Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold555
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: 85217
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:339 original size:33 final size:33
Alignment explanation
Indices: 293--364 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
283 CACATCTAGA
* *
293 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCAACACATTATGCTTTGTATCGATACAT
326 TGTATCAACACATTATGCTTTGTATCGATACAT
1 TGTATCAACACATTATGCTTTGTATCGATACAT
359 TGTATC
1 TGTATC
365 GATACATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCAACACATTATGCTTTGTATCGATACAT
Found at i:363 original size:13 final size:13
Alignment explanation
Indices: 345--371 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
335 ACATTATGCT
345 TTGTATCGATACA
1 TTGTATCGATACA
358 TTGTATCGATACA
1 TTGTATCGATACA
371 T
1 T
372 GCACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:6514 original size:49 final size:49
Alignment explanation
Indices: 6456--6555 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
6446 ATAAGTTTAA
6456 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
1 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
6505 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
1 TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
6554 TT
1 TT
6556 TGATACGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (49 bp):
TTGTTTATGAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTG
Found at i:6566 original size:49 final size:49
Alignment explanation
Indices: 6464--6566 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
6454 AATTGTTTAT
* *
6464 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTTTAT
1 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTATAC
6513 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTT-TGATAC
1 GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGT-ATAC
6562 GAATT
1 GAATT
6567 AAGTAAGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.98
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (49 bp):
GAATTTGATGTTCTTCATGATTGATGATTGAGTTGTAGTTGTTGTATAC
Found at i:6815 original size:21 final size:22
Alignment explanation
Indices: 6778--6823 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
6768 CAAACCCTAA
*
6778 CAAATCATTTATCAAATTTCTT
1 CAAATCAATTATCAAATTTCTT
6800 CAAATCAATT-TCAAATTTCTT
1 CAAATCAATTATCAAATTTCTT
6821 CAA
1 CAA
6824 TTTCACATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (22 bp):
CAAATCAATTATCAAATTTCTT
Found at i:9212 original size:19 final size:20
Alignment explanation
Indices: 9188--9241 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
9178 ACTTTATGCT
* **
9188 TTGTATAGATACATGTTC-A
1 TTGTATCGATACATGCACAA
9207 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
9227 TTGTATCGATACATG
1 TTGTATCGATACATG
9242 AAACTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:23361 original size:11 final size:12
Alignment explanation
Indices: 23311--23372 Score: 65
Period size: 11 Copynumber: 5.1 Consensus size: 12
23301 AATATTTTAT
23311 TTAAATATAA-A
1 TTAAATATAATA
23322 TTAAATATTAATTA
1 TTAAATA-TAA-TA
* *
23336 TGTAATTTTAATA
1 T-TAAATATAATA
23349 TTAAATA-AATA
1 TTAAATATAATA
23360 TTAAATATAATA
1 TTAAATATAATA
23372 T
1 T
23373 ATATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
11 18 0.43
12 12 0.29
13 3 0.07
14 5 0.12
15 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:23646 original size:19 final size:19
Alignment explanation
Indices: 23610--23649 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
