Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007036.1 Corchorus capsularis cultivar CVL-1 contig07057, 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: 48846
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3989 original size:437 final size:436
Alignment explanation
Indices: 3402--4751 Score: 1489
Period size: 438 Copynumber: 3.1 Consensus size: 436
3392 TAAGTAACAT
* * * * * *
3402 ATATGAGGGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGGATATATTGAAACAT
1 ATATGAGGATCATTTGATAAATAA-TCCAATAAGAAAATGTTTATTAATGGAGATATTG-AACAT
* * * **
3467 GAAAA-TTCCCTTTTGTACCCTTCATAAAACTCGTAGATCAAA-TTA-ACTTTCGGGTTTTTCAT
64 AAAAACTT-CCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGA-TTTCGGGTCCTTCAT
* * ** * * *
3529 AAAAGTCATAGGTCATACAATAACCTTTTAACCGACACTTGAATAACTTTAATCGGACATGTGGA
127 GAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGA
* * * ** ** ** * *
3594 TC-GAAAATTATATGGTATTAAATAGATTAACAATTGAAATAACCAAATTTAGGAAGCATTTTTT
192 -CAAAAAATTATATGATATTAAATTGACCAACAATCAAAACCACAAAATTTTGGAAGCATTTTTT
* * * * * *
3658 TGAATTAAAATATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTT
256 AGAATTAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTT
* * * *
3723 TTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAAT-CTTAA
321 TTAATAGATACTTGAATCACCTTAATCGGACAAATAGAA-AAA-AATAAAAAAATAAATGC-GAA
* * * *
3787 -ACATTATAT-T-AAAATAGAATTTGTAAAAAACTAAGTAGTATAAAGTAGAAAA
383 CACATTAAATCTCAAAATAGAA-TTGTAAAAAACTAAATAGCATAAAATAGAAAA
* *
3839 ATATGAGAATCATTTGATAAATAATCCAGATAAGAAAATGTTTATTAATGGAGATTTTGAACATA
1 ATATGAGGATCATTTGATAAATAATCCA-ATAAGAAAATGTTTATTAATGGAGATATTGAACATA
* *
3904 AAAACTTCCTGTTGAACCCTTCATGAAACTTGTAGATCAAATTTAGATTTCGGGTCCTTCATGAA
65 AAAACTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGATTTCGGGTCCTTCATGAA
* * *
3969 AGTCGTAAATCATGCAATAACCTTTTGACCGACCCTTCAATAACTTCAATCAGACATGTGGACAA
130 AGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGAC-A
*
4034 AAAAATTATATGATGTTAAATTGACCAACAATCAAAACCACAAAATTTTGGAAGCATTTTTTAG-
194 AAAAATTATATGATATTAAATTGACCAACAATCAAAACCACAAAATTTTGGAAGCATTTTTTAGA
* *
4098 ATTCAAAACATTAAAATTGGCTTTTGAGTTCTTCATAAAAATTGTAGATCATGAAATTACTTTTT
259 ATT-AAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTT
* * *
4163 AATAGATACTTGAATCACCTTAATCGGACAAATAGGAAAAAAATACAAAAATAAATGCGAACGCG
323 AATAGATACTTGAATCACCTTAATCGGACAAATA-GAAAAAAATAAAAAAATAAATGCGAACACA
** * ** *
4228 TTAAATCGTCCAACCTATAATTGTAAAGGACTAAATAGCATAAAATATAAAA
387 TTAAATC-T-CAAAATAGAATTGTAAAAAACTAAATAGCATAAAATAGAAAA
* * * * * * *
4280 ATATGAGGACCATTAGATAAATAATCCAACAAAAAAATGTTTGTTAATGGAGATCTTAAACATAA
1 ATATGAGGATCATTTGATAAATAATCCAATAAGAAAATGTTTATTAATGGAGATATTGAACATAA
* * * * *
4345 AAACTCCCTTTTGAACCCTTCTTGAAACTCGCAGATCAAATTTAGCTTTCGGCTCCTTCATGAAA
66 AAACTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGATTTCGGGTCCTTCATGAAA
* * *
4410 GTCGTAAATCATGCAATATAACCTTCTAACC-AGCACTTCAATAACTTCAATTGGACATGTGGCC
131 GTCGTAAATCATGC-A-ATAACCTTTTAACCGA-CACTTCAATAACTTCAATCGGACATGTGGAC
* **
4474 AAAAAATTATACGATATTAAATTGACCGGCAATCAAAACCACATAAATTTTGGAAGCATTTTTTA
193 AAAAAATTATATGATATTAAATTGACCAACAATCAAAACCACA-AAATTTTGGAAGCATTTTTTA
