Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013516.1 Corchorus capsularis cultivar CVL-1 contig13537, 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: 75880
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA
35 AATGTTAGGG
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):
TA
Found at i:274 original size:44 final size:43
Alignment explanation
Indices: 226--480 Score: 261
Period size: 44 Copynumber: 6.0 Consensus size: 43
216 ACCCAATAAT
*
226 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTTCTTA
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTC-TATTA
* * * *
270 CAAAGTCTTCAAACACATTTATAACACAGGGGCAATTCTCTTT
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTATTA
* * *
313 CTAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATT-
1 C-AAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTATTA
* * * *
356 -AAAGTCCCCAAACACAATTATAACACAGGGGCATCTCTATTC
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTATTA
* * * *
398 CAAAGTTCTCAAGCACATTTATAACACAGAGAC-AC-CTA-TA
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTATTA
* *
438 CTAAAGTCC-CTAAACACAATTATAACACAAGGGCAACTTCTAT
1 C-AAAGTCCTC-AAACACATTTATAACACAGGGGCAAC-TCTAT
481 ATGGTAAAGG
Statistics
Matches: 175, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
40 3 0.02
41 64 0.37
42 3 0.02
43 31 0.18
44 74 0.42
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (43 bp):
CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTATTA
Found at i:420 original size:43 final size:43
Alignment explanation
Indices: 226--472 Score: 263
Period size: 41 Copynumber: 5.8 Consensus size: 43
216 ACCCAATAAT
* * *
226 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCTTCTTA
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCATCTC-TATTC
*
270 CAAAGTCTTCAAACACATTTATAACACAGGGGCAATTCTCT-TTC
1 CAAAGTCCTCAAACACATTTATAACACAGGGGC-A-TCTCTATTC
* * *
314 TAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATT-
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCATCTCTATTC
* *
356 -AAAGTCCCCAAACACAATTATAACACAGGGGCATCTCTATTC
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCATCTCTATTC
* * * * *
398 CAAAGTTCTCAAGCACATTTATAACACAGAGACA-C-CTATAC
1 CAAAGTCCTCAAACACATTTATAACACAGGGGCATCTCTATTC
* * *
439 TAAAGTCC-CTAAACACAATTATAACACAAGGGCA
1 CAAAGTCCTC-AAACACATTTATAACACAGGGGCA
473 ACTTCTATAT
Statistics
Matches: 172, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.01
41 67 0.39
42 5 0.03
43 30 0.17
44 64 0.37
45 2 0.01
46 3 0.02
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (43 bp):
CAAAGTCCTCAAACACATTTATAACACAGGGGCATCTCTATTC
Found at i:437 original size:84 final size:84
Alignment explanation
Indices: 226--472 Score: 309
Period size: 84 Copynumber: 2.9 Consensus size: 84
216 ACCCAATAAT
* * ** *
226 CAAAGTCCTCAAACACATTTATAACACAGGGGCAACTCT-TCTTACAAAGTCTTCAAACACATTT
1 CAAAGTCCTCAAACACATTTATAACACAGAGGC-AC-CTATATT--AAAGTCCCCAAACACAATT
290 ATAACACAGGGGCAATTCTCTTTC
62 ATAACACAGGGGC-ATTCTCTTTC
* *
314 TAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATTAAAGTCCCCAAACACAATTATAA
1 CAAAGTCCTCAAACACATTTATAACACAGAGGCACCTATATTAAAGTCCCCAAACACAATTATAA
379 CACAGGGGCA-TCTCTATTC
66 CACAGGGGCATTCTCT-TTC
* * * * *
398 CAAAGTTCTCAAGCACATTTATAACACAGAGACACCTATACTAAAGTCCCTAAACACAATTATAA
1 CAAAGTCCTCAAACACATTTATAACACAGAGGCACCTATATTAAAGTCCCCAAACACAATTATAA