23600 TTTTTAGTAT
23610 TAAAAAAATAATAAAAATA
1 TAAAAAAATAATAAAAATA
*
23629 TAAAATAAAT-ATATAAATA
1 TAAAA-AAATAATAAAAATA
23648 TA
1 TA
23650 TTAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAAATAATAAAAATA
Found at i:23655 original size:28 final size:27
Alignment explanation
Indices: 23624--23682 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
23614 AAAATAATAA
23624 AAATATAAAATAAATATATAAATATATT
1 AAATATAAAATAAATATATAAAT-TATT
* * *
23652 AAATATGATATAAATATATAAATTTTT
1 AAATATAAAATAAATATATAAATTATT
23679 AAAT
1 AAAT
23683 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
AAATATAAAATAAATATATAAATTATT
Found at i:23667 original size:11 final size:10
Alignment explanation
Indices: 23637--23671 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
23627 TATAAAATAA
23637 ATATATAAAT
1 ATATATAAAT
23647 ATAT-TAAAT
1 ATATATAAAT
23656 ATGATATAAAT
1 AT-ATATAAAT
23667 ATATA
1 ATATA
23672 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 9 0.39
11 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
ATATATAAAT
Found at i:23842 original size:2 final size:2
Alignment explanation
Indices: 23835--23863 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23825 AAAATTACTT
23835 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
23864 CGTCAATGTC
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:24169 original size:23 final size:24
Alignment explanation
Indices: 24129--24175 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24119 TATAAAATTA
*
24129 AAAAAATAAAATATAATATTATAT
1 AAAAAATAAAATATAATATAATAT
*
24153 AAAAAATAATATA-AATATAATAT
1 AAAAAATAAAATATAATATAATAT
24176 TTATATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATAAAATATAATATAATAT
Found at i:24173 original size:28 final size:27
Alignment explanation
Indices: 24128--24182 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
24118 ATATAAAATT
24128 AAAAAAATAAAATATAATA-TTATATA
1 AAAAAAATAAAATATAATATTTATATA
24154 AAAAATAATATAAATATAATATTTATATA
1 AAAAA-AATA-AAATATAATATTTATATA
24183 TGATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 10 0.38
29 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAAAAATAAAATATAATATTTATATA
Found at i:24181 original size:17 final size:16
Alignment explanation
Indices: 24137--24182 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
24127 TAAAAAAATA
24137 AAATATAATATTATAT
1 AAATATAATATTATAT
24153 AAA-A-AATA--ATAT
1 AAATATAATATTATAT
24165 AAATATAATATTTATAT
1 AAATATAATA-TTATAT
24182 A
1 A
24183 TGATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.28
13 1 0.04
14 8 0.32
15 1 0.04
16 3 0.12
17 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAATATTATAT
Found at i:24209 original size:29 final size:28
Alignment explanation
Indices: 24177--24238 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
24167 ATATAATATT
* *
24177 TATATATGATTATTTTAGAATTTATATAA
1 TATATATGATT-TATTAAAATTTATATAA
* *
24206 TATAAATTATTTATTAAAATTTATATAA
1 TATATATGATTTATTAAAATTTATATAA
24234 -ATATA
1 TATATA
24239 AATTATGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 4 0.14
28 15 0.54
29 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATATATGATTTATTAAAATTTATATAA
Found at i:24215 original size:26 final size:28
Alignment explanation
Indices: 24185--24244 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
24175 TTTATATATG
*
24185 ATTATT-TTAGAATTTATAT-AATATAA
1 ATTATTATTAAAATTTATATAAATATAA
24211 ATTATTTATTAAAATTTATATAAATATAA
1 ATTA-TTATTAAAATTTATATAAATATAA
24240 ATTAT
1 ATTAT
