG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 83 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (111 bp):
AAACCCCAAATCTTAATGATCAAACTACAAATCATGTATGGTCAAAATGTAAAGCATCAATAGAC
AAACCAGTACTAGTAATGGAATCAAACCCCCAAAGCATCCATTGTG
Found at i:8402 original size:88 final size:88
Alignment explanation
Indices: 8263--8722 Score: 409
Period size: 88 Copynumber: 5.2 Consensus size: 88
8253 GATCAAGCTA
* * * * * *** *
8263 CAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGCAAACTAGTACTAGTAATGGAATCAAAG
1 CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAACCCCTACTAGTAATGGAATCAAAC
8328 CCCAAGTCGTAATGGTCAAACCC
66 CCCAAGTCGTAATGGTCAAACCC
* ** *
8351 CATATCATGTACGGTGAAACTTTAAAGCATGATT-CCCTAAACCCCTACTAGTAATGGGATCAAA
1 CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGC-AAACCCCTACTAGTAATGGAATCAAA
*
8415 CCCCAAAG-CGTAATGGTCATACCC
65 CCCC-AAGTCGTAATGGTCAAACCC
* **
8439 CAAATCATGTACGGTGAAA-TTATAAAGCATGATTAGGCAAA-TCC-AGGGATGTAAT-GAGATC
1 CAAATCATGTACGGTGAAACTT-TAAAGCATGATTAGGCAAACCCCTA-CTA-GTAATGGA-ATC
* * * **
8500 AAACCCCAAATCTTAATAGTCAAACTA
62 AAACCCCAAGTCGTAATGGTCAAACCC
* * * * * * ** *
8527 GAAATCATGTATGGTCAAAAC-GTAAAGCATCAATAGGCAAACCAATACTAGTAATGGGATCAAA
1 CAAATCATGTACGGT-GAAACTTTAAAGCATGATTAGGCAAACCCCTACTAGTAATGGAATCAAA
*
8591 CTCCAAAG-CGTAATGGTCAAACCC
65 C-CCCAAGTCGTAATGGTCAAACCC
* * **
8615 GAAATCATGTATGGTGAAACTTTAAAGCATGATTAGGCAAAAACCTACTAGTAAT-GAGATCAAA
1 CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAACCCCTACTAGTAATGGA-ATCAAA
8679 CCCCAA-TCGTAATGGTCAAACCC
65 CCCCAAGTCGTAATGGTCAAACCC
* * *
8702 ATAAATCATGTATGGTCAAAC
1 -CAAATCATGTACGGTGAAAC
8723 CCCCAATCAT
Statistics
Matches: 297, Mismatches: 57, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
86 1 0.00
87 34 0.11
88 248 0.84
89 13 0.04
90 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (88 bp):
CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAACCCCTACTAGTAATGGAATCAAAC
CCCAAGTCGTAATGGTCAAACCC
Found at i:8427 original size:23 final size:21
Alignment explanation
Indices: 8401--8442 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
8391 ACCCCTACTA
8401 GTAATGGGATCAAACCCCAAAGC
1 GTAAT-GG-TCAAACCCCAAAGC
*
8424 GTAATGGTCATACCCCAAA
1 GTAATGGTCAAACCCCAAA
8443 TCATGTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (21 bp):
GTAATGGTCAAACCCCAAAGC
Found at i:8536 original size:176 final size:175
Alignment explanation
Indices: 8263--8722 Score: 477
Period size: 176 Copynumber: 2.6 Consensus size: 175
8253 GATCAAGCTA
* * * * * * * *
8263 CAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGCAAACTA-GTACTAGTAATG-GAATCAA
