Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007122.1 Corchorus capsularis cultivar CVL-1 contig07143, 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: 27963
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4185 original size:28 final size:30
Alignment explanation
Indices: 4144--4213 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
4134 TTACAAATGC
4144 GGGTTGTGCACTTGGG-TTG-ATTCAAGTGT
1 GGGTT-TGCACTTGGGATTGTATTCAAGTGT
**
4173 GGGTTTGCACTTGGGATTGTATTTGAGTGT
1 GGGTTTGCACTTGGGATTGTATTCAAGTGT
4203 GGGTTTGCACT
1 GGGTTTGCACT
4214 CGGTGTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.27
29 8 0.22
30 19 0.51
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (30 bp):
GGGTTTGCACTTGGGATTGTATTCAAGTGT
Found at i:9386 original size:30 final size:30
Alignment explanation
Indices: 9330--9389 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
9320 AAAGGAGAGG
*
9330 ATGGAATCGCAAAGTATCATGAAGATGCCA
1 ATGGAATCGCAAAGCATCATGAAGATGCCA
* * *
9360 ATGGAATCGCAAAGCCTCTTGGAGATGCCA
1 ATGGAATCGCAAAGCATCATGAAGATGCCA
9390 TTAAGATGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (30 bp):
ATGGAATCGCAAAGCATCATGAAGATGCCA
Found at i:11102 original size:18 final size:18
Alignment explanation
Indices: 11071--11107 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11061 ATAGGCACAC
* *
11071 AGATATATCGCCATAAAT
1 AGATACATCACCATAAAT
11089 AGATACATCACCATAAAT
1 AGATACATCACCATAAAT
11107 A
1 A
11108 TAAGGGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (18 bp):
AGATACATCACCATAAAT
Found at i:11236 original size:11 final size:11
Alignment explanation
Indices: 11222--11259 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11212 ATTCATAACA
11222 AATTTATAATT
1 AATTTATAATT
11233 AATTTATAATT
1 AATTTATAATT
11244 -ATTTGATAATT
1 AATTT-ATAATT
*
11255 TATTT
1 AATTT
11260 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11808 original size:107 final size:105
Alignment explanation
Indices: 11550--11917 Score: 573
Period size: 107 Copynumber: 3.5 Consensus size: 105
11540 AATTTTTCTA
** * * * *
11550 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
* *
11613 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATAATTATTAATTTTGAAATTT
11653 ACCCTTAAAATGAAAAT-AAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
11717 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT-AATTATTAATTTTGAAATTT
*
11759 ACCCTTAAAATAAACATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAA-ATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
11824 TTTCTAAAACCCTATAACAATAGATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAATA-ATTATTAATTTTGAAATTT
11866 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
11918 AGGCTAAACT
Statistics
Matches: 247, Mismatches: 9, Indels: 14
0.91 0.03 0.05
Matches are distributed among these distances:
102 11 0.04
103 26 0.11
104 40 0.16
105 3 0.01
106 31 0.13
107 133 0.54
108 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTTTGAAATTT
Found at i:16261 original size:14 final size:12
Alignment explanation
Indices: 16230--16297 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
16220 AGAAATAGAG
16230 AGAAAAGAAAAA
1 AGAAAAGAAAAA
16242 AG-AAAGAAGAAGA
1 AGAAAAGAA-AA-A
*
16255 AGAAAAGAAATA
1 AGAAAAGAAAAA
**
16267 AGAATCGGAAAAA
1 AGAA-AAGAAAAA
*
16280 A-AAAGAGAAATA
1 AGAAA-AGAAAAA
16292 AGAAAA
1 AGAAAA
16298 AGAATAACGA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
11 6 0.14
12 18 0.42
13 13 0.30
14 6 0.14
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:16262 original size:18 final size:18
Alignment explanation
Indices: 16218--16270 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
16208 GGTGAGGGAG
*
16218 GAAGAAATAGAGAGAA-AA
1 GAAGAAA-AGAAAGAAGAA
16236 GAA-AAAAGAAAGAAGAA
1 GAAGAAAAGAAAGAAGAA
*
16253 GAAGAAAAGAAATAAGAA
1 GAAGAAAAGAAAGAAGAA
16271 TCGGAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.23
17 8 0.26
18 16 0.52
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (18 bp):
GAAGAAAAGAAAGAAGAA