24245 GTTAAACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 2 0.07
28 13 0.43
29 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTATTATTAAAATTTATATAAATATAA
Found at i:25375 original size:23 final size:23
Alignment explanation
Indices: 25314--25378 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
25304 GTACATATCA
* * *
25314 AATT-TTAAATAAATTAATATTT
1 AATTATTAAATATATAAAAATTT
* *
25336 AATTATT-TATTTAATAAAAATTT
1 AATTATTAAATAT-ATAAAAATTT
25359 AATTATTAAATATATAAAAA
1 AATTATTAAATATATAAAAA
25379 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 6 0.18
23 24 0.73
24 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTATTAAATATATAAAAATTT
Found at i:29185 original size:2 final size:2
Alignment explanation
Indices: 29178--29212 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
29168 TAAAAAGTAA
*
29178 AT AT AT AT AT AT CAA 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
29213 CCAATACGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29196 original size:15 final size:15
Alignment explanation
Indices: 29176--29204 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29166 TTTAAAAAGT
29176 AAATATATATATATC
1 AAATATATATATATC
29191 AAATATATATATAT
1 AAATATATATATAT
29205 ATATATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATATATATATC
Found at i:30338 original size:2 final size:2
Alignment explanation
Indices: 30331--30357 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30321 GAACACATGA
30331 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
30358 AGAGATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33985 original size:16 final size:16
Alignment explanation
Indices: 33947--33989 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
33937 CTCTTAAATT
*
33947 TTAATTTTTATCTAAA
1 TTAATTTTTTTCTAAA
*
33963 TTCATTTTTTTCATAAA
1 TTAATTTTTTTC-TAAA
33980 -TAATTTTTTT
1 TTAATTTTTTT
33990 TGTTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAATTTTTTTCTAAA
Found at i:34593 original size:283 final size:279
Alignment explanation
Indices: 34071--34631 Score: 770
Period size: 283 Copynumber: 2.0 Consensus size: 279
34061 TAGGCCTTAA
*
34071 AAAATGAAAAAAATAGGATTTATTTAATCTTTTAATTATCATTTATAATAAATTAAGTGAGTATA
1 AAAATGAAAAAAATAGGATTTATTTAATCTTTTAATCATCATTTATAATAAATTAAGTGAGTATA
*
34136 TTGTTAAATTTAAATTTTGATTTCCATTGTCAATGTTTCGTTGTTGATACAGCTTTCATAACGAT
66 TTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTCGTTGTTGATACAGCTTTCATAACGAT
* ** * * * * *
34201 TTGATCATTAATAATTTTGAAATTCATTACAATAAATTATTTTATTAATTTTGTTATATACTAAA
131 TTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATTAACTTTGTTAGATACTAAA
* *
34266 ATATCATAAGATAATATTTAAATAAGTATGCAAAGTTTATAAAAATAAGAAAAAAAGAATTC-GT
196 ATATCATAAGATAATATTTAAATAAGCATGCAAAATTTAT-AAAA-AAGAAAAAAA-AATTCAG-
*
34330 TATTTTTTATGGAATTAAAATTG
257 TATTTTTTATAGAATTAAAATTG
* *
34353 AAAATGAAAAAAATAGGGATTTATTTAA-CGTTTTAGTCATCATTTATAATGAACTTAAGTGAGT
1 AAAATGAAAAAAATA-GGATTTATTTAATC-TTTTAATCATCATTTATAAT-AAATTAAGTGAGT
* * * * *
34417 ATATTGTTAGATTTATA-TTTGATCTCGATTGTCAGTGTTTCAG-TGTTGATACAGCTTTTATAA
63 ATATTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTC-GTTGTTGATACAGCTTTCATAA
* * * *
34480 TGATTTAATTACAAACAATTTTGAAATTCACTATAAGAAATTATTTTATTAACTTTGTTAGATAT
127 CGATTTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATTAACTTTGTTAGATAC
* * * *
34545 TAAAGTATCATGAGATAATATTTAAATAAGCATGTAAAATTTATAAAAAATAAAAAAAAATTCAG
192 TAAAATATCATAAGATAATATTTAAATAAGCATGCAAAATTTATAAAAAAGAAAAAAAAATTCAG
34610 TATTTTTTATAGAATTAAAATT
257 TATTTTTTATAGAATTAAAATT
