Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007312.1 Corchorus capsularis cultivar CVL-1 contig07333, 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: 39869
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--37 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 A
2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38 CTGTGAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:300 original size:30 final size:30
Alignment explanation
Indices: 266--328 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
256 TCTCACGGAA
266 TGTGAGTTTTCTCTGTAACTTATTTGTTTG
1 TGTGAGTTTTCTCTGTAACTTATTTGTTTG
* *
296 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
1 TGTGAGTTTTCTCTGTAACTTATTTGTTTG
326 TGT
1 TGT
329 ATTTAGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.06, G:0.21, T:0.60
Consensus pattern (30 bp):
TGTGAGTTTTCTCTGTAACTTATTTGTTTG
Found at i:1190 original size:26 final size:26
Alignment explanation
Indices: 1154--1217 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
1144 CTTAAAATTC
*
1154 AGTAAATTTTTTTGGCAAAAAAAAAAA
1 AGTAAATTTTTCTGGC-AAAAAAAAAA
* *
1181 AGTAAATTTTTCTGGCAAAAATAAAG
1 AGTAAATTTTTCTGGCAAAAAAAAAA
1207 AGTAAATTTTT
1 AGTAAATTTTT
1218 AGATTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.34
Consensus pattern (26 bp):
AGTAAATTTTTCTGGCAAAAAAAAAA
Found at i:1290 original size:51 final size:54
Alignment explanation
Indices: 1235--1356 Score: 151
Period size: 56 Copynumber: 2.3 Consensus size: 54
1225 TTATCTCTAC
* *
1235 TTCTAAACAATTAATTCCCTTTGTAG-AA-A-TTGGTTTTAGAATTAAATCTCT
1 TTCTAAACAATTAATTCCCTTTGGAGAAATATTTGGTTCTAGAATTAAATCTCT
* * * *
1286 TTCTAAACGATTAATTCTCTTTGGAGAAATTATTTTGGTTCTAGAATTAATTTTCT
1 TTCTAAACAATTAATTCCCTTTGGAGAAA-TA-TTTGGTTCTAGAATTAAATCTCT
1342 TTCTAAACAATTAAT
1 TTCTAAACAATTAAT
1357 ATTCTAAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
51 23 0.39
52 2 0.03
54 1 0.02
56 33 0.56
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (54 bp):
TTCTAAACAATTAATTCCCTTTGGAGAAATATTTGGTTCTAGAATTAAATCTCT
Found at i:1466 original size:33 final size:35
Alignment explanation
Indices: 1399--1475 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 35
1389 TTCTCTTTTT
* *
1399 AAACAATTAATTATTCTCTATGTTGCCCAAAAAAA
1 AAACAATTAATTATCCTCTATGGTGCCCAAAAAAA
*
1434 AAACAATT-A-TATCCTCTATGGTG-CC--AAGAA
1 AAACAATTAATTATCCTCTATGGTGCCCAAAAAAA
1464 AAACAATTAATT
1 AAACAATTAATT
1476 TTCTCAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 12 0.32
31 1 0.03
32 3 0.08
33 12 0.32
34 1 0.03
35 8 0.22
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (35 bp):
AAACAATTAATTATCCTCTATGGTGCCCAAAAAAA
Found at i:4156 original size:2 final size:2
Alignment explanation
Indices: 4114--4145 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4104 ATATTGTAGC
4114 AT AT -T AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4146 TTGCGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4950 original size:21 final size:21
Alignment explanation
Indices: 4924--4997 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
4914 TGAACATTCA
4924 TAGTTTTTCTAGCCACAAATT
1 TAGTTTTTCTAGCCACAAATT
