Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1516
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: 97767
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Found at i:939 original size:25 final size:23
Alignment explanation
Indices: 883--943 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 23
873 TTAAAATAAT
*
883 TATGTATTAAAATAAAAGAAGTA
1 TATGTATTAAAATAAAAAAAGTA
*
906 TATAATATTAAAATAAAAAATACGTA
1 TAT-GTATTAAAATAAAAAA-A-GTA
932 TATGTATTAAAA
1 TATGTATTAAAA
944 CTATGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 3 0.09
24 14 0.44
25 9 0.28
26 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (23 bp):
TATGTATTAAAATAAAAAAAGTA
Found at i:992 original size:17 final size:18
Alignment explanation
Indices: 949--997 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
939 TAAAACTATG
949 TAATATAAATATTATTATGA
1 TAATATAAA-ATTATTA-GA
*
969 AATATATAAAATTATTA-A
1 TA-ATATAAAATTATTAGA
987 TAATATAAAAT
1 TAATATAAAAT
998 AAATCATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 9 0.35
18 2 0.08
20 8 0.31
21 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAATATAAAATTATTAGA
Found at i:1393 original size:24 final size:25
Alignment explanation
Indices: 1338--1399 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
1328 AATTTCTATC
* *
1338 AAAATAAATTTTTTTTTTTATTATATT
1 AAAATAAA--TTTTTTTTTATAATATA
*
1365 TAAATAAATTTTTTTTTA-AATATA
1 AAAATAAATTTTTTTTTATAATATA
*
1389 AAAATATATTT
1 AAAATAAATTT
1400 GAATAAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.43
25 10 0.33
27 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAATAAATTTTTTTTTATAATATA
Found at i:1586 original size:2 final size:2
Alignment explanation
Indices: 1579--1611 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1569 TAGCTCAGAT
1579 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1612 ACGTACTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:15353 original size:14 final size:15
Alignment explanation
Indices: 15334--15370 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
15324 GTGTATTATA
15334 ATATAATATTAAT-G
1 ATATAATATTAATAG
*
15348 ATATAATAATAATAG
1 ATATAATATTAATAG
15363 ATA-AATAT
1 ATATAATAT
15371 GTCACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATATTAATAG
Found at i:17328 original size:180 final size:183
Alignment explanation
Indices: 17017--17344 Score: 419
Period size: 180 Copynumber: 1.8 Consensus size: 183
17007 GCACGACGAG
* **
17017 AGAAAGCGAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGTGTGATCCATCAAGGTTAAG
1 AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGCCT-ATCCATCAAGGTTAAG
* * ** * **
17082 GCGGCAGTGACTTCCGTTGTGGTAGAGAAGTCGAGGAGAGACACCGTCTCTCAGATCAGTTTTGC
65 GCGGCAGTGACTTCCATTGTAGTAGAGAAGTCGAGGAGAGACACCGGATCCCAGATCAACTTTGC
17147 TTTCGAGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
130 TTTCGAGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
* * * * **
17201 AGAAAGCAAAGCTTTTAGGGTTTTGGAGGCGGTGGTGCTTCGAA-CCT-T-CATCAAGGTTGGGG
1 AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGCCTATCCATCAAGGTTAAGG
* * **
17263 CGGCAGTGACTTCCATTGTAGTAGAGAAGTCGATGAGAGGCAGTGGATCCCAGATCAACTTTGCT
