Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006953.1 Corchorus capsularis cultivar CVL-1 contig06974, 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: 26034
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:46 original size:2 final size:2
Alignment explanation
Indices: 39--72 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29 AATAGCTTAC
39 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
73 TAAGAACAAT
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):
AT
Found at i:1093 original size:32 final size:31
Alignment explanation
Indices: 1035--1095 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
1025 TTAATTAAAA
1035 TTTTTTTTACAATGTTTTCATAAAATATAAT
1 TTTTTTTTACAATGTTTTCATAAAATATAAT
*
1066 TTTTTTTTGGCAATAGTTTTCAT-AAATATA
1 TTTTTTTT-ACAAT-GTTTTCATAAAATATA
1096 CTATTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.30
32 11 0.41
33 8 0.30
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTTTTTTACAATGTTTTCATAAAATATAAT
Found at i:1207 original size:12 final size:12
Alignment explanation
Indices: 1190--1214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1180 AAATTATAGA
1190 AAAGATGAATTC
1 AAAGATGAATTC
1202 AAAGATGAATTC
1 AAAGATGAATTC
1214 A
1 A
1215 TCTAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AAAGATGAATTC
Found at i:1409 original size:16 final size:17
Alignment explanation
Indices: 1388--1422 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1378 GGACCGGGAT
*
1388 TACTAGT-ATATATAAA
1 TACTAGTAATAAATAAA
1404 TACTAGTAATAAATAAA
1 TACTAGTAATAAATAAA
1421 TA
1 TA
1423 AATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
TACTAGTAATAAATAAA
Found at i:1609 original size:1 final size:1
Alignment explanation
Indices: 1565--1598 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
1555 TCTCAGCCTC
1565 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1599 CTATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9518 original size:13 final size:13
Alignment explanation
Indices: 9500--9525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9490 GTGACATGGA
9500 TATCAGAAAGAAC
1 TATCAGAAAGAAC
9513 TATCAGAAAGAAC
1 TATCAGAAAGAAC
9526 AACAGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
TATCAGAAAGAAC
Found at i:11159 original size:12 final size:11
Alignment explanation
Indices: 11126--11158 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
11116 AAGTACTTTG
11126 AATTTTTTTTT
1 AATTTTTTTTT
11137 AATTTTTTTTT
1 AATTTTTTTTT
11148 AATTTTTTTTT
1 AATTTTTTTTT
11159 TTATAGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:12473 original size:23 final size:23
Alignment explanation
Indices: 12416--12515 Score: 149
Period size: 20 Copynumber: 4.6 Consensus size: 23
12406 TTGGGTTATC
12416 AGTCTCCAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTGGATGTTTG
12439 AGT-T--AGATCTTGGATGTTTG
1 AGTCTCCAGATCTTGGATGTTTG
12459 AGTCTCCAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTGGATGTTTG
*
12482 AGT-T--AGATCTTGGATGCTTG
1 AGTCTCCAGATCTTGGATGTTTG
12502 AGTCTCCAGATCTT
1 AGTCTCCAGATCTT
12516 TAGATCTTGG
Statistics
Matches: 70, Mismatches: 1, Indels: 12
0.84 0.01 0.14
Matches are distributed among these distances:
20 37 0.53
21 2 0.03
22 2 0.03
23 29 0.41
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (23 bp):
AGTCTCCAGATCTTGGATGTTTG
Found at i:12477 original size:43 final size:43
Alignment explanation
