Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2512
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: 88623
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:908 original size:21 final size:22
Alignment explanation
Indices: 882--931 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
872 TATTTATATG
882 TAAATATAAAT-TTAAAAATTT
1 TAAATATAAATATTAAAAATTT
* *
903 TAAATATTAATATTCAAAATTT
1 TAAATATAAATATTAAAAATTT
925 TAAATAT
1 TAAATAT
932 TTAATAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATAAATATTAAAAATTT
Found at i:924 original size:22 final size:22
Alignment explanation
Indices: 882--948 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
872 TATTTATATG
* *
882 TAAATATAAAT-TTAAAAATTT
1 TAAATATTAATATTCAAAATTT
903 TAAATATTAATATTCAAAATTT
1 TAAATATTAATATTCAAAATTT
*
925 TAAATATTTAATAGTCAAAATTT
1 TAAATA-TTAATATTCAAAATTT
948 T
1 T
949 TAAACTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.24
22 15 0.37
23 16 0.39
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (22 bp):
TAAATATTAATATTCAAAATTT
Found at i:1194 original size:20 final size:20
Alignment explanation
Indices: 1157--1194 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147 GCATGACTAT
*
1157 TAAATATATCAAATTTTATA
1 TAAATATATCAAACTTTATA
1177 TAAATATAT-AATACTTTA
1 TAAATATATCAA-ACTTTA
1195 AATATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATATCAAACTTTATA
Found at i:1450 original size:14 final size:15
Alignment explanation
Indices: 1433--1498 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 15
1423 TAATATACAA
1433 ATATATCAAAAT-TT
1 ATATATCAAAATATT
1447 ATATGA-CATAAATTATT
1 ATAT-ATCA-AAA-TATT
1464 AATATATCAAAAT-TT
1 -ATATATCAAAATATT
*
1479 AT-TAT-AAAATATA
1 ATATATCAAAATATT
1492 ATATATC
1 ATATATC
1499 TCAAATATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
14 11 0.26
15 6 0.14
16 2 0.05
17 6 0.14
18 6 0.14
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (15 bp):
ATATATCAAAATATT
Found at i:1511 original size:29 final size:28
Alignment explanation
Indices: 1454--1514 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1444 TTTATATGAC
* *
1454 ATAAATTATTAATATATCAAAATTTATT
1 ATAAAATATTAATATATCAAAATTAATT
*
1482 ATAAAATA-TAATATATCTCAAATATAATT
1 ATAAAATATTAATATATC-AAAAT-TAATT
1511 ATAA
1 ATAA
1515 TATGAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.32
28 11 0.39
29 8 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAAATATTAATATATCAAAATTAATT
Found at i:3539 original size:126 final size:126
Alignment explanation
Indices: 3314--3554 Score: 306
Period size: 126 Copynumber: 1.9 Consensus size: 126
3304 AAAAATTGTG
* * * ** *
3314 CTCTAGGATAAATATTAACATTCAATTTCTATTGATAGAAGTATAATAATTAATTTACATTCGTC
1 CTCTAAGATAAATATTAACATTCAATTTCTATTCAAAGAAGTATAATAATTAATCCACATTCATC
* * * * * *
3379 ATTTTTTCTATTGAAGACAATATATAACTTGCTAGAAAGGGTACCATTTTCTCTCCTCATA
66 ATTTTTTCTATTGAAAACAACAAACAACTTGCTAGAAAGGGCACAATTTTCTCTCCTCATA
* * *
3440 CTCTAAGATAAATATTAGCATTTAATTT-TCATTCAAAGAAGTATAATAATTAATCCACCTT-AT
1 CTCTAAGATAAATATTAACATTCAATTTCT-ATTCAAAGAAGTATAATAATTAATCCACATTCAT
*
3503 CATTTTTTTCTATTGAAAATAACAAACAACTTGCTAGAAAGGGCACAATTTT
65 CA-TTTTTTCTATTGAAAACAACAAACAACTTGCTAGAAAGGGCACAATTTT
3555 TTTTCTAATT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
125 4 0.04
126 93 0.96
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (126 bp):
CTCTAAGATAAATATTAACATTCAATTTCTATTCAAAGAAGTATAATAATTAATCCACATTCATC
ATTTTTTCTATTGAAAACAACAAACAACTTGCTAGAAAGGGCACAATTTTCTCTCCTCATA
Found at i:5245 original size:2 final size:2
Alignment explanation
Indices: 5238--5273 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5228 CAAAGCTTCA
5238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5274 CTTACCATTA
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):
AT
Found at i:11394 original size:27 final size:27
Alignment explanation
Indices: 11356--11408 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
11346 TGCAACCTTC
*
11356 ACTGTTTCAAATTGAATTTCATAATTT
1 ACTGTTTCAAATTGAATTTCAAAATTT
11383 ACTGTTTCAAATTGAATTTCAAAATT
1 ACTGTTTCAAATTGAATTTCAAAATT
11409 GGCGGCACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTT
Found at i:13272 original size:349 final size:347
Alignment explanation
Indices: 12560--14216 Score: 1151
Period size: 349 Copynumber: 4.7 Consensus size: 347
12550 TAGTAAAAGG
* * * * * *
12560 TGAAATTTCACTTAAAACATTAAATTAAATCTCTT-AAAAATTAAAAAC-TAATTTATTTCTTGA
1 TGAAATTTCACCTAAAACATTGAATTAAATC-CTTCACAAA-TCAAAACTTAATTTATTTTTTAA
* * ** * * * *
12623 GTGTTATAAATATCTATTTTATTTTTTGTTTTTCAAGATGCAACATT-TATTTATTTTTATAATA
64 GCGCTATAAGCATATATTTTATTTTTTTTTTTTAAACATGCAAC-TTCTATTTATTTTTATAATA
* *
12687 TT--TTGATA-A--TTTAAATGGTTTTTATTATTATTATGATGAATCTCAAATTTATAGCTTAAA
