Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023929.1 Corchorus olitorius cultivar O-4 contig23962, 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: 60132
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12346 original size:14 final size:12
Alignment explanation
Indices: 12326--12390 Score: 76
Period size: 12 Copynumber: 4.9 Consensus size: 12
12316 GGGCCAAGAA
12326 AAAAAGATAAAAG
1 AAAAAGA-AAAAG
12339 ATAAAAGATAAAAAG
1 A-AAAAG--AAAAAG
12354 AAAAAAGAAAAAAG
1 -AAAAAG-AAAAAG
12368 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12380 AAAAAGAAAAA
1 AAAAAGAAAAA
12391 AAGAAATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
12 17 0.36
13 7 0.15
14 11 0.23
15 10 0.21
16 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:12391 original size:7 final size:7
Alignment explanation
Indices: 12325--12396 Score: 87
Period size: 7 Copynumber: 10.4 Consensus size: 7
12315 TGGGCCAAGA
12325 AAAAAAG
1 AAAAAAG
*
12332 ATAAAAG
1 AAAAAAG
*
12339 ATAAAAG
1 AAAAAAG
12346 ATAAAAAG
1 A-AAAAAG
12354 AAAAAAG
1 AAAAAAG
12361 AAAAAAG
1 AAAAAAG
12368 -AAAAAG
1 AAAAAAG
12374 -AAAAAG
1 AAAAAAG
12380 -AAAAAG
1 AAAAAAG
12386 AAAAAAAG
1 -AAAAAAG
12394 AAA
1 AAA
12397 TTAAAATAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
6 18 0.30
7 30 0.50
8 12 0.20
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:12402 original size:18 final size:18
Alignment explanation
Indices: 12326--12390 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 18
12316 GGGCCAAGAA
12326 AAAAAGATAAAAGATAAAAG
1 AAAAAGA-AAAAGA-AAAAG
12346 ATAAAAAGAAAAAAGAAAAAAG
1 --AAAAAG-AAAAAG-AAAAAG
12368 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAG
12386 AAAAA
1 AAAAA
12391 AAGAAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.27
19 6 0.15
20 6 0.15
22 16 0.39
23 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:21004 original size:20 final size:21
Alignment explanation
Indices: 20979--21020 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20969 TTATTGATTC
20979 TTTTCCGTTT-TTTTTTCATT
1 TTTTCCGTTTCTTTTTTCATT
*
20999 TTTTCCTTTTCTTTTTTCATT
1 TTTTCCGTTTCTTTTTTCATT
21020 T
1 T
21021 CATTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCCGTTTCTTTTTTCATT
Found at i:21013 original size:13 final size:14
Alignment explanation
Indices: 20991--21029 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
20981 TTCCGTTTTT
20991 TTTTCATTTTTTCC
1 TTTTCATTTTTTCC
21005 TTTTC-TTTTTT-C
1 TTTTCATTTTTTCC
*
21017 ATTTCATTTTTTC
1 TTTTCATTTTTTC
21030 TTCAACTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.23
13 12 0.55
14 5 0.23
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTTTCC
Found at i:23422 original size:18 final size:18
Alignment explanation
Indices: 23383--23423 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23373 ACTGTTATTG
*
23383 TGTGTATCCAATTTCTTG
1 TGTGTATCCAATTTCTTA
* *
23401 TGTGTATCCCATTTTTTA
1 TGTGTATCCAATTTCTTA
23419 TGTGT
1 TGTGT
23424 CCCGATTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.54
Consensus pattern (18 bp):
TGTGTATCCAATTTCTTA
Found at i:23423 original size:20 final size:18
Alignment explanation
Indices: 23380--23414 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23370 AAAACTGTTA
23380 TTGTGTGTATCCAATTTC
1 TTGTGTGTATCCAATTTC
*
23398 TTGTGTGTATCCCATTT
1 TTGTGTGTATCCAATTT
23415 TTTATGTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (18 bp):
TTGTGTGTATCCAATTTC
Found at i:25482 original size:28 final size:28
Alignment explanation
Indices: 25408--25482 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
25398 AAGTGAGCTT
* * **
25408 AAAATGACCGAAATGCCCATGAATGTGC
1 AAAATGACCAAAATGCCCCTGAACATGC
25436 AAAATGACCAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAACATGC
25464 -AAATGACCCAAAATGCCCC
1 AAAATGA-CCAAAATGCCCC
25483 ATAGATGACC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.14
28 36 0.86
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAACATGC
Found at i:25629 original size:5 final size:5
Alignment explanation
Indices: 25613--25643 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
25603 AATGCAAAAG
*
25613 AAGCA AAACA AAGCA AAGCA AAGCA AAGCA A
1 AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA A