Indices: 12416--12515 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
12406 TTGGGTTATC
*
12416 AGTCTCCAGATCTTGGATGTTTGAGTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTGGATGTTTGAGTTAGATCTTGGATGCTTG
12459 AGTCTCCAGATCTTGGATGTTTGAGTTAGATCTTGGATGCTTG
1 AGTCTCCAGATCTTGGATGTTTGAGTTAGATCTTGGATGCTTG
12502 AGTCTCCAGATCTT
1 AGTCTCCAGATCTT
12516 TAGATCTTGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (43 bp):
AGTCTCCAGATCTTGGATGTTTGAGTTAGATCTTGGATGCTTG
Found at i:13082 original size:23 final size:23
Alignment explanation
Indices: 13056--13104 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
13046 AACAAATTCA
13056 ATAAGTTATC-AAAAAATATATAT
1 ATAA-TTATCTAAAAAATATATAT
* * *
13079 ATAATTCTCTAATATATATATAT
1 ATAATTATCTAAAAAATATATAT
13102 ATA
1 ATA
13105 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATTATCTAAAAAATATATAT
Found at i:13095 original size:2 final size:2
Alignment explanation
Indices: 13090--13118 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13080 TAATTCTCTA
13090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13119 AAAGCAGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14863 original size:19 final size:19
Alignment explanation
Indices: 14834--14877 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
14824 GCCTGCCACA
14834 TGGCA-TTTTGGTCCAACG
1 TGGCATTTTTGGTCCAACG
* *
14852 TGGCATTTTTGGTCCGAGG
1 TGGCATTTTTGGTCCAACG
14871 TGGCATT
1 TGGCATT
14878 GCCAAGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (19 bp):
TGGCATTTTTGGTCCAACG
Found at i:16925 original size:15 final size:16
Alignment explanation
Indices: 16900--16929 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16890 AATAATTATT
16900 TTTAGATTATAATATA
1 TTTAGATTATAATATA
16916 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
16930 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:18661 original size:332 final size:331
Alignment explanation
Indices: 17264--21410 Score: 3604
Period size: 332 Copynumber: 12.5 Consensus size: 331
17254 ATACTTTACG
* * * * * * *
17264 TCATCTAACCAAATTTCAGCAACACTGGATTTAAGAATCTGTTTTTACGAGCATCTGAATCTTTT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTG
* * * ** *
17329 TTTCGATTTAATTAGAAATTAATTTTTTA-AAAAATAAGAAATACGATATTAAAATTGTGTAAAG
65 TTTCGATTTAATTAGAAATTAA---TTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAG
* * * * * *
17393 ACCTCCAATTTTTTTTGTG-TGAATTATATA-TTTTTATGACTATTTTAGGC-AAAAATTGAGGA
127 TCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTT-GGCTAAAAATTGAGGA
* ** * * * * *
17455 GAAATCTTACGTGTCAATTTTTGCAAAATTTTAGCTGTAATCGTGCACTAACCATCACGGTTTTT
191 AAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTT
* * * ** * * * * *
17520 GCCTAAAAACGCGTTCCGGGGATCCGCCTCAATTTTGCATGATTTTTGGCTCCGAGACTACTTGA
256 GGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
17585 AATGTCTATAT
321 AATATCTATAT
* * * * * * *
17596 TCGTCTAATCAAATTTTCAGCGACATTGGATTTAAGGACTTGTTTCTACGAGCATCTAAATCATG
1 TCATCTAATCAAA-TCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * * * *
17661 TTTTGATTTAGTTAGAAATTAGTTCAG-AAAATACTAGGAAAACGATATTAGAAGCATGAAAAGC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATA-T-GAAAAACGATATTAAAAGCGTGAAAAGT
* * * * *
17725 CCTTCGATCTTTTTGGCGTTGAATTATATAATTTTTATGATTATTGTGGCAAAAAATTGAGGAAA
128 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAA
* ** * * * * *
17790 CAA-CTTTTGGGTCAATTTTTGTAAAATTTTAGTTGAAATTGTGTAATAATCATCATGATTTCTG
