Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 174 of 214
Found at i:51121254 original size:9 final size:9
Alignment explanation
Indices: 51121240--51121280 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
51121230 AGTCCAGGTT
51121240 TTTTTTCTG
1 TTTTTTCTG
*
51121249 TTTTTTAT-
1 TTTTTTCTG
51121257 TTTTTTCTG
1 TTTTTTCTG
*
51121266 TTTTTTTTG
1 TTTTTTCTG
51121275 TTTTTT
1 TTTTTT
51121281 TTATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (9 bp):
TTTTTTCTG
Found at i:51121279 original size:17 final size:17
Alignment explanation
Indices: 51121239--51121271 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51121229 CAGTCCAGGT
51121239 TTTTTTTCTGTTTTTTA
1 TTTTTTTCTGTTTTTTA
51121256 TTTTTTTCTGTTTTTT
1 TTTTTTTCTGTTTTTT
51121272 TTGTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTGTTTTTTA
Found at i:51121281 original size:9 final size:9
Alignment explanation
Indices: 51121237--51121282 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
51121227 ATCAGTCCAG
51121237 GTTTTTTTT
1 GTTTTTTTT
* *
51121246 CTGTTTTTT
1 GTTTTTTTT
*
51121255 ATTTTTTTCT
1 GTTTTTTT-T
51121265 GTTTTTTTT
1 GTTTTTTTT
51121274 GTTTTTTTT
1 GTTTTTTTT
51121283 ATATATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:51121339 original size:27 final size:26
Alignment explanation
Indices: 51121281--51121339 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
51121271 TTTGTTTTTT
*
51121281 TTATATATTTTAGTAAATAAAAAAAT
1 TTATATATTTTAGTAAATAAAAAAAA
*
51121307 TATATATATTTTGGTAAATAAAAAAAAA
1 T-TATATATTTTAGTAAAT-AAAAAAAA
51121335 TTATA
1 TTATA
51121340 ACATTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 20 0.69
28 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (26 bp):
TTATATATTTTAGTAAATAAAAAAAA
Found at i:51121765 original size:20 final size:21
Alignment explanation
Indices: 51121742--51121793 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
51121732 CTTATTTTCA
*
51121742 ATTTATTAATTTTATAAAA-T
1 ATTTATTAATTTTAGAAAATT
51121762 ATTT-TTAATGTTTAGAAAATT
1 ATTTATTAAT-TTTAGAAAATT
*
51121783 ATTTAGTAATT
1 ATTTATTAATT
51121794 GATTTAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 6 0.22
22 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (21 bp):
ATTTATTAATTTTAGAAAATT
Found at i:51122529 original size:28 final size:28
Alignment explanation
Indices: 51122498--51122559 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
51122488 ACAAAAACGA
*
51122498 TCTCTTTTTATTTAACCCAAACGGAATT
1 TCTCTTTTTATTTAACCCAAACGGAACT
* *
51122526 TCTC-TTTTCTTTAATCCAAACGGAACT
1 TCTCTTTTTATTTAACCCAAACGGAACT
51122553 TCTCTTT
1 TCTCTTT
51122560 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (28 bp):
TCTCTTTTTATTTAACCCAAACGGAACT
Found at i:51133664 original size:22 final size:22
Alignment explanation
Indices: 51133638--51133705 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
51133628 ATATTCAAAT
51133638 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * *
51133660 TATAATAGCAAAAT-GATAGCAA
1 AATAACAACAAAATAG-TAGCAA
* * *
51133682 AACAACAACATAACAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
51133704 AA
1 AA
51133706 CATGGAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:51134971 original size:61 final size:61
Alignment explanation
Indices: 51134892--51135006 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
51134882 TATTTTTTAA
* * * * *
51134892 TTTTTAGAGTTAGGACTAAATTGACAATTTTTGTAAATATTGAGGACCAAATTTATTGAAT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTTATTGAAT
* * *
51134953 TTTTTTGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCTAAATTT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTT
51135007 GTTGGTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGACCAAATTTATTGAAT
Found at i:51136303 original size:23 final size:23
Alignment explanation
Indices: 51136277--51136329 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
51136267 ATAAGTGCCA
51136277 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
51136300 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
51136323 CACTGAT
1 CACTGAT
51136330 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:51141794 original size:22 final size:22
Alignment explanation
Indices: 51141764--51142017 Score: 102
Period size: 21 Copynumber: 11.3 Consensus size: 22
51141754 TGGATTAGAA
* *
51141764 TTTTGTATGAATATTCTAATTT
1 TTTTATATGAATATTGTAATTT
*
51141786 TTTTATATGAACATTGTAA-TT
1 TTTTATATGAATATTGTAATTT
*
51141807 TTTT-TATGAATATTGTAATTA
1 TTTTATATGAATATTGTAATTT
*
51141828 TTTTATAATTAA-ATTTGT-ATTT
1 TTTTAT-ATGAATA-TTGTAATTT
* * *
51141850 ATAGTT-T-TGGAT-TAGT-A---
1 -T-TTTATATGAATATTGTAATTT
*
51141867 TTTTGTATGAATATTGTAATTTTAT
1 TTTTATATGAATATTGTAA--TT-T
*
51141892 AATTTTATATGAATATTGCAA-TT
1 --TTTTATATGAATATTGTAATTT
*
51141915 TTTTGTATGAATATTGTAATATTGT
1 TTTTATATGAATATTGT-A-ATT-T
*
51141940 AATTTTGTATGAATATTGTAATGTCT
1 --TTTTATATGAATATTGTAAT-T-T
***
51141966 AGATATACTGTAATATTGTAA-TT
1 TTTTATA-TG-AATATTGTAATTT
* *
51141989 TTTTGTATGAATATTGTAATTA
1 TTTTATATGAATATTGTAATTT
51142011 TTTTATA
1 TTTTATA
51142018 ATTAATTTGT
Statistics
Matches: 174, Mismatches: 29, Indels: 58
0.67 0.11 0.22
Matches are distributed among these distances:
15 2 0.01
16 2 0.01
17 4 0.02
18 3 0.02
19 1 0.01
20 17 0.10
21 38 0.22
22 31 0.18
23 16 0.09
24 8 0.05
25 5 0.03
26 13 0.07
27 34 0.20
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (22 bp):
TTTTATATGAATATTGTAATTT
Found at i:51141814 original size:20 final size:20
Alignment explanation
Indices: 51141764--51141833 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
51141754 TGGATTAGAA
* *
51141764 TTTTGTATGAATATTCTAATT
1 TTTTTTATGAATATTGTAA-T
*
51141785 TTTTTATATGAACATTGTAAT
1 TTTTT-TATGAATATTGTAAT
51141806 TTTTTTATGAATATTGTAAT
1 TTTTTTATGAATATTGTAAT
*
51141826 TATTTTAT
1 TTTTTTAT
51141834 AATTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.49
21 10 0.23
22 12 0.28
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.59
Consensus pattern (20 bp):
TTTTTTATGAATATTGTAAT
Found at i:51141826 original size:103 final size:107
Alignment explanation
Indices: 51141719--51141934 Score: 273
Period size: 103 Copynumber: 2.0 Consensus size: 107
51141709 TATTAATTAT
* * *
51141719 TAATTA-TAAATTATCTATATTTAGTGTTTATAG-TTTGGATTAGAATTTTGTATGAATATTCTA
1 TAATTATTAAATAAT-TAAATTT-GTATTTATAGTTTTGGATTAGAATTTTGTATGAATATTCTA
*
51141782 A-TT-T-TTTTATATGAACATTGTAATTTTTT-TATGAATATTG
64 ATTTATATTTTATATGAACATTGCAATTTTTTGTATGAATATTG
** * *
51141822 TAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAAT
1 TAATTATTAAATAATTAAATTTGTATTTATAGTTTTGGATTAGAATTTTGTATGAATATTCTAA-
*
51141887 TTTATAATTTTATATGAATATTGCAATTTTTTGTATGAATATTG
65 TTTAT-ATTTTATATGAACATTGCAATTTTTTGTATGAATATTG
51141931 TAAT
1 TAAT
51141935 ATTGTAATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
102 9 0.09
103 41 0.43
104 5 0.05
105 2 0.02
106 1 0.01
108 23 0.24
109 15 0.16
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (107 bp):
TAATTATTAAATAATTAAATTTGTATTTATAGTTTTGGATTAGAATTTTGTATGAATATTCTAAT
TTATATTTTATATGAACATTGCAATTTTTTGTATGAATATTG
Found at i:51141896 original size:27 final size:25
Alignment explanation
Indices: 51141866--51141961 Score: 110
Period size: 27 Copynumber: 3.8 Consensus size: 25
51141856 TTGGATTAGT
51141866 ATTTTGTATGAATATTGTAATTTTATA
1 ATTTTGTATGAATATTGTAA-TTT-TA
* *
51141893 ATTTTATATGAATATTGCAA--TT-
1 ATTTTGTATGAATATTGTAATTTTA
51141915 -TTTTGTATGAATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAAT-TT-TA
51141941 ATTTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
51141962 GTCTAGATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
21 17 0.29
23 1 0.02
24 2 0.03
25 1 0.02
27 38 0.64
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.53
Consensus pattern (25 bp):
ATTTTGTATGAATATTGTAATTTTA
Found at i:51142206 original size:37 final size:37
Alignment explanation
Indices: 51142155--51142235 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
51142145 CATATAAAGT
*
51142155 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGATTAA
51142193 TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
51142230 TTATAA
1 TTATAA
51142236 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 38 0.90
38 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGATTAA
Found at i:51145420 original size:22 final size:22
Alignment explanation
Indices: 51145393--51145434 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
51145383 AAAATACCTT
*
51145393 TTTTTTTCTTCT-TTTCCTTCC
1 TTTTTTTCTTCTGCTTCCTTCC
51145414 TTTTTTTCTTCTGCTTCCTTC
1 TTTTTTTCTTCTGCTTCCTTC
51145435 TTATTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTCTTCTGCTTCCTTCC
Found at i:51145422 original size:18 final size:18
Alignment explanation
Indices: 51145395--51145444 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
51145385 AATACCTTTT
*
51145395 TTTTTCTTCTTTTCCTTCC
1 TTTTT-TTCTTCTCCTTCC
*
51145414 TTTTTTTCTTCTGCTTCC
1 TTTTTTTCTTCTCCTTCC
51145432 TTCTTATTTCTTC
1 TT-TT-TTTCTTC
51145445 CGTTTCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTTTCTTCTCCTTCC
Found at i:51145551 original size:27 final size:27
Alignment explanation