1 CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAA-AACCTACGAGTAATGAG-ATCAA
* * * * * * * * *
8326 AGCCCAAGTCGTAATGGTCAAACCC-CATATCATGTACGGTGAAACTTTAAAGCAT-GATTCCCT
64 ACCCCAA-TCGTAATAGTCAAACCCAGAAATCATGTATGGTAAAAC-GTAAAGCATCAATACCC-
** *
8389 AAACCCCTACTAGTAATGGGATCAAACCCCAAAGCGTAATGGTCATACCC
126 AAACCAATACTAGTAATGGGATCAAACCCCAAAGCGTAATGGTCAAACCC
* *
8439 CAAATCATGTACGGTGAAA-TTATAAAGCATGATTAGGC-AAATCC-AGGGATGTAATGAGATCA
1 CAAATCATGTACGGTGAAACTT-TAAAGCATGATTAGGCAAAAACCTA-CGA-GTAATGAGATCA
* * **
8501 AACCCCAAATCTTAATAGTCAAA-CTAGAAATCATGTATGGTCAAAACGTAAAGCATCAATAGGC
63 AACCCC-AATCGTAATAGTCAAACCCAGAAATCATGTATGGT-AAAACGTAAAGCATCAATACCC
*
8565 AAACCAATACTAGTAATGGGATCAAACTCCAAAGCGTAATGGTCAAACCC
126 AAACCAATACTAGTAATGGGATCAAACCCCAAAGCGTAATGGTCAAACCC
* * *
8615 GAAATCATGTATGGTGAAACTTTAAAGCATGATTAGGCAAAAACCTACTAGTAATGAGATCAAAC
1 CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAAAACCTACGAGTAATGAGATCAAAC
* * *
8680 CCCAATCGTAATGGTCAAACCCATAAATCATGTATGGTCAAAC
66 CCCAATCGTAATAGTCAAACCCAGAAATCATGTATGGTAAAAC
8723 CCCCAATCAT
Statistics
Matches: 235, Mismatches: 36, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
174 1 0.00
175 23 0.10
176 192 0.82
177 18 0.08
178 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (175 bp):
CAAATCATGTACGGTGAAACTTTAAAGCATGATTAGGCAAAAACCTACGAGTAATGAGATCAAAC
CCCAATCGTAATAGTCAAACCCAGAAATCATGTATGGTAAAACGTAAAGCATCAATACCCAAACC
AATACTAGTAATGGGATCAAACCCCAAAGCGTAATGGTCAAACCC
Found at i:8605 original size:264 final size:264
Alignment explanation
Indices: 8236--8713 Score: 705
Period size: 264 Copynumber: 1.8 Consensus size: 264
8226 ATCCATTGTG
* * * *
8236 AAACCTCAAATCTTAATGATCAAGCTACAAATCATGTATGGTCAAAATGTAAAGCATGAATAGGC
1 AAACCCCAAATCTTAATGATCAAACTACAAATCATGTATGGTCAAAACGTAAAGCATCAATAGGC
* * *
8301 AAACTAGTACTAGTAATGGAATCAAAGCCCAAGTCGTAATGGTCAAACCCCATATCATGTACGGT
66 AAACCAATACTAGTAATGGAATCAAAGCCCAAGTCGTAATGGTCAAACCCCAAATCATGTACGGT
** *
8366 GAAACTTTAAAGCATGATT-CCCTAAACCCCTACTAGTAATGGGATCAAACCCCAAAGCGTAATG
131 GAAACTTTAAAGCATGATTACCC-AAAAACCTACTAGTAATGAGATCAAACCCC-AAGCGTAATG
*
8430 GTCATACCC-CAAATCATGTACGGTGAAATTATAAAGCATGATTAGGCAAATCCAGGGATGTAAT
194 GTCAAACCCACAAATCATGTACGGTGAAATTATAAAGCATGATTAGGCAAATCCAGGGATGTAAT
8494 GAGATC
259 GAGATC
*
8500 AAACCCCAAATCTTAAT-AGTCAAACTAGAAATCATGTATGGTCAAAACGTAAAGCATCAATAGG
1 AAACCCCAAATCTTAATGA-TCAAACTACAAATCATGTATGGTCAAAACGTAAAGCATCAATAGG
* * *
8564 CAAACCAATACTAGTAATGGGATCAAA-CTCCAAAG-CGTAATGGTCAAACCCGAAATCATGTAT
65 CAAACCAATACTAGTAATGGAATCAAAGC-CC-AAGTCGTAATGGTCAAACCCCAAATCATGTAC
** *
8627 GGTGAAACTTTAAAGCATGATTAGGCAAAAACCTACTAGTAATGAGATCAAACCCCAATCGTAAT