* * *
4539 AAATTTAAACATTAAAATTGGCTTTTGAGTTTTTCATGAAAATTGTAGAT-ATGAAATTACCTTT
257 GAATTAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTT
* * * * *
4603 TAATAGGTGTACTTGAATCACCTTAATCGGACAAATAGGGAAAAAATACAATAATAAATGCCAAC
322 TAATA-G-ATACTTGAATCACCTTAATCGGACAAATA-GAAAAAAATAAAAAAATAAATGCGAAC
*** ** * ** * * *
4668 GTGTTAAATCGTCCAACCTATAATTGTAAAGGACTAGATAGCATAAACTATAAAA
384 ACATTAAATC-T-CAAAATAGAATTGTAAAAAACTAAATAGCATAAAATAGAAAA
* * *
4723 GTATGAGGACCATTAGATAAATAATCCAA
1 ATATGAGGATCATTTGATAAATAATCCAA
4752 CAAAAAAAAT
Statistics
Matches: 792, Mismatches: 100, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
436 43 0.05
437 139 0.18
438 147 0.19
439 3 0.00
440 105 0.13
441 110 0.14
442 109 0.14
443 136 0.17
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (436 bp):
ATATGAGGATCATTTGATAAATAATCCAATAAGAAAATGTTTATTAATGGAGATATTGAACATAA
AAACTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGATTTCGGGTCCTTCATGAAA
GTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGACAAA
AAATTATATGATATTAAATTGACCAACAATCAAAACCACAAAATTTTGGAAGCATTTTTTAGAAT
TAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAAT
AGATACTTGAATCACCTTAATCGGACAAATAGAAAAAAATAAAAAAATAAATGCGAACACATTAA
ATCTCAAAATAGAATTGTAAAAAACTAAATAGCATAAAATAGAAAA
Found at i:4722 original size:443 final size:437
Alignment explanation
Indices: 3436--4759 Score: 1592
Period size: 443 Copynumber: 3.0 Consensus size: 437
3426 TTCAAATAAG
* * * * * * *
3436 AAAATATTTCTTAATGGATATATTGAAACATGAAAATTCCCTTTTGTACCCTTCATAAAACTCGT
1 AAAATGTTTATTAATGGAGATATT-AAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGT
* ** * * ** *
3501 AGATCAAA-TTAACTTTCGGGTTTTTCATAAAAGTCATAGGTCATACAATAACCTTTTAACCGAC
65 AGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGAC
* * * * * * ** *
3565 ACTTGAATAACTTTAATCGGACATGTGGATC-GAAAATTATATGGTATTAAATAGATTAACAATT
130 ACTTCAATAACTTCAATCGGACATGTGGACCAAAAAATTATATGATATTAAATTGACCAACAATC
* ** * * * * * * *
3629 GAAATAACCAAATTTAGGAAGCATTTTTTTGAATTAAAATATAAAAATTTGCTTTTGAGTCCTTC
195 AAAACCACAAAATTTTGGAAGCA-TTTTTTAAATTAAAACATTAAAATTGGCTTTTGAGTTCTTC
* * * *
3694 ATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATA
259 ATGAAAATTGTAGATCATGAAATTACCTTTTAATAGATACTTGAATCACCTTAATCGGACAAATA
* * * ** * **
3759 -GAACAAAGAATAAAAAAATAAAT-CTTAAAC-ATTATAT--T--AAAATAGAATTTGTAAAAAA
324 GGAA-AAA-AATACAAAAATAAATGC--AAACGGTTAAATCGTCCAACCTATAA-TTGTAAAGGA
* * * * * * * *
3817 CTAAGTAGTATAAAGTAGAAAAATATGAGAATCATTTGATAAATAATCCAGATAAG
384 CTAA-TAGCATAAAATATAAAAATATGAGGACCATTAGATAAATAATCCA-ACAAA
* * * * *
3873 AAAATGTTTATTAATGGAGATTTTGAACATAAAAACTTCCTGTTGAACCCTTCATGAAACTTGTA
1 AAAATGTTTATTAATGGAGATATTAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTA
* * *
3938 GATCAAATTTAGATTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTGACCGACC
66 GATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACA
* * *
4003 CTTCAATAACTTCAATCAGACATGTGGACAAAAAAATTATATGATGTTAAATTGACCAACAATCA
131 CTTCAATAACTTCAATCGGACATGTGGACCAAAAAATTATATGATATTAAATTGACCAACAATCA
*
4068 AAACCACAAAATTTTGGAAGCATTTTTTAGATTCAAAACATTAAAATTGGCTTTTGAGTTCTTCA