34632 CTTTTAATGT
Statistics
Matches: 246, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
280 26 0.11
281 10 0.04
282 20 0.08
283 162 0.66
284 28 0.11
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (279 bp):
AAAATGAAAAAAATAGGATTTATTTAATCTTTTAATCATCATTTATAATAAATTAAGTGAGTATA
TTGTTAAATTTAAATTTTGATCTCCATTGTCAATGTTTCGTTGTTGATACAGCTTTCATAACGAT
TTAATCACAAACAATTTTGAAATTCACTACAAGAAATTATTTTATTAACTTTGTTAGATACTAAA
ATATCATAAGATAATATTTAAATAAGCATGCAAAATTTATAAAAAAGAAAAAAAAATTCAGTATT
TTTTATAGAATTAAAATTG
Found at i:34841 original size:16 final size:16
Alignment explanation
Indices: 34817--34849 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34807 ATTTATGTTT
34817 ATTTAATTTTTTAAAA
1 ATTTAATTTTTTAAAA
*
34833 ATTTTATTTTTTAAAA
1 ATTTAATTTTTTAAAA
34849 A
1 A
34850 AATTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAATTTTTTAAAA
Found at i:34843 original size:17 final size:17
Alignment explanation
Indices: 34817--34856 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34807 ATTTATGTTT
34817 ATTTAATTTTTT-AAAAA
1 ATTT-ATTTTTTAAAAAA
*
34834 TTTTATTTTTTAAAAAA
1 ATTTATTTTTTAAAAAA
34851 ATTTAT
1 ATTTAT
34857 AATGCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTATTTTTTAAAAAA
Found at i:35425 original size:67 final size:67
Alignment explanation
Indices: 35317--35451 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
35307 CAGCAAAATA
* *
35317 ATTGCAATGGAATATTATTTCCAGTCTTTTAGTTATGTATGAACACTCTTATTCGATCATTTATG
1 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTCGATCATTTATG
35382 AC
66 AC
*
35384 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTTGATCATTTATG
1 ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTCGATCATTTATG
35449 AC
66 AC
35451 A
1 A
35452 ACTCTTATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (67 bp):
ATTGCAATGGAATATTATTACCAGTCTTTTAGTTATGTATGAACACTCTGATTCGATCATTTATG
AC
Found at i:35669 original size:16 final size:15
Alignment explanation
Indices: 35636--35684 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
35626 AAAGTATTAG
*
35636 AATTCAAAAAATTCA
1 AATTTAAAAAATTCA
*
35651 AATTTAAAATAATTTA
1 AATTTAAAA-AATTCA
35667 AATTTAAAAAGATTCA
1 AATTTAAAAA-ATTCA
35683 AA
1 AA
35685 CTCAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTTAAAAAATTCA
Found at i:44422 original size:16 final size:16
Alignment explanation
Indices: 44403--44461 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
44393 GATTAAAATC
44403 TAAAAAGATCTAAACT
1 TAAAAAGATCTAAACT
* *
44419 TAAAATA-ATTTAAATT
1 TAAAA-AGATCTAAACT
*
44435 TAAAAAGATTTAAACT
1 TAAAAAGATCTAAACT
* *
44451 CAAAAAAATCT
1 TAAAAAGATCT
44462 CAAATTCGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 1 0.03
16 33 0.94
17 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAAAAGATCTAAACT
Found at i:45902 original size:27 final size:26
Alignment explanation
Indices: 45853--45953 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 26
45843 TTTTTATGTT
*
45853 AATTTATTT-TTT-TTAAA-AT-AAA
1 AATTTATTTATTTAGTAAATATAAAA
45875 AATTTATTTAATTTAAGTAAAT-TAAAA
1 AATTTATTT-ATTT-AGTAAATATAAAA
* *
45902 ATATTTAATTATTTATTAAATATAAAA
1 A-ATTTATTTATTTAGTAAATATAAAA
*
45929 AA--T-TTTATTT-TTAAATATAAAA
1 AATTTATTTATTTAGTAAATATAAAA
45951 AAT
1 AAT
45954 AATTTTTGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
22 23 0.35
23 6 0.09
24 4 0.06
26 12 0.18
27 14 0.21
28 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
AATTTATTTATTTAGTAAATATAAAA
Found at i:45921 original size:26 final size:25
Alignment explanation
Indices: 45853--45960 Score: 72