25644 GAGAAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.65, C:0.19, G:0.16, T:0.00
Consensus pattern (5 bp):
AAGCA
Found at i:28762 original size:21 final size:21
Alignment explanation
Indices: 28736--28777 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28726 TAAGGAAGAA
28736 GTTTCAAGCTCATCAGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
*
28757 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCAGAGTTG
28778 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCAGAGTTG
Found at i:30216 original size:710 final size:710
Alignment explanation
Indices: 28857--30275 Score: 2829
Period size: 710 Copynumber: 2.0 Consensus size: 710
28847 AGGAAGCTTT
28857 GTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCATTTGAAGCCCATTG
1 GTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCATTTGAAGCCCATTG
28922 GAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTCTTGAAATCGATGAG
66 GAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTCTTGAAATCGATGAG
28987 CATTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTT
131 CATTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTT
29052 TTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTC
196 TTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTC
29117 TTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAAT
261 TTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAAT
29182 TAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGT
326 TAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGT
29247 AAACACAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATTATCTTAGCTTCTTT
391 AAACACAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATTATCTTAGCTTCTTT
29312 GTTCTAGTTTGAGCAAAATTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGT
456 GTTCTAGTTTGAGCAAAATTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGT
29377 GATACTTGATTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTT
521 GATACTTGATTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTT
29442 GGGCCGACGAAAGAAGAGGAATCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGA
586 GGGCCGACGAAAGAAGAGGAATCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGA
29507 AGTTAAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATCTAACACAACTAGATTC
651 AGTTAAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATCTAACACAACTAGATTC
29567 GTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCATTTGAAGCCCATTG
1 GTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCATTTGAAGCCCATTG
29632 GAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTCTTGAAATCGATGAG
66 GAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTCTTGAAATCGATGAG
29697 CATTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTT
131 CATTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTT
29762 TTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTC
196 TTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTC
29827 TTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAAT
261 TTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAAT
29892 TAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGT
326 TAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGT
29957 AAACACAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATTATCTTAGCTTCTTT
391 AAACACAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATTATCTTAGCTTCTTT
30022 GTTCTAGTTTGAGCAAAATTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGT
456 GTTCTAGTTTGAGCAAAATTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGT
30087 GATACTTGATTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTT
521 GATACTTGATTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTT
30152 GGGCCGACGAAAGAAGAGGAATCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGA
586 GGGCCGACGAAAGAAGAGGAATCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGA
*
30217 AGTTCAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATCTAACACAACTAGATT
651 AGTTAAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATCTAACACAACTAGATT
30276 TCGGTGAGGA
Statistics
Matches: 708, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
710 708 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (710 bp):
GTTTGGCCTCATTAGAGTTCATCTTGAAGAGTTTAAAGCCATCGGAGATCATTTGAAGCCCATTG