66 CGGCAGTGACTTCCATTGTAGTAGAGAAGTCGAGGAGAGACACCGGATCCCAGATCAACTTTGCT
* * *
17328 TTTGGGGCTTCAACAGC
131 TTCGAGCCTTCAACAGC
17345 TTTGAAAATC
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
180 80 0.66
181 1 0.01
183 1 0.01
184 39 0.32
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (183 bp):
AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGCCTATCCATCAAGGTTAAGG
CGGCAGTGACTTCCATTGTAGTAGAGAAGTCGAGGAGAGACACCGGATCCCAGATCAACTTTGCT
TTCGAGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
Found at i:26604 original size:240 final size:232
Alignment explanation
Indices: 26181--26644 Score: 669
Period size: 240 Copynumber: 2.0 Consensus size: 232
26171 AACCAGTTTT
*
26181 TAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTGTTCTTCTATG
1 TAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTATTCTTCTATG
* * * * *
26246 AACCCAATTGATTTAGGGTAACTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCTAGATTTCTTT
66 AACCCAATTGATTTAGAGTAACTAAGCAAGGTCATGGAGTTGGCCTTGGTGTTCCAGATTTCTTT
26311 TTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTGTCTTCCTGTA
131 TTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTG-C--C-T-TCTT--T-TA
26376 GTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAAACCAGCTC
188 GTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAAACCAGCTC
* * * * *
26421 TAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTTGTCCATTTCCGAGCTATTCTTTTTAT
1 TAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTATTC-TTCTAT
* * *
26486 GAATCCAATTGATTTAGAGTAATTAAGCAAGGTCCTGG-GTTGGCCTTGGTGTTCCAGATTTCTT
65 GAACCCAATTGATTTAGAGTAACTAAGCAAGGTCATGGAGTTGGCCTTGGTGTTCCAGATTTCTT
* * * *
26550 TTTTATTTTAGTTTTAAAAGGTTTCTTTTTTATATTGTATTCTGTTTGCCTTCTTTTAGTTTGTT
130 TTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTTTAGTTTGGT
*
26615 AGATAGGCCAAGTGGAAGATAATGAAGCAA
195 AGATAGGCCAAGTGGAAGACAATGAAGCAA
26645 TCAATTTTCG
Statistics
Matches: 204, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
232 37 0.18
233 1 0.00
235 4 0.02
236 1 0.00
237 1 0.00
239 1 0.00
240 122 0.60
241 37 0.18
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (232 bp):
TAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTATTCTTCTATG
AACCCAATTGATTTAGAGTAACTAAGCAAGGTCATGGAGTTGGCCTTGGTGTTCCAGATTTCTTT
TTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTTTAGTTTGGTA
GATAGGCCAAGTGGAAGACAATGAAGCAAACCAGCTC
Found at i:28334 original size:22 final size:22
Alignment explanation
Indices: 28300--28343 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28290 TAATTACTTT
28300 TTTATTTTCTTTCGAT-TTTTCA
1 TTTATTTTCTTTC-ATCTTTTCA
28322 TTTATTTGT-TTTCATCTTTTCA
1 TTTATTT-TCTTTCATCTTTTCA
28344 GCGCTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 17 0.85
23 1 0.05
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTATTTTCTTTCATCTTTTCA
Found at i:31156 original size:22 final size:22
Alignment explanation
Indices: 31131--31183 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
31121 ATTAAGTAAT
* *
31131 ATAAATATTATTTATAAAATAA
1 ATAAAAATTATTAATAAAATAA
31153 ATAAAAATTATTAATAAAATAA
1 ATAAAAATTATTAATAAAATAA
31175 A-ACAAAATT
