Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011131.1 Corchorus capsularis cultivar CVL-1 contig11152, 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: 108904
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1076 original size:332 final size:321
Alignment explanation
Indices: 244--1354 Score: 1152
Period size: 332 Copynumber: 3.4 Consensus size: 321
234 TTTTTCCATT
* * * *
244 TTTTTTTCCGAATTTAGTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCT
1 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
* * * ** * * * * *
309 TAAATCCAATTTCCCTGAGAAATTT-TTAGATGAATACAGATATTTGAATGAGTATTT-CTGCCA
66 TATATTCAATGTGGCTGAG-ATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCA
* * * * * * * * *
372 AAAATCATACAAAACTTAGCCGGGGCCCCCGAATGCGTTTTTAGCCCAAAAACCGTGATGGTT--
129 AAAATCATGCAAAACTGAACCAGGGCCCCGGAACGCGATTTTAGCACAAAAATCGTGATGGTTAG
* * *
435 ----CG-----GCTAAAAACTGACCCGAAAGATTTTTTTTTTGAAATTTTTGCAACAATACTCTT
194 CACACGATTCAGCTAAAAACTGACCCGAAA-A-ATTTTTTCTGAAATTTTTGCCACAATACTCTT
* * ** *
491 AAAAAATATATAATTCAATGCCAAAAAGATTGACGGACTTTTCACCGCTTCTAATAT-C-TTTTC
257 AAAAAATATATAATTTAACGCCAAAAAGATTGAAAGATTTTTCA-CGCTTCTAATATCCTTTTTC
554 -
321 A
* *
554 TATTTTTTCCAGAATTAATTTCTAATTAAATTGAAACAAG-TGTCAAATACTCGTAAAAACAAAT
1 T-TTTTTTCC-GAATTAATTTCTAATTAAATCGAAACAAGAT-TCAAATGCTCGTAAAAACAAAT
* * * * *
618 CCTTATATCCAATGTGGCTGAGATTTAGTTCGATGAATATAGATATTTCAAAGAGTCTTTGCGCT
63 CCTTATATTCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCC
* * * * * * *
683 AAAAATCATGCAAAATTGAACCAGGGCTCCGGAATGCGTTTTTAGCATAAAATTTGTGATGGTTA
128 AAAAATCATGCAAAACTGAACCAGGGCCCCGGAACGCGATTTTAGCACAAAAATCGTGATGGTTA
* * * *
748 GCACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAAATTTTGGCCA
193 GCACACGA-TTCAGC--------T--AAAAACTGACCCGAAAAATTTTTTCTGAAATTTTTGCCA
* *
813 CAATAGTCTTAAAAAATATATAATTTAACG-CAAAAAAATTTGAAAGATTTTTCACGCTTCTAAT
247 CAATACTCTTAAAAAATATATAATTTAACGCCAAAAAGA-TTGAAAGATTTTTCACGCTTCTAAT
877 ATCCTTTTTCA
311 ATCCTTTTTCA
* * * * *
888 TTTTTTTTCGAATTTATTTATAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCT
1 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
* *
953 TAAATTCAATGTGTCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAA
66 TATATTCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAA
* *
1017 AAATCATGCAAAACTGAA-CTGAGGCCCCGGAACGCGATTTTAGCCCAAAAATCGTGATGGTTAG
130 AAATCATGCAAAACTGAACCAG-GGCCCCGGAACGCGATTTTAGCACAAAAATCGTGATGGTTAG
* **
1081 TACACGATTCAGCTAAAAACTGACCCGAAAAAATATTTTTCTGAAATTTTTGCCACAATACTCAG
194 CACACGATTCAGCTAAAAACTGACCCG-AAAAAT-TTTTTCTGAAATTTTTGCCACAATACTCTT
* * * *
1146 AAAAAATATATAATTTAACGCCAAAAAGATTG-ACG-TGCTTTTCAAGTTTCTAATATCGTTTTT
257 AAAAAATATATAATTTAACGCCAAAAAGATTGAAAGAT--TTTTCACGCTTCTAATATCCTTTTT
*
1209 AAA
320 -CA
*
1212 TTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTC
1 TTTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCC
* *
1277 TTATATTTAATGTGGCTGAGA-TTTGATTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCA
65 TTATATTCAATGTGGCTGAGATTTTG-TTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCA
*
1341 AAAATCAAGCAAAA
129 AAAATCATGCAAAA
1355 TTCAGCCGGG
Statistics
Matches: 667, Mismatches: 91, Indels: 71
0.80 0.11 0.09
Matches are distributed among these distances:
310 1 0.00
311 12 0.02
312 144 0.22
313 1 0.00
318 2 0.00
321 14 0.02
322 7 0.01
323 70 0.10
324 21 0.03
325 117 0.18
326 1 0.00
331 28 0.04
332 218 0.33
333 14 0.02