128 TTAATT-ATATAGCTTTAAATGGTTCTTA-T-TTATTATGATGAATCTCAAATTTATAGC-TCAA
* * *
12747 TGATAAAAAAAATA-TTGATACATGTTTATAAGTAAAGTTTTAA-TTGTTGTTATCAAATTTTCA
189 --AT----AAACTAGTTGATACATGTTTATAAGTAAAGTTTTAATTTTTTGTTATCAAATTCTCA
* * * * * * *
12810 CTCAAAAATTGAGAAAAGTATAAGAAAAATGAAATTATACCTGTTAAGTTGTTACTAGAAAGATC
248 CCCAAAAATTGAGAAAAGTAGAAGAAAAATGAAATTATACCTATTAAGTTGTTATTAAAAAAAGC
* * * *
12875 AAGGTACTT-GAGAGAAGTCAAATTTCTAATAATTGG
313 AAGG-A-TTCTAGAGAAGTCAATTTTCAAATAATTGA
* * ** * * *
12911 TGGAATTTCACCTGAAACATTGAATTAAATATTTTACAAGTCAAAACTTAATTTATTTCTTAAGC
1 TGAAATTTCACCTAAAACATTGAATTAAATCCTTCACAAATCAAAACTTAATTTATTTTTTAAGC
** ** * *
12976 GCTATTGGTGTATATTTTATTTTTTATTTTTAAACATGCAACTTCTATTTATTATTATAATACTT
66 GCTATAAGCATATATTTTATTTTTTTTTTTTAAACATGCAACTTCTATTTATTTTTATAATA-TT
*
13041 AATTATGATAGCTTTAAATGGTTCTTATTTATTATGATAAATCTCAAATTTATAGCTCAAAT-AA
130 AATTAT-ATAGCTTTAAATGGTTCTTATTTATTATGATGAATCTCAAATTTATAGCTCAAATAAA
*
13105 CTAGTTGATACATGTTTATAAGTAAAGTTTTAATTTTTTGTTATCAAGTTCTCACCCAAAAATTG
194 CTAGTTGATACATGTTTATAAGTAAAGTTTTAATTTTTTGTTATCAAATTCTCACCCAAAAATTG
* *
13170 AGAAAAGTAGAAGAAAGACGAAATTATA-CTAGTTGAA-TTGTTATTAAAAAAAGCAAGGCATTC
259 AGAAAAGTAGAAGAAAAATGAAATTATACCTA-TT-AAGTTGTTATTAAAAAAAGCAAGG-ATTC
13233 TAGAGAAGTCAAGTTTTC-AATAATTGA
321 TAGAGAAGTCAA-TTTTCAAATAATTGA
* * * *
13260 TGAAATTTCACCTAAAACGTTGAATTAAATCCCTT-ACAAGTCAAAACTCAATTTATTTTTTGAG
1 TGAAATTTCACCTAAAACATTGAATTAAAT-CCTTCACAAATCAAAACTTAATTTATTTTTTAAG
* * * * ** * * *
13324 TGTTATAGGC-T-TA---TATTTTATTTTTTTAAACATAAAATTTTTATTTATTTTTATAATACA
65 CGCTATAAGCATATATTTTATTTTTTTTTTTTAAACATGCAACTTCTATTTATTTTTATAATA-T
* * * * * *
13384 TAATTATTTA--TTGTGACAA---ATCTTA--AATT-T-AT--AGCTCAAA-TGATA----AAAA
129 TAATTATATAGCTT-T-A-AATGGTTCTTATTTATTATGATGAATCTCAAATTTATAGCTCAAAT
* * * * * *
13433 AAACTGGTTGATATATATTTAGAAGTAAAGTTTTAATTTTTTTTATTATCAAATTCTCA-CCTAA
191 AAACTAGTTGATACATGTTTATAAGTAAAGTTTTAA--TTTTTTGTTATCAAATTCTCACCCAAA
* ** *
13497 AATTGAGAAAAGTAGAAGAAATGA-GAAATTATATTTATTAAGTTGTTATCTATAAGAAA--AA-
254 AATTGAGAAAAGTAGAAGAAA-AATGAAATTATACCTATTAAGTTGTTAT-TA-AAAAAAGCAAG
* * ** * *
13558 GATACTTGAG-AG--AA--ACCAAGT--TTGG
316 GATTCTAGAGAAGTCAATTTTCAAATAATTGA
* * * * * *
13583 TGAAATTTTACCTAAAACATTGAATTAAAT-TTCTCATAAATCAAAACTTAATTTACTTATTACG
1 TGAAATTTCACCTAAAACATTGAATTAAATCCT-TCACAAATCAAAACTTAATTTATTTTTTAAG
* *
13647 CGTTATAAGCATATATTTTATTTTTATTTTTTTAAACATGCAAATTCTATTTATTTTTATAATAT
65 CGCTATAAGCATATATTTTATTTTT-TTTTTTTAAACATGCAACTTCTATTTATTTTTATAATAT
* *
13712 GTAATTATACTAGCTTCAAATGGTTCTTATTTATTATGACGAATCTCAAATTTATAGCTCAAATA
129 -TAATTATA-TAGCTTTAAATGGTTCTTATTTATTATGATGAATCTCAAATTTATAGCTC--A-A
* * *
13777 ATACAAAAAAAAAAACTAATTGATGCATGCTTATATA-TGAAA-TTTTAATTTTTTGTTATCAAA
189 AT----------AAACTAGTTGATACATGTTTATA-AGT-AAAGTTTTAATTTTTTGTTATCAAA
* * * * *
13840 TTATAACCTAAAAATTGAGAAAGGTAGAAGAAAAATGAAATTATGCC-ATTAAGTTGTTA-TAAG
242 TTCTCACCCAAAAATTGAGAAAAGTAGAAGAAAAATGAAATTATACCTATTAAGTTGTTATTAA-
* * * *
13903 TAAGAGCAAGG-TGCTAAAGAGAAGTCAGGTTTTCAAATAATTAGA
306 AAAAAGCAAGGATTCT--AGAGAAGTCA-ATTTTCAAATAATT-GA
* * * * * * *
13948 AG-AATTTTACTTGAAATATTAAATTAAATCCTTCACAAATCAAAATTTAATTTATTTTTTAAGC
1 TGAAATTTCACCTAAAACATTGAATTAAATCCTTCACAAATCAAAACTTAATTTATTTTTTAAGC
* * * * *
14012 ACTGTAAGCATATATTTTATTTTAATTTTTTTTAAACATGTAATTTTTATTTATTTTTATAATAT
66 GCTATAAGCATATATTTTATTTT--TTTTTTTTAAACATGCAACTTCTATTTATTTTTATAATA-
* * * * * *
14077 TTAATTATAACAGCTTCAAATGGTTCTTATTTATTATAACGAATCTTATATTTATAGCTCAAATG
128 TTAATTAT-ATAGCTTTAAATGGTTCTTATTTATTATGATGAATCTCAAATTTATAGCTC-AA--
* * * * *
14142 ATAAAAAAAACTAATTAATACATGTTTTTAAGTAAAATTTTAA-TATTTGTTATCAAATTCTCAC
189 AT-----AAACTAGTTGATACATGTTTATAAGTAAAGTTTTAATTTTTTGTTATCAAATTCTCAC
**
14206 CTTAAAATTGA
249 CCAAAAATTGA
14217 AATTTAAAGG
Statistics
Matches: 1046, Mismatches: 164, Indels: 184
0.75 0.12 0.13
Matches are distributed among these distances:
321 1 0.00
322 1 0.00
323 61 0.06
324 2 0.00
325 4 0.00
327 2 0.00
328 6 0.01
329 45 0.04
330 13 0.01
331 34 0.03
332 52 0.05
333 25 0.02
334 12 0.01
335 8 0.01
336 1 0.00
337 2 0.00
338 8 0.01
339 7 0.01
341 7 0.01
342 1 0.00
343 3 0.00
344 48 0.05
345 1 0.00
346 2 0.00
347 6 0.01
348 34 0.03
349 150 0.14
350 18 0.02
351 94 0.09
352 8 0.01
353 2 0.00
354 42 0.04
355 60 0.06
356 27 0.03
357 20 0.02
359 33 0.03
360 31 0.03
362 4 0.00
363 1 0.00
364 74 0.07
365 93 0.09
366 3 0.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (347 bp):
TGAAATTTCACCTAAAACATTGAATTAAATCCTTCACAAATCAAAACTTAATTTATTTTTTAAGC
GCTATAAGCATATATTTTATTTTTTTTTTTTAAACATGCAACTTCTATTTATTTTTATAATATTA
ATTATATAGCTTTAAATGGTTCTTATTTATTATGATGAATCTCAAATTTATAGCTCAAATAAACT
AGTTGATACATGTTTATAAGTAAAGTTTTAATTTTTTGTTATCAAATTCTCACCCAAAAATTGAG