196 AAACCACAAAATTTTGGAAGCATTTTTTAAATT-AAAACATTAAAATTGGCTTTTGAGTTCTTCA
* *
4133 TAAAAATTGTAGATCATGAAATTACTTTTTAATAGATACTTGAATCACCTTAATCGGACAAATAG
260 TGAAAATTGTAGATCATGAAATTACCTTTTAATAGATACTTGAATCACCTTAATCGGACAAATAG
*
4198 GAAAAAAATACAAAAATAAATGCGAACGCGTTAAATCGTCCAACCTATAATTGTAAAGGACTAAA
325 GAAAAAAATACAAAAATAAATGCAAACG-GTTAAATCGTCCAACCTATAATTGTAAAGGACT-AA
4263 TAGCATAAAATATAAAAATATGAGGACCATTAGATAAATAATCCAACAAA
388 TAGCATAAAATATAAAAATATGAGGACCATTAGATAAATAATCCAACAAA
* * * *
4313 AAAATGTTTGTTAATGGAGATCTTAAACATAAAAACTCCCTTTTGAACCCTTCTTGAAACTCGCA
1 AAAATGTTTATTAATGGAGATATTAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTA
* *
4378 GATCAAATTTAGCTTTCGGCTCCTTCATGAAAGTCGTAAATCATGCAATATAACCTTCTAACC-A
66 GATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGC-A-ATAACCTTTTAACCGA
* * **
4442 GCACTTCAATAACTTCAATTGGACATGTGG-CCAAAAAATTATACGATATTAAATTGACCGGCAA
129 -CACTTCAATAACTTCAATCGGACATGTGGACCAAAAAATTATATGATATTAAATTGACCAACAA
* *
4506 TCAAAACCACATAAATTTTGGAAGCATTTTTTAAAATTTAAACATTAAAATTGGCTTTTGAGTTT
193 TCAAAACCACA-AAATTTTGGAAGCATTTTTT-AAATTAAAACATTAAAATTGGCTTTTGAGTTC
*
4571 TTCATGAAAATTGTAGAT-ATGAAATTACCTTTTAATAGGTGTACTTGAATCACCTTAATCGGAC
256 TTCATGAAAATTGTAGATCATGAAATTACCTTTTAATA-G-ATACTTGAATCACCTTAATCGGAC
* * *
4635 AAATAGGGAAAAAATACAATAATAAATGCCAACGTGTTAAATCGTCCAACCTATAATTGTAAAGG
319 AAATAGGAAAAAAATACAAAAATAAATGCAAACG-GTTAAATCGTCCAACCTATAATTGTAAAGG
* *
4700 ACTAGATAGCATAAACTATAAAAGTATGAGGACCATTAGATAAATAATCCAACAAA
383 ACTA-ATAGCATAAAATATAAAAATATGAGGACCATTAGATAAATAATCCAACAAA
4756 AAAA
1 AAAA
4760 ATATTAGTTT
Statistics
Matches: 766, Mismatches: 101, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
436 43 0.06
437 114 0.15
438 138 0.18
439 3 0.00
440 105 0.14
441 109 0.14
442 110 0.14
443 144 0.19
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (437 bp):
AAAATGTTTATTAATGGAGATATTAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTA
GATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACA
CTTCAATAACTTCAATCGGACATGTGGACCAAAAAATTATATGATATTAAATTGACCAACAATCA
AAACCACAAAATTTTGGAAGCATTTTTTAAATTAAAACATTAAAATTGGCTTTTGAGTTCTTCAT
GAAAATTGTAGATCATGAAATTACCTTTTAATAGATACTTGAATCACCTTAATCGGACAAATAGG
AAAAAAATACAAAAATAAATGCAAACGGTTAAATCGTCCAACCTATAATTGTAAAGGACTAATAG
CATAAAATATAAAAATATGAGGACCATTAGATAAATAATCCAACAAA
Found at i:4971 original size:2 final size:2
Alignment explanation
Indices: 4964--5002 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
4954 GTTTCTTGTA
4964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5003 ATTCTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:9433 original size:21 final size:21
Alignment explanation
Indices: 9409--9456 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
9399 GAAGAGAGAG
* *
9409 ATGATGAAGATGAAGATGAAA
1 ATGAAGAAGATGAAGATAAAA
* *
9430 ATGAAGAATATGTAGATAAAA
1 ATGAAGAAGATGAAGATAAAA
9451 ATGAAG
1 ATGAAG
9457 CTGATGATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (21 bp):
ATGAAGAAGATGAAGATAAAA
Found at i:12702 original size:31 final size:31
Alignment explanation
Indices: 12657--12740 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