Indices: 51145521--51145584 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
51145511 CTCTTAGTAT
51145521 GGCACCAATAATGGCGCCTCCCAGATA
1 GGCACCAATAATGGCGCCTCCCAGATA
** * **
51145548 GGCACCACCATTGGCGCCTCTGAGATA
1 GGCACCAATAATGGCGCCTCCCAGATA
*
51145575 GGCGCCAATA
1 GGCACCAATA
51145585 CTATGTATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.16
Consensus pattern (27 bp):
GGCACCAATAATGGCGCCTCCCAGATA
Found at i:51146316 original size:56 final size:56
Alignment explanation
Indices: 51146230--51146341 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
51146220 CATTCCGGTG
51146230 TAAATTTTGGTTGGTACCGGTCGTATCAGTCTGTACTAGTTGATTTCTCCCATACC
1 TAAATTTTGGTTGGTACCGGTCGTATCAGTCTGTACTAGTTGATTTCTCCCATACC
51146286 TAAATTTTGGTTGGTACCGGTCGTATCAGTCTGTACTAGTTGATTTCTCCCATACC
1 TAAATTTTGGTTGGTACCGGTCGTATCAGTCTGTACTAGTTGATTTCTCCCATACC
51146342 GATCAAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (56 bp):
TAAATTTTGGTTGGTACCGGTCGTATCAGTCTGTACTAGTTGATTTCTCCCATACC
Found at i:51147358 original size:17 final size:17
Alignment explanation
Indices: 51147313--51147358 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
51147303 AAACTATAAC
51147313 AAAATTATTT--TTTAA
1 AAAATTATTTAATTTAA
*
51147328 AATATT-TTTAAATTTAA
1 AAAATTATTT-AATTTAA
51147345 AAAATTATTTAATT
1 AAAATTATTTAATT
51147359 ATTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 3 0.12
15 5 0.20
17 14 0.56
18 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATTATTTAATTTAA
Found at i:51151576 original size:21 final size:21
Alignment explanation
Indices: 51151530--51151580 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
51151520 TATCTGATAA
*
51151530 AAAAATAAATTAATTTATTAG
1 AAAAATAAATTAATTTATCAG
*
51151551 AAAAATAAATTTATTTATCA-
1 AAAAATAAATTAATTTATCAG
51151571 ATAAAATAAA
1 A-AAAATAAA
51151581 AATACTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATAAATTAATTTATCAG
Found at i:51154376 original size:39 final size:39
Alignment explanation
Indices: 51154333--51154427 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
51154323 CCCGGTGCTT
51154333 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
51154372 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
* *
51154411 GTCCCTGTGGTTGGTGT
1 GTCCCTGTTGTCGGTGT
51154428 TGAGGTAGGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.04, C:0.20, G:0.39, T:0.37
Consensus pattern (39 bp):
GTCCCTGTTGTCGGTGTCCCCGTTGTTGGTGTGGTAGGA
Found at i:51154423 original size:24 final size:24
Alignment explanation
Indices: 51154387--51154478 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
51154377 TGTTGTCGGT
* *
51154387 GTCCCCGTTGTTGGTGTGGTAGGA
1 GTCCCTGTGGTTGGTGTGGTAGGA
*
51154411 GTCCCTGTGGTTGGTGTTGAGGTAGGC
1 GTCCCTGTGGTTGGTG-T--GGTAGGA
* * *
51154438 GTCCCTGTGGTCGGTGTCGTCGGA
1 GTCCCTGTGGTTGGTGTGGTAGGA
*
51154462 GTCCCTGTGGATGGTGT
1 GTCCCTGTGGTTGGTGT
51154479 TGTGCTTGTA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
24 33 0.59
25 1 0.02
26 1 0.02
27 21 0.38
ACGTcount: A:0.07, C:0.18, G:0.42, T:0.33
Consensus pattern (24 bp):
GTCCCTGTGGTTGGTGTGGTAGGA
Found at i:51155964 original size:19 final size:19
Alignment explanation
Indices: 51155885--51155970 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 19
51155875 TCGAATTTAA
* *
51155885 ATTTATTTAAAAATATAAA
1 ATTTTTTTAAAAATATAAT
* *
51155904 ATTATTTTT-ATATTATAAT
1 ATT-TTTTTAAAAATATAAT
*
51155923 ATTTAAATTTT--AAATAT-AC
1 ATTT---TTTTAAAAATATAAT
51155942 ATTTTTTTAAAAATATAAT
1 ATTTTTTTAAAAATATAAT
*
51155961 ATTTTATTAA
1 ATTTTTTTAA
51155971 TTAAATTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.08
18 7 0.14
19 28 0.55
20 8 0.16
21 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTTAAAAATATAAT
Found at i:51162991 original size:39 final size:38
Alignment explanation
Indices: 51162943--51163131 Score: 118
Period size: 39 Copynumber: 4.8 Consensus size: 38
51162933 GTTTAGTTAT
*
51162943 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAAC
1 TAAT-ATTATTGTTAGTTAGTATTATTATTAGT-AAAAAC
* * **
51162983 TAATATTATTATCATGGTTAGTTATTAGGATTAGTAAAAACCC
1 TAATATTATTGT--TAGTTAG-TATTATTATTAGTAAAAA--C
* * ****
51163026 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTAC
1 TAA-TATTATTGTTAGTTAGTATTATTATTAGTAAAAAC
*
51163064 ATTATATTATTGTTAGTTAGTATTATT-TTGAGT-AAAAC
1 -TAATATTATTGTTAGTTAGTATTATTATT-AGTAAAAAC
* *
51163102 TATTATTATTGTTA-TT-GTGTTAGTTATTAG
1 TAATATTATTGTTAGTTAGTATTA-TTATTAG
51163132 GATTAGTGGT
Statistics
Matches: 116, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
35 5 0.04
36 6 0.05
37 14 0.12
38 12 0.10
39 26 0.22
40 14 0.12
41 16 0.14
42 11 0.09
43 5 0.04
44 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (38 bp):
TAATATTATTGTTAGTTAGTATTATTATTAGTAAAAAC
Found at i:51165978 original size:8 final size:8
Alignment explanation
Indices: 51165946--51166001 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
51165936 GGAATTGAGC
51165946 TAATGTTG
1 TAATGTTG
**
51165954 TAAAATTG
1 TAATGTTG
*
51165962 TTATG-TG
1 TAATGTTG
51165969 TAATGTTG
1 TAATGTTG
51165977 TAATGTTG
1 TAATGTTG
51165985 TAATGTTG
1 TAATGTTG
*
51165993 CAATGTTG
1 TAATGTTG
51166001 T
1 T
51166002 TTTAACACCC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 6 0.15
8 33 0.85
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.48
Consensus pattern (8 bp):
TAATGTTG
Found at i:51168351 original size:153 final size:156
Alignment explanation
Indices: 51168151--51168450 Score: 441
Period size: 157 Copynumber: 1.9 Consensus size: 156
51168141 TGCCTGCAAC
* * *
51168151 TTAAAAAAGAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCGTA-TTTTTTCCCGAATTTT
1 TTAAAAAAGAATTTAGAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTT
* *
51168215 ATTACTTT-A-AAAAATATAATATTTTC-TAATTTTATTGTATTACATTATTTTAGTACATTATG
66 ATTACTTTAATAAAAATATAATATTTTCGT-ATTTTATTATATTACATTATTTAAGTACATTATG
51168277 TTTGAAAT-TCATTAATTTAGTGAGTTT
130 TTTGAAATGT-ATTAATTTAGTGAGTTT
* *
51168304 TTAAAATA-AATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGGATTT
1 TTAAAAAAGAATTTAGAAAAA-AACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTT
* *
51168368 TATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTAAGTACATTAT
65 TATTACTTT-AATAAAAATATAATATTTTCGTATTTTATTATATTACATTATTTAAGTACATTAT
51168433 GTTTGAAATGTATTAATT
129 GTTTGAAATGTATTAATT
51168451 AATTCTATTT
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
152 11 0.08
153 32 0.24
154 23 0.18
156 1 0.01
157 62 0.47
158 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (156 bp):
TTAAAAAAGAATTTAGAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTT
ATTACTTTAATAAAAATATAATATTTTCGTATTTTATTATATTACATTATTTAAGTACATTATGT
TTGAAATGTATTAATTTAGTGAGTTT
Found at i:51168526 original size:120 final size:119
Alignment explanation
Indices: 51168401--51168618 Score: 330
Period size: 120 Copynumber: 1.8 Consensus size: 119
51168391 TATTTTCGTA
* *
51168401 TTTTATTATTTTACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAATTCTATTTTTTTA
1 TTTTATTATTTTACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCT-GTTTTTTA
*
51168466 AA-AAATAGTAAAAAACTCTTATTTCTGCCCTTTAAAAAAATATACTACTTTTTAT
65 AATAAAT-GTAAAAAACTCTTATTTCGGCCCTTTAAAAAAATATACTACTTTTTAT
* * * * *
51168521 TTTTATTATTTTACATTATTTTAGTACATTATGTTTTAAATTTATTAATTTAGTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCTGTTTTTTAA
*
51168586 ATAAATTTAAAAAACTCTTATTTCGGCCCTTTA
66 ATAAATGTAAAAAACTCTTATTTCGGCCCTTTA
51168619 CTCGTATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
119 34 0.39
120 54 0.61
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (119 bp):
TTTTATTATTTTACATTATTTAAGTACATTATGTTTGAAATGTATTAATTAAGTCTGTTTTTTAA
ATAAATGTAAAAAACTCTTATTTCGGCCCTTTAAAAAAATATACTACTTTTTAT
Found at i:51168680 original size:152 final size:151
Alignment explanation
Indices: 51168501--51168999 Score: 600
Period size: 152 Copynumber: 3.3 Consensus size: 151
51168491 TGCCCTTTAA
* *
51168501 AAAAATATACTACTTTTTATTTTTATTATTTTACATTATTTTAGTACATTATGTTTTAAATTTAT
1 AAAAATATACTATTTTTTA-TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* * *
51168566 TAATTTAGTGTGTTTTTTAAATAAATTTAAAAAACTCTTATTTCGGCCCTTTACTCGTATTTTTT
65 TAATTTAGTATGTTTTTTAAATAAATTTAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTT
51168631 CCCGAATTTTATTACTTTCAAT
130 CCCGAATTTTATTACTTTCAAT
* *
51168653 AAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
1 AAAAATATACTATTTTT-TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* ** * * * *
51168718 TAAGTAATT-CTAT-TTTTTTAAATTTA-GTAAAATACCCTTATTTCGACCCTTTGTTCGTATTT
65 TAA-T--TTAGTATGTTTTTTAAATAAATTTAAAAAACCCTTATTTCGGCCCTTTGCTCGTA--T
*
51168780 TTTTTCTCCGGATTTTATTACTTT--A-
125 TTTTTC-CCGAATTTTATTACTTTCAAT
* * *
51168805 CAAAATATACGATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
1 AAAAATATACTATTTT-TTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* * * * *
51168870 TAATTTAGTATGTTTTCTAAATAAAGTTCAAAAAATAACCCTTATTTCGGCCATTTGCTTGTCTT
65 TAATTTAGTATGTTTTTTAAATAAA-TT--TAAAA-AACCCTTATTTCGGCCCTTTGCTCGTATT
*
51168935 TTTTCCCAAATTTTATTACTTTCAAT
126 TTTTCCCGAATTTTATTACTTTCAAT
*
51168961 AAAAATATA-TATTTTTTATTTTGTTATTTTACATT-TTTT
1 AAAAATATACTATTTTTTATTTTATTATTTTACATTATTTT
51169000 CGGATTTTAT
Statistics
Matches: 291, Mismatches: 38, Indels: 35