* * * *
4945 TAGTTTTAGC-CGCAATGAACATT
1 TAGTTTT-TCTAGCCA-CAA-ATT
4968 CATAGTTTTTCTAGCCACAAATT
1 --TAGTTTTTCTAGCCACAAATT
4991 TAGTTTT
1 TAGTTTT
4998 AGCCGCACTA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
21 17 0.44
22 3 0.08
23 6 0.15
24 3 0.08
25 10 0.26
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (21 bp):
TAGTTTTTCTAGCCACAAATT
Found at i:4964 original size:46 final size:46
Alignment explanation
Indices: 4911--5004 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
4901 CGAGGGGATC
4911 CAATGAACATTCATAGTTTTTCTAGCCACAAATTTAGTTTTAGCCG
1 CAATGAACATTCATAGTTTTTCTAGCCACAAATTTAGTTTTAGCCG
4957 CAATGAACATTCATAGTTTTTCTAGCCACAAATTTAGTTTTAGCCG
1 CAATGAACATTCATAGTTTTTCTAGCCACAAATTTAGTTTTAGCCG
5003 CA
1 CA
5005 CTAAGATGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (46 bp):
CAATGAACATTCATAGTTTTTCTAGCCACAAATTTAGTTTTAGCCG
Found at i:15272 original size:3 final size:3
Alignment explanation
Indices: 15264--15314 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
15254 TATAGTAATA
15264 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15312 TAT
1 TAT
15315 AGATAAATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15603 original size:80 final size:80
Alignment explanation
Indices: 15470--15709 Score: 282
Period size: 80 Copynumber: 3.0 Consensus size: 80
15460 TCACTAACAC
15470 AAATCAAATAACAACTTTTACCAATCAATAATACTAATC-AATGGACCTCCATCAATTATTAATT
1 AAATCAAATAACAA-TTTTACCAATCAATAATACTAATCAAAT-GACCTCCATCAATTATTAATT
15534 TCTAAAAATTTATCA-T
64 TCTAAAAATTTATCATT
15550 AAATCAAATAACAATTTTTACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAA-TT
1 AAATCAAATAACAA-TTTTACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTT
*
15614 CTAATAATTTATCATT
65 CTAAAAATTTATCATT
* * * * * *
15630 AATTTC-AATAGTCCA---TAGCTAATCAATAATACTAACCAAATGACCTCCATTAATTATTAA-
1 AA-ATCAAATA-ACAATTTTA-CCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAAT
*
15690 TTC-AAATAATTCATCATT
63 TTCTAAA-AATTTATCATT
15708 AA
1 AA
15710 TTTCAATAGT
Statistics
Matches: 144, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
77 4 0.03
78 54 0.38
79 15 0.10
80 64 0.44
81 7 0.05
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.35
Consensus pattern (80 bp):
AAATCAAATAACAATTTTACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTTC
TAAAAATTTATCATT
Found at i:15671 original size:78 final size:77
Alignment explanation
Indices: 15488--15724 Score: 293
Period size: 78 Copynumber: 3.0 Consensus size: 77
15478 TAACAACTTT
*
15488 TACCAATCAATAATACTAATC-AATGGACCTCCATCAATTATTAATTTCTAAAAATTTATCA-TA
1 TACCAATCAATAATACTAATCAAAT-GACCTCCATCAATTATTAA-TTCTAATAATTTATCATTA
* * *
15551 A-ATCAAATA-ACAA
64 ATTTC-AATAGTCCA
15564 TTTTTACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTCTAATAATTTATCAT
1 ----TACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTCTAATAATTTATCAT
15629 TAATTTCAATAGTCCA
62 TAATTTCAATAGTCCA
* * * * *
15645 TAGCTAATCAATAATACTAACCAAATGACCTCCATTAATTATTAATTCAAATAATTCATCATTAA
1 TA-CCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTCTAATAATTTATCATTAA
15710 TTTCAATAGTCCA
65 TTTCAATAGTCCA
15723 TA
1 TA