1 ATA-AAAATT
31184 TATATCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAAAATTATTAATAAAATAA
Found at i:31186 original size:23 final size:23
Alignment explanation
Indices: 31128--31186 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
31118 AAAATTAAGT
* *
31128 AATATAAATATTATTTATAAAATA
1 AATAAAAAT-TTATTAATAAAATA
31152 AATAAAAA-TTATTAATAAAATA
1 AATAAAAATTTATTAATAAAATA
31174 AA-ACAAAATTTAT
1 AATA-AAAATTTAT
31187 ATCATAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 19 0.61
23 4 0.13
24 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAAAATTTATTAATAAAATA
Found at i:31538 original size:22 final size:23
Alignment explanation
Indices: 31511--31569 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
31501 AAGTCAATAA
*
31511 TTTTAATTTATATT-AAATAAAT
1 TTTTAATTTTTATTAAAATAAAT
*
31533 TTTTAATTTTTATTAAAATAATT
1 TTTTAATTTTTATTAAAATAAAT
*
31556 TTTTTATTTTTATT
1 TTTTAATTTTTATT
31570 TATATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAATTTTTATTAAAATAAAT
Found at i:31567 original size:30 final size:29
Alignment explanation
Indices: 31531--31590 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
31521 TATTAAATAA
* *
31531 ATTTTTAATTTTTATTAAAATAATTTTTTT
1 ATTTTT-ATTTATATTAAAATAAATTTTTT
*
31561 ATTTTTATTTATATTTAAATAAATTTTTT
1 ATTTTTATTTATATTAAAATAAATTTTTT
31590 A
1 A
31591 ATTTAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTTTATTTATATTAAAATAAATTTTTT
Found at i:31705 original size:18 final size:18
Alignment explanation
Indices: 31682--31717 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31672 AAAATTAAAA
31682 TCTTGAGAAATTATAATC
1 TCTTGAGAAATTATAATC
*
31700 TCTTGAGAATTTATAATC
1 TCTTGAGAAATTATAATC
31718 GATCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
TCTTGAGAAATTATAATC
Found at i:32109 original size:2 final size:2
Alignment explanation
Indices: 32104--32135 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
32094 TCTCTCCAAC
*
32104 CT CT CT CT CT CT CT CG CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
32136 TCACGTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:34147 original size:22 final size:22
Alignment explanation
Indices: 34119--34162 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34109 GATTATGTAC
34119 GTTTAGATATTACAAGCTTAGT
1 GTTTAGATATTACAAGCTTAGT
34141 GTTTAGATATTACAAGCTTAGT
1 GTTTAGATATTACAAGCTTAGT
34163 ACCGTAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (22 bp):
GTTTAGATATTACAAGCTTAGT
Found at i:43848 original size:2 final size:2
Alignment explanation
Indices: 43835--43878 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
43825 CTTTCTTCTT
* *
43835 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43877 TA
1 TA
43879 ATTTCTGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44425 original size:25 final size:26
Alignment explanation
Indices: 44365--44429 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
44355 TTAAAATAAT
*
44365 TATGTATTAAAATTATAAAAGAAGTA
1 TATGTATTAAAATTAAAAAAGAAGTA
* * *
44391 TAATAATATTAAAA-TAAAAAATACGTA
1 T-AT-GTATTAAAATTAAAAAAGAAGTA
44418 TATGTATTAAAA
1 TATGTATTAAAA
44430 CTATGTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.25