193 -AATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTG
* * **
17854 GCTAAAAAACGCGTTTCAGGG-CCCGGCTAAGTTTTGCATGATTTTTGGTGCCAAGACTTTTTGA
257 GCT-AAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
* *
17918 GATATCCATAT
321 AATATCTATAT
* **
17929 TCATCTAATCAAATCTCAGCTACATTGTATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
17994 TTCGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAATCGTGAAAAATCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * * * ** * * *
18058 CCAATATTTTTGGTGTTAAATAATATATATTTTATGAGTATTTTATCAAAAAATTGAGAAAAAAA
131 TCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAAT
* * * * * * * *
18123 ATTTCGGGTCATTTTTTACAAAATTTTAGACAAAATCATGTACTAACCATCACGGTTTTTTTGG-
196 CTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG--TTTTTGGC
* * * ** ** *
18187 TAAAAACGTGTTTCGGGGCCCCGGTTCAGTTTTGCATGATTTTTTACTTCGAGACTCCTTGAAAT
259 TAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
18252 ATCTATAT
324 ATCTATAT
* * * * * * * *
18260 TGATCTAATAAAATTTTATCCT-CATTGCATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTG
1 TCATCTAATCAAATCTCA-GCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * **
18324 TTTCGATTTAATTAGAAATTAATTTTAGAAAAAGTATGAAAAACAATATTAAAAGTGTGAAAAAC
65 TTTCGATTTAATTAGAAATTAA-TTCAGAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGT
* *
18389 CCTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAA
128 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAA
* * * * *
18454 TATCTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCATGTAATAATCATCACGGTTTTTGC
193 AATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGG
* * * *
18519 CTAAAAATGCG-TTCAGGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAATAATCCTTGAAA
258 CTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
*
18583 TATCTATAC
323 TATCTATAT
* * *
18592 TCATCTAATCAAATCTCAGCTACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
18657 TTCGATTTAATTAGAAATTAATTCGGAAAAAAGTAGGAAAAACAATATTAGAAGCGTAAAAAATC
66 TTCGATTTAATTAGAAATTAATTCAG-AAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * *
18722 CTTCAATATTTTTGGCGTTGAATTATATATTTTTTTATGAGTACTTTAGCTAGAAATTGAGGAAA
129 CTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAA
* * * * * *
18787 TATCTTTCGGGTCAATGTTTGCAAAATTTTAGCCGAAATTGTGTAATAATCATTACGGTTTTTTG
193 AATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG-TTTTTG
* * * * * *
18852 ACTAACAAC-C-ATTCTAGGGCCCCGGGTCGGTTTTGCATGATTTTTAGCGCCAAGACTCCTTGA
257 GCTAAAAACGCGTTTC-AGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
* *
18915 GATATCCATAT
321 AATATCTATAT
* * * * * *
18926 TCATCTAATCCAATCTTAG-TCACATTGCATTTAAGGATTTATTTTTACGAGCATTTAAATCTTG
1 TCATCTAATCAAATCTCAGCT-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* *
18990 TTTCGA--TAA--A-AAA--AA---AG-AAAA-AT-------GATATGAAAAGTGTGAAAAGTCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * * * *
19036 TCCAATCTTATTGGCGTTAAATTATATATATTTCATGAGTATTGTAGCCAAAAAATGAGGAAAAA
130 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAA
* * * ** * *
19101 TTTTTTTGGGT-AATTTTTTGCAAAATATTAGCTGAAATC--GT-ATATTCATCATGGTTTTTTG
195 -TCTTTTGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGG
* * * * * ** *
19162 CTAAAAAACGCGTTTCAGGGCCCTGACTTAGTTTTGTATGATTTTTGGCGTCGTGATTCCTTGAA
258 CT-AAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
19227 ATATCTATAT
322 ATATCTATAT
* * *
19237 TCATCTAATCAAATCTCAGCCACATTGTATTTAAGTATTTGTTTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTG
19302 TTTCGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* **** *
19366 TCCAATCTTTTTGTAAATGAATTATATATATTTTATGAGTATTTTAGG-TAAAAATTGAGGAAAA
130 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTT-GGCTAAAAATTGAGGAAAA
* * * * * *
19430 ATATTTAT-GGTCATTTTTTTGCAAAATATTAGGCGAAATCGTGTACGTTAGTCAA-AATCACGA
194 ATCTTT-TGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTA----A-T-AACCATCACGG
* * * * * * * *
19493 TTTTTGGCTAAAAACGTGTTTC-GGGACTCAGTTCAGTGTTGCATAATTTTTGGCGCCGAGACTC
251 TTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
*
19557 CTCG-AATATCTATAT
316 CTTGAAATATCTATAT
* * * *** * *
19572 TCATATAACCAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTGAATCATGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * ** * *
19636 TTCTATTTAGTTAG-AATTAATTCAG---AATAGGAAAAACGATTTTAGCAGCATGAAAAGCCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * * *
19697 TCAATCTTTTTGGCATTTAATTATATAATTTTTATGAGTATTGTGG--GAAAATCGAGGAAATAA
131 TCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAA-AA
* * * *
19760 -CTTTTGGGT-AATTTTTTGTAAAATTTTAGCTGAAATCGTGTGATAACCATCACAGTTTTTGGC
195 TCTTTTGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGC
* * * * * * ** * *
19823 TTAAAATGCG-TTCCGGGGCCCGGCTAAGTTTTGCATGATTTTTGGCACCAAGGTTCTTTGAGAT
259 TAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
*
19887 ATCCATAT
324 ATCTATAT
* ** *
19895 TCATCTAATCAAATCTCAGCTACATTGGATATAACAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
19960 TTCGATTTAATTAGAAATTAATTCAG-CAAATATGAAATACAATTTTAAAATCGTGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * *
20024 CCAATATTTTTGGCGTTAAATTTATATATATATATATATATTATGAGTATTTTAGCCAAAAATTG
131 TCAATCTTTTTGGCGTT-GA---AT-TATATAT-T-T-T-TTATGAGTATTTTGGCTAAAAATTG
* ** ** * * * *
20089 TGGAAAAAAAAATTTTCAAGTCATTTTTTGCAAAATTTTAGTCGAAAT--TGT-GT-ACCATCAT
187 AGG--AAAAATCTTTT-GGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAC
** * * * * * ** *
20150 TTTTTTTGGCTAAAAACACGTTT-TGGTGCTCCGGGTCAATTTTGCATGATTTTTTGTTG-CAAA
249 GGTTTTTGGCTAAAAACGCGTTTCAGG-GCCCCGGCTCAGTTTTGCATGA-TTTTTGGCGCCAAG
20213 ACTCCTTGAAATATCTATAT
312 ACTCCTTGAAATATCTATAT
* * * ** * * * *
20233 TCATATAACCAAATCTTAGCCCCATTAGATTTAAGGATTTGTTTTTACGAGCATTTAAATCATGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
20298 TTCGATTTAATTAGAAATTAATTTGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCC
66 TTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * *
20363 TTTAATCCTTTTGGGGTTGAGTTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA-GAAAAA
130 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAA
* * * *
20427 TATTTTAGGTCAATTTTTGCAAAATTTTAGCCGAAAATCGTGTACTAACTAACCATCATGATTTT
195 TCTTTTGGGTCAATTTTTGCAAAATTTTAGCCG-AAATCGTG---TAA-TAACCATCACGGTTTT
* * * * **
20492 CGGCTAAAAACGCGTTTC-GGAG-CCTGACTCAGTTTTGCATGATTTTTGGTGTTAAGACTCCTT
255 TGGCTAAAAACGCGTTTCAGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
*
20555 GAAGTATCTATAT
319 GAAATATCTATAT
* * * * * *
20568 TCATCTAACCAAATCTCAG-TCACATTGTATTTAAGGATTTGTTTTTTATGAGTATCTAAATCGT
1 TCATCTAATCAAATCTCAGCT-ACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTT
* * * * * * *
20632 ATTTCGATTTAATCAGAAATTAATTTGGAAATAAAATAGGAAAAACAATATTGAAAGCGTGAAAA
64 GTTTCGATTTAATTAGAAATTAA-TT-CAGA-AAAATATGAAAAACGATATTAAAAGCGTG-AAA
* * * * * ** *
20697 AGGCTTTCAATTTTTTTGACATTGAATTATATATTTTTTATGAGTATTTTCACTAGAAATTGAGG