0.80 0.10 0.10
Matches are distributed among these distances:
149 2 0.01
150 3 0.01
151 11 0.04
152 149 0.51
153 35 0.12
154 34 0.12
155 28 0.10
156 29 0.10
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (151 bp):
AAAAATATACTATTTTTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATT
AATTTAGTATGTTTTTTAAATAAATTTAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTC
CCGAATTTTATTACTTTCAAT
Found at i:51168714 original size:272 final size:273
Alignment explanation
Indices: 51168219--51168769 Score: 851
Period size: 272 Copynumber: 2.0 Consensus size: 273
51168209 AATTTTATTA
*
51168219 CTTTAAAAAATATAATATTTTCTAATTTTATTGTATTACATTATTTTAGTACATTATGTTTGAAA
1 CTTTAAAAAATATAATATTTTCTAATTTTATTATATTACATTATTTTAGTACATTATGTTTGAAA
*
51168284 TTCATTAATTTAGTGAGTTTTTAAAATAAATTTAGAAAAATAACCCTTATTTCGGCCCTTTGCTC
66 TTCATTAATTTAGTGAGTTTTTAAAATAAATTT--AAAAATAACCCTTATTTCGGCCCTTTACTC
*
51168349 GTATTTTTTTCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
129 GTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
*
51168414 CATTATTTAAGTACATTATGTTTGAAATGTATTAATTAATTCTATTTTTTTAAAAAATAGTAAAA
194 CATTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTT-AAAAATAGTAAAA
*
51168479 AACTCTTATTTCTG-CC
258 AACCCTTATTTC-GACC
* * * *
51168495 CTTTAAAAAAATATACTACTTTT-TATTTTTATTATTTTACATTATTTTAGTACATTATGTTTTA
1 CTTT-AAAAAATATAATA-TTTTCTAATTTTATTATATTACATTATTTTAGTACATTATGTTTGA
* * * *
51168559 AATTTATTAATTTAGTGTGTTTTTTAAATAAATTT-AAAA-AACTCTTATTTCGGCCCTTTACTC
64 AATTCATTAATTTAGTGAGTTTTTAAAATAAATTTAAAAATAACCCTTATTTCGGCCCTTTACTC
*
51168622 GTA-TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTA
129 GTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
* ** *
51168686 CATTATTTTAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTAAATTTAGTAAAAT
194 CATTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTAAAAATAGTAAAAA
51168751 ACCCTTATTTCGACC
259 ACCCTTATTTCGACC
51168766 CTTT
1 CTTT
51168770 GTTCGTATTT
Statistics
Matches: 254, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
270 1 0.00
271 27 0.11
272 108 0.43
273 25 0.10
274 4 0.02
276 4 0.02
277 81 0.32
278 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (273 bp):
CTTTAAAAAATATAATATTTTCTAATTTTATTATATTACATTATTTTAGTACATTATGTTTGAAA
TTCATTAATTTAGTGAGTTTTTAAAATAAATTTAAAAATAACCCTTATTTCGGCCCTTTACTCGT
ATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACA
TTATTTAAGTACATTATGTTTGAAATGTATTAAGTAATTCTATTTTTTTAAAAATAGTAAAAAAC
CCTTATTTCGACC
Found at i:51169354 original size:21 final size:19
Alignment explanation
Indices: 51169328--51169377 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
51169318 TTATTTATTT
51169328 CTTTCTTTTTCCTTCCTTCC
1 CTTTCTTTTTCC-TCCTTCC
* *
51169348 CTCTTCTTCTT-CTCCTTTC
1 CT-TTCTTTTTCCTCCTTCC
51169367 CTTTCTTTTTC
1 CTTTCTTTTTC
51169378 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
20 3 0.12
21 7 0.28
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
CTTTCTTTTTCCTCCTTCC
Found at i:51169394 original size:14 final size:14
Alignment explanation
Indices: 51169354--51169400 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
51169344 TTCCCTCTTC
51169354 TTCTTCTCCTTTCCT
1 TTCTTCTCCTTT-CT
* *
51169369 TTCTTTTTCTTTCT
1 TTCTTCTCCTTTCT
*
51169383 TTCTTCTCCTTTCC
1 TTCTTCTCCTTTCT
51169397 TTCT
1 TTCT
51169401 CCACCCCACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCTTCTCCTTTCT
Found at i:51169541 original size:5 final size:5
Alignment explanation
Indices: 51169533--51169607 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
51169523 TGGGGTGGAG
* *
51169533 AAGGA AAGGA GAA-GA AA-GA AAGAA AATGA AAGGA GAA-GA AAGGA AAGGA
1 AAGGA AAGGA -AAGGA AAGGA AAGGA AAGGA AAGGA -AAGGA AAGGA AAGGA
* *
51169582 AAGGA GAA-G- AAGAA AAGGG AAGGA AA
1 AAGGA -AAGGA AAGGA AAGGA AAGGA AA
51169608 AAGAAAGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
3 2 0.04
4 8 0.15
5 39 0.71
6 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (5 bp):
AAGGA
Found at i:51169573 original size:10 final size:11
Alignment explanation
Indices: 51169529--51169590 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 11
51169519 CTGGTGGGGT
51169529 GGAGAAGGAAA
1 GGAGAAGGAAA
51169540 GGAGAA-GAAA
1 GGAGAAGGAAA
* *
51169550 GAAAGAAAATGAAA
1 G---GAGAAGGAAA
51169564 GGAGAA-GAAA
1 GGAGAAGGAAA
51169574 GGA-AAGGAAA
1 GGAGAAGGAAA
51169584 GGAGAAG
1 GGAGAAG
51169591 AAGAAAAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 2 0.05
10 19 0.44
11 13 0.30
13 4 0.09
14 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.39, T:0.02
Consensus pattern (11 bp):
GGAGAAGGAAA
Found at i:51169573 original size:20 final size:20
Alignment explanation
Indices: 51169548--51169618 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
51169538 AAGGAGAAGA
*
51169548 AAGAAAGAAAATGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
*
51169568 AAGAAAGGAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
* *
51169588 AAG-AAGAAAAGGGAAGGAAA
1 AAGAAAGAAAAGGAAAGG-AG
51169608 AAGAAAGAAAA
1 AAGAAAGAAAA
51169619 AAAATAAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 12 0.27
20 25 0.57
21 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAAGGAG
Found at i:51169604 original size:24 final size:24
Alignment explanation
Indices: 51169533--51169607 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
51169523 TGGGGTGGAG
*
51169533 AAGGAAAGGAGAAGAA-AGAAAGAA
1 AAGGAAAGGAGAAGAAGA-AAAGGA
*
51169557 AATGAAA-G-G-AGAAG-AAAGGA
1 AAGGAAAGGAGAAGAAGAAAAGGA
*
51169577 AAGGAAAGGAGAAGAAGAAAAGGG
1 AAGGAAAGGAGAAGAAGAAAAGGA
51169601 AAGGAAA
1 AAGGAAA
51169608 AAGAAAGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 11 0.26
21 5 0.12
22 2 0.05
23 6 0.14
24 18 0.43
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (24 bp):
AAGGAAAGGAGAAGAAGAAAAGGA
Found at i:51170155 original size:154 final size:151
Alignment explanation
Indices: 51169942--51170795 Score: 944
Period size: 154 Copynumber: 5.6 Consensus size: 151
51169932 ATAAAATCTG
* * * *
51169942 AAAAAAATATAAAATAACAAAATAAAAAATA-TATATATTTTTATTGAAAGTAATAAAATTCGGG
1 AAAATAATGTAAAATAATAAAATAGAAAATAGTATAT-TTTTTA---AAAGTAATAAAATTCGGG
* * *
51170006 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTTAACAAACACATTAA
62 AAAAAATACGAATAAAGGGCCGAAATAAGGGTT-TTTTTT-AAATTTATTTAAAAAACAAATTAA
*
51170071 ATTAATAAATTTCAAACATAATGTACT
125 ATTAATAAATTTAAAACATAATGTACT
* *
51170098 AAAATAATGTACAATAATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGAAAA
1 AAAATAATGTAAAATAATAAAA-TAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGGAAA
* ** * ***
51170163 AAATACGAACAAAGGGCCGAAATAAGAATATTTTACCAATTTA---AAAAAACAGAATT-AATTA
65 AAATACGAATAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACA-AATTAAATTA
* *
51170224 ATACATTTCAAACATAATGTACT
129 ATAAATTTAAAACATAATGTACT
*
51170247 AAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATA-GAAAATAGTATA-TTTT-TTAAAAGTAATAAAATTCGGGA
* * * * *
51170312 AAAAATACTAGTAAACGGCCGAAATAA-GGCTTTTTTTAAATTTATTTAAAAAAACAAACTAAAT
63 AAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTT-AAAAAACAAATTAAAT
51170376 TAATAAATTTAAAACATAATGTACT
127 TAATAAATTTAAAACATAATGTACT
* *
51170401 AAAATAATGTAAAATAATAAAAATAAAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGGAA
1 AAAATAATGTAAAATAAT-AAAATAGAAAATAGTATATTTTTTAAAAGTAATAAAATTC-GGG-A
* * *
51170466 AAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTTACTAAA-TTA---AAAAAACAGAATT-AA
63 AAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT-TTAAATTTATTTAAAAAACA-AATTAAA
* *
51170526 TTAATACATTTGAAACATAATG---T
126 TTAATAAATTTAAAACATAATGTACT
** *
51170549 AAAATAA--TAAAATACA-AAAAT--AAAATA-T-T-TTAATTGAAAGTAATAAAATTCGGGAAA
1 AAAATAATGTAAAATA-ATAAAATAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGGAAA
* * * *
51170606 AAATACGAGTAAAGGGCCGAAATAAGGGTTACTTTTCTAAATTTATTTAAAAAAACACACTAAAT
65 AAATACGAATAAAGGGCCGAAATAAGGGTT--TTTTTTAAATTTATTT-AAAAAACAAATTAAAT
* *
51170671 TAATGAATTTAAAATATAATGTACT
127 TAATAAATTTAAAACATAATGTACT
* *
51170696 AAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTT-AAAGTATTAAAATCCGGGGAA
1 AAAATAATGTAAAATAATAAAA-TAGAAAATAGTATATTTTTTAAAAGTAATAAAATTC-GGG-A
51170760 AAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
63 AAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
51170796 ACTAATTTTT
Statistics
Matches: 596, Mismatches: 62, Indels: 82
0.81 0.08 0.11
Matches are distributed among these distances:
138 30 0.05
139 8 0.01
140 26 0.04
141 1 0.00
142 1 0.00
143 8 0.01
144 28 0.05
145 5 0.01
146 7 0.01
147 9 0.02
148 11 0.02
149 77 0.13
150 18 0.03
151 74 0.12
152 32 0.05
153 15 0.03
154 150 0.25
155 23 0.04
156 54 0.09
157 14 0.02
158 5 0.01
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.30
Consensus pattern (151 bp):
AAAATAATGTAAAATAATAAAATAGAAAATAGTATATTTTTTAAAAGTAATAAAATTCGGGAAAA
AATACGAATAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACAAATTAAATTAAT
AAATTTAAAACATAATGTACT
Found at i:51170715 original size:144 final size:140
Alignment explanation
Indices: 51170404--51170800 Score: 400
Period size: 138 Copynumber: 2.8 Consensus size: 140
51170394 ATGTACTAAA
** *
51170404 ATAATGTAAAATAATAAAAATA-AAAAATAGTATATTTT--TTTAAAGTAATAAAATTCGGGGAA