Period size: 26 Copynumber: 4.5 Consensus size: 25
45843 TTTTTATGTT
*
45853 AATTT-ATTTTTTTTAAA-ATAAAA
1 AATTTAATTTTTATTAAATATAAAA
* *
45876 ATTTATTTAA-TTTAAGTAAAT-TAAAA
1 A---ATTTAATTTTTATTAAATATAAAA
45902 ATATTTAATTATTTATTAAATATAAAA
1 A-ATTTAATT-TTTATTAAATATAAAA
*
45929 AATTT--TATTT-TTAAATATAAAA
1 AATTTAATTTTTATTAAATATAAAA
45951 AA--TAATTTTT
1 AATTTAATTTTT
45961 GACGTGATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.01
22 18 0.26
23 4 0.06
24 8 0.12
25 1 0.01
26 29 0.43
27 7 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (25 bp):
AATTTAATTTTTATTAAATATAAAA
Found at i:45944 original size:22 final size:23
Alignment explanation
Indices: 45910--45953 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
45900 AAATATTTAA
45910 TTATTTATTAAATATAAAAAATT
1 TTATTTATTAAATATAAAAAATT
45933 TTATTT-TTAAATATAAAAAAT
1 TTATTTATTAAATATAAAAAAT
45954 AATTTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTTATTAAATATAAAAAATT
Found at i:45958 original size:20 final size:21
Alignment explanation
Indices: 45908--45960 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
45898 AAAAATATTT
45908 AATT-ATTTATTAAATATAAAA
1 AATTAATTT-TTAAATATAAAA
*
45929 AATTTTATTTTTAAATATAAAA
1 AA-TTAATTTTTAAATATAAAA
45951 AA-TAATTTTT
1 AATTAATTTTT
45961 GACGTGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 16 0.55
23 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAATTTTTAAATATAAAA
Found at i:47399 original size:34 final size:34
Alignment explanation
Indices: 47357--47525 Score: 230
Period size: 34 Copynumber: 5.0 Consensus size: 34
47347 TAGGTGAAGC
* *
47357 ATGTTAGGTATGTTAAGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
*
47391 ATGTTAGGTGTGTTAAGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
*
47425 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAAA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
* * * *
47459 ATATTAGATGTGTTAGGTAATGTATTTGGTGAAA
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
* * * *
47493 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAG
47526 TAAGATATTT
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 125 1.00
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (34 bp):
ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
Found at i:52291 original size:34 final size:34
Alignment explanation
Indices: 52252--52383 Score: 165
Period size: 34 Copynumber: 3.9 Consensus size: 34
52242 GTGAAGCATG
* * * *
52252 TTAGGTATGTTAAGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAAAATA
* *
52286 TTAGGTGTATTAGGAGATGTATTTGGTGAAAATA
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAAAATA
* *
52320 TTAGATGTGTTAGGTAATGTATTTGGTGAAAATA
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAAAATA
* * *
52354 TTAGGTGTGTTAGGTAATGTGTTAGGTGAA
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAA
52384 TAAGATATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 85 1.00
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTGGTGAAAATA
Found at i:52382 original size:68 final size:69
Alignment explanation
Indices: 52234--52383 Score: 178
Period size: 68 Copynumber: 2.2 Consensus size: 69
52224 CTTTGTTAAG
* * * * * *
52234 TGTGTTAGGTGAAGCATGTTAGGTATGTTAAGTGATGTATTTGGTGAGAATGTTAGGTGTATTAG
1 TGTGTTAGGTGAAGAATATTAGATATGTTAAGTAATGTATTTGGTGAAAATATTAGGTGTATTAG
52299 GAGA
66 GAGA
* * * * *
52303 TGTATTTGGTGAA-AATATTAGATGTGTTAGGTAATGTATTTGGTGAAAATATTAGGTGTGTTAG
1 TGTGTTAGGTGAAGAATATTAGATATGTTAAGTAATGTATTTGGTGAAAATATTAGGTGTATTAG
52367 GTA-A
66 G-AGA