AAAAGTAGAAGAAAAATGAAATTATACCTATTAAGTTGTTATTAAAAAAAGCAAGGATTCTAGAG
AAGTCAATTTTCAAATAATTGA
Found at i:13393 original size:27 final size:26
Alignment explanation
Indices: 13340--13395 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
13330 AGGCTTATAT
*
13340 TTTATTTTTTTAAACATAAAATTTTTA
1 TTTATTTTTATAAACAT-AAATTTTTA
13367 TTTATTTTTATAATACAT-AATTATTTA
1 TTTATTTTTATAA-ACATAAATT-TTTA
13394 TT
1 TT
13396 GTGACAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 18 0.69
28 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTTTTATAAACATAAATTTTTA
Found at i:16501 original size:17 final size:18
Alignment explanation
Indices: 16481--16524 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
16471 TATTTGAATT
*
16481 TAAATAATATTATAAA-A
1 TAAATAAAATTATAAAGA
*
16498 TAAA-AAAATTTTAAAGA
1 TAAATAAAATTATAAAGA
16515 TAAATAAAAT
1 TAAATAAAAT
16525 GACTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
TAAATAAAATTATAAAGA
Found at i:20750 original size:14 final size:14
Alignment explanation
Indices: 20728--20765 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20718 TCTCTCTTTC
*
20728 TAATCTTTAACCAA
1 TAATGTTTAACCAA
20742 TAATGTTTAACCAA
1 TAATGTTTAACCAA
*
20756 TAATGATTAA
1 TAATGTTTAA
20766 TAAGTCTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (14 bp):
TAATGTTTAACCAA
Found at i:21881 original size:12 final size:12
Alignment explanation
Indices: 21864--21900 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
21854 TTCCTTCTAA
21864 AATAGCAACAGC
1 AATAGCAACAGC
21876 AATAGCAACAGC
1 AATAGCAACAGC
21888 AATAGCAACAGC
1 AATAGCAACAGC
21900 A
1 A
21901 TATATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.08
Consensus pattern (12 bp):
AATAGCAACAGC
Found at i:21882 original size:6 final size:6
Alignment explanation
Indices: 21867--21900 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
21857 CTTCTAAAAT
* *
21867 AGCAAC AGCAAT AGCAAC AGCAAT AGCAAC AGCA
1 AGCAAC AGCAAC AGCAAC AGCAAC AGCAAC AGCA
21901 TATATTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.26, G:0.18, T:0.06
Consensus pattern (6 bp):
AGCAAC
Found at i:22638 original size:121 final size:121
Alignment explanation
Indices: 22485--22729 Score: 463
Period size: 121 Copynumber: 2.0 Consensus size: 121
22475 CAGTTAATTT
* *
22485 GATTCTCTACATGCTACATTATACTATTAGGCGAAATTAATTCCTTTAGTGAGGTCTCAGCTTGC
1 GATTCTCTAAATGCTACATTATACTATTAGGCGAAATTAATTCCTTTAGTCAGGTCTCAGCTTGC
22550 ACAGTGGCCATAAAATTTATAAACTCATAGAGAGAATGAACCTGCCATGCTGTCTG
66 ACAGTGGCCATAAAATTTATAAACTCATAGAGAGAATGAACCTGCCATGCTGTCTG
22606 GATTCTCTAAATGCTACATTATACTATTAGGCGAAATTAATTCCTTTAGTCAGGTCTCAGCTTGC
1 GATTCTCTAAATGCTACATTATACTATTAGGCGAAATTAATTCCTTTAGTCAGGTCTCAGCTTGC
*
22671 GCAGTGGCCATAAAATTTATAAACTCATAGAGAGAATGAACCTGCCATGCTGTCTG
66 ACAGTGGCCATAAAATTTATAAACTCATAGAGAGAATGAACCTGCCATGCTGTCTG
22727 GAT
1 GAT
22730 GAAGATCAAT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (121 bp):
GATTCTCTAAATGCTACATTATACTATTAGGCGAAATTAATTCCTTTAGTCAGGTCTCAGCTTGC
ACAGTGGCCATAAAATTTATAAACTCATAGAGAGAATGAACCTGCCATGCTGTCTG
Found at i:26295 original size:17 final size:16
Alignment explanation
Indices: 26268--26309 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
26258 GCTGCCTGTG
26268 AAAAAGAAAGAAAACA
1 AAAAAGAAAGAAAACA
*
26284 AAAAAGAGAAGAAAAGA
1 AAAAAGA-AAGAAAACA
*
26301 ACAAAGAAA
1 AAAAAGAAA
26310 ATAAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAACA
Found at i:27927 original size:5 final size:5
Alignment explanation
Indices: 27914--27946 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
27904 CTTAAACAGA
*
27914 AAAAT AAAAC AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
27947 GGGGGAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:28107 original size:18 final size:18
Alignment explanation
Indices: 28084--28150 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
28074 AGAATGTAAT
28084 AAATTTATTAATATATTA
1 AAATTTATTAATATATTA
28102 AAATTTATATAA-ATATATA
1 AAATTTAT-TAATATAT-TA
*
28121 AAA-TT-TTAATATAATA
1 AAATTTATTAATATATTA
* *
28137 AAATATATAAATAT
1 AAATTTATTAATAT
28151 GATATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 8 0.20
17 5 0.12
18 20 0.49
19 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTATTAATATATTA
Found at i:28118 original size:8 final size:8
Alignment explanation
Indices: 28107--28166 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
28097 TATTAAAATT
28107 TATATAAA
1 TATATAAA
28115 TATATAAA
1 TATATAAA
* *
28123 -ATTTTAA
1 TATATAAA
28130 TATAATAAAA
1 TAT-AT-AAA
28140 TATATAAATA
1 TATAT-AA-A
28150 TGATATAAA
1 T-ATATAAA
28159 TATATAAA
1 TATATAAA
28167 ATTTTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.12
8 17 0.40
9 8 0.19
10 9 0.21
11 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:28118 original size:20 final size:19