*
463 CACAAGGGCA
66 CACAGGGGCA
473 ACTTCTATAT
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
83 5 0.04
84 71 0.50
85 29 0.20
86 2 0.01
87 4 0.03
88 31 0.22
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (84 bp):
CAAAGTCCTCAAACACATTTATAACACAGAGGCACCTATATTAAAGTCCCCAAACACAATTATAA
CACAGGGGCATTCTCTTTC
Found at i:8729 original size:24 final size:24
Alignment explanation
Indices: 8688--8748 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
8678 GTCACCAATG
* * * *
8688 CCCTTTTCCTTTTCCTGTTGTTCA
1 CCCTTTTTCTTCTGCTGTTGCTCA
* *
8712 TCTTTTTTCTTCTGCTGTTGCTCA
1 CCCTTTTTCTTCTGCTGTTGCTCA
8736 CCCTTTTTCTTCT
1 CCCTTTTTCTTCT
8749 ACATCTGCTC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.03, C:0.31, G:0.08, T:0.57
Consensus pattern (24 bp):
CCCTTTTTCTTCTGCTGTTGCTCA
Found at i:12243 original size:30 final size:31
Alignment explanation
Indices: 12202--12259 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
12192 CTTGCATCGC
12202 AATTGATGCGCCCAAGG-CTTATCATGGAAGG
1 AATTGATGCG-CCAAGGACTTATCATGGAAGG
*
12233 AATT-ATGCGCCAAGGACTTATTATGGA
1 AATTGATGCGCCAAGGACTTATCATGGA
12260 CTTGAAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (31 bp):
AATTGATGCGCCAAGGACTTATCATGGAAGG
Found at i:15503 original size:21 final size:22
Alignment explanation
Indices: 15456--15503 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
15446 GTTCCAGCCA
**
15456 TCATTG-CCTTCTTCTTTTTCT
1 TCATTGTCCTTCTTCTGATTCT
15477 TC-TTGTCCTTCTTCTGATTC-
1 TCATTGTCCTTCTTCTGATTCT
15497 TCATTGT
1 TCATTGT
15504 TGTTCAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.06, C:0.27, G:0.08, T:0.58
Consensus pattern (22 bp):
TCATTGTCCTTCTTCTGATTCT
Found at i:18850 original size:21 final size:21
Alignment explanation
Indices: 18824--18863 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18814 TCCAATATAG
18824 TTCCTCTAAGT-GCTCCTAATT
1 TTCCTC-AAGTAGCTCCTAATT
*
18845 TTCCTCAATTAGCTCCTAA
1 TTCCTCAAGTAGCTCCTAA
18864 ATGGTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCCTCAAGTAGCTCCTAATT
Found at i:21860 original size:19 final size:21
Alignment explanation
Indices: 21816--21855 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
21806 GATTTTATTT
21816 CTCTTTCCTCTTCCCCAAAAA
1 CTCTTTCCTCTTCCCCAAAAA
21837 CTCTTT-CTCTTCCCCAAAA
1 CTCTTTCCTCTTCCCCAAAA
21856 TTCTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCTTTCCTCTTCCCCAAAAA
Found at i:26644 original size:2 final size:2
Alignment explanation
Indices: 26639--26670 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26629 TATATATATA
26639 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
26671 CTAAAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27830 original size:15 final size:15
Alignment explanation
Indices: 27810--27843 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
27800 TTACGAAGTG
*
27810 TTCAATTCGAGTTGC
1 TTCAATTCGAGCTGC
27825 TTCAATTCGAGCTGC
1 TTCAATTCGAGCTGC
27840 TTCA
1 TTCA
27844 CTAGCTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (15 bp):
TTCAATTCGAGCTGC
Found at i:29499 original size:15 final size:15
Alignment explanation
Indices: 29475--29505 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29465 CACGTCAGCG
*
29475 CTCATGTGGGGCCCA
1 CTCATATGGGGCCCA
29490 CTCATATGGGGCCCA
1 CTCATATGGGGCCCA
29505 C
1 C