52371 TGTGTTAGGTGAA
1 TGTGTTAGGTGAA
52384 TAAGATATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
68 55 0.82
69 12 0.18
ACGTcount: A:0.28, C:0.01, G:0.32, T:0.39
Consensus pattern (69 bp):
TGTGTTAGGTGAAGAATATTAGATATGTTAAGTAATGTATTTGGTGAAAATATTAGGTGTATTAG
GAGA
Found at i:55874 original size:20 final size:21
Alignment explanation
Indices: 55839--55882 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
55829 GTCAGAAAGA
* *
55839 AAAGTAAAAAGATGAAAAATT
1 AAAGAAAAAAGATGAAAAAAT
55860 AAAGAAAAAAG-TGAAAAAAT
1 AAAGAAAAAAGATGAAAAAAT
55880 AAA
1 AAA
55883 ATATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAGAAAAAAGATGAAAAAAT
Found at i:57543 original size:2 final size:2
Alignment explanation
Indices: 57498--57534 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
57488 ACTTCTAGTC
57498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57535 CTCATATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61156 original size:26 final size:25
Alignment explanation
Indices: 61113--61185 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
61103 AGATTTTAAG
*
61113 AAAAAAAAGCAAAG-AAAAAACAGA-
1 AAAAAAAAACAAAGCAAAAAA-AGAT
61137 AAAAACAAAA-AGAAGCAAAAAAAGATT
1 AAAAA-AAAACA-AAGCAAAAAAAGA-T
61164 AAAAAAAAACAAAGCAAAAAAA
1 AAAAAAAAACAAAGCAAAAAAA
61186 AAACGAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
24 6 0.14
25 9 0.21
26 21 0.50
27 6 0.14
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (25 bp):
AAAAAAAAACAAAGCAAAAAAAGAT
Found at i:61183 original size:16 final size:17
Alignment explanation
Indices: 61164--61201 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
61154 AAAAAAGATT
61164 AAAAAAAAAC-AAAGCA
1 AAAAAAAAACAAAAGCA
61180 AAAAAAAAACGAAAAGCA
1 AAAAAAAAAC-AAAAGCA
61198 AAAA
1 AAAA
61202 TAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAGCA
Found at i:61187 original size:18 final size:18
Alignment explanation
Indices: 61116--61201 Score: 54
Period size: 20 Copynumber: 4.7 Consensus size: 18
61106 TTTTAAGAAA
*
61116 AAAAAGCAAAGAAAAAACAG
1 AAAAAGCAAA-AAAAAA-AC
* *
61136 AAAAAACAAAAAGAAGCAA-
1 AAAAAGCAAAAA-AA-AAAC
61155 AAAAAG-ATTAAAAAAAAAC
1 AAAAAGCA--AAAAAAAAAC
61174 --AAAGCAAAAAAAAAAC
1 AAAAAGCAAAAAAAAAAC
*
61190 GAAAAGCAAAAA
1 AAAAAGCAAAAA
61202 TAATTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
16 10 0.19
17 4 0.07
18 14 0.26
19 9 0.17
20 16 0.30
21 1 0.02
ACGTcount: A:0.78, C:0.09, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAGCAAAAAAAAAAC
Found at i:61194 original size:26 final size:25
Alignment explanation
Indices: 61113--61194 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 25
61103 AGATTTTAAG
*
61113 AAAAAAAAGCAAAGAAAAAACAGAAA
1 AAAAAAAAGCAAAAAAAAAAC-GAAA
**
61139 AAACAAAAAG-AAGCAAAAAAAGATTAAAA
1 AAA-AAAAAGCAA--AAAAAAA-A-CGAAA
61168 AAAAACAAAGCAAAAAAAAAACGAAA
1 AAAAA-AAAGCAAAAAAAAAACGAAA
61194 A
1 A
61195 GCAAAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
26 9 0.20
27 7 0.16
28 15 0.34
29 11 0.25
30 2 0.05
ACGTcount: A:0.79, C:0.09, G:0.10, T:0.02
Consensus pattern (25 bp):
AAAAAAAAGCAAAAAAAAAACGAAA
Found at i:62572 original size:28 final size:26
Alignment explanation
Indices: 62536--62726 Score: 96
Period size: 28 Copynumber: 7.0 Consensus size: 26
62526 GATAGCATTT
* * *
62536 AAGTAAAAGCCTACATTTGTTGGCATCC
1 AAGTCAAAGCCCACATTTGCTGGCA--C
* *
62564 GAGTCAAAGCCCACACTTGCTGGCAC
1 AAGTCAAAGCCCACATTTGCTGGCAC
* *
62590 AAGTCAAAGCCCACATTCG-TCGGTACAT
1 AAGTCAAAGCCCACATTTGCT-GG--CAC
* * * *
62618 AAGTCTAAGCCCACATTCGTTAGCAC