Alignment explanation
Indices: 28084--28180 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 19
28074 AGAATGTAAT
28084 AAATTTAT-T-AATATATTA
1 AAATTTATATAAATATA-TA
28102 AAATTTATATAAATATATA
1 AAATTTATATAAATATATA
*
28121 AAATTTTAATATAATAAAATATA
1 AAA-TTT-ATAT-A-AATATATA
*
28144 TAAATATGATATAAATATATA
1 -AAAT-TTATATAAATATATA
*
28165 AAATTTTAAATAAATA
1 AAA-TTTATATAAATA
28181 AAATTATTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
18 8 0.12
19 6 0.09
20 21 0.32
21 12 0.18
22 2 0.03
23 12 0.18
24 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
AAATTTATATAAATATATA
Found at i:28131 original size:35 final size:35
Alignment explanation
Indices: 28082--28159 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
28072 TAAGAATGTA
* *
28082 ATAAATTTATTAATATATTAAAATTTATATAAATAT-
1 ATAAAATTATTAATATAATAAAA--TATATAAATATG
28118 ATAAAATT-TTAATATAATAAAATATATAAATATG
1 ATAAAATTATTAATATAATAAAATATATAAATATG
28152 ATATAAAT
1 ATA-AAAT
28160 ATATAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 11 0.29
34 3 0.08
35 17 0.45
36 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
ATAAAATTATTAATATAATAAAATATATAAATATG
Found at i:28223 original size:20 final size:19
Alignment explanation
Indices: 28182--28226 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
28172 AAATAAATAA
*
28182 AATTATTAAAAATTAGTTT
1 AATTATTAAAAATTAGTGT
*
28201 AATTCATTAAAAATTTGTGT
1 AATT-ATTAAAAATTAGTGT
28221 AATTAT
1 AATTAT
28227 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTATTAAAAATTAGTGT
Found at i:28511 original size:8 final size:8
Alignment explanation
Indices: 28498--28530 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
28488 ACTTTTTTCA
28498 TTCTTTTT
1 TTCTTTTT
28506 TTCTTTTT
1 TTCTTTTT
*
28514 TCCTTTTT
1 TTCTTTTT
28522 TT-TTTTT
1 TTCTTTTT
28529 TT
1 TT
28531 GGTTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:28513 original size:19 final size:18
Alignment explanation
Indices: 28489--28530 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
28479 AGATGGATGA
28489 CTTTTTTCATTCTTTTTTT
1 CTTTTTTCATT-TTTTTTT
*
28508 CTTTTTTCCTTTTTTTTT
1 CTTTTTTCATTTTTTTTT
28526 -TTTTT
1 CTTTTT
28531 GGTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTTTTCATTTTTTTTT
Found at i:28779 original size:28 final size:29
Alignment explanation
Indices: 28728--28793 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
28718 TAAATGGTTT
* * * *
28728 AATATTTTTATTATATTAGTTAAAGATAT
1 AATATTTTTAATACATTAGTTAAAAATAA
* *
28757 TATATTTTTAATACA-TATTTAAAAATAA
1 AATATTTTTAATACATTAGTTAAAAATAA
28785 AATATTTTT
1 AATATTTTT
28794 TTACATAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (29 bp):
AATATTTTTAATACATTAGTTAAAAATAA
Found at i:36901 original size:79 final size:79
Alignment explanation
Indices: 36768--36922 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 79
36758 TATCAACAAA
* * *
36768 TACTCTAAGGTTATAGAATTTTCTCATCAAATCTTTGTTTTTAGTTCTAGAAGTGTCTATTTAGA
1 TACTCTAAGGTTATAGAATTTTCTCATCAAATCTTTATTTTTAGTTCTAAAAGTGTCTATCTAGA
36833 ATACTCTTCAAAAC
66 ATACTCTTCAAAAC
* * *
36847 TACTCTAAGGTTTTAGATTTTTCTCATCAAATCTTTATTTTTAGTTCTAAAAGTGTTTATCTAGA
1 TACTCTAAGGTTATAGAATTTTCTCATCAAATCTTTATTTTTAGTTCTAAAAGTGTCTATCTAGA
*
36912 ATACTTTTCAA
66 ATACTCTTCAA
36923 TCTCTTACTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (79 bp):
TACTCTAAGGTTATAGAATTTTCTCATCAAATCTTTATTTTTAGTTCTAAAAGTGTCTATCTAGA
ATACTCTTCAAAAC
Found at i:46359 original size:32 final size:32
Alignment explanation
Indices: 46318--46393 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
46308 AAGACAAACG
*
46318 TGTTGATTAAATAGGTGCAAAGGTGCTGCCAT
1 TGTTGATTAAATAGGTGCAAAGGTGCTACCAT
*
46350 TGTTGATTAAATTGGTGCAAAGGTGCTACCAT
1 TGTTGATTAAATAGGTGCAAAGGTGCTACCAT
*
46382 TATTGATTAAAT
1 TGTTGATTAAAT
46394 GGCTAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (32 bp):
TGTTGATTAAATAGGTGCAAAGGTGCTACCAT
Found at i:52410 original size:24 final size:25
Alignment explanation
Indices: 52381--52442 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
52371 AACATAAATC
** *
52381 TTATTAATTATTAAATTTAA-GTTA
1 TTATTAATTATTAAAAATAATATTA
52405 TTATTAATTATATTAAAAATAATATTA
1 TTATTAA-T-TATTAAAAATAATATTA
52432 TTATTAATTAT
1 TTATTAATTAT
52443 ATTGTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 7 0.22
25 4 0.12
26 11 0.34
27 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTATTAATTATTAAAAATAATATTA
Found at i:52991 original size:18 final size:20
Alignment explanation
Indices: 52970--53016 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
52960 ACTTTCGGTG
52970 AAAATTATAAT-A-AATAAA
1 AAAATTATAATGATAATAAA
* *
52988 AAAATAATTAATGATATTAAA
1 AAAATTA-TAATGATAATAAA
53009 AAAATTAT