128 GGTGAAACTTTAAAGCATGATTACCCAAAAACCTACTAGTAATGAGATCAAACCCCAAGCGTAAT
*
8692 GGTCAAACCCATAAATCATGTA
193 GGTCAAACCCACAAATCATGTA
8714 TGGTCAAACC
Statistics
Matches: 190, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
263 19 0.10
264 167 0.88
265 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (264 bp):
AAACCCCAAATCTTAATGATCAAACTACAAATCATGTATGGTCAAAACGTAAAGCATCAATAGGC
AAACCAATACTAGTAATGGAATCAAAGCCCAAGTCGTAATGGTCAAACCCCAAATCATGTACGGT
GAAACTTTAAAGCATGATTACCCAAAAACCTACTAGTAATGAGATCAAACCCCAAGCGTAATGGT
CAAACCCACAAATCATGTACGGTGAAATTATAAAGCATGATTAGGCAAATCCAGGGATGTAATGA
GATC
Found at i:8714 original size:551 final size:550
Alignment explanation
Indices: 7666--8721 Score: 1646
Period size: 551 Copynumber: 1.9 Consensus size: 550
7656 AATGGTTAAA
7666 CCCCAAAGCATCCATTGTGAAACCCCAAATATTAATAGTCAAACTACAAATCATGTATGGTCAAA
1 CCCCAAAGCATCCATTGTGAAACCCCAAATATTAATAGTCAAACTACAAATCATGTATGGTCAAA
* *
7731 ATGTAAAGCATGAATAGGCAAACCAATACTATTAATGGAATCGAAGCCCAAATCATAATGGTCAA
66 ATGTAAAGCATGAATAGGCAAACCAATACTAGTAATGGAATCAAAGCCCAAATCATAATGGTCAA
7796 ACCCCAAATCATGTACGGTGAACTTTAAAGCATGATTCCCTAAACCCCTACTAGTAATAGGATCA
131 ACCCCAAATCATGTACGGTGAACTTTAAAGCATGATTCCCTAAACCCCTACTAGTAATAGGATCA
* * *
7861 AACCCCAAAGCGTTAGGTCAAACCCAAATCATGTATGGTGAAATTGTAAAGCATGATTAGGCAAA
196 AACCCCAAAGCGTAAGGTCAAACCCAAATCATGTACGGTGAAATTATAAAGCATGATTAGGCAAA
* * *
7926 CCTAGGGATGTAATGGGATCAAACCACAAATCTTAGTGGTCAAACTAGAAATCATGTATGGTCAA
261 CCTAGGGATGTAATGAGATCAAACCACAAATCTTAATAGTCAAACTAGAAATCATGTATGGTCAA
*
7991 AATGTAAAGCATCAATAGGCAAACTCATACTAGTAATGGGATCAAACCCCAAACGTAATGGTCAA
326 AACGTAAAGCATCAATAGGCAAACTCATACTAGTAATGGGATCAAACCCCAAACGTAATGGTCAA
* *
8056 ACCCCAAATCATGTATGGTGAAATTGTAAAACATGATTAGGCAAACCCAGGGATGTAATTAATAG
391 ACCCCAAATCATGTATGGTGAAATTGTAAAACATGATTAGGCAAACCCAGCGATGTAATT-AGAG
* * *
8121 GATCAAACCCCAAATCTTAGTGATCAAACTAGAAATCATGTATGGTCAAAATGTAAAGCATCAAT
455 GATCAAACCCCAAATCGTAATGATCAAACCAGAAATCATGTATGGTCAAAATGTAAAGCATCAAT
8186 AGACAAACCAGTACTAGTAATGGGATCAAAC
520 AGACAAACCAGTACTAGTAATGGGATCAAAC
* * *
8217 CCCCAAAGCATCCATTGTGAAACCTCAAATCTTAAT-GATCAAGCTACAAATCATGTATGGTCAA
1 CCCCAAAGCATCCATTGTGAAACCCCAAATATTAATAG-TCAAACTACAAATCATGTATGGTCAA
* * * *
8281 AATGTAAAGCATGAATAGGCAAACTAGTACTAGTAATGGAATCAAAGCCCAAGTCGTAATGGTCA
65 AATGTAAAGCATGAATAGGCAAACCAATACTAGTAATGGAATCAAAGCCCAAATCATAATGGTCA
* *
8346 AACCCCATATCATGTACGGTGAAACTTTAAAGCATGATTCCCTAAACCCCTACTAGTAATGGGAT
130 AACCCCAAATCATGTACGGTG-AACTTTAAAGCATGATTCCCTAAACCCCTACTAGTAATAGGAT
*
8411 CAAACCCCAAAGCGTAATGGTCATACCCCAAATCATGTACGGTGAAATTATAAAGCATGATTAGG
194 CAAACCCCAAAGCGTAA-GGTCA-AACCCAAATCATGTACGGTGAAATTATAAAGCATGATTAGG