26 3 0.09
27 13 0.41
28 8 0.25
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.34
Consensus pattern (26 bp):
TATGTATTAAAATTAAAAAAGAAGTA
Found at i:44462 original size:22 final size:23
Alignment explanation
Indices: 44435--44491 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
44425 TAAAACTATG
*
44435 TAATATAAATATTATTCATAAAA
1 TAATATAAATATTATTAATAAAA
* *
44458 T-ATATAAAAATTATTAATAATA
1 TAATATAAATATTATTAATAAAA
*
44480 TAAAATAAATAT
1 TAATATAAATAT
44492 CATAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAATATTATTAATAAAA
Found at i:44807 original size:23 final size:21
Alignment explanation
Indices: 44768--44815 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
44758 TTGTGATTGT
*
44768 ATTTAAATAAGTCAATAACTTTA
1 ATTTAAATAAGTAAAT-AC-TTA
44791 ATTTAAATTAA-TAAATACTTA
1 ATTTAAA-TAAGTAAATACTTA
44812 ATTT
1 ATTT
44816 TGAATTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 11 0.48
24 3 0.13
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTAAATAAGTAAATACTTA
Found at i:45083 original size:2 final size:2
Alignment explanation
Indices: 45076--45100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45066 TGGCTCAGAT
45076 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
45101 TCGCGTACTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45310 original size:3 final size:3
Alignment explanation
Indices: 45304--45328 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45294 TTAGCATTTG
45304 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
45329 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:57995 original size:14 final size:14
Alignment explanation
Indices: 57976--58003 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57966 CTTGTTAACA
57976 CTTCTTTAGTAGAT
1 CTTCTTTAGTAGAT
57990 CTTCTTTAGTAGAT
1 CTTCTTTAGTAGAT
58004 ATTACAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
CTTCTTTAGTAGAT
Found at i:58999 original size:239 final size:234
Alignment explanation
Indices: 58567--59037 Score: 639
Period size: 242 Copynumber: 2.0 Consensus size: 234
58557 CATTGAGAAG
58567 CAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTGTTCT
1 CAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTGTTCT
* * *
58632 TTTATGAACCCAACTGATTTAGGGTAACTACGCAAGGTGATGGATTTGGCCTTGGTGTTCTAGAT
66 TTTATGAACCCAACTGATTGAGAGTAACTAAGCAAGGTGATGGATTTGGCCTTGGTGTTCTAGAT
* *
58697 TTTTTTTTTAATTTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTGTC
131 TTCTTTTTTAATTTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTATGCTTG-C--C-T-TC
58762 TTCCTGTAGTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAAAC
191 -T--TGTAGTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAAAC
* * * **
58809 CAGTTCTAGAAAGGATACTGGTGAAAGA-GTTTTTTGAATGATTTGTCCGTTTCTGAGC-GATTC
1 CAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTG-TTC
* * * *
58872 TTTTTATGAACCCAATTGATTGAGAGTAATTAAG-ACAGGTGCTGGA-TTGGCCTTGGTGTTCTG
65 -TTTTATGAACCCAACTGATTGAGAGTAACTAAGCA-AGGTGATGGATTTGGCCTTGGTGTTCTA
* *
58935 GATTTCTTTTTT-A-TTTTAGTTTTAAAAGGTTTCTTTTTTGTAATGTATTATGCTTGCCTTCTT
128 GATTTCTTTTTTAATTTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTATGCTTGCCTTCTT
* *
58998 GTAGTTTGTTAGATAGGCCACGTGGAAGACAATGAAGCAA
193 GTAGTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAA
59038 TCGATTTTCT
Statistics
Matches: 208, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
231 39 0.19
233 1 0.00
234 2 0.01
235 1 0.00
236 1 0.00
238 1 0.00
239 40 0.19
240 2 0.01
241 57 0.27
242 64 0.31
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (234 bp):
CAGTTCTAGAAAGGAAACTGGTGAAAGAGGTTTTTTGAATGATATGTCCATTTCCAAGCTGTTCT
TTTATGAACCCAACTGATTGAGAGTAACTAAGCAAGGTGATGGATTTGGCCTTGGTGTTCTAGAT
TTCTTTTTTAATTTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTATGCTTGCCTTCTTGTA
GTTTGGTAGATAGGCCAAGTGGAAGACAATGAAGCAAAC
Found at i:63809 original size:26 final size:26
Alignment explanation
Indices: 63780--63833 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
63770 TATGATTTCG
*
63780 TTATTATTTAAAAAATTATTTATTTT
1 TTATAATTTAAAAAATTATTTATTTT
** *
63806 TTATAATTTAATTATTTATTTATTTT
1 TTATAATTTAAAAAATTATTTATTTT
63832 TT
1 TT
63834 GGTTGTACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATAATTTAAAAAATTATTTATTTT
Found at i:65371 original size:24 final size:24
Alignment explanation
Indices: 65295--65361 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 24
65285 AAGTCAATAA
* *
65295 TTTTAATTTACATTAAAAAAATTTTAAT
1 TTTTAATTTATATTAAAACAA--TT--T
65323 TTTTAATTTATATTAAAACAATTT
1 TTTTAATTTATATTAAAACAATTT
*
65347 TTTTTATTTATATTA
1 TTTTAATTTATATTA
65362 TATAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 15 0.42
26 2 0.06
28 19 0.53
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATTTATATTAAAACAATTT
Found at i:65874 original size:2 final size:2
Alignment explanation
Indices: 65869--65896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65859 TCTCTCCAAC
65869 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65897 TCACGTACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:71996 original size:26 final size:26
Alignment explanation
Indices: 71967--72017 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
71957 TATTTTCTGA
71967 ACTTGTTATAATAAAGTAATAATTAG
1 ACTTGTTATAATAAAGTAATAATTAG
71993 ACTTGTTATAATAAAGTAATAATTA
1 ACTTGTTATAATAAAGTAATAATTA
72018 ATAAACCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (26 bp):
ACTTGTTATAATAAAGTAATAATTAG
Found at i:75316 original size:382 final size:382
Alignment explanation
Indices: 74609--75376 Score: 1410
Period size: 382 Copynumber: 2.0 Consensus size: 382
74599 AAGGTCCGGG
*
74609 ATTTAGACCTTATTTTCTTTTCCTTGTTTGTTTTCTCGTCTTCTTCTCTTTTATCCTTCCAAAAT
1 ATTTAGACCTTATTTTCTTTTCCTTGTTTGTTTTCTCGTCTCCTTCTCTTTTATCCTTCCAAAAT
*
74674 TTCTTTTTCTTCACTTTTACACTTGATCCCTTTCGCTGAAGGAGGTGCTTGGTCGTAGCTGATTC
66 TTCTTTTTCTTCACTTTTACACTTGATCCCTTTCGCTGAAGGAGGTGCTTGGTCATAGCTGATTC
74739 TTCAAGTGGAGCCAGTGTGAGCACAGCAAAGTCCCCTTCCTCATCATGATCAACCTCAAGCGTGG
131 TTCAAGTGGAGCCAGTGTGAGCACAGCAAAGTCCCCTTCCTCATCATGATCAACCTCAAGCGTGG
*
74804 TGACTCCATCCATCTCCGCAAGTATGTAAAATATATTTCCAATTTTCTTTTCTTATTTTGCATTT
196 TGACTCCATCCATCTCCGCAAGTAGGTAAAATATATTTCCAATTTTCTTTTCTTATTTTGCATTT
* *
74869 CCTCCCCTTTTTTTTAGAGCTGATCGCCACTCTATCTACAGAAGCAGCACTCCATCTCTGATATG