334 17 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (321 bp):
TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
TATATTCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAA
AATCATGCAAAACTGAACCAGGGCCCCGGAACGCGATTTTAGCACAAAAATCGTGATGGTTAGCA
CACGATTCAGCTAAAAACTGACCCGAAAAATTTTTTCTGAAATTTTTGCCACAATACTCTTAAAA
AATATATAATTTAACGCCAAAAAGATTGAAAGATTTTTCACGCTTCTAATATCCTTTTTCA
Found at i:1866 original size:25 final size:27
Alignment explanation
Indices: 1819--1874 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1809 TTCCATAATT
*
1819 AATAAAAAAGTTGAATCATCTAAAAA-
1 AATAAAAAAGTTAAATCATCTAAAAAG
* *
1845 AATAAAATAGTTAAATGA-CTAAAAAG
1 AATAAAAAAGTTAAATCATCTAAAAAG
1871 AATA
1 AATA
1875 CTTATATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23
Consensus pattern (27 bp):
AATAAAAAAGTTAAATCATCTAAAAAG
Found at i:4315 original size:19 final size:20
Alignment explanation
Indices: 4286--4324 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4276 TTTTTTTTTC
*
4286 TCAAGGAAAATTTAAAAAAA
1 TCAAGGAAAATTGAAAAAAA
4306 TCAA-GAAAATTGAAAAAAA
1 TCAAGGAAAATTGAAAAAAA
4325 AATTTGGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (20 bp):
TCAAGGAAAATTGAAAAAAA
Found at i:4322 original size:20 final size:20
Alignment explanation
Indices: 4286--4325 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4276 TTTTTTTTTC
*
4286 TCAAGGAAAATTTAAAAAAA
1 TCAAGGAAAATTAAAAAAAA
4306 TCAA-GAAAATTGAAAAAAAA
1 TCAAGGAAAATT-AAAAAAAA
4326 ATTTGGCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (20 bp):
TCAAGGAAAATTAAAAAAAA
Found at i:5018 original size:30 final size:29
Alignment explanation
Indices: 4956--5025 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
4946 ACCGAACCGT
****
4956 CAAATAAGCCCCTGAACTATTATTTCAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
*
4985 CAAATAAGCCCCTGAACTCTTAAAAAAAGC
1 CAAATAAGCCCCTGAACTATT-AAAAAAGC
5015 CAAATAAGCCC
1 CAAATAAGCCC
5026 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:6330 original size:2 final size:2
Alignment explanation
Indices: 6323--6347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6313 TGAGATGTGA
6323 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 A
6348 GGGGAGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7747 original size:2 final size:2
Alignment explanation
Indices: 7701--7735 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7691 GAAATTGAAG
7701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7736 GCTCATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13705 original size:48 final size:48
Alignment explanation
Indices: 13634--13740 Score: 180
Period size: 48 Copynumber: 2.2 Consensus size: 48
13624 TGCCTTCTAC
13634 GTATACAAAATGTCAATCCTAATTCAAGTAAATTTCTTATGCTTGAAG
1 GTATACAAAATGTCAATCCTAATTCAAGTAAATTTCTTATGCTTGAAG
* *
13682 GTATATAAAGTGTCAATCCTAATTCAAGTAAATTTCTTATGCTTGAAG
1 GTATACAAAATGTCAATCCTAATTCAAGTAAATTTCTTATGCTTGAAG
*
13730 GTAGA-AAAATG
1 GTATACAAAATG
13741 ATCACTTGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
47 5 0.09
48 50 0.91
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (48 bp):
GTATACAAAATGTCAATCCTAATTCAAGTAAATTTCTTATGCTTGAAG
Found at i:19476 original size:40 final size:40
Alignment explanation
Indices: 19418--19494 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
19408 TTTATAACTA
*
19418 GGGGCTAAACCTGGATTTAATTTCTCACCTTAATTATCAG
1 GGGGCTAAACCTGAATTTAATTTCTCACCTTAATTATCAG