1 AAAATTAT
53017 TTATATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 2 0.09
21 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATTATAATGATAATAAA
Found at i:52997 original size:21 final size:21
Alignment explanation
Indices: 52972--53032 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
52962 TTTCGGTGAA
52972 AATTATAATAAATAAAAAAA-T
1 AATTATAAT-AATAAAAAAATT
* *
52993 AATTAATGATATTAAAAAAATT
1 AATT-ATAATAATAAAAAAATT
*
53015 ATTTATATATTAATAAAA
1 AATTATA-A-TAATAAAA
53033 TATTGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 15 0.48
22 9 0.29
23 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTATAATAATAAAAAAATT
Found at i:53011 original size:20 final size:20
Alignment explanation
Indices: 52984--53034 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
52974 TTATAATAAA
52984 TAAAAAAATAATTAATGATAT
1 TAAAAAAATAATTAAT-ATAT
* *
53005 TAAAAAAATTATTTATATAT
1 TAAAAAAATAATTAATATAT
*
53025 TAATAAAATA
1 TAAAAAAATA
53035 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAAAATAATTAATATAT
Found at i:53032 original size:22 final size:22
Alignment explanation
Indices: 52986--53056 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 22
52976 ATAATAAATA
* *
52986 AAAAAATAATTAATGATATT-A-
1 AAAAAATTATTTAT-ATATTAAT
53007 AAAAAATTATTTATATATTAAT
1 AAAAAATTATTTATATATTAAT
*
53029 AAAATATTGATTT-T-T-TTAAT
1 AAAAAATT-ATTTATATATTAAT
*
53049 ATAAAATT
1 AAAAAATT
53057 TTAAATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 16 0.38
21 14 0.33
22 8 0.19
23 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
AAAAAATTATTTATATATTAAT
Found at i:53232 original size:13 final size:15
Alignment explanation
Indices: 53208--53240 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53198 CTTTATTTGT
53208 TATAATTTTTAAAA-
1 TATAATTTTTAAAAG
53222 TATAA-TTTTAAAAG
1 TATAATTTTTAAAAG
53236 TATAA
1 TATAA
53241 AGACTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TATAATTTTTAAAAG
Found at i:55712 original size:21 final size:21
Alignment explanation
Indices: 55688--55731 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55678 AATAAAAAAT
55688 TATT-AATTAATTTATAATTTA
1 TATTAAATTAATTTA-AATTTA
55709 TATTAAATTAATTTAAATTTA
1 TATTAAATTAATTTAAATTTA
55730 TA
1 TA
55732 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTAAATTAATTTAAATTTA
Found at i:55899 original size:38 final size:38
Alignment explanation
Indices: 55864--55945 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
55854 TAATTATATT
* * *
55864 ATATTTATTATGATTATAAAT-ATAATAAATATTATAA
1 ATATTAATTATGAATATAAATAATAAAAAATATTATAA
*
55901 ATATTAATTATGAATATCAATAATAAAAAATATTA-AA
1 ATATTAATTATGAATATAAATAATAAAAAATATTATAA
55938 ATTATTAA
1 A-TATTAA
55946 ATAATGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 21 0.54
38 18 0.46
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (38 bp):
ATATTAATTATGAATATAAATAATAAAAAATATTATAA
Found at i:55905 original size:9 final size:9
Alignment explanation
Indices: 55876--55906 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55866 ATTTATTATG
55876 ATTATAAAT
1 ATTATAAAT
*
55885 ATAATAAAT
1 ATTATAAAT
55894 ATTATAAAT
1 ATTATAAAT
55903 ATTA
1 ATTA
55907 ATTATGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTATAAAT
Found at i:57041 original size:16 final size:16
Alignment explanation
Indices: 57022--57145 Score: 72
Period size: 16 Copynumber: 7.8 Consensus size: 16
57012 AAGTAACTCA
57022 TATTTAAAATAATTTT
1 TATTTAAAATAATTTT
* *
57038 TA-TTCAAGTAATTTT
1 TATTTAAAATAATTTT
* ** *
57053 TGTTTAAAATAAAAATA
1 TATTTAAAAT-AATTTT
* *
57070 AATTTAAAATAATTCT
1 TATTTAAAATAATTTT
* * *
57086 TATTCAAAAAAATTCT
1 TATTTAAAATAATTTT
* * **
57102 TGTTCAAAATAAAATT
1 TATTTAAAATAATTTT
57118 T-TTTAAAATAACTTTT
1 TATTTAAAATAA-TTTT
*
57134 TATTCAAAATAA
1 TATTTAAAATAA
57146 AATCTTTATG
Statistics
Matches: 78, Mismatches: 26, Indels: 7
0.70 0.23 0.06
Matches are distributed among these distances:
15 21 0.27
16 37 0.47
17 20 0.26
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (16 bp):
TATTTAAAATAATTTT
Found at i:57077 original size:48 final size:46
Alignment explanation
Indices: 57023--57142 Score: 141
Period size: 48 Copynumber: 2.5 Consensus size: 46
57013 AGTAACTCAT
** * *
57023 ATTTAAAATAATTTTTATTCAAGTAATTTTTGTTTAAAATAAAAATAA
1 ATTTAAAATAATTTTTATTCAAAAAATTCTTGTTCAAAAT-AAAAT-A
* *
57071 ATTTAAAATAATTCTTATTCAAAAAAATTCTTGTTCAAAATAAAATT
1 ATTTAAAATAATTTTTATTC-AAAAAATTCTTGTTCAAAATAAAATA
*
57118 TTTTAAAATAACTTTTTATTCAAAA
1 ATTTAAAATAA-TTTTTATTCAAAA
57143 TAAAATCTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
47 14 0.23
48 32 0.52
49 16 0.26
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (46 bp):
ATTTAAAATAATTTTTATTCAAAAAATTCTTGTTCAAAATAAAATA