1 ATAATGTAAAATAAT-AAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAA
* * *
51170466 AAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACAGAATTAATTAAT
65 AAAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACACAATAAATTAAT
*
51170531 ACATTTGAAAC
130 ACATTTAAAAC
51170542 ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTC-GGG-AA
1 ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAAA
*
51170605 AAAATACG-AGTAAAGGGCCGAAATAAGGGTTACTTTT-CTAAATTTATTTAAAAAAACACACTA
66 AAAATACGAAG-AAAGGGCCGAAATAAGGGTT--TTTTACT-AA---A-TTAAAAAAACACAATA
*
51170668 AATTAATGA-ATTTAAAAT
123 AATTAAT-ACATTTAAAAC
* * *
51170686 ATAATGTACTAAAATAATGTAAAATA-ATAAAATTAGAAAATAGTATATT-TTTTAAAGTATTAA
1 ATAATG---TAAAATAA--TAAAATACA-AAAA-T--AAAATA-T-T-TTAATTGAAAGTAATAA
* *
51170749 AATCCGGGGAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTACTAA
54 AATTCGGGGAAAAAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAA
51170801 TTTTTTTTGA
Statistics
Matches: 217, Mismatches: 14, Indels: 40
0.80 0.05 0.15
Matches are distributed among these distances:
137 8 0.04
138 58 0.27
139 5 0.02
140 23 0.11
143 1 0.00
144 33 0.15
145 1 0.00
147 8 0.04
148 1 0.00
149 11 0.05
150 1 0.00
152 6 0.03
153 1 0.00
154 22 0.10
155 7 0.03
156 30 0.14
157 1 0.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAATGTAAAATAATAAAATACAAAAATAAAATATTTTAATTGAAAGTAATAAAATTCGGGGAAA
AAAATACGAAGAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAAAAAAACACAATAAATTAATA
CATTTAAAAC
Found at i:51170734 original size:295 final size:294
Alignment explanation
Indices: 51169950--51170800 Score: 1230
Period size: 305 Copynumber: 2.9 Consensus size: 294
51169940 TGAAAAAAAT
* *
51169950 ATAAAATAACAAAATAAAAAATATATATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATAC
1 ATAAAATAATAAAATAAAAAATATAAATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATAC
** * *
51170015 GAACAAAGGGCCGAAATAAGGGTTATTTTTTGAAATTTATTT-AACAAACACATTAAATTAATAA
66 GAGTAAAGGGCCGAAATAAGGGTTA-TTTTT-AAATTTATTTAAAAAAACACACTAAATTAATAA
* * *
51170079 ATTTCAAACATAATGTACTAAAATAATGTACAATAATAAAATTAGAAAATAGTATATTTTTTAAA
129 ATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAA
** * * *
51170144 AGTAATAAAATTC--GGAAAAAAATACGAACAAAGGGCCGAAATAAGAATATTTTACCAATTTAA
194 AGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAA
51170207 AAAAACAGAATTAATTAATACATTTCAAACATAATG
259 AAAAACAGAATTAATTAATACATTTCAAACATAATG
*
51170243 TACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTAAAAGTAATAAAATTC
1 -A-TAAAATAA--TAAAATAA-AAAAT------ATAA-ATATTTTTATTGAAAGTAATAAAATTC
* * * *
51170308 GGGAAAAAATACTAGTAAACGGCCGAAATAAGGCTT-TTTTTAAATTTATTTAAAAAAACAAACT
54 GGGAAAAAATACGAGTAAAGGGCCGAAATAAGGGTTATTTTTAAATTTATTTAAAAAAACACACT
* *
51170372 AAATTAATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAAATAAAAAATAGTAT
119 AAATTAATAAATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTAT
* *
51170437 ATTTTTTTAAAGTAATAAAATTCGGGGAAAAAAATACGAAGAAAGTGCCGAAATAAGGGTTTTTT
184 ATTTTTTTAAAGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
*
51170502 ACTAAATTAAAAAAACAGAATTAATTAATACATTTGAAACATAATG
249 ACTAAATTAAAAAAACAGAATTAATTAATACATTTCAAACATAATG
*
51170548 -TAAAATAATAAAATACAAAAATA-AAATATTTTAATTGAAAGTAATAAAATTCGGGAAAAAATA
1 ATAAAATAATAAAATA-AAAAATATAAATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATA
*
51170611 CGAGTAAAGGGCCGAAATAAGGGTTACTTTTCTAAATTTATTTAAAAAAACACACTAAATTAATG
65 CGAGTAAAGGGCCGAAATAAGGGTTA-TTTT-TAAATTTATTTAAAAAAACACACTAAATTAATA
*
51170676 AATTTAAAATATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATA-TTTTTTA
128 AATTTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTA
* * *
51170740 AAGTATTAAAATCCGGGGAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTTACTAA
193 AAGTAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAA
51170801 TTTTTTTTGA
Statistics
Matches: 501, Mismatches: 38, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
292 58 0.12
293 2 0.00
294 70 0.14
295 93 0.19
297 7 0.01
298 5 0.01
300 12 0.02
301 1 0.00
302 18 0.04
303 97 0.19
304 3 0.01
305 135 0.27
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (294 bp):
ATAAAATAATAAAATAAAAAATATAAATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAATAC
GAGTAAAGGGCCGAAATAAGGGTTATTTTTAAATTTATTTAAAAAAACACACTAAATTAATAAAT
TTAAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAG
TAATAAAATTCGGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTACTAAATTAAAA
AAACAGAATTAATTAATACATTTCAAACATAATG
Found at i:51174214 original size:43 final size:42
Alignment explanation
Indices: 51174148--51174317 Score: 188
Period size: 43 Copynumber: 4.0 Consensus size: 42
51174138 ATAGGATTTC
*
51174148 CGATATGTG-TTATCGTGTAAGACCACGTTTGGGACGTTGGCAT
1 CGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
51174191 CGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
*
51174234 CGTATT-TGATT-CGTGTAAGACC-CTATCTGGGACAG-TGGCAT
1 CG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
51174275 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
51174318 TGTACGAGTC
Statistics
Matches: 108, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
40 2 0.02
41 28 0.26
42 10 0.09
43 62 0.57
44 6 0.06
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
CGATTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:51174305 original size:84 final size:84
Alignment explanation
Indices: 51174160--51174317 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
51174150 ATATGTGTTA
* * *
51174160 TCGTGTAAGACCACGTTTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTTTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
51174225 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
51174244 TCGTGTAAGACC-C-TATCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCT
1 TCGTGTAAGACCACGT-T-TGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCT
*
51174305 GGGACGTTGGCAT
62 GGGACATTGGCAT
51174318 TGTACGAGTC
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
82 1 0.02
83 3 0.05
84 61 0.92
85 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTTTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:51174506 original size:16 final size:17
Alignment explanation
Indices: 51174477--51174508 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
51174467 TGAATTGATG
51174477 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
51174494 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
51174509 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:51177159 original size:39 final size:38
Alignment explanation
Indices: 51177115--51177316 Score: 155
Period size: 39 Copynumber: 5.3 Consensus size: 38
51177105 ACTAACACAA
51177115 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGTTTTTTACT-AAAATAATACTAAC
** *
51177154 TAACAATAATAATTAGAGTTTTACT-AAA-AATAATAAC
1 TAACAATAATAA-TAGTTTTTTACTAAAATAATACTAAC
* **** *
51177191 TAACAATAAT-ATAATGTAAAAACTAACAATCATACTAAC
1 TAACAATAATAATAGT-TTTTTACTAA-AATAATACTAAC
* *
51177230 TAA-AATAATAATTAGGGTTTTTACT-AATTAATAACTAAC
1 TAACAATAATAA-TA-GTTTTTTACTAAAATAAT-ACTAAC
* * * *
51177269 -CATAATAATATTAGTTTTTTACTAATAATAATACTAAG
1 TAACAATAATAATAGTTTTTTACTAA-AATAATACTAAC
51177307 TAACAATAAT
1 TAACAATAAT
51177317 TATTAATAAC
Statistics
Matches: 123, Mismatches: 27, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
35 2 0.02
36 4 0.03
37 28 0.23
38 24 0.20
39 49 0.40
40 16 0.13
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (38 bp):
TAACAATAATAATAGTTTTTTACTAAAATAATACTAAC
Found at i:51177200 original size:37 final size:38
Alignment explanation
Indices: 51177115--51177316 Score: 125
Period size: 37 Copynumber: 5.3 Consensus size: 38
51177105 ACTAACACAA
** *
51177115 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGAGTTTTACT-AAAATAATAATAAC
51177154 TAACAATAATAATTAGAGTTTTACT-AAA-AATAATAAC
1 TAACAATAATAA-TAGAGTTTTACTAAAATAATAATAAC
*** * *
51177191 TAACAATAAT-ATA-ATGTAAAAACTAACAATCATACTAAC
1 TAACAATAATAATAGA-GT-TTTACTAA-AATAATAATAAC
*
51177230 TAA-AATAATAATTAGGGTTTTTACT--AAT--TAATAAC
1 TAACAATAATAA-TAGAG-TTTTACTAAAATAATAATAAC
* * * *
51177265 TAACCATAATAATATTAGTTTTTTACTAATAATAATACTAAG
1 TAACAATAATAATA-GAG--TTTTACTAA-AATAATAATAAC
51177307 TAACAATAAT
1 TAACAATAAT
51177317 TATTAATAAC
Statistics
Matches: 126, Mismatches: 19, Indels: 33
0.71 0.11 0.19
Matches are distributed among these distances:
34 1 0.01
35 15 0.12
36 12 0.10
37 30 0.24
38 11 0.09
39 23 0.18
40 19 0.15
41 1 0.01
42 14 0.11
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (38 bp):
TAACAATAATAATAGAGTTTTACTAAAATAATAATAAC
Found at i:51177233 original size:23 final size:23
Alignment explanation
Indices: 51177188--51177234 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
51177178 TAAAAATAAT
*
51177188 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
51177211 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
51177234 A
1 A
51177235 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:51177923 original size:21 final size:22
Alignment explanation
Indices: 51177899--51177950 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
51177889 TGGCCAGTAC
*
51177899 AAATAACAA-AAACAATAGC-AA
1 AAATAACAACAAA-AACAGCAAA
51177920 AAATAACAACAAAAACAGCAGAA