125 AGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGG
* * * *
20762 AAAAATCTTTCGGGTTAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTAAACATTCATG
190 AAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-TAACCA-TCACG
* * ** *
20827 ATTTTCGGCTAAAAACGCGTTTC-GAGG-CGTGGCTCAGTTTTGGATGATTTTTGGTGTCAAGAG
250 GTTTTTGGCTAAAAACGCGTTTCAG-GGCCCCGGCTCAGTTTTGCATGATTTTT-G-G-C----G
* * *
20890 TCAAGACTCCTTGAATTATTTATAT
307 CCAAGACTCCTTGAAATATCTATAT
* * * * *
20915 TCATATAACCAAGAATCTCAGCCATATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
1 TCATCTAATC-A-AATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * * * * *
20980 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAACTAGGAAAAACAATATTAGAAGCTTTAAAAG
64 GTTTCGATTTAATTAGAAATTAATTCAG-AAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAG
* ** * * *
21045 CCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
127 TCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAA
* * * * *
21110 ATATATTTCGTGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATAACCATCACGGTTT
192 AAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAATAACCATCACGGTTT
* * * * *
21175 TTGGCTAAAAACGCG-TTCCGGAGTCACGGCTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCT
254 TTGGCTAAAAACGCGTTTCAGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
* *
21239 TGAAATCTCTTTAT
318 TGAAATATCTATAT
* * * * * * *
21253 TCATCTAATCAAGTCTCAGCCACATTGGATTTAAGGATTGGTTTTTACGTGCATCGGAATCCTAT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
21318 TTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAATTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* *
21383 ACAATCTTTTTGGCTTTGAATTATATAT
131 TCAATCTTTTTGGCGTTGAATTATATAT
21411 ATATATATAT
Statistics
Matches: 3108, Mismatches: 579, Indels: 254
0.79 0.15 0.06
Matches are distributed among these distances:
309 7 0.00
310 15 0.00
311 83 0.03
312 61 0.02
313 70 0.02
314 3 0.00
316 1 0.00
317 3 0.00
319 2 0.00
320 1 0.00
321 5 0.00
322 64 0.02
323 47 0.02
324 32 0.01
325 11 0.00
327 95 0.03
328 33 0.01
329 25 0.01
330 298 0.10
331 180 0.06
332 347 0.11
333 305 0.10
334 333 0.11
335 132 0.04
336 188 0.06
337 42 0.01
338 187 0.06
339 88 0.03
340 135 0.04
341 25 0.01
342 3 0.00
343 5 0.00
344 24 0.01
345 26 0.01
346 109 0.04
347 56 0.02
348 40 0.01
349 27 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (331 bp):
TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
TCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCTAAAAATTGAGGAAAAAT
CTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTA
AAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
CTATAT
Found at i:24445 original size:5 final size:5
Alignment explanation
Indices: 24435--24473 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
24425 CGAGGAGCAC
*
24435 ATCTT ATCTT ATCTT ATTTT A-C-T ATCTT ATCTT ATCTT A
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT A
24474 CTACTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 1 0.03
5 27 0.90
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (5 bp):
ATCTT
Found at i:24462 original size:18 final size:18
Alignment explanation
Indices: 24439--24476 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
24429 GAGCACATCT
*
24439 TATCTTATCTTATTTTAC
1 TATCTTATCTTATCTTAC
24457 TATCTTATCTTATCTTAC
1 TATCTTATCTTATCTTAC
24475 TA
1 TA
24477 CTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (18 bp):
TATCTTATCTTATCTTAC
Done.