Found at i:57125 original size:15 final size:17
Alignment explanation
Indices: 57080--57154 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 17
57070 AATTTAAAAT
57080 AATTCTTATTC-AAA-AA
1 AATT-TTATTCAAAATAA
*
57096 AATTCTTGTTCAAAATAA
1 AATT-TTATTCAAAATAA
57114 AATTTT-TT-AAAATAA
1 AATTTTATTCAAAATAA
**
57129 CTTTTTATTCAAAATAA
1 AATTTTATTCAAAATAA
57146 AATCTTTAT
1 AAT-TTTAT
57155 GAAATAAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
15 11 0.22
16 14 0.29
17 13 0.27
18 11 0.22
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTTATTCAAAATAA
Found at i:64877 original size:2 final size:2
Alignment explanation
Indices: 64862--64909 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
64852 CTACTCAGTT
* *
64862 TC TC TC TG TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
64904 TC TC TC
1 TC TC TC
64910 ACTGGGGATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:65718 original size:2 final size:2
Alignment explanation
Indices: 65713--65742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65703 AATCTTTTTG
65713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65743 TAACGGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66983 original size:18 final size:18
Alignment explanation
Indices: 66960--66997 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
66950 TAAAAGTATG
66960 ATTATGATGAGATTTATC
1 ATTATGATGAGATTTATC
66978 ATTATGATGAGATTTATC
1 ATTATGATGAGATTTATC
66996 AT
1 AT
66998 GTAACAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (18 bp):
ATTATGATGAGATTTATC
Found at i:67043 original size:18 final size:21
Alignment explanation
Indices: 67005--67047 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
66995 CATGTAACAG
67005 TAAAATTAAATATTGTAATAA
1 TAAAATTAAATATTGTAATAA
67026 TAAAATTAAA-A-T-TAATAA
1 TAAAATTAAATATTGTAATAA
67044 TAAA
1 TAAA
67048 TTTATGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 1 0.05
21 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAATTAAATATTGTAATAA
Found at i:68663 original size:4 final size:4
Alignment explanation
Indices: 68654--68703 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
68644 TTTATTCATT
* *
68654 TTTC TTTC TTT- TTTC -TCC TTTC TTTC TTTCC TTTTG TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC
68702 TT
1 TT
68704 AGCTACCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 29 0.76
5 1 0.03
6 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:68676 original size:14 final size:13
Alignment explanation
Indices: 68657--68703 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
68647 ATTCATTTTT
*
68657 CTTTCTTTTTTCTC
1 CTTTCTTTCTT-TC
68671 CTTTCTTTCTTTC
1 CTTTCTTTCTTTC
*
68684 CTTTTGTTTCTTT-
1 C-TTTCTTTCTTTC
68697 CTTTCTT
1 CTTTCTT
68704 AGCTACCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 5 0.17
13 4 0.14
14 20 0.69
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (13 bp):
CTTTCTTTCTTTC
Found at i:68679 original size:22 final size:22
Alignment explanation
Indices: 68654--68703 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
68644 TTTATTCATT
68654 TTTCTTT-CTTTT-TTCTCCTTTC
1 TTTCTTTCCTTTTGTT-T-CTTTC
68676 TTTCTTTCCTTTTGTTTCTTTC
1 TTTCTTTCCTTTTGTTTCTTTC
68698 TTTCTT
1 TTTCTT
68704 AGCTACCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 18 0.69
23 6 0.23
24 2 0.08
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTCTTTCCTTTTGTTTCTTTC
Found at i:70071 original size:2 final size:2
Alignment explanation
Indices: 70064--70092 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70054 GGTTAGTGTT
70064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70093 TTAGGTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71831 original size:38 final size:38
Alignment explanation
Indices: 71774--71942 Score: 230
Period size: 38 Copynumber: 4.4 Consensus size: 38
71764 GTTCAATTTG
** *
71774 GAATTCTCTAGCCACCAGCCACCAGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
* *
71812 GAATTCTCTAGTCGTCAGCCGCCGGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
* * *
71850 GAATTCTCTAGTCGTCAGCCGCCGGCAAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
* * *
71888 GAATTCTCTAGCCGTCAGCCGCCAGTCAATTTCATATT
1 GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
*
71926 GAATTCTCTAACCGTCA
1 GAATTCTCTAGCCGTCA
71943 ACTAATTCAA
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 118 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (38 bp):
GAATTCTCTAGCCGTCAGCCGCCAGCCAATTCCAAATT
Found at i:75630 original size:38 final size:38
Alignment explanation
Indices: 75510--75647 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
75500 CCAGCCACTG
* * *
75510 GCCAATTCCAAATTGAATTCTCTAGTCGTCAGCCACCG
1 GCCAATTCCAAATTGAATTCTCTAGCCGTCAGCCGCCA