261 CCTCCCCTTTTGTTTAGAGCTGATCGCCACTCTATCTACAGAAGCAGCACTCCATCTCCGATATG
* *
74934 GAGATTAGACCCATCTACTACTTAGCTTTTTTTACTTGTGTATTCTGCCTTGGGTGT
326 GAGATTAGACCCATCTACTACTTAGCTTTTTTTACTCGTGTATTCTGCCTTGGGTAT
*
74991 ATTTAGACCTTATTTTCTTTTCCTTTTTTGTTTTCTCGTCTCCTTCTCTTTTATCCTTCCAAAAT
1 ATTTAGACCTTATTTTCTTTTCCTTGTTTGTTTTCTCGTCTCCTTCTCTTTTATCCTTCCAAAAT
* *
75056 TTCTTTTTCTTCACTTTTACACTTGATCCCTTTTGCTGAAGGAGGTGCTTGGTCATGGCTGATTC
66 TTCTTTTTCTTCACTTTTACACTTGATCCCTTTCGCTGAAGGAGGTGCTTGGTCATAGCTGATTC
*
75121 TTCAAGTGGAGCCAGTGTGAGCACAGCAAAGTCCCCTTCCTCATCATGATCAACCTCAAGTGTGG
131 TTCAAGTGGAGCCAGTGTGAGCACAGCAAAGTCCCCTTCCTCATCATGATCAACCTCAAGCGTGG
75186 TGACTCCATCCATCTCCGCAAGTAGGTAAAATATATTTCCAATTTTCTTTTCTTATTTTGCATTT
196 TGACTCCATCCATCTCCGCAAGTAGGTAAAATATATTTCCAATTTTCTTTTCTTATTTTGCATTT
* **
75251 CCTCCCCTTTTGTTTAGAGCTGATTGCCACTCTATCTATGGAAGCAGCACTCCATCTCCGATATG
261 CCTCCCCTTTTGTTTAGAGCTGATCGCCACTCTATCTACAGAAGCAGCACTCCATCTCCGATATG
75316 GAGATTAGACCCATCTACTACTTAGCTTTTTTTACTCGTGTATTCTGCCTTGGGTAT
326 GAGATTAGACCCATCTACTACTTAGCTTTTTTTACTCGTGTATTCTGCCTTGGGTAT
75373 ATTT
1 ATTT
75377 TGTTTTTATA
Statistics
Matches: 372, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
382 372 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.41
Consensus pattern (382 bp):
ATTTAGACCTTATTTTCTTTTCCTTGTTTGTTTTCTCGTCTCCTTCTCTTTTATCCTTCCAAAAT
TTCTTTTTCTTCACTTTTACACTTGATCCCTTTCGCTGAAGGAGGTGCTTGGTCATAGCTGATTC
TTCAAGTGGAGCCAGTGTGAGCACAGCAAAGTCCCCTTCCTCATCATGATCAACCTCAAGCGTGG
TGACTCCATCCATCTCCGCAAGTAGGTAAAATATATTTCCAATTTTCTTTTCTTATTTTGCATTT
CCTCCCCTTTTGTTTAGAGCTGATCGCCACTCTATCTACAGAAGCAGCACTCCATCTCCGATATG
GAGATTAGACCCATCTACTACTTAGCTTTTTTTACTCGTGTATTCTGCCTTGGGTAT
Found at i:76658 original size:22 final size:22
Alignment explanation
Indices: 76630--76673 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
76620 CAGGTTGTCT
76630 CTCTCAATTCTCCTCTTCTTTA
1 CTCTCAATTCTCCTCTTCTTTA
76652 CTCTCAATTCTCCTCTTCTTTA
1 CTCTCAATTCTCCTCTTCTTTA
76674 TTTTCCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (22 bp):
CTCTCAATTCTCCTCTTCTTTA
Found at i:78013 original size:25 final size:26
Alignment explanation
Indices: 77953--78017 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
77943 TTAAAATAAT
*
77953 TATGTATTAAAATTATAAAAGAAGTA
1 TATGTATTAAAATTAAAAAAGAAGTA
* * *
77979 TAATAATATTAAAA-TAAAAAATATGTA
1 T-AT-GTATTAAAATTAAAAAAGAAGTA
78006 TATGTATTAAAA
1 TATGTATTAAAA
78018 CTATGTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.25
26 3 0.09
27 13 0.41
28 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (26 bp):
TATGTATTAAAATTAAAAAAGAAGTA
Found at i:78050 original size:22 final size:23
Alignment explanation
Indices: 78023--78079 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
78013 TAAAACTATG
*
78023 TAATATAAATATTATTCATAAAA
1 TAATATAAATATTATTAATAAAA
* *
78046 T-ATATAAAAATTATTAATAATA
1 TAATATAAATATTATTAATAAAA
*
78068 TAAAATAAATAT
1 TAATATAAATAT
78080 CATAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAATATTATTAATAAAA
Found at i:78405 original size:23 final size:22
Alignment explanation
Indices: 78362--78410 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