1 AAATAACAACAAAAACAGCA-AA
51177943 AAATAACA
1 AAATAACA
51177951 GCACCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 3 0.11
23 10 0.37
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAACAACAAAAACAGCAAA
Found at i:51177944 original size:23 final size:24
Alignment explanation
Indices: 51177903--51177950 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
51177893 CAGTACAAAT
*
51177903 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
51177927 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
51177950 A
1 A
51177951 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:51180417 original size:16 final size:16
Alignment explanation
Indices: 51180396--51180449 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
51180386 AAATTTTATC
*
51180396 TTTAAAAATAATATAT
1 TTTAAAAATATTATAT
* *
51180412 TTTAAATATTTTATAAT
1 TTTAAAAATATTAT-AT
*
51180429 ATTAAAAA-ATTATAT
1 TTTAAAAATATTATAT
51180444 TTTAAA
1 TTTAAA
51180450 TTTTATAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 7 0.23
16 15 0.50
17 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAAATATTATAT
Found at i:51180425 original size:31 final size:32
Alignment explanation
Indices: 51180397--51180457 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
51180387 AATTTTATCT
51180397 TTAAAAATAATATATTTTAAATATTTTATAATA
1 TTAAAAA-AATATATTTTAAATATTTTATAATA
*
51180430 TTAAAAAATTATATTTT-AA-ATTTTATAA
1 TTAAAAAAATATATTTTAAATATTTTATAA
51180458 AATCAGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.33
31 2 0.07
32 9 0.33
33 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAAAAAAATATATTTTAAATATTTTATAATA
Found at i:51180445 original size:32 final size:31
Alignment explanation
Indices: 51180385--51180457 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
51180375 AAACAAACAA
*
51180385 TAAATTTTAT-CT-TTAAAAATAATATATTT
1 TAAATTTTATAATATTAAAAATAATATATTT
*
51180414 TAAATATTTTATAATATTAAAAA-ATTATATTT
1 T-AA-ATTTTATAATATTAAAAATAATATATTT
51180446 TAAATTTTATAA
1 TAAATTTTATAA
51180458 AATCAGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 1 0.03
30 11 0.29
31 9 0.24
32 10 0.26
33 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TAAATTTTATAATATTAAAAATAATATATTT
Found at i:51180446 original size:23 final size:22
Alignment explanation
Indices: 51180417--51180460 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
51180407 TATATTTTAA
51180417 ATATTTTATAATATTAAAAAATT
1 ATATTTTA-AATATTAAAAAATT
* *
51180440 ATATTTTAAATTTTATAAAAT
1 ATATTTTAAATATTAAAAAAT
51180461 CAGTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTTTAAATATTAAAAAATT
Found at i:51181109 original size:18 final size:20
Alignment explanation
Indices: 51181086--51181128 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
51181076 TTTATAATAT
*
51181086 TATTTTTTAA-ATT-TTAAA
1 TATTTTTTAATATTATAAAA
51181104 TATTTTTTAATATTATAAAA
1 TATTTTTTAATATTATAAAA
51181124 TATTT
1 TATTT
51181129 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 3 0.14
20 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTTAATATTATAAAA
Found at i:51181197 original size:13 final size:13
Alignment explanation
Indices: 51181181--51181228 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 13
51181171 TGTTTTTATA
51181181 ATATTTTAAATAT
1 ATATTTTAAATAT
51181194 ATATTTT-AA-A-
1 ATATTTTAAATAT
51181204 A-ATTTTAAATAT
1 ATATTTTAAATAT
*
51181216 AATTTTTTAAATA
1 -ATATTTTAAATA
51181229 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 2 0.07
12 2 0.07
13 8 0.28
14 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:51181211 original size:22 final size:23
Alignment explanation
Indices: 51181174--51181231 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
51181164 TATTATTTGT
*
51181174 TTTTATAATATTTTAAATAT-ATA
1 TTTTA-AAAATTTTAAATATAATA
*
51181197 TTTTAAAAATTTTAAATATAATT
1 TTTTAAAAATTTTAAATATAATA
51181220 TTTTAAATAATT
1 TTTTAAA-AATT
51181232 ATTTTTTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.42
23 14 0.45
24 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAAAAATTTTAAATATAATA
Found at i:51181225 original size:14 final size:15
Alignment explanation
Indices: 51181206--51181239 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51181196 ATTTTAAAAA
51181206 TTTTAAAT-ATAATT
1 TTTTAAATAATAATT
*
51181220 TTTTAAATAATTATT
1 TTTTAAATAATAATT
51181235 TTTTA
1 TTTTA
51181240 GAGATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAATAATAATT
Found at i:51181303 original size:22 final size:23
Alignment explanation
Indices: 51181261--51181311 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
51181251 ACGTTTTAAA
*
51181261 AAAAATTATATTTAAAATTTTTT
1 AAAAATAATATTTAAAATTTTTT
*
51181284 AAAAATAATATTT-AATTTTTTT
1 AAAAATAATATTTAAAATTTTTT
51181306 AAAAAT
1 AAAAAT
51181312 TTTAAATGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAAATAATATTTAAAATTTTTT
Found at i:51181368 original size:21 final size:22
Alignment explanation
Indices: 51181333--51181374 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
51181323 GCACCGAGTA
*
51181333 AAATATTATTTTTAAAAATTTT
1 AAATATTAATTTTAAAAATTTT
51181355 AAATA-TAATTTTAAAAATTT
1 AAATATTAATTTTAAAAATTT
51181375 CGAATATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTAATTTTAAAAATTTT
Found at i:51181380 original size:21 final size:21
Alignment explanation
Indices: 51181333--51181381 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
51181323 GCACCGAGTA
* *
51181333 AAATATTATTTTTAAAAATTTT
1 AAATA-TAATTTTAAAAATTTC
51181355 AAATATAATTTTAAAAATTTC
1 AAATATAATTTTAAAAATTTC
*
51181376 GAATAT
1 AAATAT
51181382 CTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATAATTTTAAAAATTTC
Found at i:51181447 original size:23 final size:22
Alignment explanation
Indices: 51181401--51181450 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
51181391 TAATTTAAAA
* *
51181401 AAAAT-TATATTTAAAAATTTT
1 AAAATATACATTTAAAAATTAT
51181422 AAAATATACATTTAAAATATTAT
1 AAAATATACATTTAAAA-ATTAT
51181445 AAAATA
1 AAAATA
51181451 AAAAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATATACATTTAAAAATTAT
Found at i:51181489 original size:24 final size:23
Alignment explanation
Indices: 51181446--51181490 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
51181436 AAATATTATA
**
51181446 AAATAAAAAAAAACTGAAAAAGT
1 AAATAAAAAAAAACAAAAAAAGT
51181469 AAATAAAGAAAAAACAAAAAAA
1 AAATAAA-AAAAAACAAAAAAA
51181491 ATGAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (23 bp):
AAATAAAAAAAAACAAAAAAAGT
Found at i:51195850 original size:11 final size:12
Alignment explanation
Indices: 51195833--51195865 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
51195823 GTATAATTTA
51195833 AAAAAATTATAT
1 AAAAAATTATAT
*
51195845 -AAAAATAATAT
1 AAAAAATTATAT
51195856 AAAAAATTAT
1 AAAAAATTAT
51195866 TCTAAGAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:51197180 original size:44 final size:44
Alignment explanation
Indices: 51197088--51197181 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
51197078 AGATAGAAAG
* * * *
51197088 AAAGTTTATATAGGATGATGATGTTAATGTATTGTTGTCCCTTA
1 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
*
51197132 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTC
1 AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
51197176 AAAGTT
1 AAAGTT
51197182 AAGTTATGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (44 bp):
AAAGTTTATACAGGATGATGATGTTAATGTATTGCTATCCCCTA
Found at i:51199075 original size:14 final size:13
Alignment explanation
Indices: 51199056--51199112 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
51199046 ATTTAGCCGA
51199056 ATATGCATCACCAC
1 ATATGCATCA-CAC
51199070 ATATGCAT-ACAC
1 ATATGCATCACAC
*
51199082 ATAGTTACATCATCAC
1 ATA--TGCATCA-CAC
51199098 ATATGCAT-ACAC
1 ATATGCATCACAC
51199110 ATA
1 ATA
51199113 GCTCACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 12 0.32
13 2 0.05
14 16 0.43
15 1 0.03
16 6 0.16
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (13 bp):
ATATGCATCACAC
Found at i:51199385 original size:43 final size:43
Alignment explanation
Indices: 51199338--51199419 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
51199328 TAATCACATA
51199338 TCGATGCC-ACTGTCCCAGACAG-GATCTTACACGAAAACATAAT
1 TCGATGCCAAC-GTCCCAGAC-GTGATCTTACACGAAAACATAAT
* *
51199381 TCGATGCCAACGTCCCGGACGTGGTCTTACACGAAAACA
1 TCGATGCCAACGTCCCAGACGTGATCTTACACGAAAACA
51199420 CAAATTGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 32 0.91
44 2 0.06
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (43 bp):
TCGATGCCAACGTCCCAGACGTGATCTTACACGAAAACATAAT
Found at i:51205288 original size:25 final size:26
Alignment explanation
Indices: 51205234--51205290 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
51205224 AGTAAATGTC
51205234 TATTTTTGTAATTAATCAATTTTCCCTA
1 TATTTTTGTAATTAATCAATTTT--CTA
*
51205262 TATTTTTCGTAATTAAT-TATTTT-TA
1 TATTTTT-GTAATTAATCAATTTTCTA
51205287 TATT
1 TATT
51205291 ATTTAGGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
28 12 0.44
29 9 0.33
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (26 bp):
TATTTTTGTAATTAATCAATTTTCTA
Found at i:51207445 original size:6 final size:6
Alignment explanation