15725 TTATTAACAA
Statistics
Matches: 143, Mismatches: 9, Indels: 12
0.87 0.05 0.07
Matches are distributed among these distances:
77 2 0.01
78 72 0.50
79 15 0.10
80 47 0.33
81 7 0.05
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (77 bp):
TACCAATCAATAATACTAATCAAATGACCTCCATCAATTATTAATTCTAATAATTTATCATTAAT
TTCAATAGTCCA
Found at i:16242 original size:19 final size:19
Alignment explanation
Indices: 16199--16235 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16189 AATTTTTTCA
*
16199 ATAATTCATAATTAACAAT
1 ATAATTCATAATTAAAAAT
*
16218 ATAATTCTTAATTAAAAA
1 ATAATTCATAATTAAAAA
16236 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATTCATAATTAAAAAT
Found at i:17312 original size:442 final size:439
Alignment explanation
Indices: 16487--17324 Score: 1043
Period size: 442 Copynumber: 1.9 Consensus size: 439
16477 TTTTTGGTTG
* * * *
16487 AATCAAATTCAGCTTTCAGACTCTTAATAAAAGTCGCAGATCACATGATAACCTTCTAAGCAACA
1 AATCAAATTCAGCTTTCAGACCCTTAACAAAAGTCACAGATCACACGATAACCTTCTAAGCAACA
* * **
16552 CTTGAACAAGCTCAATCGGACAAGTGGATCGAAAATTATACAATATTAAATTGACCAGCAATCGA
66 CTTAAACAAGCTCAATCGGACAAGTGGAACGAAAATTATACAATATTAAAGAGACCAGCAATCGA
** * * * *
16617 GAACACAAAATTTCAGAAGCATTTTTTAGAATTGAAACCTCAAATTTGACTTATGAGTTATTAAT
131 GAACACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTATGAATCATTAAT
* * *
16682 GAAAGTTATAGATAATGAAATTACCTTTCAATGGACACTTGAATCACCTTGATCGGACAAATAGA
196 GAAAGTTATAGATAATGAAATTACCTTTCAATAGACACTTGAATCACCTTGATCGGACAAACAAA
** * * * *
16747 ACAAAAAATAAAAAATAAAAGGCAACGCGTTAAATCGTCCGACCGATAATTGTAAAGGATTAAAT
261 ACAAAAAATAAAAAATAAAAGGCAAAACGTTAAATCGTCCAACCCAAAATTGTAAAGGACTAAAT
* * *
16812 AGCATAAAGCATAAAAAGTGTGAGGATCATTTGATAAATAATCCAGCAAAACAAATATTTGTTTA
326 AGCAAAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAACAAATATTTGTTTA
16877 TAGAGACCAAACATAAAAATTCTATCTCGAACCCTCCACGAAAGTCATT
391 TAGAGACCAAACATAAAAATTCTATCTCGAACCCTCCACGAAAGTCATT
* * * * * * *
16926 AATCAAATTCAGCTTTCAGGCCCTTGACGAAAGTCATAGATCACACGATAACCTTTTAATCGACA
1 AATCAAATTCAGCTTTCAGACCCTTAACAAAAGTCACAGATCACACGATAACCTTCTAAGCAACA
* * * * ***
16991 CTTAAACAATCTCAATCGGAGAAGTGGAACGAAAATTATATAATAATATTAGAGAGATTGGCAAT
66 CTTAAACAAGCTCAATCGGACAAGTGGAACGAAAA-T-TAT-ACAATATTAAAGAGACCAGCAAT
* * * *
17056 CGAGACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTCTGAATCCTT
128 CGAGAACACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTATGAATCATT
* * * * * * * * *
17121 CATGAAAGTTGTAGATCATGGAATTACCTTTTAATAGACACTTGAATCATCTTGATTGGATAAGC
193 AATGAAAGTTATAGATAATGAAATTACCTTTCAATAGACACTTGAATCACCTTGATCGGACAAAC
* * * * ***
17186 AAAACAAAAAATATAAGAATTAAAGTCAAAACGTTCAATCGTCCAACCCAAAACTTGTGGGGGAC
258 AAAACAAAAAATA-AAAAATAAAAGGCAAAACGTTAAATCGTCCAACCCAAAA-TTGTAAAGGAC
*
17251 TAAATAGCAAAAAGCGT-AAAAGTAT-AGGGATCATTTGATAAATAATCCAACAAAA-AAATATT
321 TAAATAGCAAAAAGCATAAAAAGTATGA-GGATCATTTGATAAATAATCCAACAAAACAAATATT
*
17313 TGTTTATTGAGA
385 TGTTTATAGAGA
17325 ATGAGACCCA
Statistics
Matches: 331, Mismatches: 62, Indels: 9
0.82 0.15 0.02
Matches are distributed among these distances:
439 85 0.26
440 1 0.00
441 3 0.01
442 156 0.47
443 64 0.19
444 22 0.07