* * **
19458 GGGGTTAAACCTGAATTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAACCTGAATTTAATTTCTCACCTTAATTAT
19495 TTAAGAGGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (40 bp):
GGGGCTAAACCTGAATTTAATTTCTCACCTTAATTATCAG
Found at i:21127 original size:333 final size:333
Alignment explanation
Indices: 20521--21192 Score: 1094
Period size: 333 Copynumber: 2.0 Consensus size: 333
20511 ATAAGTTCAA
*
20521 TAAACTCCCACGACAAGAGTCTCTAAATCCTTAAAAAGGTTGATGGTAACTTACCATGATCTTTT
1 TAAACTCCCACAACAAGAGTCTCTAAATCCTTAAAAAGGTTGATGGTAACTTACCATGATCTTTT
* * **
20586 GATTGAGTATATGTAAAATTTTATTACAATCTGAATAAATCTCTATATTTCAAACATCTAAATGA
66 GATTGAGTACATGTAAAATCTTATTACAATCTGAATAAATCTCTATATGCCAAACATCTAAATGA
* *
20651 GGAATCAACTCAAAGTAAGAAATTATCATAAACAAACCATCTACCAACCAAATACACAAATAAAC
131 GAAATCAACTCAAAGTAAGAAACTATCATAAACAAACCATCTACCAACCAAATACACAAATAAAC
* * *
20716 AAATTACAAACTAAACTCACATTCCGTGAGACTTGAACCCAGAACCTTGCGATCCAGGCACGGTG
196 AAATTACAAACTAAACTCACATTCCGTGAGACTCGAACCCAGAACCTTGCGACCCAGACACGGTG
*
20781 CACCTACCAGTTGAACTAACAACTCTACTGCAACTAACCATGATCTTAGAAATGAAATAAGGTAT
261 CACCTACCAGTTGAACTAACAACTCTACTGCAACTAACCATGATCTTAGAAATGAAATAAGGTAC
20846 CATGCTTC
326 CATGCTTC
*
20854 TAAACTCCCACAAGAAGAGTCTCTAAATCCTTAAAAAGGTTGATGGTAACTTACCATGATCTTTT
1 TAAACTCCCACAACAAGAGTCTCTAAATCCTTAAAAAGGTTGATGGTAACTTACCATGATCTTTT
* *
20919 GATTGAGTACATGTGAAATCTTATTATAATCTGAATAAATCTCTATATGCCTAAACATCTAAATG
66 GATTGAGTACATGTAAAATCTTATTACAATCTGAATAAATCTCTATATGCC-AAACATCTAAATG
* * *
20984 AGAAATCAACTCAAAGTAAGAAACTATCATAAATAAACCATGTACCTACCAAATACACAAATAAA
130 AGAAATCAACTCAAAGTAAGAAACTATCATAAACAAACCATCTACCAACCAAATACACAAATAAA
* * * *
21049 TAAATTACAAACTAAACTCACATTCCGTGAGACTCGAACTCAGGACCTTGC-ACCCAGATACGGT
195 CAAATTACAAACTAAACTCACATTCCGTGAGACTCGAACCCAGAACCTTGCGACCCAGACACGGT
* ** * *
21113 GCACCTACCAGTTGAGCTAACAACTCTGGTGCAACTTACCATGATCTTAGAAATGAAATAATGTA
260 GCACCTACCAGTTGAACTAACAACTCTACTGCAACTAACCATGATCTTAGAAATGAAATAAGGTA
21178 CCATGCTTC
325 CCATGCTTC
21187 TAAACT
1 TAAACT
21193 TTTCCATAGC
Statistics
Matches: 312, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
333 192 0.62
334 120 0.38
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (333 bp):
TAAACTCCCACAACAAGAGTCTCTAAATCCTTAAAAAGGTTGATGGTAACTTACCATGATCTTTT
GATTGAGTACATGTAAAATCTTATTACAATCTGAATAAATCTCTATATGCCAAACATCTAAATGA
GAAATCAACTCAAAGTAAGAAACTATCATAAACAAACCATCTACCAACCAAATACACAAATAAAC
AAATTACAAACTAAACTCACATTCCGTGAGACTCGAACCCAGAACCTTGCGACCCAGACACGGTG
CACCTACCAGTTGAACTAACAACTCTACTGCAACTAACCATGATCTTAGAAATGAAATAAGGTAC
CATGCTTC
Found at i:22003 original size:5 final size:5
Alignment explanation
Indices: 21993--22018 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21983 TTTATCAAAC
21993 AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A
22019 TTCAAGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:28752 original size:11 final size:11
Alignment explanation
Indices: 28736--28770 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28726 TTGACAGCGC
28736 AACGAAAACAA
1 AACGAAAACAA
*
28747 AACGAAAACGA
1 AACGAAAACAA
*
28758 AACAAAAACAA
1 AACGAAAACAA
28769 AA
1 AA
28771 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (11 bp):
AACGAAAACAA
Found at i:40855 original size:13 final size:13
Alignment explanation
Indices: 40837--40866 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40827 AGTTATATGT
40837 AAAAGTAAATAAG
1 AAAAGTAAATAAG
40850 AAAAGTAAATAAG