1 AAGTCAAAGCCCACATTTGCTGGCAC
* * * *
62644 GTAAGTCGAAGCCCACACTTGTTGTCAC
1 --AAGTCAAAGCCCACATTTGCTGGCAC
* * * *
62672 AAGTCAAAGCCTACATTCGTTGTCACAC
1 AAGTCAAAGCCCACATTTGCTG--GCAC
* * *
62700 AAGTCTAAGCCTACATTGGCTGGCAC
1 AAGTCAAAGCCCACATTTGCTGGCAC
62726 A
1 A
62727 TAAATTAATA
Statistics
Matches: 129, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
25 1 0.01
26 43 0.33
28 84 0.65
29 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGTCAAAGCCCACATTTGCTGGCAC
Found at i:62628 original size:82 final size:81
Alignment explanation
Indices: 62542--62716 Score: 219
Period size: 82 Copynumber: 2.1 Consensus size: 81
62532 ATTTAAGTAA
* *
62542 AAGCCTACATTTGTTGGCATCCG-AGTCAAAGCCCACACTTGCTGGCACAAGTCAAAGCCCACAT
1 AAGCCTACATTCGTTAGCA--CGAAGTCAAAGCCCACACTTGCTGGCACAAGTCAAAGCCCACAT
*
62606 TCGTCGGT-ACATAAGTCT
64 TCGT-GGTCACACAAGTCT
* * * * *
62624 AAGCCCACATTCGTTAGCACGTAAGTCGAAGCCCACACTTGTTGTCACAAGTCAAAGCCTACATT
1 AAGCCTACATTCGTTAGCACG-AAGTCAAAGCCCACACTTGCTGGCACAAGTCAAAGCCCACATT
*
62689 CGTTGTCACACAAGTCT
65 CGTGGTCACACAAGTCT
62706 AAGCCTACATT
1 AAGCCTACATT
62717 GGCTGGCACA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 76 0.95
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (81 bp):
AAGCCTACATTCGTTAGCACGAAGTCAAAGCCCACACTTGCTGGCACAAGTCAAAGCCCACATTC
GTGGTCACACAAGTCT
Found at i:62704 original size:54 final size:56
Alignment explanation
Indices: 62587--62716 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 56
62577 CACTTGCTGG
* *
62587 CACAAGTCAAAGCCCACATTCGTCGGTACATAAGTCTAAGCCCACATTCGTTAGCA
1 CACAAGTCAAAGCCCACATTCGTCGGTACACAAGTCAAAGCCCACATTCGTTAGCA
** * * *
62643 CGTAAGTCGAAGCCCACACTT-GT-TGT-CACAAGTCAAAGCCTACATTCGTT-GTCA
1 CACAAGTCAAAGCCCACA-TTCGTCGGTACACAAGTCAAAGCCCACATTCGTTAG-CA
* *
62697 CACAAGTCTAAGCCTACATT
1 CACAAGTCAAAGCCCACATT
62717 GGCTGGCACA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
53 3 0.05
54 37 0.61
55 2 0.03
56 17 0.28
57 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (56 bp):
CACAAGTCAAAGCCCACATTCGTCGGTACACAAGTCAAAGCCCACATTCGTTAGCA
Found at i:62773 original size:28 final size:27
Alignment explanation
Indices: 62742--62837 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
62732 TAATACCCAT
*
62742 ACTAGTTGGCACTTGAGTCAAAGCCTAC
1 ACTAGTTAGCACTT-AGTCAAAGCCTAC
* * *
62770 ACTAGCTAGCACCTACGTCAAAG-CTCAT
1 ACTAGTTAGCACTTA-GTCAAAGCCT-AC
* *
62798 ACTAGTTAGCATCTAAGTCAAAGCCCAC
1 ACTAGTTAGCA-CTTAGTCAAAGCCTAC
*
62826 ACTAGTTGGCAC
1 ACTAGTTAGCAC
62838 CTCGTAGGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.07
28 47 0.87
29 3 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (27 bp):
ACTAGTTAGCACTTAGTCAAAGCCTAC
Found at i:65527 original size:22 final size:22
Alignment explanation
Indices: 65476--65552 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 22
65466 AAATTTGCCT
*
65476 GCATGTATCGACACAA-TA-GA
1 GCATGTATCGATACAATTATGA
** *
65496 TAATATATCGATACAATTATGA
1 GCATGTATCGATACAATTATGA
65518 GCATGTATCGATAC-ATT-T-A
1 GCATGTATCGATACAATTATGA
*
65537 CTCATGTATCGATACA
1 -GCATGTATCGATACA
65553 TTTCCTTTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
20 26 0.58
21 5 0.11
22 13 0.29
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (22 bp):
GCATGTATCGATACAATTATGA
Found at i:66287 original size:51 final size:51
Alignment explanation
Indices: 66232--66333 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
66222 TCTTCTACCT
66232 TGTTAAAAGTCATTGACCTCTCAAATAACAAGTTTGAAGGAGAAATTCCTA
1 TGTTAAAAGTCATTGACCTCTCAAATAACAAGTTTGAAGGAGAAATTCCTA
*