Found at i:16304 original size:37 final size:39
Alignment explanation
Indices: 16236--16309 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 39
16226 AGAGAGAAAA
16236 GAAAAAAGAAAGAAGAAGAAGAAAAGAAATAA-GAATCG
1 GAAAAAAGAAAGAAGAAGAAGAAAAGAAATAACGAATCG
*
16274 GAAAAAA-AAAG-AGAAATAAGAAAA-AGAATAACGAAT
1 GAAAAAAGAAAGAAG-AAGAAGAAAAGA-AATAACGAAT
16310 AAAAAATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 3 0.09
37 18 0.56
38 11 0.34
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (39 bp):
GAAAAAAGAAAGAAGAAGAAGAAAAGAAATAACGAATCG
Found at i:17001 original size:21 final size:23
Alignment explanation
Indices: 16948--17002 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
16938 CATTTCCTTT
*
16948 TAATATTAAATAAAACTATTATA
1 TAATAATAAATAAAACTATTATA
16971 TATATGAATAAATAAAA-T-TTATA
1 TA-AT-AATAAATAAAACTATTATA
16994 TAATAATAA
1 TAATAATAA
17003 TCACAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 9 0.31
24 3 0.10
25 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
TAATAATAAATAAAACTATTATA
Found at i:17354 original size:31 final size:31
Alignment explanation
Indices: 17283--17354 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
17273 GTCTATCAGC
*
17283 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
* *
17314 TAATT-ATTTGTTTAATTTAATAC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGACTTTAATTT
17344 GTTTTAATTTG
1 -TTTTAATTTG
17355 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:18747 original size:17 final size:15
Alignment explanation
Indices: 18708--18756 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
18698 CAATTGATAG
*
18708 ATTTTAAAATCCTTC
1 ATTTTAAAATTCTTC
*
18723 ACTTTAAAATTCTTC
1 ATTTTAAAATTCTTC
*
18738 AAATTTTAAAATTCCTC
1 --ATTTTAAAATTCTTC
18755 AT
1 AT
18757 CCAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 15 0.54
17 13 0.46
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTAAAATTCTTC
Found at i:21387 original size:69 final size:68
Alignment explanation
Indices: 21246--21394 Score: 192
Period size: 69 Copynumber: 2.2 Consensus size: 68
21236 GATAACGTTA
* * *
21246 TGTCATATTTCTTGCATTTAAGTCTAATTTCGTTTCCCGAAATACCCTTTCGGATAAAGGGTCAA
1 TGTCATATTTCTTGCATTTAAGTCTAATTTCGTTTCCCAAAATACCCTTTCAGAAAAAGGGTCAA
21311 TTT
66 TTT
* ** * *
21314 TGTCATATTTCTTGCATTTAGGT-TAAATTTTTTATTTCCAAAATGCCCTTTCAGAAAAAGGGTC
1 TGTCATATTTCTTGCATTTAAGTCT-AATTTCGT-TTCCCAAAATACCCTTTCAGAAAAAGGGTC
21378 AATTT
64 AATTT
*
21383 TGTCATGTTTCT
1 TGTCATATTTCT
21395 ACATACAAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
67 1 0.01
68 28 0.40
69 41 0.59
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (68 bp):
TGTCATATTTCTTGCATTTAAGTCTAATTTCGTTTCCCAAAATACCCTTTCAGAAAAAGGGTCAA
TTT
Found at i:21447 original size:68 final size:67
Alignment explanation
Indices: 21285--21538 Score: 237
Period size: 68 Copynumber: 3.7 Consensus size: 67
21275 TCGTTTCCCG
* * ** *
21285 AAATACCCTTTCGGATAAAGGGTCAATTTTGTCATATTTCTTGCATTTAGGTTAAATTTTTTATT
1 AAATACCCTTTCGGAAAAAGGGTCAATTTTGTCATGTTTC-TGCATACAAGTTAAA--TTTTATT
21350 TCC-A
63 TCCTA
* * * *
21354 AAATGCCCTTTCAGAAAAAGGGTCAATTTTGTCATGTTTCTACATACAAGTTCAATTTTGATTTC
1 AAATACCCTTTCGGAAAAAGGGTCAATTTTGTCATGTTTCTGCATACAAGTTAAATTTT-ATTTC
21419 CTA
65 CTA
* * * * * *
21422 AAATACTCGTTT-GGAAAAAGGGTCAATCTTCTCATGCTTTC-GCGTACAAGTTAAATTCT-CTT
1 AAATAC-CCTTTCGGAAAAAGGGTCAATTTTGTCATG-TTTCTGCATACAAGTTAAATTTTATTT
21484 CCTA
64 CCTA
** * * *
21488 AAATACCCTTTCGGTCAAAGGGTCAGTTTTGTTATGTTTCTTGCATTCAAG
1 AAATACCCTTTCGGAAAAAGGGTCAATTTTGTCATGTTTC-TGCATACAAG
21539 AGAATAAAAG
Statistics
Matches: 150, Mismatches: 28, Indels: 16
0.77 0.14 0.08
Matches are distributed among these distances:
65 8 0.05
66 34 0.23
67 13 0.09
68 51 0.34
69 44 0.29
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (67 bp):
AAATACCCTTTCGGAAAAAGGGTCAATTTTGTCATGTTTCTGCATACAAGTTAAATTTTATTTCC
TA
Found at i:26481 original size:23 final size:22
Alignment explanation
Indices: 26445--26509 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