12647 ACTATTTCTT
*
12657 GAAAAATAT-AGGGATTATTTTGTCCCAAAA
1 GAAAAACATAAGGGATTATTTTGTCCCAAAA
*
12687 GAAAAACATAAGGGATTATTTTGTCCTAAAA
1 GAAAAACATAAGGGATTATTTTGTCCCAAAA
*
12718 GAAAAACATAAGGGATTTTTTTG
1 GAAAAACATAAGGGATTATTTTG
12741 GGTATTTAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 8 0.16
31 42 0.84
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (31 bp):
GAAAAACATAAGGGATTATTTTGTCCCAAAA
Found at i:16140 original size:29 final size:31
Alignment explanation
Indices: 16095--16169 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 31
16085 TATATTTTTG
* *
16095 ATATA-ATAT-TAT-TATTTCTAAATTTTTA
1 ATATATATATATATATATTTCTAAAATTATA
*
16123 ATA-ATATATATA-ATATTTTTAAAATTATA
1 ATATATATATATATATATTTCTAAAATTATA
*
16152 TTATATATATATATATAT
1 ATATATATATATATATAT
16170 ATTGTAGTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.03
28 7 0.18
29 17 0.45
30 9 0.24
31 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATATATATATATATATTTCTAAAATTATA
Found at i:16159 original size:21 final size:21
Alignment explanation
Indices: 16116--16157 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
16106 TTATTTCTAA
16116 ATTTTTAATAATATATATAAT
1 ATTTTTAATAATATATATAAT
*
16137 ATTTTTAA-AAT-TATATTAT
1 ATTTTTAATAATATATATAAT
16156 AT
1 AT
16158 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTAATAATATATATAAT
Found at i:22826 original size:78 final size:79
Alignment explanation
Indices: 22696--22852 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 79
22686 ATCAACTCTA
* *
22696 AAAATGAGCTGTTTTGGGTTCAAGATCAAGGGACATTTTCCATTTATATGCCATGGTTGATTGAT
1 AAAATGAGCTGTTTTGGGTTCAAGATCAAGGGACATTTTACATTTATATGCCATAGTTGATTGAT
22761 CCCATTGAACAATT
66 CCCATTGAACAATT
*
22775 AAAATGAGCT-TTTTGGGTTTAAGATCAAGGGACATTTTACATTTATATGCCATAGTTGATTGAT
1 AAAATGAGCTGTTTTGGGTTCAAGATCAAGGGACATTTTACATTTATATGCCATAGTTGATTGAT
22839 CCCATTGAACAATT
66 CCCATTGAACAATT
22853 CAGCCCGAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 65 0.87
79 10 0.13
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (79 bp):
AAAATGAGCTGTTTTGGGTTCAAGATCAAGGGACATTTTACATTTATATGCCATAGTTGATTGAT
CCCATTGAACAATT
Found at i:23329 original size:2 final size:2
Alignment explanation
Indices: 23322--23347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23312 TCAATGTCTT
23322 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
23348 ATAAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32627 original size:21 final size:22
Alignment explanation
Indices: 32603--32648 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
32593 GCTGTAAATA
32603 AATT-CTTTATT-TGTTTTATAT
1 AATTACTTTATTAT-TTTTATAT
32624 AATTACTTTATTCATTTTTATAT
1 AATTACTTTATT-ATTTTTATAT
32647 AA
1 AA
32649 AGTTTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 7 0.32
23 10 0.45
24 1 0.05
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
AATTACTTTATTATTTTTATAT
Found at i:44459 original size:328 final size:328
Alignment explanation
Indices: 43833--44459 Score: 820
Period size: 328 Copynumber: 1.9 Consensus size: 328
43823 GATAAAAAAA
* * *