Indices: 51207434--51207465 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
51207424 AGCTGTGATT
51207434 TCCATC TCCATC TCCATC TCCATC TCCATC TC
1 TCCATC TCCATC TCCATC TCCATC TCCATC TC
51207466 TAACCAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCATC
Found at i:51210048 original size:21 final size:21
Alignment explanation
Indices: 51210024--51210067 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
51210014 TTTTGTTACA
51210024 ATGGCTTCGACAGATTCATCC
1 ATGGCTTCGACAGATTCATCC
*
51210045 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCGACAGATTCATCC
51210066 AT
1 AT
51210068 TCTTTGGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (21 bp):
ATGGCTTCGACAGATTCATCC
Found at i:51220088 original size:9 final size:9
Alignment explanation
Indices: 51220074--51220099 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
51220064 CGTGTTATAA
51220074 AATAAAGAG
1 AATAAAGAG
51220083 AATAAAGAG
1 AATAAAGAG
51220092 AATAAAGA
1 AATAAAGA
51220100 ACAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
AATAAAGAG
Found at i:51238654 original size:11 final size:11
Alignment explanation
Indices: 51238632--51238693 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
51238622 AACTAATCTT
51238632 CTCTCAAATTTC
1 CTCTC-AATTTC
51238644 CTCTCAATTTC
1 CTCTCAATTTC
* *
51238655 TTCTAAATTTC
1 CTCTCAATTTC
* *
51238666 CTCCCAATTTG
1 CTCTCAATTTC
*
51238677 CTCTCAAATTC
1 CTCTCAATTTC
51238688 CT-TCAA
1 CTCTCAA
51238694 AATTTCTCTC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 4 0.10
11 32 0.78
12 5 0.12
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:51238655 original size:22 final size:22
Alignment explanation
Indices: 51238630--51238705 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 22
51238620 CAAACTAATC
51238630 TTCTCTCAAATTTCCTCTCAAT
1 TTCTCTCAAATTTCCTCTCAAT
*
51238652 TTCT-TCTAAATTTCCTCCCAAT
1 TTCTCTC-AAATTTCCTCTCAAT
51238674 TTGCTCTCAAA-TTCCT-TCAAAAT
1 TT-CTCTCAAATTTCCTCTC--AAT
51238697 TTCTCTCAA
1 TTCTCTCAA
51238706 GTCCATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.06
22 32 0.68
23 10 0.21
24 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.43
Consensus pattern (22 bp):
TTCTCTCAAATTTCCTCTCAAT
Found at i:51238766 original size:51 final size:51
Alignment explanation
Indices: 51238670--51238766 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
51238660 AATTTCCTCC
* *
51238670 CAATTTGCTCTCAAATTCCTTCAAAATTTCTCTCAAGTCCATATTTATTTT
1 CAATTTGCTCTCAAACTCCTTCAAAATTTCTCTCAAATCCATATTTATTTT
* * * *
51238721 CAATTTGCTCTCAAGCTCC-TCTTAAATTTCTCTTAAATCCCTATTT
1 CAATTTGCTCTCAAACTCCTTC-AAAATTTCTCTCAAATCCATATTT
51238767 TTAAATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.05
51 37 0.95
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (51 bp):
CAATTTGCTCTCAAACTCCTTCAAAATTTCTCTCAAATCCATATTTATTTT
Found at i:51240018 original size:16 final size:17
Alignment explanation
Indices: 51239997--51240032 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
51239987 TACAGTAAGC
51239997 TTTTTTAATATAT-ATA
1 TTTTTTAATATATAATA
*
51240013 TTTTTTAATTTATAATA
1 TTTTTTAATATATAATA
51240030 TTT
1 TTT
51240033 AGATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAATATATAATA
Found at i:51240994 original size:12 final size:12
Alignment explanation
Indices: 51240979--51241003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51240969 TTGTAAGTTT
51240979 TGCAACAAAAGG
1 TGCAACAAAAGG
51240991 TGCAACAAAAGG
1 TGCAACAAAAGG
51241003 T
1 T
51241004 TCTCATGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (12 bp):
TGCAACAAAAGG
Found at i:51247825 original size:6 final size:6
Alignment explanation
Indices: 51247812--51247844 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
51247802 TAAAAGTAAA
*
51247812 TTTA-T TTTACT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
51247845 ATAATACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:51257458 original size:18 final size:18
Alignment explanation
Indices: 51257431--51257465 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51257421 TATATGTGAT
51257431 ATTAATTA-TTATAAAAC
1 ATTAATTATTTATAAAAC
51257448 ATTATATTATTTATAAAA
1 ATTA-ATTATTTATAAAA
51257466 ATAATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATTATTTATAAAAC
Found at i:51257472 original size:18 final size:18
Alignment explanation
Indices: 51257435--51257473 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
51257425 TGTGATATTA
*
51257435 ATTATTATAAAACATTAT
1 ATTATTATAAAACATAAT
51257453 ATTATTTATAAAA-ATAAT
1 ATTA-TTATAAAACATAAT
51257471 ATT
1 ATT
51257474 TGATTGCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATTATAAAACATAAT
Found at i:51263673 original size:18 final size:19
Alignment explanation
Indices: 51263636--51263673 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51263626 TTATAAATAT
*
51263636 AAATAAAAACTCTTGTAAA
1 AAATAAAAACTCTTGCAAA
*
51263655 AAATAAAACCTCTT-CAAA
1 AAATAAAAACTCTTGCAAA
51263673 A
1 A
51263674 CAAGTCTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (19 bp):
AAATAAAAACTCTTGCAAA
Found at i:51265312 original size:18 final size:18
Alignment explanation
Indices: 51265289--51265324 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51265279 TGGAGCATAT
*
51265289 TATGACCTTTGAATTTTC
1 TATGACCTTTGAACTTTC
51265307 TATGACCTTTGAACTTTC
1 TATGACCTTTGAACTTTC
51265325 ACTTTATAAT
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:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (18 bp):
TATGACCTTTGAACTTTC
Found at i:51274431 original size:13 final size:13
Alignment explanation
Indices: 51274413--51274439 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51274403 TATAATTATT
51274413 TTATTTTATTTGA
1 TTATTTTATTTGA
51274426 TTATTTTATTTGA
1 TTATTTTATTTGA
51274439 T
1 T
51274440 AATAGTAAAT
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:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TTATTTTATTTGA
Found at i:51274784 original size:23 final size:23
Alignment explanation
Indices: 51274754--51274797 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
51274744 TTGGTTTGGT
*
51274754 TTTTAAAA-ATATTTTCTATTTTA
1 TTTTAAAATA-ATTTTATATTTTA
51274777 TTTTAAAATAATTTTATATTT
1 TTTTAAAATAATTTTATATTT
51274798 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAAATAATTTTATATTTTA
Found at i:51283122 original size:20 final size:22
Alignment explanation
Indices: 51283079--51283126 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
51283069 CTACTAAAAA
*
51283079 TTAAAGAAAAACATCAAAGATT
1 TTAAAGAAAAACATAAAAGATT
* *
51283101 TTAAA-AAAATCATAAAAGTTT
1 TTAAAGAAAAACATAAAAGATT
51283122 TTAAA
1 TTAAA
51283127 TTTTGAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (22 bp):
TTAAAGAAAAACATAAAAGATT
Found at i:51283319 original size:112 final size:112
Alignment explanation
Indices: 51283182--51283396 Score: 369
Period size: 112 Copynumber: 1.9 Consensus size: 112
51283172 GGGTTCTATA
* *
51283182 TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAATCTTCAAAATCAAAACTATGAACTTTTTAA
1 TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTAAA
51283247 TATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
66 TATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
* **
51283294 TTTTAAAATAAAAAA-AATGATTTTTTGAAAAAAGCTCTTCAAAATCAAAACTATGAACTTCTAA
1 TTTTAAAATAAAAAACAAT-AATTTTTGAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTAA
51283358 ATATTAGATCTGAAATATATAAAAATAGAAAATCCAATT
65 ATATTAGATCTGAAATATATAAAAATAGAAAATCCAATT
51283397 GCAGTTTTAG
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 3 0.03
112 94 0.97
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (112 bp):
TTTTAAAATAAAAAACAATAATTTTTGAAAAAAAATCTTCAAAATCAAAACTATGAACTTCTAAA
TATTAGATCTGAAATATATAAAAATAGAAAATCCAATTAGTTTTGTG
Found at i:51286844 original size:184 final size:174
Alignment explanation
Indices: 51286544--51286913 Score: 436
Period size: 184 Copynumber: 2.1 Consensus size: 174
51286534 AGGGGCATCA
* * * *
51286544 TCTTCCAATTCCGCAACATGTATCAAGCCATCTTCAGTGAAAATATGGAGCATGGACAAGGTATG
1 TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAGGTATG
* * * * *
51286609 TGAAAGTTTGGGAATCGTAGTAGGAGTGATGCCATCATTACTTTCAGCATTGAGAGGGAACTGAA
66 TGAAAGTTGGGGAATCGTAGTAGGAGTGATACCAACATCACTTTCAGCATTGAGAGGGAACCGAA
* * * *
51286674 GAGCCTCCAAAAAAATCAGAGGCATTAAAGAGTAATGCAGCGTCG
131 GAG-CTCCAAAAAAATCAAAGGCATTAAAAAGTAAAGCAGAGTCG
* * *
51286719 TCTTCCAATTCCTCAACATATATCAAACTATCTTCACTGAAAACATGGAGCATTGACAAGATATG
1 TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAG----G
* *
51286784 ATGATCGTGTGAAAGTTGGGGAATCGTAGTAGGGGT-ATTATCAACATCACTTTCAGCATTGAGA
62 -T-A---TGTGAAAGTTGGGGAATCGTAGTAGGAGTGA-TACCAACATCACTTTCAGCATTGAGA
* * *
51286848 GGGAACCGAAGAGCTCCCAGAAAATCAAAGGCATTAAAAAGTAAAGCGGAGTCG
121 GGGAACCGAAGAGCTCCAAAAAAATCAAAGGCATTAAAAAGTAAAGCAGAGTCG
*
51286902 TCTTCCATTTCC
1 TCTTCCAATTCC
51286914 ATACTGTCTT
Statistics
Matches: 163, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
175 53 0.33
179 1 0.01
180 1 0.01
181 1 0.01
183 46 0.28
184 61 0.37
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (174 bp):
TCTTCCAATTCCGCAACATATATCAAACCATCTTCACTGAAAACATGGAGCATGGACAAGGTATG
TGAAAGTTGGGGAATCGTAGTAGGAGTGATACCAACATCACTTTCAGCATTGAGAGGGAACCGAA