29506 ATGACCGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.19
Consensus pattern (15 bp):
CTCATATGGGGCCCA
Found at i:33505 original size:157 final size:157
Alignment explanation
Indices: 33219--33526 Score: 598
Period size: 157 Copynumber: 2.0 Consensus size: 157
33209 ATAATTAATG
33219 ATAAATTACAAAATTGCCTAATAAATAAAATAACTAACAAAATTAAGTATAGGGGTATTGGAGTC
1 ATAAATTACAAAATTGCCTAATAAATAAAATAACTAACAAAATTAAGTATAGGGGTATTGGAGTC
*
33284 TTTCTTTAGACTTAAAATATAAAGATATTAAAAGCCTCTAGGAGATTTTGCCCAAAAGAGAGTTA
66 TTTCCTTAGACTTAAAATATAAAGATATTAAAAGCCTCTAGGAGATTTTGCCCAAAAGAGAGTTA
33349 AATCCACCAAATTCTGCTTTCTAGATA
131 AATCCACCAAATTCTGCTTTCTAGATA
33376 ATAAATTACAAAATTGCCTAATAAATAAAATAACTAACAAAATTAAGTATAGGGGTATTGGAGTC
1 ATAAATTACAAAATTGCCTAATAAATAAAATAACTAACAAAATTAAGTATAGGGGTATTGGAGTC
*
33441 TTTCCTTAGGCTTAAAATATAAAGATATTAAAAGCCTCTAGGAGATTTTGCCCAAAAGAGAGTTA
66 TTTCCTTAGACTTAAAATATAAAGATATTAAAAGCCTCTAGGAGATTTTGCCCAAAAGAGAGTTA
33506 AATCCACCAAATTCTGCTTTC
131 AATCCACCAAATTCTGCTTTC
33527 CATATTTAAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (157 bp):
ATAAATTACAAAATTGCCTAATAAATAAAATAACTAACAAAATTAAGTATAGGGGTATTGGAGTC
TTTCCTTAGACTTAAAATATAAAGATATTAAAAGCCTCTAGGAGATTTTGCCCAAAAGAGAGTTA
AATCCACCAAATTCTGCTTTCTAGATA
Found at i:37187 original size:8 final size:7
Alignment explanation
Indices: 37176--37224 Score: 61
Period size: 6 Copynumber: 7.4 Consensus size: 7
37166 AGAAAAACAC
37176 AAAAACG
1 AAAAACG
37183 AAAAACG
1 AAAAACG
37190 AAAAAC-
1 AAAAACG
37196 AAAAAC-
1 AAAAACG
37202 AAAAAC-
1 AAAAACG
37208 AAAAAC-
1 AAAAACG
37214 AAAATACG
1 AAAA-ACG
37222 AAA
1 AAA
37225 CTAAACAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.55
7 15 0.38
8 3 0.08
ACGTcount: A:0.78, C:0.14, G:0.06, T:0.02
Consensus pattern (7 bp):
AAAAACG
Found at i:37193 original size:6 final size:6
Alignment explanation
Indices: 37169--37217 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
37159 AAAGTTAAGA
37169 AAAACAC AAAAAC GAAAAAC GAAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAA-AC AAAAAC -AAAAAC -AAAAAC AAAAAC AAAAAC AAAAAC AAAA
37218 TACGAAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 24 0.59
7 17 0.41
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:38069 original size:46 final size:46
Alignment explanation
Indices: 37997--38089 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
37987 GAGAATTGAA
* *
37997 AGTAACCCGTTGCTTTAAGAACTAGAAAGGTCTTAGCCAACAATAG
1 AGTAACCCGTTGCTTTAAGAACTAGAAAGATATTAGCCAACAATAG
*
38043 AGTAACCCGTTGCTTTAAGAATTAGAAAGATATTAGCCAACAATAG
1 AGTAACCCGTTGCTTTAAGAACTAGAAAGATATTAGCCAACAATAG
38089 A
1 A
38090 CAATGTTCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (46 bp):
AGTAACCCGTTGCTTTAAGAACTAGAAAGATATTAGCCAACAATAG
Found at i:44398 original size:42 final size:42
Alignment explanation
Indices: 44323--44406 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
44313 GCTTCACTCG
* * *
44323 AAACATATTAGGTTCTTCTGATGGTGACCCAAAACAGATCAC
1 AAACAGATTAGGTTCTTATGATGGTCACCCAAAACAGATCAC
** *
44365 AAACAGATTAGGTTCTTATGATGGTCATTCAAAATAGATCAC
1 AAACAGATTAGGTTCTTATGATGGTCACCCAAAACAGATCAC
44407 TTATTGTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (42 bp):
AAACAGATTAGGTTCTTATGATGGTCACCCAAAACAGATCAC
Found at i:44428 original size:30 final size:30
Alignment explanation
Indices: 44409--44492 Score: 159