1 AAAAGTAAATAAG
40863 AAAA
1 AAAA
40867 AAGGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAAGTAAATAAG
Found at i:43379 original size:5 final size:5
Alignment explanation
Indices: 43371--43405 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
43361 AAGTAAAGCC
43371 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
43406 GCTTTCTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:48060 original size:9 final size:9
Alignment explanation
Indices: 48046--48070 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
48036 TTAGATTCAG
48046 CATCAAAAT
1 CATCAAAAT
48055 CATCAAAAT
1 CATCAAAAT
48064 CATCAAA
1 CATCAAA
48071 TTCCAGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (9 bp):
CATCAAAAT
Found at i:51649 original size:12 final size:11
Alignment explanation
Indices: 51629--51658 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
51619 AACGTTTACC
51629 AAAAAAAAAAG
1 AAAAAAAAAAG
51640 AAAAAGAAAAAG
1 AAAAA-AAAAAG
51652 AAAAAAA
1 AAAAAAA
51659 CAAGCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:69038 original size:19 final size:20
Alignment explanation
Indices: 68995--69039 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
68985 GGCACGCCAT
*
68995 ATGTACCAAAAAGTCGTGCCAC
1 ATGTACCAAAAA--CGTGACAC
69017 ATGTACCAAAAA-GTGACAC
1 ATGTACCAAAAACGTGACAC
69036 ATGT
1 ATGT
69040 CACGCCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATGTACCAAAAACGTGACAC
Found at i:69044 original size:53 final size:53
Alignment explanation
Indices: 68959--69061 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
68949 GACGTGACAC
* **
68959 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCATATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCATATGTACCAAAAAGTCGT
* *
69012 GCCACATGTACCAAAAAGTGACACATGTCACGCCATGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCATATGTACCAAAAAGT
69062 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCATATGTACCAAAAAGTCGT
Found at i:78303 original size:51 final size:51
Alignment explanation
Indices: 78231--78338 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 51
78221 AGAATTTTTC
*
78231 ATGAAGCATGACCTCTGCTTAAGTCCCCACTAAACAAATGGAGAATGGCAA
1 ATGAAGCATGACCTCTACTTAAGTCCCCACTAAACAAATGGAGAATGGCAA
* * *
78282 ATGAAGCATGACTTCTACTTAAGTCCCCTCTAAACAAATGGAGAATGGGAA
1 ATGAAGCATGACCTCTACTTAAGTCCCCACTAAACAAATGGAGAATGGCAA
78333 ATGAAG
1 ATGAAG
78339 AAGGAATACG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (51 bp):
ATGAAGCATGACCTCTACTTAAGTCCCCACTAAACAAATGGAGAATGGCAA
Found at i:84402 original size:2 final size:2
Alignment explanation
Indices: 84395--84420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
84385 AATTAAAACC
84395 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
84421 ATAGTGAATT
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:84808 original size:15 final size:14
Alignment explanation
Indices: 84782--84817 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
84772 AAAAGCCTTT
84782 AAAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
*
84796 AAAGAAGGAAAAAA
1 AAAGAAGAAAAAAA
84810 AAA-AAGAA
1 AAAGAAGAA
84818 CAGCGGGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAAAAA
Found at i:87356 original size:24 final size:25
Alignment explanation
Indices: 87329--87496 Score: 181
Period size: 24 Copynumber: 6.8 Consensus size: 25
87319 GTATGACCGA
87329 CAAGGGAATCCAATGCA-A-AACCAG
1 CAAGGGAATCCAAT-CATACAACCAG