**
75548 GCCAATTCCAAATTGAATTCTCTAGCCGTCAGTTGCCA
1 GCCAATTCCAAATTGAATTCTCTAGCCGTCAGCCGCCA
* *
75586 GCCAATTTCAAATTGAATTCTCTAGCCGTCAGCCGTCA
1 GCCAATTCCAAATTGAATTCTCTAGCCGTCAGCCGCCA
* * * *
75624 GTCAATTTCATATTGAACTCTCTA
1 GCCAATTCCAAATTGAATTCTCTA
75648 ACCATCAACT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 88 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (38 bp):
GCCAATTCCAAATTGAATTCTCTAGCCGTCAGCCGCCA
Found at i:76730 original size:22 final size:22
Alignment explanation
Indices: 76687--76730 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
76677 TATACAAGAC
** *
76687 TTTAATTAAATGTATTTTTGAT
1 TTTAATTAAATGTACATGTGAT
76709 TTTAATTAAATGTACATGTGAT
1 TTTAATTAAATGTACATGTGAT
76731 AAAAATGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (22 bp):
TTTAATTAAATGTACATGTGAT
Found at i:77047 original size:22 final size:22
Alignment explanation
Indices: 76999--77071 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
76989 TAAAATTGAT
*
76999 TACATATGATCATAACTGAATA
1 TACATATGATAATAACTGAATA
* * *
77021 CACATATGATAATAACTTAATG
1 TACATATGATAATAACTGAATA
* * *
77043 TACATATAACT-TTAATTGAATA
1 TACATATGA-TAATAACTGAATA
77065 TACATAT
1 TACATAT
77072 AATTTTTTAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 39 0.98
23 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (22 bp):
TACATATGATAATAACTGAATA
Found at i:77158 original size:22 final size:22
Alignment explanation
Indices: 77133--77224 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
77123 TTGAATATAA
*
77133 ATAT-AATTATAACTGAATGTAT
1 ATATGAATT-TAACTAAATGTAT
* *
77155 ATATGAATATAACTAAATATAT
1 ATATGAATTTAACTAAATGTAT
* *
77177 ATTTGACTTTAACTAAATGTAT
1 ATATGAATTTAACTAAATGTAT
* *
77199 ATCTGACTTTAACTAAATGTAT
1 ATATGAATTTAACTAAATGTAT
77221 ATAT
1 ATAT
77225 TTTTAGCCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
22 57 0.95
23 3 0.05
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (22 bp):
ATATGAATTTAACTAAATGTAT
Found at i:77475 original size:22 final size:23
Alignment explanation
Indices: 77418--77475 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
77408 CAAATAAAAT
*
77418 TAAATGTATATA-TGATTATAAT
1 TAAATGTATATATTGATTATAAC
* * *
77440 TGAATGTACATATTG-TTATAGC
1 TAAATGTATATATTGATTATAAC
77462 TAAATGTATATATT
1 TAAATGTATATATT
77476 ATTGAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TAAATGTATATATTGATTATAAC
Found at i:78502 original size:20 final size:22
Alignment explanation
Indices: 78473--78512 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
78463 TAATTATTTA
78473 TGTAA-ATTT-TAATATTTATG
1 TGTAATATTTGTAATATTTATG
*
78493 TGTAATTTTTGTAATATTTA
1 TGTAATATTTGTAATATTTA
78513 ATTCTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (22 bp):
TGTAATATTTGTAATATTTATG
Found at i:78863 original size:419 final size:414
Alignment explanation
Indices: 78016--78809 Score: 958
Period size: 419 Copynumber: 1.9 Consensus size: 414
78006 TCTACAACAC
* ** *
78016 ATATTACATACAAACATTACCTA-AACTCTAATTATTTATATAAATTGTAATATTTATATGTAAT
1 ATATTACATACAAGCATTATTTACAAAT-TAATTATTTATATAAATTGTAATATTTATATGTAAT
* * * * *
78080 TTTCATAATATTTAGTTGTAATTCTTACGAACTAATAAAAAATCTAAACTTTATTATAACATTGA
65 TTTCATAATATTTAATTCTAATTCTTACCAACTAATAAAAAATCTAAACTTTATCATAACATTAA
* * *
78145 TTTTTTATTAATATATTATATTTATTGTTAATATTAAAAAATATAAATAAAATATAAATTTTTTT
130 TTTTTTATTAATATATTATATTTAATGCTAATATTAAAAAATATAAATAAAATATAAAATTTTTT
*
78210 TAACTTCAAAAATTACTTAAAAAATCAACTTTTTTTACATATATAATATATTTAATGAAAAATAA
195 TAACTTCAAAAATTACTTAAAAAATCAA--TTTTCTA-ATATATAATATATTTAATGAAAAATAA
* **
78275 AAAAAATTTGAAAAAATTAAACTTTATTTTTCTTATAAGAATTTTTTATTTAAATACATTACAGT
257 AAAAAATTTGAAAAAATTAAACTTTATTTTTCTTAAAAGAATTTTTTACATAAATACATTACAGT
* * *** *
78340 TTTCGTAATATTTTATGTAAATATGTAATTTTTTTGTAATTTTTATACACAAATATTACCTTTAA
322 TTTCGTAATATTTTACGTAAATATGTAATTTGTTTGTAATTCCGATACACAAATATTACATTT-A
* * *
78405 AGAATCTTTACACAAGTGCATTAACCACAT
386 AGAATCTATACAAAAGTCCATTAA-CACAT
* * *
78435 ATATTACATACAAGCATTATTTACAAATTAATTATTTATGTAAATTTTAATATTTATGTGTAATT
1 ATATTACATACAAGCATTATTTACAAATTAATTATTTATATAAATTGTAATATTTATATGTAATT
** *
78500 TTTGTAATATTTAATTCTAATTCTTACCAACTAATAAAAAAATCTAAATTTTATCAT-ACATTAA
66 TTCATAATATTTAATTCTAATTCTTACCAACTAAT-AAAAAATCTAAACTTTATCATAACATTAA
78564 TTTTTTATTAATATATTATATTTAATGCTAATATTAATATATAA-ATAAAATAGAAATATAAAAT
130 TTTTTTATTAATATATTATATTTAATGCTAATATTAA-A-A-AATAT-AAATA-AAATATAAAAT
* *
78628 TTTTTTAACTTCAAAAAATTAC-TACGAAAATTAA-TTTCT-ATATATAATATATTTAAT-AAAA
190 TTTTTTAACTTC-AAAAATTACTTA-AAAAATCAATTTTCTAATATATAATATATTTAATGAAAA
* ** * * * *
78689 ATCAAAAATAATTTTGAAATGATTATACTTTATTTTTCTTAAAATATTTTTTTTACATAAATATA
253 AT-AAAAA-AAATTTGAAAAAATTAAACTTTATTTTTCTTAAAAGA-ATTTTTTACATAAATACA
* * *
78754 TTATAG-TTTCGGTAATATTTTACGTAAATTTTTAATGATTGTTTGTAA-TCCGATAC