26435 GAACACCTCA
*
26445 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
26467 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
26490 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
26510 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:26503 original size:22 final size:22
Alignment explanation
Indices: 26402--26508 Score: 72
Period size: 22 Copynumber: 4.8 Consensus size: 22
26392 TAAACTTTCT
* * *
26402 TATGAAATTTTGTTAACCTCCC
1 TATGAAATATTGATAACCTCCA
* * * *
26424 TAAGGAATTTTGA-ACACCTCAA
1 TATGAAATATTGATA-ACCTCCA
* **
26446 TATGAAATTTTGATAACCAACA
1 TATGAAATATTGATAACCTCCA
* *
26468 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATATTGATAACCTCCA
*
26491 TATGATATATTGATAACC
1 TATGAAATATTGATAACC
26509 ACTTTATAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 46 0.70
23 19 0.29
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (22 bp):
TATGAAATATTGATAACCTCCA
Found at i:26635 original size:23 final size:22
Alignment explanation
Indices: 26604--26688 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
26594 ACCTTGATCG
*
26604 CTATGAAATTTTGATAAATCTTT
1 CTATAAAATTTTGATAAA-CTTT
* **
26627 CTATAAAATTTTAATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTT
26650 CTATAAAATTTTGAT-AACTTT
1 CTATAAAATTTTGATAAACTTT
* *
26671 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
26689 CTACAAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.06
22 14 0.28
23 33 0.66
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTT
Found at i:26743 original size:22 final size:22
Alignment explanation
Indices: 26655--26857 Score: 99
Period size: 22 Copynumber: 9.5 Consensus size: 22
26645 CCTCCCTATA
26655 AAATTTTGATAACTTTC-TTATG
1 AAATTTTGATAAC-TTCATTATG
* *
26677 AAATCTTGATAA---C--TA-C
1 AAATTTTGATAACTTCATTATG
*
26693 AAATTTTGATAAGC-TCCTTATG
1 AAATTTTGATAA-CTTCATTATG
**
26715 ATTTTTTGATAACTTCATTATG
1 AAATTTTGATAACTTCATTATG
* **
26737 AAATTTTGTTAA-TCTCCCTATG
1 AAATTTTGATAACT-TCATTATG
*
26759 AAATTTTGAT--CTACATACTATG
1 AAATTTTGATAACTTCAT--TATG
* *
26781 AAAATTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CTTCATTATG
* ** *
26803 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAACTTCATTATG
*
26825 AAAATTTGATAACCTTCA-TATG
1 AAATTTTGATAA-CTTCATTATG
*
26847 AAATATTGATA
1 AAATTTTGATA
26858 TTCTCACTGA
Statistics
Matches: 134, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
16 11 0.08
17 2 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 6 0.04
22 106 0.79
23 3 0.02
24 1 0.01
25 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACTTCATTATG
Found at i:26920 original size:19 final size:19
Alignment explanation
Indices: 26847--26914 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
26837 CCTTCATATG
* * *
26847 AAATATTGATATTCTCACT
1 AAATTTTGATATCCTCCCT
*
26866 GAATTTTGATATCCTCCCT
1 AAATTTTGATATCCTCCCT
* *
26885 GAATTTTGGTATCCTCCCT
1 AAATTTTGATATCCTCCCT
26904 AAAATTTTGAT
1 -AAATTTTGAT
26915 TACTCCATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 33 0.80
20 8 0.20
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (19 bp):
AAATTTTGATATCCTCCCT
Found at i:27051 original size:22 final size:22
Alignment explanation
Indices: 27020--27205 Score: 119
Period size: 22 Copynumber: 8.4 Consensus size: 22
27010 AATCAGATTT
*
27020 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
**
27042 TGAAATTTTGATAATATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * **
27064 TAAAATTTTGTTGACCCCACTA
1 TGAAATTTTGATAACCTCTTTA
* * *
27086 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
27108 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
27130 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
27152 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
*
27174 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-C--CTCTTTA
27198 TGAAATTT
1 TGAAATTT
27206 CAATAATCAC
Statistics
Matches: 125, Mismatches: 29, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 13 0.10
22 96 0.77
23 2 0.02