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (439 bp):
AATCAAATTCAGCTTTCAGACCCTTAACAAAAGTCACAGATCACACGATAACCTTCTAAGCAACA
CTTAAACAAGCTCAATCGGACAAGTGGAACGAAAATTATACAATATTAAAGAGACCAGCAATCGA
GAACACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTATGAATCATTAAT
GAAAGTTATAGATAATGAAATTACCTTTCAATAGACACTTGAATCACCTTGATCGGACAAACAAA
ACAAAAAATAAAAAATAAAAGGCAAAACGTTAAATCGTCCAACCCAAAATTGTAAAGGACTAAAT
AGCAAAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAACAAATATTTGTTTA
TAGAGACCAAACATAAAAATTCTATCTCGAACCCTCCACGAAAGTCATT
Found at i:20511 original size:25 final size:25
Alignment explanation
Indices: 20459--20524 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
20449 CACTCATATT
*
20459 CTTGCGTTTGGCAAACGAGCCTACG
1 CTTGCGTTTAGCAAACGAGCCTACG
** **
20484 CTTGCGTTTAGCAAACGAGTTTGTG
1 CTTGCGTTTAGCAAACGAGCCTACG
20509 CTTGCGTTTAGCAAAC
1 CTTGCGTTTAGCAAAC
20525 ACATAGGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTACG
Found at i:24493 original size:9 final size:9
Alignment explanation
Indices: 24478--24508 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
24468 CCATGTCACC
24478 CTTTTTTTT
1 CTTTTTTTT
24487 -TTTTTTTT
1 CTTTTTTTT
24495 CTTTTTTTT
1 CTTTTTTTT
24504 CTTTT
1 CTTTT
24509 GACATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:32921 original size:13 final size:13
Alignment explanation
Indices: 32903--32927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32893 TGTTGTTATT
32903 TTGTAGATCTAAG
1 TTGTAGATCTAAG
32916 TTGTAGATCTAA
1 TTGTAGATCTAA
32928 AATTTTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:37452 original size:22 final size:22
Alignment explanation
Indices: 37419--37476 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
37409 ACCACACTGT
* *
37419 GGTTACCCAAATTTCGTAGTGCA
1 GGTTACCAAAATTTCGTA-TGAA
37442 -GTTACCAAAATTTCGTATGAA
1 GGTTACCAAAATTTCGTATGAA
*
37463 GGTTATCAAAATTT
1 GGTTACCAAAATTT
37477 TCATCGGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTTCGTATGAA
Found at i:37611 original size:22 final size:22
Alignment explanation
Indices: 37568--37612 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
37558 AAAGATTATT
* *
37568 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGTGAGGCTATC
37590 AAAATTTCATAGAT-AGGCTATC
1 AAAATTTCATAG-TGAGGCTATC
37612 A
1 A
37613 GAGAGGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGCTATC
Found at i:37623 original size:34 final size:34
Alignment explanation
Indices: 37583--37648 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
37573 TTCATAGTGT
*
37583 GGTTATCAAAATTTCATAGAT-AGGCTATCAGAGA
1 GGTTATCAAAATTCCATAG-TGAGGCTATCAGAGA
*
37617 GGTTATCAAAATTCCATAGTGAGGGTATCAGA
1 GGTTATCAAAATTCCATAGTGAGGCTATCAGA
37649 ATTTCATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (34 bp):
GGTTATCAAAATTCCATAGTGAGGCTATCAGAGA
Found at i:37674 original size:22 final size:22
Alignment explanation
Indices: 37616--37740 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
37606 GCTATCAGAG
* *
37616 AGGTTATCAAAATTCCATAGTG
1 AGGTTATCAAAATTTCATAGTA
* * *
37638 AGGGTATCAGAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTA
* *
37660 TGGTTATCAAAATTTTATAAG-A