GAGCTCCAAAAAAATCAAAGGCATTAAAAAGTAAAGCAGAGTCG
Found at i:51287681 original size:22 final size:22
Alignment explanation
Indices: 51287618--51287672 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
51287608 CCACCAAATA
*
51287618 AGAAAACGATGGAAGAAGAAGC
1 AGAAATCGATGGAAGAAGAAGC
51287640 AGAAATCGATGGAAGAAGAAGC
1 AGAAATCGATGGAAGAAGAAGC
51287662 AGAAATCGATG
1 AGAAATCGATG
51287673 AGGGCAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.31, T:0.09
Consensus pattern (22 bp):
AGAAATCGATGGAAGAAGAAGC
Found at i:51289218 original size:18 final size:18
Alignment explanation
Indices: 51289197--51289231 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51289187 TGAGTTTTCG
51289197 AATTCAAATAACTCGAAC
1 AATTCAAATAACTCGAAC
* *
51289215 AATTCGAATAATTCGAA
1 AATTCAAATAACTCGAA
51289232 TATCAAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTCAAATAACTCGAAC
Found at i:51289625 original size:17 final size:16
Alignment explanation
Indices: 51289591--51289621 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51289581 CCTATTTACT
51289591 TTCCCTCAAACTTTTA
1 TTCCCTCAAACTTTTA
51289607 TTCCCTCAAACTTTT
1 TTCCCTCAAACTTTT
51289622 TATTTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTCAAACTTTTA
Found at i:51289650 original size:20 final size:21
Alignment explanation
Indices: 51289608--51289653 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
51289598 AAACTTTTAT
*
51289608 TCCCTCAAACTTTTTATTTTC
1 TCCCTCAAACTTTTTATTCTC
51289629 TCCCT-AAAC-TTTTACTTCTC
1 TCCCTCAAACTTTTTA-TTCTC
51289649 TCCCT
1 TCCCT
51289654 TTACTCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.48
Consensus pattern (21 bp):
TCCCTCAAACTTTTTATTCTC
Found at i:51304071 original size:31 final size:31
Alignment explanation
Indices: 51304031--51304091 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
51304021 AAAATAACAA
*
51304031 TTCAGTAACTTAAAAT-AAAAATTTTGAATAG
1 TTCAATAACTT-AAATGAAAAATTTTGAATAG
*
51304062 TTCAATAACTTAAATGAAAACTTTTGAATA
1 TTCAATAACTTAAATGAAAAATTTTGAATA
51304092 ACTAAATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (31 bp):
TTCAATAACTTAAATGAAAAATTTTGAATAG
Found at i:51304911 original size:22 final size:22
Alignment explanation
Indices: 51304863--51304904 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
51304853 CTTTGGAATA
* *
51304863 TTATTTTAAAGAAAGTGGGTAG
1 TTATTGTAAAGAAAGTGAGTAG
51304885 TTATTGTAAAGAAAGTGAGT
1 TTATTGTAAAGAAAGTGAGT
51304905 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (22 bp):
TTATTGTAAAGAAAGTGAGTAG
Found at i:51308350 original size:10 final size:10
Alignment explanation
Indices: 51308335--51308365 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
51308325 TTAAAAAAAA
51308335 ATTATTTTTT
1 ATTATTTTTT
51308345 ATTATTTTTT
1 ATTATTTTTT
51308355 ATTATTTTTT
1 ATTATTTTTT
51308365 A
1 A
51308366 ATAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:51308757 original size:6 final size:6
Alignment explanation
Indices: 51308746--51308774 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
51308736 GTAGTTATAC
51308746 TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
51308775 AAGAAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:51311316 original size:32 final size:32
Alignment explanation
Indices: 51311280--51311346 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
51311270 ACATGACAGC
* *
51311280 CTGGTGGAGGGCCTGCCACAGGCGACACTGGA
1 CTGGTGGAGGGCCTGCCACAAGCGACACCGGA
*
51311312 CTGGTGGAGGGCCTGCTACAAGCGACACCGGA
1 CTGGTGGAGGGCCTGCCACAAGCGACACCGGA
51311344 CTG
1 CTG
51311347 AAATGTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.39, T:0.13
Consensus pattern (32 bp):
CTGGTGGAGGGCCTGCCACAAGCGACACCGGA
Found at i:51323886 original size:16 final size:16
Alignment explanation
Indices: 51323865--51323910 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
51323855 TCTTAATCCT
51323865 TTATTTGTTTATTTAG
1 TTATTTGTTTATTTAG
* *
51323881 TTATTTGTTTGTTTAT
1 TTATTTGTTTATTTAG
* *
51323897 TTATATCTTTATTT
1 TTATTTGTTTATTT
51323911 GAAATTTTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (16 bp):
TTATTTGTTTATTTAG
Found at i:51323911 original size:20 final size:20
Alignment explanation
Indices: 51323863--51323911 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
51323853 TCTCTTAATC
51323863 CTTTATTTGTTTATTTAGTT
1 CTTTATTTGTTTATTTAGTT
* *
51323883 ATTTGTTTGTTTATTTA-TAT
1 CTTTATTTGTTTATTTAGT-T
51323903 CTTTATTTG
1 CTTTATTTG
51323912 AAATTTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.69
Consensus pattern (20 bp):
CTTTATTTGTTTATTTAGTT
Found at i:51324649 original size:107 final size:106
Alignment explanation
Indices: 51324463--51324684 Score: 322
Period size: 107 Copynumber: 2.1 Consensus size: 106
51324453 CATCAAAAAG
* * *
51324463 AAACTTTCAAAATAAGGCAATATTTCGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
*
51324528 GTTTCAATTTCTCGTTTGACCAAATAGCAAAATATCCTTT-TT
66 GTTTCAATTTCTCGTTCGACCAAATAGCAAAATAT--TTTCTT
* * * * *
51324570 AAACTTTCAAAACGAGGCAATGTTTTGTGTTTGAAAATTCGAGAGAACGTACCCTAACGTGCTGG
1 AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
*
51324635 GTTTCAATTTCTCGTTCGACCAAATAGCTAAATATTTTCTT
66 GTTTCAATTTCTCGTTCGACCAAATAGCAAAATATTTTCTT
51324676 -AACTTTCAA
1 AAACTTTCAA
51324685 TCAATATTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
105 12 0.12
106 2 0.02
107 90 0.87
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (106 bp):
AAACTTTCAAAACAAGGCAATATTTCGCGTTTGAAAATTCGAGAAAACGTACCCTAACGTGCTGG
GTTTCAATTTCTCGTTCGACCAAATAGCAAAATATTTTCTT
Found at i:51328155 original size:21 final size:20
Alignment explanation
Indices: 51328106--51328160 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
51328096 ATCTAAAATA
*
51328106 AAATATAATTTAAATATTTTT
1 AAAT-TAATTTAAATAGTTTT
*
51328127 ATAA-TAATTTAAGGTAGTTTT
1 A-AATTAATTTAA-ATAGTTTT
51328148 AAATTAA-TTAAAT
1 AAATTAATTTAAAT
51328161 TTTCATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 11 0.39
22 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATTAATTTAAATAGTTTT
Found at i:51329242 original size:153 final size:149
Alignment explanation
Indices: 51328963--51329246 Score: 356
Period size: 153 Copynumber: 1.9 Consensus size: 149
51328953 AATTAGTCCA
* * * *
51328963 AAACTTTAGTTAAAAGTCAATAGAAAATTACTACATGTCATTCATTGAGCTAATGTGCCATGTAG
1 AAACTTTAGTCAAAAGTCAATAAAAAATTACTACATGTCAATCAATGAGCTAATGTGCCATGTAG
* * * * * * *
51329028 TAATTTGTTAAAAGAAAACGAAAATGTTAAGAACGATAAATAATTCGCACAATCATCTTATTTAA
66 CAATATGTTAAAAGAAAACAAAAATGTTAACAACAACAAATAATTCGCACAATCATATTATTTAA
51329093 ATTTTATAGAGTGATCACT
131 ATTTTATAGAGTGATCACT
51329112 AAACTTTAGTCAAAAGTCAATAAAAAAATATCACATATCA-GTCAATCAATGAGCTAATGTGCCA
1 AAACTTTAGTCAAAAGTCAAT-AAAAAAT-T-AC-TA-CATGTCAATCAATGAGCTAATGTGCCA
* * * * *
51329176 TGTAGCAATATGTTAAAA-ATAGATAAAAATGTTATCAACAACAAATAATTCGTACAATTATATT
61 TGTAGCAATATGTTAAAAGA-AAACAAAAATGTTAACAACAACAAATAATTCGCACAATCATATT
51329240 ATTTAAA
125 ATTTAAA
51329247 GTGATTAAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
149 20 0.18
150 6 0.05
151 1 0.01
152 3 0.03
153 81 0.72
154 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (149 bp):
AAACTTTAGTCAAAAGTCAATAAAAAATTACTACATGTCAATCAATGAGCTAATGTGCCATGTAG
CAATATGTTAAAAGAAAACAAAAATGTTAACAACAACAAATAATTCGCACAATCATATTATTTAA
ATTTTATAGAGTGATCACT
Found at i:51329434 original size:6 final size:6
Alignment explanation
Indices: 51329423--51329448 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51329413 TCGTAAACAG
51329423 GCCGAC GCCGAC GCCGAC GCCGAC GC
1 GCCGAC GCCGAC GCCGAC GCCGAC GC
51329449 GGCTCAGGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.35, T:0.00
Consensus pattern (6 bp):
GCCGAC
Found at i:51335312 original size:28 final size:27
Alignment explanation
Indices: 51335278--51335352 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
51335268 TGTTTTAAAT
**
51335278 AATTAAAAAAGCATTAAAATTATTTTAA
1 AATTAAAAAAAAATTAAAATT-TTTTAA
**
51335306 AATTAAAAAAAAATTAATCTTTTTTAA
1 AATTAAAAAAAAATTAAAATTTTTTAA
* *
51335333 ATTTAAAAAATTAATTAAAA
1 AATTAAAAAA-AAATTAAAA
51335353 GCTGATTTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 15 0.39
28 23 0.61
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (27 bp):
AATTAAAAAAAAATTAAAATTTTTTAA
Found at i:51345897 original size:14 final size:14
Alignment explanation
Indices: 51345878--51345909 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
51345868 AGGTCATTTA
51345878 GCCCAACCAAACTG
1 GCCCAACCAAACTG
51345892 GCCCAACCAAACTG
1 GCCCAACCAAACTG
51345906 GCCC
1 GCCC
51345910 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:51351020 original size:14 final size:14
Alignment explanation
Indices: 51351001--51351032 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
51350991 AGGTCATTTA
51351001 GCCCAACCAAACTG
1 GCCCAACCAAACTG
51351015 GCCCAACCAAACTG
1 GCCCAACCAAACTG
51351029 GCCC
1 GCCC
51351033 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:51356556 original size:39 final size:40
Alignment explanation
Indices: 51356513--51356680 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
51356503 CTCGTTCAAG
* * * *
51356513 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
51356552 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