43833 AACAAAAACCACTAGCTCAAAAGAGTAAAGAATAAAAGAGGGAGTGAGCAACCAATGAACATGCT
1 AACAAAAACCACTAGCCCAAAAGAATAAAGAATAAAAGAGAGAGTGAGCAACCAATGAACATGCT
* *
43898 CCATATGTCAACAACAAAGGGATGAATAATGAAAACTAATGATGAGGGATAAACATTATTGTTTG
66 CCATATGTCAACAACAAAGGGATGAATAATGAAAACTAATGATGAGGGATAAACATTATTATTTA
* ** *
43963 AATTTCGGAAGTTTAAGGGGCTAATGATCTTAAATTTGCAAATTCATGGGGCAAAATGTCTTAAT
131 AATTTCGGAAGTTTAAAGGGCTAATGATCTTAAATTTAAAAATTCATGGGGCAAAATGTCCTAAT
*
44028 TTGAAGTTTATGAGACAAAACGTTATTAACGTAATAGTTCGAGGGACAAAAAGGCGAATAAGCCA
196 TTGAAGTTTATGAGACAAAACGGTATTAACGTAATAGTTCGAGGGACAAAAAGGCGAATAAGCCA
** * ** * * *
44093 TCAAACCTAAGTCTGGCCCAAAGAAATGTTTGGCCCAAAACCAAAGCCATATATAATTCAGCCCA
261 TCAAACAAAAATCTACCCCAAACAAATGTCTAGCCCAAAACCAAAGCCATATATAATTCAGCCCA
44158 CAT
326 CAT
* *
44161 AACAAAAACCAAC-AGCCCAAAAGAATAAAGAATTAAAGAGAGAGTGAGCAACCAATGAAGATGC
1 AACAAAAACC-ACTAGCCCAAAAGAATAAAGAATAAAAGAGAGAGTGAGCAACCAATGAACATGC
* * * **
44225 TCCATATTTCAACACCAAAGGGATGAATAATGAAAACTATTTTTGAGGGATAAACATTATTATTT
65 TCCATATGTCAACAACAAAGGGATGAATAATGAAAACTAATGATGAGGGATAAACATTATTATTT
*
44290 AAAATTT-GCGAAG-TTAAAGGGCTAATGATCTTAAATTTAAAAATTCATGGGGCAGAATGTCCT
130 -AAATTTCG-GAAGTTTAAAGGGCTAATGATCTTAAATTTAAAAATTCATGGGGCAAAATGTCCT
* * * * * *
44353 AATTTGATGTTTATGAGACAAAATGGTATTGAA-GTGATAGTTTG-GGGATAAAAAGGTGAATAA
193 AATTTGAAGTTTATGAGACAAAACGGTATT-AACGTAATAGTTCGAGGGACAAAAAGGCGAATAA
* *
44416 GCCATTAAA-AAAACATC-ACCATCCAAACCCAAT-TCTAGCCCAAA
257 GCCATCAAACAAAA-ATCTACC--CCAAA-CAAATGTCTAGCCCAAA
44460 GAAATGCTTC
Statistics
Matches: 257, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
326 3 0.01
327 27 0.11
328 211 0.82
329 16 0.06
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (328 bp):
AACAAAAACCACTAGCCCAAAAGAATAAAGAATAAAAGAGAGAGTGAGCAACCAATGAACATGCT
CCATATGTCAACAACAAAGGGATGAATAATGAAAACTAATGATGAGGGATAAACATTATTATTTA
AATTTCGGAAGTTTAAAGGGCTAATGATCTTAAATTTAAAAATTCATGGGGCAAAATGTCCTAAT
TTGAAGTTTATGAGACAAAACGGTATTAACGTAATAGTTCGAGGGACAAAAAGGCGAATAAGCCA
TCAAACAAAAATCTACCCCAAACAAATGTCTAGCCCAAAACCAAAGCCATATATAATTCAGCCCA
CAT
Found at i:48360 original size:3 final size:3
Alignment explanation
Indices: 48352--48389 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
48342 AAAAATTAAA
48352 ATT ATT ATT ATT ATT CATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A
48390 AATTCTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:48371 original size:22 final size:22
Alignment explanation
Indices: 48346--48388 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
48336 CATGTCAAAA
48346 ATTAAAATTATTATTATTATTC
1 ATTAAAATTATTATTATTATTC
**
48368 ATTATTATTATTATTATTATT
1 ATTAAAATTATTATTATTATT
48389 AAATTCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTAAAATTATTATTATTATTC
Found at i:48403 original size:22 final size:22
Alignment explanation
Indices: 48354--48404 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
48344 AAATTAAAAT
* *
48354 TATTATTATTATTCATTATTAT
1 TATTATTATTATTAATTATTAA
*
48376 TATTATTATTATTAAATTCTTAA
1 TATTATTATTATT-AATTATTAA
48399 T-TTATT
1 TATTATT
48405 GATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTATTATTAATTATTAA
Done.