1 AGGTTATCAAAATTTCAT-AGTA
*
37682 AGGTTATTAAAGATTTCATAGTA
1 AGGTTATCAAA-ATTTCATAGTA
* * * *
37705 TGGTTACCAAAATTTGATTGTA
1 AGGTTATCAAAATTTCATAGTA
*
37727 ATGTTAT-AAAATTT
1 AGGTTATCAAAATTT
37741 TAAATTTCAT
Statistics
Matches: 81, Mismatches: 19, Indels: 7
0.76 0.18 0.07
Matches are distributed among these distances:
21 7 0.09
22 57 0.70
23 17 0.21
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTA
Found at i:37733 original size:45 final size:43
Alignment explanation
Indices: 37648--37740 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 43
37638 AGGGTATCAG
* * *
37648 AATTTCATAGTGTGGTTATCAAAATTTTATAAGAAGGTTATTAA
1 AATTTCATAGTATGGTTACCAAAATTTGATAAGAAGGTTA-TAA
* *
37692 AGATTTCATAGTATGGTTACCAAAATTTGAT-TGTAATGTTATAA
1 A-ATTTCATAGTATGGTTACCAAAATTTGATAAG-AAGGTTATAA
37736 AATTT
1 AATTT
37741 TAAATTTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
43 4 0.10
44 6 0.14
45 32 0.76
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (43 bp):
AATTTCATAGTATGGTTACCAAAATTTGATAAGAAGGTTATAA
Found at i:37892 original size:22 final size:22
Alignment explanation
Indices: 37846--37908 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
37836 TTGCATAGGA
* *
37846 AGGTTATCAAACTTTTAAAGCG
1 AGGTTATCAAAATTTTCAAGCG
* *
37868 AGGTTATCAAAATTTTCCAGTG
1 AGGTTATCAAAATTTTCAAGCG
*
37890 AGGTTATGAAAAATTTTCA
1 AGGTTAT-CAAAATTTTCA
37909 TATTGTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTTCAAGCG
Found at i:38011 original size:22 final size:22
Alignment explanation
Indices: 37986--38035 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
37976 GAGATCAGCA
* * *
37986 AAATTTCATTAGGAGGTTATCG
1 AAATTTCATAAGAAGATTATCG
*
38008 AAATTTCATAAGAAGATTATTG
1 AAATTTCATAAGAAGATTATCG
38030 AAATTT
1 AAATTT
38036 AAAAGTACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (22 bp):
AAATTTCATAAGAAGATTATCG
Found at i:38165 original size:22 final size:22
Alignment explanation
Indices: 38132--38256 Score: 110
Period size: 22 Copynumber: 5.7 Consensus size: 22
38122 TTTGGTATGA
*
38132 AGGTTATTAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGGG
* **
38154 AGGATATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GG
*
38177 A-GTTTTCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGGG
* ** **
38198 AGCTTAAAAAAATTTCATAATG
1 AGGTTATCAAAATTTCATAGGG
* *
38220 AAGTTATCGAAAA-ATCATAGGG
1 AGGTTATC-AAAATTTCATAGGG
38242 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
38257 GTGATTATCA
Statistics
Matches: 76, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
21 5 0.07
22 66 0.87
23 5 0.07
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGG
Found at i:38188 original size:44 final size:45
Alignment explanation
Indices: 38140--38256 Score: 139
Period size: 44 Copynumber: 2.6 Consensus size: 45
38130 GAAGGTTATT
* * ** *
38140 AAAATTTCATAGGGAGGATATCAAAATTTCATAGTTTAGTTTTC-
1 AAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAAGTTATCG
* **
38184 AAAATTTCATAGGGAGCTTAAAAAAATTTCATAATGAAGTTATCG
1 AAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAAGTTATCG
*
38229 AAAA-ATCATAGGGAGGTTATCAAAATTT
1 AAAATTTCATAGGGAGGTTATCAAAATTT