GAGATCATCAACAAAGGAATATTCCCATCGATTCCAAGTTGTGCATTCTTCTTGAAATCGATGAG
CATTAGGTCATTAGAGTTGTAATTTGGCCATTGTGGGCTTTATTCTATCTTTAATTAGCTTATTT
TTAAGTTTGGATGTTATTTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTGTTTAATTATGTC
TTTATTTCCTTTTCCTAGTTGGGTTTGGACTAGTTTTACCCTAGGCCATATATTTGGACGAAAAT
TAGGTTATTTTTCTAGATCTAGGGCATCACCCTATGCCTATATAAAGGCACCAAACCCCTCTTGT
AAACACAAGTTGAGTTGATTAATAAAATTGAGGTTTTTACCCAAATTGATTATCTTAGCTTCTTT
GTTCTAGTTTGAGCAAAATTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAAGTTGT
GATACTTGATTGTTTGTGAATCTTGTGTTCTAGAGTTAACAATTGCAGGTCTAATTGGAGACTTT
GGGCCGACGAAAGAAGAGGAATCACCTTGTGAAGGTCATCGACATACACATCTAGAAGTTGAGGA
AGTTAAAGTCGACTTTGATAGATATTCAAGGCTAGATTTGAATCTAACACAACTAGATTC
Found at i:31134 original size:20 final size:21
Alignment explanation
Indices: 31109--31153 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
31099 AGAGATTAAT
*
31109 TAAAAAGAAAACAAT-TAAAA
1 TAAAAACAAAACAATGTAAAA
* *
31129 TAAAAACAAAGCAATGTAAAT
1 TAAAAACAAAACAATGTAAAA
31150 TAAA
1 TAAA
31154 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (21 bp):
TAAAAACAAAACAATGTAAAA
Found at i:34826 original size:7 final size:8
Alignment explanation
Indices: 34812--34836 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34802 CAAAAAATAT
34812 TAAAAAAA
1 TAAAAAAA
34820 TAAAAAAA
1 TAAAAAAA
34828 TAAAAAAA
1 TAAAAAAA
34836 T
1 T
34837 TTTCGGAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:39099 original size:22 final size:22
Alignment explanation
Indices: 39069--39111 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39059 AAAATTCATA
* *
39069 ACAAGTCCTGCCGAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
*
39091 ACAACTCCTGCCCATGACTTG
1 ACAACTCCTGCCCAGGACTTG
39112 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:44404 original size:4 final size:4
Alignment explanation
Indices: 44395--44478 Score: 52
Period size: 4 Copynumber: 21.2 Consensus size: 4
44385 AAAATTATTA
* * *
44395 AAAT AAAT AAAT AATT AAGT -AAT AGAT AAAT ATATAT AAAT AGAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT A-AAT AAAT
* *
44444 AAGT AAA- AAAT -AAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A
44479 TGTATATAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
3 12 0.19
4 41 0.66
5 6 0.10
6 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:44438 original size:18 final size:18
Alignment explanation
Indices: 44415--44490 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
44405 ATAATTAAGT
44415 AATAGATAAATATATATA
1 AATAGATAAATATATATA
44433 AATAGA-AAA-ATA-AGTA
1 AATAGATAAATATATA-TA
* * *
44449 AA-AAATAATAGATAAATA
1 AATAGATAA-ATATATATA
*
44467 AAAAGATAAATATGTATATA
1 AATAGATAAATA--TATATA
44487 AATA
1 AATA
44491 ATTAGATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
15 3 0.07
16 9 0.20
17 4 0.09
18 15 0.33
19 6 0.13
20 8 0.18
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (18 bp):
AATAGATAAATATATATA
Found at i:44499 original size:12 final size:12
Alignment explanation
Indices: 44451--44500 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
44441 AATAAGTAAA
44451 AAATAA-TAGAT
1 AAATAATTAGAT
**
44462 AAATAAAAAGAT
1 AAATAATTAGAT
*
44474 AAAT-ATGTATAT
1 AAATAAT-TAGAT
44486 AAATAATTAGAT
1 AAATAATTAGAT
44498 AAA
1 AAA
44501 GAGGTAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.23
12 22 0.71
13 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
AAATAATTAGAT
Found at i:44560 original size:19 final size:18
Alignment explanation
Indices: 44524--44595 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 18
44514 AAAAAAAAAC
44524 GATAATAGTAAATAAATA
1 GATAATAGTAAATAAATA
*
44542 GATAATAGCTAAATTAATA
1 GATAATAG-TAAATAAATA
*
44561 AATAA-A--AAGATAAATA
1 GATAATAGTAA-ATAAATA
44577 G-TAA-A-TAAAT-AATA
1 GATAATAGTAAATAAATA
44591 GATAA
1 GATAA
44596 ATAGCTCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
14 5 0.11
15 11 0.24
16 8 0.17
18 9 0.20
19 13 0.28
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.26
Consensus pattern (18 bp):
GATAATAGTAAATAAATA
Found at i:44562 original size:27 final size:27
Alignment explanation
Indices: 44532--44588 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
44522 ACGATAATAG
* *
44532 TAAATAAATAGAT-AATAGCTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATAAA
44559 TAAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAAAAGATAAATAGTAAATAAA
44586 TAA
1 TAA
44589 TAGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATAAA
Found at i:47887 original size:72 final size:72
Alignment explanation
Indices: 47773--47914 Score: 266
Period size: 72 Copynumber: 2.0 Consensus size: 72
47763 GATAAATTTT
*
47773 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTTTTATAGATGTGTATCCTTATTTTCTTGACAA
1 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTTGACAA
47838 TGCAAAA
66 TGCAAAA
*
47845 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTCTTTTCTTGACAA
1 TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTTGACAA
47910 TGCAA
66 TGCAA
47915 TTTTAGTTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (72 bp):
TTTTTTCTAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTATTTTCTTGACAA
TGCAAAA
Found at i:49709 original size:9 final size:9
Alignment explanation
Indices: 49691--49724 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
49681 GATTATATCG
*
49691 AAAAATATA
1 AAAAAAATA
49700 AAAAAAAT-
1 AAAAAAATA
49708 AAAAAAATA
1 AAAAAAATA
49717 AAAAAAAT
1 AAAAAAAT
49725 TTCGACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATA
Found at i:49717 original size:17 final size:17
Alignment explanation
Indices: 49691--49724 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49681 GATTATATCG
*
49691 AAAAATATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
49708 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
49725 TTCGACCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:54108 original size:16 final size:17
Alignment explanation
Indices: 54089--54126 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
54079 TACCCTTATC
54089 TTTTTATTTTTC-ATTA
1 TTTTTATTTTTCTATTA
* *
54105 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTATTA
54122 TTTTT
1 TTTTT
54127 TTTATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTATTA
Found at i:55307 original size:21 final size:21
Alignment explanation
Indices: 55268--55316 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
55258 TCAATGCTTT
**
55268 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
55290 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
55311 A-GAAGC
1 AGGAAGC
55317 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:58035 original size:8 final size:8
Alignment explanation
Indices: 58013--58046 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
58003 ACATTTTCCA
58013 TCAAATTT
1 TCAAATTT
58021 ATCAAATTT
1 -TCAAATTT
58030 TCAAATTT
1 TCAAATTT
*
58038 TCAAGTTT
1 TCAAATTT
58046 T
1 T
58047 GGAAAAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (8 bp):
TCAAATTT
Found at i:59482 original size:29 final size:29
Alignment explanation
Indices: 59463--59832 Score: 392
Period size: 29 Copynumber: 12.8 Consensus size: 29
59453 GCGAATCTAG
* *
59463 GGGCATTTTGGTCATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCCAA
59492 GGGCATTTTGGTCA-TTTTGCACATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* *
59520 GGGTATTTTGGTCATTTTTGCACATTC-A
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* ** *
59548 GGAGCATCTTGGTCATTTACGCATATCCAA
1 GG-GCATTTTGGTCATTTTTGCACATCCAA
* * *
59578 GGGCGTTTTGGTCATTTTCGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* *
59607 GGGCATTTTGGTCATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCCAA
59636 GGGCATTTTGGTCA-TTTTGCACATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* *
59664 GGGCATTTTGGTCATTTATGCACATTCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* *
59693 GAGCATTTTGGTCA--TTTACACATGTCCAA
1 GGGCATTTTGGTCATTTTTGCACA--TCCAA
** *
59722 GGAGCATTTTGGTCATTTACGCATATCCAA
1 GG-GCATTTTGGTCATTTTTGCACATCCAA
* * * *
59752 AGGCATTTTGGTCGTATTTACACATCC-A
1 GGGCATTTTGGTCATTTTTGCACATCCAA
* * * *
59780 GGGACATTTTGATCATTTTTTTCACGTCCAG
1 GGG-CATTTTGGTCA-TTTTTGCACATCCAA
59811 GGGCATTTTGGTCATTTTTGCA
1 GGGCATTTTGGTCATTTTTGCA
59833 TACTCTGGTT
Statistics
Matches: 282, Mismatches: 47, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
27 6 0.02
28 57 0.20
29 171 0.61
30 41 0.15
31 3 0.01
32 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACATCCAA
Found at i:59537 original size:57 final size:58
Alignment explanation