87353 CAAGGGAAT-CAATCATACAACCAG
1 CAAGGGAATCCAATCATACAACCAG
87377 CAAGGGAAT-CAATCATACAACCAG
1 CAAGGGAATCCAATCATACAACCAG
*
87401 CAAGGGAATCCAAATCCAATGCAAAACCAG
1 CAAGGGAATCC-AAT-C-AT--ACAACCAG
* *
87431 CCAGGGAGTCC-ATCATACAACCAG
1 CAAGGGAATCCAATCATACAACCAG
*
87455 CAAGGAAATCCAATGCA-A-AACCAG
1 CAAGGGAATCCAAT-CATACAACCAG
87479 CAAGGGAATCC-ATCATAC
1 CAAGGGAATCCAATCATAC
87497 CAGCAGGGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 24
0.79 0.05 0.15
Matches are distributed among these distances:
22 4 0.03
23 8 0.06
24 79 0.64
25 4 0.03
26 7 0.06
27 2 0.02
28 4 0.03
30 16 0.13
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (25 bp):
CAAGGGAATCCAATCATACAACCAG
Found at i:87425 original size:78 final size:78
Alignment explanation
Indices: 87335--87490 Score: 244
Period size: 78 Copynumber: 2.0 Consensus size: 78
87325 CCGACAAGGG
*
87335 AATCCAATGCAAAACCAGCAAGGGAATCAATCATACAACCAGCAAGGGAAT-CAAT-CATACAAC
1 AATCCAATGCAAAACCAGCAAGGGAATCAATCATACAACCAGCAAGGAAATCCAATGCA-A-AAC
87398 CAGCAAGGGAATCCA
64 CAGCAAGGGAATCCA
* * *
87413 AATCCAATGCAAAACCAGCCAGGGAGTCCATCATACAACCAGCAAGGAAATCCAATGCAAAACCA
1 AATCCAATGCAAAACCAGCAAGGGAATCAATCATACAACCAGCAAGGAAATCCAATGCAAAACCA
87478 GCAAGGGAATCCA
66 GCAAGGGAATCCA
87491 TCATACCAGC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
78 65 0.90
79 5 0.07
80 2 0.03
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (78 bp):
AATCCAATGCAAAACCAGCAAGGGAATCAATCATACAACCAGCAAGGAAATCCAATGCAAAACCA
GCAAGGGAATCCA
Found at i:87767 original size:36 final size:36
Alignment explanation
Indices: 87718--87994 Score: 281
Period size: 36 Copynumber: 7.7 Consensus size: 36
87708 CACCTGGTGG
* *
87718 GAATTATGTGCAAGGGGCAAATCCAGGCTATGGGCA
1 GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
* * *
87754 GAATTATGGGCAAGGGACAGATCCTGGCTTTGGGCA
1 GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
* **
87790 GAAATATGGGCAACAGGCAAATCCTGGCTATGGGCA
1 GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
** *
87826 GAATTATGGGCAACAGGCAAATCCTGGCCATGGGCA
1 GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
** ** *
87862 GAATTATGGGCAACAGGCAAATCCTGGCTACAGTCA
1 GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
* **
87898 GAACTTCA--GGCAAGGGGCAAATCCTGGGTATGCCCA
1 GAA-TT-ATGGGCAAGGGGCAAATCCTGGCTATGGGCA
* * *
87934 GAATTTTGGGCAAGGAGCAAATCCT-GCTTATGGACA
1 GAATTATGGGCAAGGGGCAAATCCTGGC-TATGGGCA
* **
87970 GAGTTATGGGCAAGGACCAAATCCT
1 GAATTATGGGCAAGGGGCAAATCCT
87995 ACATCTGGTC
Statistics
Matches: 204, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
35 3 0.01
36 198 0.97
37 2 0.01
38 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.19
Consensus pattern (36 bp):
GAATTATGGGCAAGGGGCAAATCCTGGCTATGGGCA
Found at i:94691 original size:13 final size:13
Alignment explanation
Indices: 94673--94698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
94663 AGTATCCATG
94673 CTTATTTGATGTT
1 CTTATTTGATGTT
94686 CTTATTTGATGTT
1 CTTATTTGATGTT
94699 TAATGTTCGC
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:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
CTTATTTGATGTT
Found at i:108859 original size:2 final size:2
Alignment explanation
Indices: 108852--108900 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
108842 TAGAAATACT
108852 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
108894 AG AG AG A
1 AG AG AG A
108901 TGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.