78352 TTGTGATTGT
* *
78362 ATTTAAATAAGTCAATAACTTTA
1 ATTTAAATAAATAAATAAC-TTA
78385 ATTTAAATTAAATAAAT-ACTTA
1 ATTTAAA-TAAATAAATAACTTA
78407 ATTT
1 ATTT
78411 TGAATTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAATAAATAACTTA
Found at i:78441 original size:30 final size:30
Alignment explanation
Indices: 78407--78470 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
78397 TAAATACTTA
*
78407 ATTTTGAATTTCTATCAAAATAAATTTTTT
1 ATTTTGAATTTATATCAAAATAAATTTTTT
** **
78437 ATTTTTTATTTATATTTAAATAAATTTTTT
1 ATTTTGAATTTATATCAAAATAAATTTTTT
78467 ATTT
1 ATTT
78471 AAATATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (30 bp):
ATTTTGAATTTATATCAAAATAAATTTTTT
Found at i:78482 original size:25 final size:23
Alignment explanation
Indices: 78437--78488 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
78427 TAAATTTTTT
**
78437 ATTTTTTATTTATATTTAAATAA
1 ATTTTTTATTTATATAAAAATAA
*
78460 ATTTTTTATTTAAATATAAAAATAT
1 ATTTTTTATTT--ATATAAAAATAA
78485 ATTT
1 ATTT
78489 GAATAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
25 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTTATTTATATAAAAATAA
Found at i:88124 original size:180 final size:181
Alignment explanation
Indices: 87818--88145 Score: 442
Period size: 180 Copynumber: 1.8 Consensus size: 181
87808 GCACGACGAG
* *
87818 AGAAAGCGAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGTGTGATCCATCAAGGTTAAG
1 AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAA--G-CATCCATCAAGGTTAAG
* * ** *
87883 GCGGCAGTGACTTCCGTTGTGGTAGAGAAATCGAGGAGAGACACCGTCTCTCAGATCAATTTTGC
63 GCGGCAGTGACTTCCATTGTAGTAGAGAAATCGAGGAGAGACACCGGATCCCAGATCAATTTTGC
*
87948 TTTCGCGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
128 TTCCGCGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
* * * * * *
88002 AGAAAGCAAAGCTTTTAGGGTTTTGGAGGCGGTGGTGCTTCGAA-CCTCCATCAAGGTTGAGGCG
1 AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGCATCCATCAAGGTTAAGGCG
* * **
88066 GCAGTGACTTCCATTGTAGTAGAGAAGTCGATGAGAGACAGTGGATCCCAGATCAATTTTGCTTC
66 GCAGTGACTTCCATTGTAGTAGAGAAATCGAGGAGAGACACCGGATCCCAGATCAATTTTGCTTC
* *
88131 CGGGGCTTCAACAGC
131 CGCGCCTTCAACAGC
88146 TTTGAAAATC
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
180 85 0.69
184 39 0.31
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (181 bp):
AGAAAGCAAAGCCTTTAAGGTGTTGGAGGCGGTGGTGATTCGAAGCATCCATCAAGGTTAAGGCG
GCAGTGACTTCCATTGTAGTAGAGAAATCGAGGAGAGACACCGGATCCCAGATCAATTTTGCTTC
CGCGCCTTCAACAGCACTTCCATCTTTCCTTCAAAATTCTTTCTCGTGCAC
Found at i:95307 original size:2 final size:2
Alignment explanation
Indices: 95300--95335 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
95290 TAGAATGTTT
95300 TA 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 TA
95336 AAGAGGCTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96035 original size:14 final size:14
Alignment explanation
Indices: 96016--96044 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
96006 ACTTGTTAAC
96016 TCTTCTTTAGTAGA
1 TCTTCTTTAGTAGA
96030 TCTTCTTTAGTAGA
1 TCTTCTTTAGTAGA
96044 T
1 T
96045 ATTACAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TCTTCTTTAGTAGA
Done.