Indices: 59463--59832 Score: 397
Period size: 57 Copynumber: 6.4 Consensus size: 58
59453 GCGAATCTAG
*
59463 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTT-TGCACATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTATGCACATCCAA
* * * * * *
59520 GGGTATTTTGGTCATTTTTGCACATTCAGGAGCATCTTGGTCATTTACGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTATGCACATCCAA
* * * * * * *
59578 GGGCGTTTTGGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACATCTAG
1 GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTATGCACATCCAA
* *
59636 GGGCATTTTGGTCA-TTTTGCACATCCAAGGGCATTTTGGTCATTTATGCACATTCAA
1 GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTATGCACATCCAA
* * * * *
59693 GAGCATTTTGGTCA--TTTACACATGTCCAAGGAGCATTTTGGTCATTTACGCATATCCAA
1 GGGCATTTTGGTCATTTTTGCACA--TCC-AGGGGCATTTTGGTCATTTATGCACATCCAA
* * * * * * * * * *
59752 AGGCATTTTGGTCGTATTTACACATCCAGGGACATTTTGATCATTTTTTTCACGTCCAG
1 GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCA-TTTATGCACATCCAA
59811 GGGCATTTTGGTCATTTTTGCA
1 GGGCATTTTGGTCATTTTTGCA
59833 TACTCTGGTT
Statistics
Matches: 256, Mismatches: 50, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
56 7 0.03
57 91 0.36
58 83 0.32
59 67 0.26
61 8 0.03
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (58 bp):
GGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTATGCACATCCAA
Found at i:59675 original size:115 final size:114
Alignment explanation
Indices: 59463--59834 Score: 404
Period size: 115 Copynumber: 3.2 Consensus size: 114
59453 GCGAATCTAG
* * * * *
59463 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCA-TTTTGCACATCCAAGGGTATT
1 GGGCATTTTGGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACATCCAAGGGCATT
* * *
59527 TTGGTCATTTTTGCACATTCAGGAGCATCTTGGTCATTTACGCATATCCAA
66 TTGGTCA-TTTTGCACATCCAGG-GCATTTTGGTCATTTACGCACATCCAA
* * *
59578 GGGCGTTTTGGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATT
1 GGGCATTTTGGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACATCCAAGGGCATT
* *
59643 TTGGTCATTTTGCACATCCAAGGGCATTTTGGTCATTTATGCACATTCAA
66 TTGGTCATTTTGCACATCC-AGGGCATTTTGGTCATTTACGCACATCCAA
* * * * ** * *
59693 GAGCATTTTGGTCATTTACACATGTCCAAGGAGCATTTTGGTCATTTACGCATATCCAAAGGCAT
1 GGGCATTTTGGTCATTTTCGCATATCCAAGG-GCATTTTGGTCATTTTTGCACATCCAAGGGCAT
* * * *** * *
59758 TTTGGTCGTATTTACACATCCAGGGACATTTTGATCATTTTTTTCACGTCCAG
65 TTTGGTCAT-TTTGCACATCCAGGG-CATTTTGGTCA-TTTACGCACATCCAA
*
59811 GGGCATTTTGGTCATTTTTGCATA
1 GGGCATTTTGGTCATTTTCGCATA
59835 CTCTGGTTTC
Statistics
Matches: 214, Mismatches: 37, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
115 98 0.46
116 67 0.31
117 20 0.09
118 29 0.14
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (114 bp):
GGGCATTTTGGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACATCCAAGGGCATT
TTGGTCATTTTGCACATCCAGGGCATTTTGGTCATTTACGCACATCCAA
Found at i:59723 original size:144 final size:145
Alignment explanation
Indices: 59463--59832 Score: 553
Period size: 144 Copynumber: 2.5 Consensus size: 145
59453 GCGAATCTAG
*
59463 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGTATTT
1 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGCATTT
* * *
59528 TGGTCATTTTTGCACATTCAGGAGCATCTTGGTCATTTACGCATATCCAAGG-GCGTTTTGGTCA
66 TGGTCATTTTTGCACATTCAAGAGCATCTTGGTCATTTACACATATCCAAGGAGCATTTTGGTCA
*
59592 TTTTCGCATATCCAA
131 TTTACGCATATCCAA
59607 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGCATTT
1 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGCATTT
* * *
59672 TGGTCATTTATGCACATTCAAGAGCATTTTGGTCATTTACACATGTCCAAGGAGCATTTTGGTCA
66 TGGTCATTTTTGCACATTCAAGAGCATCTTGGTCATTTACACATATCCAAGGAGCATTTTGGTCA
59737 TTTACGCATATCCAA
131 TTTACGCATATCCAA
* * * * * * * * * *
59752 AGGCATTTTGGTCGTATTTACACATCCAGGGACATTTTGATCATTTTTTTCACGTCCAGGGGCAT
1 GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCA--TTTTGCACATCCAAGGGCAT
59817 TTTGGTCATTTTTGCA
64 TTTGGTCATTTTTGCA
59833 TACTCTGGTT
Statistics
Matches: 204, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
144 111 0.54
145 61 0.30
147 32 0.16
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (145 bp):
GGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGCATTT
TGGTCATTTTTGCACATTCAAGAGCATCTTGGTCATTTACACATATCCAAGGAGCATTTTGGTCA
TTTACGCATATCCAA
Done.