315 TTACAGTTTTC-GTAATATTTTACGTAAATATGTAAT--TTGTTTGTAATTCCGATAC
78810 TATTTATATG
Statistics
Matches: 321, Mismatches: 39, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
418 6 0.02
419 148 0.46
420 58 0.18
421 48 0.15
422 12 0.04
423 33 0.10
424 16 0.05
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (414 bp):
ATATTACATACAAGCATTATTTACAAATTAATTATTTATATAAATTGTAATATTTATATGTAATT
TTCATAATATTTAATTCTAATTCTTACCAACTAATAAAAAATCTAAACTTTATCATAACATTAAT
TTTTTATTAATATATTATATTTAATGCTAATATTAAAAAATATAAATAAAATATAAAATTTTTTT
AACTTCAAAAATTACTTAAAAAATCAATTTTCTAATATATAATATATTTAATGAAAAATAAAAAA
AATTTGAAAAAATTAAACTTTATTTTTCTTAAAAGAATTTTTTACATAAATACATTACAGTTTTC
GTAATATTTTACGTAAATATGTAATTTGTTTGTAATTCCGATACACAAATATTACATTTAAGAAT
CTATACAAAAGTCCATTAACACAT
Found at i:80287 original size:21 final size:22
Alignment explanation
Indices: 80244--80307 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 22
80234 TTTTTGTTAC
*
80244 ATATGATAAT-TAACTTATGTA
1 ATATGATAATATAATTTATGTA
*
80265 ATA-GATAATATAATTTGTGTA
1 ATATGATAATATAATTTATGTA
*
80286 AT-T-AT--TATATTTTATGTA
1 ATATGATAATATAATTTATGTA
80304 ATAT
1 ATAT
80308 TATTTTCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 13 0.36
19 1 0.03
20 8 0.22
21 14 0.39
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
ATATGATAATATAATTTATGTA
Found at i:84197 original size:13 final size:13
Alignment explanation
Indices: 84179--84204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84169 GCAGATAAAC
84179 TTATTTAAATATA
1 TTATTTAAATATA
84192 TTATTTAAATATA
1 TTATTTAAATATA
84205 AAAAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTAAATATA
Found at i:86942 original size:41 final size:41
Alignment explanation
Indices: 86895--87112 Score: 267
Period size: 41 Copynumber: 5.3 Consensus size: 41
86885 GTCATCCAAG
* * **
86895 ATAAAATCATATAGCGGCGTTTTA-ATGTAAAATGCCACTAA
1 ATAAAATCATATAGCGACGTTTTACAT-TAAAATGTCGTTAA
* * *
86936 ATAAAATCGTATAGCGACGTTTTACATTAAAATATTGTTAA
1 ATAAAATCATATAGCGACGTTTTACATTAAAATGTCGTTAA
* ** *
86977 ATAAAATCATATAGCGACGTTTTATATTAAAACATCGCTAA
1 ATAAAATCATATAGCGACGTTTTACATTAAAATGTCGTTAA
*
87018 ATAAAATCATATAACGACGTTTTACATTAAAATGTCGTTAA
1 ATAAAATCATATAGCGACGTTTTACATTAAAATGTCGTTAA
* ** * *
87059 ATAAAATCATATAACGATATTTTACATTAAAACGCCGTTAA
1 ATAAAATCATATAGCGACGTTTTACATTAAAATGTCGTTAA
87100 ATAAAATCATATA
1 ATAAAATCATATA
87113 AAGTTTTAAT
Statistics
Matches: 155, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 153 0.99
42 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (41 bp):
ATAAAATCATATAGCGACGTTTTACATTAAAATGTCGTTAA
Found at i:87040 original size:123 final size:119
Alignment explanation
Indices: 86895--87163 Score: 308
Period size: 123 Copynumber: 2.2 Consensus size: 119
86885 GTCATCCAAG
* * * * *
86895 ATAAAATCATATAGCGGCGTTTTAATGTAAAATGCCACTAAATAAAATCGTATAGCGACGTTTTA
1 ATAAAATCATATAACGACGTTTTAAT-TAAAATGCCACTAAATAAAATCATATAACGACATTTTA
* ** * *
86960 CATTAAAATATTGTTAAATAAAATCATATAGCGACGTTTTATAT-TAAAACA-TCGCTAA
65 CATTAAAACACCGTTAAATAAAATCATATA---AAGTTTTA-ATGTAAAACAGT-ACTAA
* ** *
87018 ATAAAATCATATAACGACGTTTTACATTAAAATGTCGTTAAATAAAATCATATAACGATATTTTA
1 ATAAAATCATATAACGACGTTTTA-ATTAAAATGCCACTAAATAAAATCATATAACGACATTTTA
*
87083 CATTAAAACGCCGTTAAATAAAATCATATAAAGTTTTAATGTAAAACAGTACTAA
65 CATTAAAACACCGTTAAATAAAATCATATAAAGTTTTAATGTAAAACAGTACTAA
* *
87138 ATAAAATCGTATAACTACGTTTTAAT
1 ATAAAATCATATAACGACGTTTTAAT
87164 AATGAAACGT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
119 4 0.03
120 40 0.32
121 1 0.01
123 79 0.63
124 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (119 bp):
ATAAAATCATATAACGACGTTTTAATTAAAATGCCACTAAATAAAATCATATAACGACATTTTAC
ATTAAAACACCGTTAAATAAAATCATATAAAGTTTTAATGTAAAACAGTACTAA
Found at i:87113 original size:41 final size:41
Alignment explanation
Indices: 86933--87161 Score: 254
Period size: 41 Copynumber: 5.7 Consensus size: 41
86923 AAAATGCCAC
* * * *
86933 TAAATAAAATCGTATAGCGACGTTTTACATTAAAATATTGT
1 TAAATAAAATCATATAACGACGTTTTACATTAAAACATCGT
* * *
86974 TAAATAAAATCATATAGCGACGTTTTATATTAAAACATCGC
1 TAAATAAAATCATATAACGACGTTTTACATTAAAACATCGT
**
87015 TAAATAAAATCATATAACGACGTTTTACATTAAAATGTCGT
1 TAAATAAAATCATATAACGACGTTTTACATTAAAACATCGT
** **
87056 TAAATAAAATCATATAACGATATTTTACATTAAAACGCCGT
1 TAAATAAAATCATATAACGACGTTTTACATTAAAACATCGT
87097 TAAATAAAATCATATAA--A-GTTTTA-ATGTAAAACA--GT
1 TAAATAAAATCATATAACGACGTTTTACAT-TAAAACATCGT
* *
87133 ACTAAATAAAATCGTATAACTACGTTTTA
1 --TAAATAAAATCATATAACGACGTTTTA
87162 ATAATGAAAC
Statistics
Matches: 165, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 27 0.16
39 1 0.01
40 1 0.01
41 132 0.80
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (41 bp):
TAAATAAAATCATATAACGACGTTTTACATTAAAACATCGT
Done.