66283 TGTTAAAAGTCATTGACCTCTCAAATAACAGGTTTGAAGGAGAAATTCCTA
1 TGTTAAAAGTCATTGACCTCTCAAATAACAAGTTTGAAGGAGAAATTCCTA
66334 AGGTTATTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTTAAAAGTCATTGACCTCTCAAATAACAAGTTTGAAGGAGAAATTCCTA
Found at i:71815 original size:17 final size:17
Alignment explanation
Indices: 71783--71816 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
71773 AAAAAAAAAT
71783 TAAAACATAATATAATA
1 TAAAACATAATATAATA
71800 TAAAA-ATAATATTAATA
1 TAAAACATAATA-TAATA
71817 CAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAACATAATATAATA
Found at i:74136 original size:8 final size:9
Alignment explanation
Indices: 74112--74150 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
74102 TGCTTAAATA
74112 ATTTTTTTCC
1 ATTTTTTT-C
*
74122 AATTTTTTTT
1 -ATTTTTTTC
74132 ATTTTTTTC
1 ATTTTTTTC
74141 ATTTTTTTC
1 ATTTTTTTC
74150 A
1 A
74151 AGAATTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:76434 original size:63 final size:63
Alignment explanation
Indices: 76367--76550 Score: 235
Period size: 62 Copynumber: 2.9 Consensus size: 63
76357 GTAAACTTTA
* ** *
76367 GTGGGTTTGGAAGATGGGTAGTGGTTCATTGGCTTGGGAGATACTGATCGATGATGGAGTTTG
1 GTGGGTTTGGAAGATGGATAGTGGTTCGGTGGCTTGGGAGATGCTGATCGATGATGGAGTTTG
* * ** * *
76430 GTGGGTTTGGAAGATGGATGGTGGTCCGGTGGCTT-AAAGGTGCTGATCGACGATGGAGTTTG
1 GTGGGTTTGGAAGATGGATAGTGGTTCGGTGGCTTGGGAGATGCTGATCGATGATGGAGTTTG
* * * *
76492 ATAGGTTTGGAGGATGGATAGTGGTTCGGTGGCTTGGGAGATGCTGATCAATGATGGAG
1 GTGGGTTTGGAAGATGGATAGTGGTTCGGTGGCTTGGGAGATGCTGATCGATGATGGAG
76551 CTTAATGGTT
Statistics
Matches: 100, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
62 52 0.52
63 48 0.48
ACGTcount: A:0.20, C:0.08, G:0.42, T:0.30
Consensus pattern (63 bp):
GTGGGTTTGGAAGATGGATAGTGGTTCGGTGGCTTGGGAGATGCTGATCGATGATGGAGTTTG
Found at i:83645 original size:19 final size:19
Alignment explanation
Indices: 83621--83688 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
83611 AATTCAACAG
83621 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
83640 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
83655 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
83672 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
83689 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:83659 original size:32 final size:32
Alignment explanation
Indices: 83623--83685 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
83613 TTCAACAGTT
*
83623 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
83655 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
83686 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:83660 original size:13 final size:13
Alignment explanation
Indices: 83642--83666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83632 ACATAAGTTT
83642 TGTATCGATACAA
1 TGTATCGATACAA
83655 TGTATCGATACA
1 TGTATCGATACA
83667 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:83746 original size:13 final size:13
Alignment explanation
Indices: 83728--83753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83718 CATTTTTCTG
83728 TGTATCGATACAT
1 TGTATCGATACAT
83741 TGTATCGATACAT
1 TGTATCGATACAT
83754 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:83750 original size:33 final size:33
Alignment explanation
Indices: 83708--83774 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
83698 GCCAAGGAAA
***
83708 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
83741 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
83774 T
1 T
83775 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.