Period size: 30 Copynumber: 2.8 Consensus size: 30
44399 TAGATCACTT
44409 ATTGTGATGGTGACCCAAAACAGATCATAC
1 ATTGTGATGGTGACCCAAAACAGATCATAC
44439 ATTGTGATGGTGACCCAAAACAGATCATAC
1 ATTGTGATGGTGACCCAAAACAGATCATAC
*
44469 ACTGTGATGGTGACCCAAAACAGA
1 ATTGTGATGGTGACCCAAAACAGA
44493 CTTTGTTTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (30 bp):
ATTGTGATGGTGACCCAAAACAGATCATAC
Found at i:45247 original size:79 final size:79
Alignment explanation
Indices: 45116--45274 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 79
45106 TTATTGGTTG
** * *
45116 AACCATGGCTTTCTTGAATTTTGATTGGCTGCATGATTTGATCATATTTATTTAATCAAATCAAG
1 AACCATGGCTTTCTTGAATTTTGATTGGCCACATGATTTGATAATACTTATTTAATCAAATCAAG
*
45181 ATAAATGCCAAATA
66 ATAAATGCAAAATA
*
45195 AACCATGGCTTTCTTGAATTTTGATTGGCCACATGATTTGATAATACTTATTTAATCAAATTAAG
1 AACCATGGCTTTCTTGAATTTTGATTGGCCACATGATTTGATAATACTTATTTAATCAAATCAAG
45260 ATAAATGCAAAATA
66 ATAAATGCAAAATA
45274 A
1 A
45275 TTAATTTAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (79 bp):
AACCATGGCTTTCTTGAATTTTGATTGGCCACATGATTTGATAATACTTATTTAATCAAATCAAG
ATAAATGCAAAATA
Found at i:50899 original size:33 final size:35
Alignment explanation
Indices: 50847--50912 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
50837 AATCTTCCTT
*
50847 AAAAGCAAAGTCTGAAATAACATCAT-AACAAATC
1 AAAAGCAAAGTCTGAAATAAAATCATGAACAAATC
*
50881 AAAAGC-AAGTCTGGAATAAAATCATGAACAAA
1 AAAAGCAAAGTCTGAAATAAAATCATGAACAAA
50913 AAACATCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (35 bp):
AAAAGCAAAGTCTGAAATAAAATCATGAACAAATC
Found at i:55456 original size:20 final size:21
Alignment explanation
Indices: 55418--55458 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
55408 TGTAAAATAG
*
55418 GGTAAAAATGCACATAAAAAT
1 GGTAAAAATGCACAGAAAAAT
*
55439 GGTAAAAAT-CATAGAAAAAT
1 GGTAAAAATGCACAGAAAAAT
55459 AGCTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
GGTAAAAATGCACAGAAAAAT
Found at i:62527 original size:20 final size:21
Alignment explanation
Indices: 62489--62529 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
62479 TGTAAAATAG
*
62489 GGTAAAAATGCACATAAAAAT
1 GGTAAAAATGCACAGAAAAAT
*
62510 GGTAAAAAT-CATAGAAAAAT
1 GGTAAAAATGCACAGAAAAAT
62530 AGCTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
GGTAAAAATGCACAGAAAAAT
Found at i:69253 original size:78 final size:78
Alignment explanation
Indices: 69171--69412 Score: 292
Period size: 70 Copynumber: 3.2 Consensus size: 78
69161 TTGTTTAGGT
* * * *
69171 TTTTA-TAGTTTTACTTAACTAAAAATTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTTAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
69235 ATTTTATTTTACTA
65 ATTATATTTTACTA
69249 TTTTA--A---T-C--AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTTAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
69306 TTATATTTTA-TCA
66 TTATATTTTACT-A
* * *
69319 TTTTATTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTAC--
1 TTTTACTATTTTACTTAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
69382 TTATATTTTACCA
66 TTATATTTTACTA
*
69395 TTTTACTATTTTAATTAA
1 TTTTACTATTTTACTTAA
69413 AAAACTTGAT
Statistics
Matches: 144, Mismatches: 10, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
69 1 0.01
70 60 0.42
72 2 0.01
73 1 0.01
75 1 0.01
76 27 0.19
77 1 0.01
78 51 0.35
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (78 bp):
TTTTACTATTTTACTTAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACTA
Found at i:69261 original size:70 final size:70
Alignment explanation
Indices: 69187--69399 Score: 259
Period size: 78 Copynumber: 3.0 Consensus size: 70
69177 AGTTTTACTT
* * * *
69187 AACTAAAAATTCTATTTTTATTTAATTAAATATAATATCTTTATAACTATTTTATTTTACTATTT
1 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTTTATTTTACTATTT
69252 TAATC
66 TAATC
69257 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTATCATTT
1 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAC-----TA-TTT-T-ATTT
* *
69322 TATTATTTTACTC
58 TACTATTTTAATC
* * *
69335 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTAC--TTATATTTTACCATTT
1 AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTTTATTTTACTATTT
69398 TA
66 TA
69400 CTATTTTAAT
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
68 12 0.10
69 1 0.01
70 45 0.36
75 2 0.02
76 3 0.02
77 1 0.01
78 61 0.49
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (70 bp):
AACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTTTATTTTACTATTT
TAATC
Found at i:73905 original size:31 final size:32
Alignment explanation
Indices: 73870--73936 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 32
73860 AACTTTATGT
*
73870 TTTCCGATTGTACCC-TTATTTTT-AAAACATA
1 TTTCCAATTGTACCCGTT-TTTTTAAAAACATA
73901 TTTCCAATTGTACCCGTTTTTTTAAAAACATA
1 TTTCCAATTGTACCCGTTTTTTTAAAAACATA
73933 TTTC
1 TTTC
73937 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (32 bp):
TTTCCAATTGTACCCGTTTTTTTAAAAACATA
Found at i:74008 original size:15 final size:15
Alignment explanation
Indices: 73962--74010 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
73952 AAATAATATT
73962 TTAATTATTCCATTA
1 TTAATTATTCCATTA
*
73977 TT--TT-TT-AATTA
1 TTAATTATTCCATTA
*
73988 TAAATTATTCCATTA
1 TTAATTATTCCATTA
74003 TTAATTAT
1 TTAATTAT
74011 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:74167 original size:19 final size:20
Alignment explanation
Indices: 74140--74177 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
74130 TACTATTAGT
74140 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
74160 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
74178 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:74371 original size:22 final size:22
Alignment explanation
Indices: 74343--74526 Score: 151
Period size: 22 Copynumber: 8.3 Consensus size: 22
74333 TATCTCTATG
*
74343 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
74365 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
74388 -GGTTATCAAAATTCCATAGCG-
1 TGGTTATCAAAATTTCATAG-GA
*
74409 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* * *
74432 -AGTTATCAAAATGTCATACTG-
1 TGGTTATCAAAATTTCATA-GGA
* *
74453 TGGTTACCGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
74475 TCGGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
**
74499 TGGTTATTGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
74521 TGGTTA
1 TGGTTA
74527 ATTTTCACAA
Statistics
Matches: 127, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
21 3 0.02
22 103 0.81
23 4 0.03
24 17 0.13
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:74587 original size:22 final size:22
Alignment explanation
Indices: 74557--74949 Score: 193
Period size: 22 Copynumber: 17.9 Consensus size: 22