*
8476 CAAATCC-AGGGATGTAATGAGATCAAACCCCAAATCTTAATAGTCAAACTAGAAATCATGTATG
257 CAAA-CCTAGGGATGTAATGAGATCAAACCACAAATCTTAATAGTCAAACTAGAAATCATGTATG
*
8540 GTCAAAACGTAAAGCATCAATAGGCAAAC-CAATACTAGTAATGGGATCAAACTCCAAAGCGTAA
321 GTCAAAACGTAAAGCATCAATAGGCAAACTC-ATACTAGTAATGGGATCAAACCCCAAA-CGTAA
* * * *
8604 TGGTCAAACCCGAAATCATGTATGGTGAAACTT-TAAAGCATGATTAGGCAAAAACCTA-CTA-G
384 TGGTCAAACCCCAAATCATGTATGGTGAAA-TTGTAAAACATGATTAGGC--AAACCCAGCGATG
* *
8666 TAA-T-GA-GATCAAACCCC-AATCGTAATGGTCAAACCCATAAATCATGTATGGTCAAA
446 TAATTAGAGGATCAAACCCCAAATCGTAATGATCAAA-CCAGAAATCATGTATGGTCAAA
8722 CCCCCAATCA
Statistics
Matches: 462, Mismatches: 32, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
550 14 0.03
551 169 0.37
552 59 0.13
553 6 0.01
554 150 0.32
555 55 0.12
556 3 0.01
557 6 0.01
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (550 bp):
CCCCAAAGCATCCATTGTGAAACCCCAAATATTAATAGTCAAACTACAAATCATGTATGGTCAAA
ATGTAAAGCATGAATAGGCAAACCAATACTAGTAATGGAATCAAAGCCCAAATCATAATGGTCAA
ACCCCAAATCATGTACGGTGAACTTTAAAGCATGATTCCCTAAACCCCTACTAGTAATAGGATCA
AACCCCAAAGCGTAAGGTCAAACCCAAATCATGTACGGTGAAATTATAAAGCATGATTAGGCAAA
CCTAGGGATGTAATGAGATCAAACCACAAATCTTAATAGTCAAACTAGAAATCATGTATGGTCAA
AACGTAAAGCATCAATAGGCAAACTCATACTAGTAATGGGATCAAACCCCAAACGTAATGGTCAA
ACCCCAAATCATGTATGGTGAAATTGTAAAACATGATTAGGCAAACCCAGCGATGTAATTAGAGG
ATCAAACCCCAAATCGTAATGATCAAACCAGAAATCATGTATGGTCAAAATGTAAAGCATCAATA
GACAAACCAGTACTAGTAATGGGATCAAAC
Found at i:8787 original size:20 final size:21
Alignment explanation
Indices: 8738--8787 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
8728 ATCATCCATT
* * *
8738 GTGAAACCCCAAATCTTAATG
1 GTGAAACCCCAAATATGAATA
*
8759 GTCAAACCCCAAATATGAA-A
1 GTGAAACCCCAAATATGAATA
8779 GTGAAACCC
1 GTGAAACCC
8788 TAACCTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (21 bp):
GTGAAACCCCAAATATGAATA
Found at i:9349 original size:30 final size:30
Alignment explanation
Indices: 9292--9350 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
9282 CAATGGGTCA
*
9292 AAAGAAATATTTTTTTATTACAACTTTTTG
1 AAAGAAATATTTTTTAATTACAACTTTTTG
* * *
9322 AAAG-AATCTTTTTTAATTTCAACCTTTTG
1 AAAGAAATATTTTTTAATTACAACTTTTTG
9351 TCCCACATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (30 bp):
AAAGAAATATTTTTTAATTACAACTTTTTG
Found at i:11255 original size:21 final size:20
Alignment explanation
Indices: 11222--11261 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11212 AATAGCATAA
*
11222 AAAATATATCAAATACATGC
1 AAAATAGATCAAATACATGC
*
11242 AAAATAGATACAAATGCATG
1 AAAATAGAT-CAAATACATG
11262 TAGCATCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAATAGATCAAATACATGC
Done.