38257 GTGATTATCA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 56 0.93
45 4 0.07
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (45 bp):
AAAATTTCATAGGGAGGTTATCAAAATTTCATAATGAAGTTATCG
Found at i:38308 original size:23 final size:20
Alignment explanation
Indices: 38241--38338 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 20
38231 AAATCATAGG
*
38241 GAGGTTATCAAAA--TTTGT
1 GAGGTTATCAAAATTTTTAT
38259 GA--TTATCAAAA-TTTTAT
1 GAGGTTATCAAAATTTTTAT
*
38276 GAGGGTATCAAAATTTTGTAGT
1 GAGGTTATCAAAATTTT-TA-T
38298 GAGGTTTATCAAAATTTTATAT
1 GAGG-TTATCAAAATTTT-TAT
*
38320 GAATGCTTATCAAAATTTT
1 G-A-GGTTATCAAAATTTT
38339 ATACCAAGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.14
17 6 0.09
18 2 0.03
19 8 0.12
20 3 0.05
21 2 0.03
22 7 0.11
23 28 0.42
24 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (20 bp):
GAGGTTATCAAAATTTTTAT
Found at i:38339 original size:23 final size:23
Alignment explanation
Indices: 38261--38341 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
38251 AAATTTGTGA
38261 TTATCAAAA-TTT-TA-TGAGG-
1 TTATCAAAATTTTATAGTGAGGC
* * *
38280 GTATCAAAATTTTGTAGTGAGGT
1 TTATCAAAATTTTATAGTGAGGC
*
38303 TTATCAAAATTTTATA-TGAATGC
1 TTATCAAAATTTTATAGTG-AGGC
38326 TTATCAAAATTTTATA
1 TTATCAAAATTTTATA
38342 CCAAGGTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
19 8 0.15
20 3 0.06
21 2 0.04
22 7 0.13
23 32 0.62
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTATAGTGAGGC
Found at i:38380 original size:22 final size:22
Alignment explanation
Indices: 38256--38392 Score: 77
Period size: 22 Copynumber: 6.3 Consensus size: 22
38246 TATCAAAATT
38256 TGTGATTATCAAAATTTTATGAG
1 TGTGATTATCAAAATTTTAT-AG
*
38279 -G-G--TATCAAAATTTTGTAG
1 TGTGATTATCAAAATTTTATAG
* *
38297 TGAGGTTTATCAAAATTTTATA-
1 TG-TGATTATCAAAATTTTATAG
* *
38319 TGAATGCTTATCAAAATTTTATAC
1 TG--TGATTATCAAAATTTTATAG
*** * * * *
38343 CAAGGTCATTACAATTTTATAG
1 TGTGATTATCAAAATTTTATAG
* *
38365 TGTGATTATCAAAATTTCACAG
1 TGTGATTATCAAAATTTTATAG
38387 TGTGAT
1 TGTGAT
38393 CACTAAGCTT
Statistics
Matches: 86, Mismatches: 21, Indels: 15
0.70 0.17 0.12
Matches are distributed among these distances:
18 2 0.02
19 14 0.16
21 2 0.02
22 36 0.42
23 32 0.37
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (22 bp):
TGTGATTATCAAAATTTTATAG
Found at i:38594 original size:22 final size:22
Alignment explanation
Indices: 38460--38597 Score: 73
Period size: 22 Copynumber: 6.3 Consensus size: 22
38450 ACATGTAGAC
* * *
38460 TATCAAAGTTTTATAGTAATGT
1 TATCAAAATTTCATAGGAATGT
* * *
38482 TTTC-AAATTTCTATAGGGAGGT
1 TATCAAAATTTC-ATAGGAATGT
* *
38504 TAACAAAATTTTATATGG-ATGT
1 TATCAAAATTTCATA-GGAATGT
* ** *
38526 TCTTGAAATTTGATAGGAATGT
1 TATCAAAATTTCATAGGAATGT
* ** * * * *
38548 TTTTGAAATTGCATAGTATTAT
1 TATCAAAATTTCATAGGAATGT
38570 TATCAAAATTTCATAGGAATGT
1 TATCAAAATTTCATAGGAATGT
38592 TATCAA
1 TATCAA
38598 GTAGAAAAAA
Statistics
Matches: 84, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
21 7 0.08
22 69 0.82
23 8 0.10
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.42
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAATGT
Done.