74547 AGGTTATCAA
*
74557 AGAGATTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
74579 CGAGGTTAT-AAGATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
74600 TGTGGTTAACAAAATTTCATTA-
1 AGAGGTTATCAAAATTTCA-TAG
* * *
74622 TGAGGTTA-CTAATATTTCATGG
1 AGAGGTTATC-AAAATTTCATAG
* *
74644 GGAGGTTATCAAAATTTTATAG
1 AGAGGTTATCAAAATTTCATAG
* *
74666 CGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
* *
74689 A-ATGTTATAAGAGTCTCAATTTCATA-
1 AGAGGTTATCA-A-----AATTTCATAG
* * *
74715 AGAAG-TACCAAAATTTGATAG
1 AGAGGTTATCAAAATTTCATAG
*
74736 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
74756 AGTGATTATCGAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
74778 AGATCAGATTATCAAAAATT-ATAG
1 AG---AGGTTATCAAAATTTCATAG
*
74802 -GAAGATTATCAAAATTTCAT--
1 AG-AGGTTATCAAAATTTCATAG
* * *
74822 A-ATGTTATCAAAATTCCACAG
1 AGAGGTTATCAAAATTTCATAG
* *
74843 CGAGGTTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG
* * *
74864 ATGTGATTATCAGAATTTCATAG
1 A-GAGGTTATCAAAATTTCATAG
* * * * *
74887 AGGGGTCAACAAAATTTTATAA
1 AGAGGTTATCAAAATTTCATAG
* *
74909 AGAGGTTATCAAAATTTCAGAA
1 AGAGGTTATCAAAATTTCATAG
*
74931 AGAGGTTATCAAATTTTCA
1 AGAGGTTATCAAAATTTCA
74950 GAATGTGATT
Statistics
Matches: 281, Mismatches: 63, Indels: 54
0.71 0.16 0.14
Matches are distributed among these distances:
19 14 0.05
20 20 0.07
21 43 0.15
22 165 0.59
23 7 0.02
24 4 0.01
25 13 0.05
26 4 0.01
27 2 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:74970 original size:22 final size:22
Alignment explanation
Indices: 74804--74971 Score: 74
Period size: 22 Copynumber: 7.8 Consensus size: 22
74794 AATTATAGGA
*
74804 AGATTATCAAAATTTCA-TAA-
1 AGATTATCAAAATTTCAGAAAG
* * * **
74824 TG-TTATCAAAATTCCACAGCG
1 AGATTATCAAAATTTCAGAAAG
* * * *
74845 AGGTTATCAAAATTACATAATG
1 AGATTATCAAAATTTCAGAAAG
* * * *
74867 TGATTATCAGAATTTCATAGAG
1 AGATTATCAAAATTTCAGAAAG
* * * * * *
74889 GGGTCAACAAAATTTTATAAAG
1 AGATTATCAAAATTTCAGAAAG
*
74911 AGGTTATCAAAATTTCAGAAAG
1 AGATTATCAAAATTTCAGAAAG
* * *
74933 AGGTTATCAAATTTTCAGAATG
1 AGATTATCAAAATTTCAGAAAG
*
74955 TGATTA-CAAAAATTTCA
1 AGATTATC-AAAATTTCA
74972 TAGTGGTATT
Statistics
Matches: 111, Mismatches: 33, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
19 13 0.12
20 1 0.01
21 2 0.02
22 95 0.86
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (22 bp):
AGATTATCAAAATTTCAGAAAG
Found at i:75043 original size:41 final size:41
Alignment explanation
Indices: 74986--75120 Score: 132
Period size: 41 Copynumber: 3.2 Consensus size: 41
74976 GGTATTTCTG
74986 GGAAGGTTATCAAAATTTCATAGTATATTGTTACCAAATTA
1 GGAAGGTTATCAAAATTTCATAGTATATTGTTACCAAATTA
* * * * *
75027 GGAAGGTTATTAAAATTTTATTATGGAGGA-TATTA--AAATTTCA
1 GGAAGGTTATCAAAATTTCA-TA-GTA-TATTGTTACCAAA-TT-A
* * *
75070 GGGAGGATATCAAAATTTCATAGTATATGGTTACCAAATTA
1 GGAAGGTTATCAAAATTTCATAGTATATTGTTACCAAATTA
75111 GGAAGGTTAT
1 GGAAGGTTAT
75121 TACACTTTTA
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
40 1 0.01
41 35 0.49
42 8 0.11
43 26 0.37
44 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (41 bp):
GGAAGGTTATCAAAATTTCATAGTATATTGTTACCAAATTA
Found at i:75076 original size:20 final size:20
Alignment explanation
Indices: 75051--75089 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
75041 ATTTTATTAT
*
75051 GGAGGATATTAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