24 3 0.02
25 6 0.05
26 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:27109 original size:66 final size:66
Alignment explanation
Indices: 27020--27205 Score: 189
Period size: 66 Copynumber: 2.8 Consensus size: 66
27010 AATCAGATTT
* * * * * * **
27020 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAATATCTTTATAAAATTTTGTTGACCCCACT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAATATCTTTATGAAATTTTGATAACAACACT
27085 A
66 A
* * ** *
27086 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACAC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAATATC-TTTATGAAATTTTGATAACAACAC
27150 TA
65 TA
27152 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCATATCTTTATGAAATTT
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGAT-A--ATATCTTTATGAAATTT
27206 CAATAATCAC
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
65 9 0.09
66 70 0.73
67 6 0.06
68 11 0.11
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAATATCTTTATGAAATTTTGATAACAACACT
A
Found at i:27115 original size:44 final size:44
Alignment explanation
Indices: 26992--27189 Score: 163
Period size: 44 Copynumber: 4.5 Consensus size: 44
26982 CCTAAAAATA
* * * *
26992 CCACTATAAAATTTTTG-TAATCAGATTTTGAAAATTTGATAACC
1 CCACTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACC
* ** * * * *
27036 TCTTTATGAAATTTTGATAAT-ATCTTTATAAAATTTTGTTGACC
1 CCACTATGAAATTTTGATAATCA-CATTATGAAATTTTGATAACC
*
27080 CCACTATGAAATTTTGATAATCACATTATGTAATTTTGATAACC
1 CCACTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC
* * * * *
27124 TCGCTTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCT
1 CCACTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA-CC
*
27169 TCA-TAT-AAATTTTGATAATCA
1 CCACTATGAAATTTTGATAATCA
27190 TATCTTTATG
Statistics
Matches: 121, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
43 20 0.17
44 97 0.80
45 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (44 bp):
CCACTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC
Found at i:27192 original size:18 final size:19
Alignment explanation
Indices: 27154--27192 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
27144 CAACACTATG
27154 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAA--TTCATAT
27175 AAATTTTGATAA-TCATAT
1 AAATTTTGATAATTCATAT
27193 CTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTTGATAATTCATAT
Found at i:27301 original size:22 final size:23
Alignment explanation
Indices: 27272--27326 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
27262 AAATTGAGAC
*
27272 TTTT-ATAACCTTCA-TATAAAA
1 TTTTGATAACCTACACTATAAAA
27293 TTTTGATAA-CTACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
27315 TTTTGATAACCT
1 TTTTGATAACCT
27327 CCCAATGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 8 0.27
22 20 0.67
23 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:27510 original size:24 final size:22
Alignment explanation
Indices: 27449--27567 Score: 89
Period size: 22 Copynumber: 5.3 Consensus size: 22
27439 TTGTGATTAT
* *
27449 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
27471 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
27493 TAACTTGATCCTATGAAATTTTGG
1 TAAC--CAACCTATGAAATTTTAA
*
27517 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
27539 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
27561 TAACCAA
1 TAACCAA
27568 AGTAAAATAT
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.04
22 56 0.74
24 17 0.22
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:27691 original size:30 final size:31
Alignment explanation
Indices: 27657--27721 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
27647 TGGCAATTTA
* *
27657 GAAATATGTTTTT-AAAA-AAGGGTATAATTG
1 GAAATAT-TTTTTAAAAATAAGGGTACAATCG
27687 GAAATATTTTTTAAAAATAAGGGTACAATCG
1 GAAATATTTTTTAAAAATAAGGGTACAATCG
27718 GAAA
1 GAAA
27722 ACATAAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.16
30 11 0.35
31 15 0.48
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
GAAATATTTTTTAAAAATAAGGGTACAATCG
Done.