75071 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
75090 TAGTATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:75134 original size:84 final size:84
Alignment explanation
Indices: 74979--75177 Score: 344
Period size: 84 Copynumber: 2.4 Consensus size: 84
74969 TCATAGTGGT
* * *
74979 ATTTCTGGGAAGGTTATCAAAATTTCATAGTATATTGTTACCAAATTAGGAAGGTTATTAAAATT
1 ATTTCAGGG-AGGATATCAAAATTTCATAGTATATGGTTACCAAATTAGGAAGGTTATTAAAATT
75044 TTATTATGGAGGATATTAAA
65 TTATTATGGAGGATATTAAA
* *
75064 ATTTCAGGGAGGATATCAAAATTTCATAGTATATGGTTACCAAATTAGGAAGGTTATTACACTTT
1 ATTTCAGGGAGGATATCAAAATTTCATAGTATATGGTTACCAAATTAGGAAGGTTATTAAAATTT
75129 TATTATGGAGGATATTAAA
66 TATTATGGAGGATATTAAA
75148 ATTTCAGGGAGGATATCAAAATTTCATAGT
1 ATTTCAGGGAGGATATCAAAATTTCATAGT
75178 TTAGTTTTCA
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 101 0.93
85 8 0.07
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (84 bp):
ATTTCAGGGAGGATATCAAAATTTCATAGTATATGGTTACCAAATTAGGAAGGTTATTAAAATTT
TATTATGGAGGATATTAAA
Found at i:75160 original size:20 final size:20
Alignment explanation
Indices: 75135--75173 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
75125 CTTTTATTAT
*
75135 GGAGGATATTAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
75155 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
75174 TAGTTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:75210 original size:22 final size:21
Alignment explanation
Indices: 75161--75699 Score: 120
Period size: 22 Copynumber: 24.7 Consensus size: 21
75151 TCAGGGAGGA
***
75161 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAG-AGGGT
* *
75183 TTTCAAAATTTTATAAGAGGGT
1 TATCAAAATTTCAT-AGAGGGT
*
75205 TATCAAAATTTCATAGTA-TGT
1 TATCAAAATTTCATAG-AGGGT
*
75226 AGATCAAAATTTCATAG-GGAGAT
1 -TATCAAAATTTCATAGAGG-G-T
* *
75249 TAACAAAATTTCATA-ATGAAGT
1 TATCAAAATTTCATAGA-G-GGT
** *
75271 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGAG-GGT
75293 TATCAAAATTT-AT--A--GT
1 TATCAAAATTTCATAGAGGGT
* **
75309 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCAT-AGAGGGT
* *
75331 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA--GAGGGT
* **
75354 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATA-G-AGGGT
* *
75377 TATCAAAATTTCATAGCGAGAT
1 TATCAAAATTTCATAGAG-GGT
* * *
75399 TATCAAAATTTCATTGTGTGAT
1 TATCAAAATTTCATAGAG-GGT
* * * *
75421 GATCAAAATTTCAGAGTATGAT
1 TATCAAAATTTCATAG-AGGGT
*
75443 TATTAACAA-TTCATATG-GAGGT
1 TATCAA-AATTTCATA-GAG-GGT
* * *
75465 TTTTAAATTTTCATA-ACGTGGT
1 TATCAAAATTTCATAGA-G-GGT
* * *
75487 TATCAATATATCATATG-GAGTT
1 TATCAAAATTTCATA-GAG-GGT
* * *
75509 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGAG--GGT
*
75532 TATCAAAATTTCATTG-GGAAGT
1 TATCAAAATTTCATAGAGG--GT
75554 TATCAAAATTTCATACTGA-GGT
1 TATCAAAATTTCATA--GAGGGT
* * *
75576 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAGAG-GGT
* * *
75598 TAACAAAATTTTATAAGAAGGT
1 TATCAAAATTTCAT-AGAGGGT
** * *
75620 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCAT-AGAGGGT
* * * ***
75641 TCTCGAAATTCCATAGTATCAT
1 TATCAAAATTTCATAG-AGGGT
* *
75663 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATA-GAGGGT
75685 TATCAAAATTTCATA
1 TATCAAAATTTCATA
75700 ATGGGATCAT
Statistics
Matches: 382, Mismatches: 91, Indels: 88
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.03
17 2 0.01
20 3 0.01
21 27 0.07
22 273 0.71
23 63 0.16
24 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATAGAGGGT
Found at i:75233 original size:44 final size:43
Alignment explanation
Indices: 75145--75568 Score: 160
Period size: 44 Copynumber: 9.8 Consensus size: 43
75135 GGAGGATATT
*
75145 AAAATTTC--AGGGAGGA-TATCAAAATTTCATAGTTTAGTTTTC
1 AAAATTTCATAGGGA-GATTATCAAAATTTCATAGTTTAG-TATC
*
75187 AAAATTTTATAAGAGG-G-TTATCAAAATTTCATAGTATGTAG-ATC
1 AAAATTTCAT-AG-GGAGATTATCAAAATTTCATAGT-T-TAGTATC
* * **
75231 AAAATTTCATAGGGAGATTAACAAAATTTCATAATGAAGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGTTTAG-TATC
** *
75275 AAAAAATCATAGGGAGGTTATCAAAATTT-ATAG--T--TATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGTTTAGTATC
* * * * **
75313 AAGATTTCATA-AGAAAGTTATCAAAATTTTATAG-GGAGGTTTATC
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTTTA-G--TATC
* * **
75358 AAAATTTTATAGGAAGATTTATCAAAATTTCATAG-CGAGATTATC
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTTTAG--TATC
* * * * * * * *
75403 AAAATTTCATTGTGTGATGATCAAAATTTCAGAGTATGATTATT
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGT-TTAGTATC
* * * * * *** *
75447 AACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATC
1 AA-AATTTCATAGGGAGATTATCAAAATTTCATAGTTTAG-TATC
* * * * * * *
75491 AATATATCATATGGAGTTTATCAACATCTCATAGTGTTGGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATAGT-TTAG-TATC
*
75536 AAAATTTCATTGGGA-AGTTATCAAAATTTCATA
1 AAAATTTCATAGGGAGA-TTATCAAAATTTCATA
75569 CTGAGGTCTT
Statistics
Matches: 281, Mismatches: 74, Indels: 51
0.69 0.18 0.13
Matches are distributed among these distances:
37 2 0.01
38 24 0.09
39 4 0.01
42 11 0.04
43 7 0.02
44 137 0.49
45 69 0.25
46 27 0.10
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (43 bp):
AAAATTTCATAGGGAGATTATCAAAATTTCATAGTTTAGTATC
Found at i:75358 original size:23 final size:23
Alignment explanation
Indices: 75330--75409 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
75320 CATAAGAAAG
75330 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
75353 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* * *
75376 TTATCAAAATTTCATAGCGA-GA
1 TTATCAAAATTTTATAGGGAGGT
75398 TTATCAAAATTT
1 TTATCAAAATTT
75410 CATTGTGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 12 0.24
23 38 0.76
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:75557 original size:45 final size:45
Alignment explanation
Indices: 75483--75568 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
75473 TTTCATAACG
* *
75483 TGGTTATCAATATATCATATGGAGTTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAGTTTATCAAAATCTCATAGTGT
* *
75528 TGGTTATCAAAATTTCAT-TGGGAAG-TTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GG-AGTTTATCAAAATCTCATA
75569 CTGAGGTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.03
45 32 0.91
46 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAGTTTATCAAAATCTCATAGTGT
Found at i:75631 original size:21 final size:22
Alignment explanation
Indices: 75594--75641 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
75584 TTCCTTAGGG
* *
75594 AGGTTAACAAAATTTTATAAGA
1 AGGTTAACAAAAATTTATAAAA
75616 AGGTTAA-AAAAATTTATAAAA
1 AGGTTAACAAAAATTTATAAAA
75637 AGGTT
1 AGGTT
75642 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (22 bp):
AGGTTAACAAAAATTTATAAAA
Done.