51356592 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
51356632 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
51356672 TGCCTTCGG
1 TGCCTTCGG
51356681 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:51356693 original size:40 final size:40
Alignment explanation
Indices: 51356550--51356680 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
51356540 TAACTCATAC
* *
51356550 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
51356590 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
51356630 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
51356670 AATGCCTTCGG
1 AATGCCTTCGG
51356681 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.04
40 79 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:51356693 original size:80 final size:80
Alignment explanation
Indices: 51356513--51356733 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 80
51356503 CTCGTTCAAG
* * * * * * * * *
51356513 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGATAT
*
51356577 TAAAACTCGCACGAA
66 TAAAACTCGCACAAA
* *
51356592 TGCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTAACCCGGA
1 TGCCTTCGGGACTTAACCCGGATA-TAGTCACT-TAGCA-AAAAGCCTTCGGGACTTAACCCGGA
51356654 -ATTAATAACTCGCACAAA
63 TATTAA-AACTCGCACAAA
** *
51356672 TGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGA
51356734 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 31 0.26
80 77 0.65
81 6 0.05
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGATAT
TAAAACTCGCACAAA
Found at i:51364500 original size:39 final size:40
Alignment explanation
Indices: 51364457--51364624 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
51364447 CTCGTTCAAG
* * * *
51364457 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
51364496 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
51364536 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
51364576 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
51364616 TGCCTTCGG
1 TGCCTTCGG
51364625 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:51364637 original size:40 final size:40
Alignment explanation
Indices: 51364494--51364624 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
51364484 TAACTCATAC
* *
51364494 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
51364534 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
51364574 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
51364614 AATGCCTTCGG
1 AATGCCTTCGG
51364625 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.04
40 79 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:51364637 original size:80 final size:80
Alignment explanation
Indices: 51364457--51364677 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 80
51364447 CTCGTTCAAG
* * * * * * * * *
51364457 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGATAT
*
51364521 TAAAACTCGCACGAA
66 TAAAACTCGCACAAA
* *
51364536 TGCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTAACCCGGA
1 TGCCTTCGGGACTTAACCCGGATA-TAGTCACT-TAGCA-AAAAGCCTTCGGGACTTAACCCGGA
51364598 -ATTAATAACTCGCACAAA
63 TATTAA-AACTCGCACAAA
** *
51364616 TGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGA
51364678 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 31 0.26
80 77 0.65
81 6 0.05
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCAAAAAGCCTTCGGGACTTAACCCGGATAT
TAAAACTCGCACAAA
Found at i:51377947 original size:7 final size:7
Alignment explanation
Indices: 51377926--51378039 Score: 94
Period size: 7 Copynumber: 16.1 Consensus size: 7
51377916 TAAGAATAAT
51377926 AATAAATA
1 AATAAA-A
51377934 AAT-AAA
1 AATAAAA
*
51377940 ATTAAAA
1 AATAAAA
51377947 AATAAAAA
1 AAT-AAAA
51377955 AATTAAAA
1 AA-TAAAA
*
51377963 AATAGTAA
1 AATA-AAA
*
51377971 AATAGTAA
1 AATA-AAA
51377979 AAT-AAA
1 AATAAAA
51377985 AATAAAA
1 AATAAAA
*
51377992 AAT--AT
1 AATAAAA
*
51377997 AATATAA
1 AATAAAA
51378004 AATAAAA
1 AATAAAA
51378011 AATAAAA
1 AATAAAA
51378018 AATAAAA
1 AATAAAA
51378025 AA-AATAA
1 AATAA-AA
51378032 AATAAAA
1 AATAAAA
51378039 A
1 A
51378040 TGGGGTGGCT
Statistics
Matches: 90, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
5 4 0.04
6 10 0.11
7 45 0.50
8 30 0.33
9 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (7 bp):
AATAAAA
Found at i:51377953 original size:6 final size:6
Alignment explanation
Indices: 51377869--51378040 Score: 61
Period size: 6 Copynumber: 27.8 Consensus size: 6
51377859 TAAAGCAACT
* * * * * **
51377869 AAAACA AAATTA AAAAGA AAGATA AAAA-A AAATTTA AAATATA AGTATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA AAA-ATA AAAATA
* * * * *
51377918 AGAATA ATAATAA ATAAATA AAATTA AAAA-A TAAA-A AAATTAA AAAATA
1 AAAATA AAAAT-A A-AAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA
*
51377967 GTAAAATA GTAAAATA AAAATA AAAA-A TATAATA TAAAATAA AAAATA
1 --AAAATA --AAAATA AAAATA AAAATA -AAAATA -AAAAT-A AAAATA
*
51378015 AAAA-A TAAA-A AAAAT- AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
51378041 GGGGTGGCTT
Statistics
Matches: 129, Mismatches: 24, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
5 25 0.19
6 58 0.45
7 28 0.22
8 18 0.14
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:51377966 original size:33 final size:30
Alignment explanation
Indices: 51377848--51378039 Score: 117
Period size: 33 Copynumber: 6.1 Consensus size: 30
51377838 TAAGTTGAAG
* * *
51377848 AAAATAAAAAATAAAGCAACTAAAACAAAATTA
1 AAAATAAAAAATAAA--AAAT-AAATAAAATAA
* *
51377881 AAAA-GAAAGATAAAAAA-AAATTTAAAATATA
1 AAAATAAAAAATAAAAAATAAA--TAAAATA-A
** *
51377912 AGTATAAGAATAATAATAAATAAATAAAATTAA
1 AAAATAA-AA-AATAAAAAATAAATAAAA-TAA
* *
51377945 AAAATAAAAAAATTAAAAAAT-AGTAAAATAGT
1 AAAAT-AAAAAA-TAAAAAATAAATAAAATA-A
51377977 AAAAT-AAAAATAAAAAATATAATATAAAATAA
1 AAAATAAAAAAT-AAAAA-ATAA-ATAAAATAA
51378009 AAAATAAAAAAT-AAAAA-AAATAAAATAA
1 AAAATAAAAAATAAAAAATAAATAAAATAA
51378037 AAA
1 AAA
51378040 TGGGGTGGCT
Statistics
Matches: 126, Mismatches: 17, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
28 15 0.12
29 3 0.02
30 18 0.14
31 11 0.09
32 28 0.22
33 37 0.29
34 11 0.09
35 3 0.02
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (30 bp):
AAAATAAAAAATAAAAAATAAATAAAATAA
Found at i:51381747 original size:5 final size:5
Alignment explanation
Indices: 51381739--51381784 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
51381729 TATTTAATTT
* * *
51381739 ATATA ATATA ATACA ATTTA TTATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
51381785 AACATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:51381765 original size:20 final size:19
Alignment explanation
Indices: 51381734--51381771 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
51381724 TCATCTATTT
51381734 AATTTATATAATATAATAC
1 AATTTATATAATATAATAC
51381753 AATTTATTATAATATAATA
1 AATTTA-TATAATATAATA
51381772 TAATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTATATAATATAATAC
Found at i:51383511 original size:23 final size:23
Alignment explanation
Indices: 51383485--51383575 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
51383475 CAACATTGAT
51383485 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
**
51383508 ATGTAGCCGAAGCTACCACTGTT
1 ATGTAGCCGAAGCTACCACTGAA
*
51383531 ATGTAGCTGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
* *
51383554 ACGTAGTCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
51383576 TCAATAACAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:51383551 original size:46 final size:46
Alignment explanation
Indices: 51383484--51383574 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
51383474 GCAACATTGA
*
51383484 TATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGT
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTGT
* *
51383530 TATGTAGCTGAAGCTACCACTGAAACGTAGTCGAAGCTACCACTG
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTG
51383575 ATCAATAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (46 bp):
TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTGT
Found at i:51399873 original size:24 final size:24
Alignment explanation
Indices: 51399844--51399889 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
51399834 ATCATCTTTT
* *
51399844 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
51399868 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
51399890 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:51405584 original size:88 final size:88
Alignment explanation
Indices: 51405481--51405659 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 88
51405471 TTATGCAATA
* *
51405481 AATACTCAAGAAAATTAAGAGCAT-AATTCGAGTAAAAACTGACAGTTTAAAGCTTATTAAAACA
1 AATACTCAAGAAAATTAAGAGAATAAATTC-AGTAAAAACCGACAGTTTAAAGCTTATTAAAACA
* * *
51405545 TTGTTAGATGATCACTTGAAGTGC
65 CTATTAGATGATCACTTAAAGTGC
*
51405569 AATACTCAAGAAAATTAAGAGAATAAATTCAGTAAAAACCGATAGTTTAAAGCTTATTAAAACAC
1 AATACTCAAGAAAATTAAGAGAATAAATTCAGTAAAAACCGACAGTTTAAAGCTTATTAAAACAC
51405634 TATTAGATGATCACTTAAAGTGC
66 TATTAGATGATCACTTAAAGTGC
51405657 AAT
1 AAT
51405660 TTTGGGGTGT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 79 0.94
89 5 0.06
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (88 bp):
AATACTCAAGAAAATTAAGAGAATAAATTCAGTAAAAACCGACAGTTTAAAGCTTATTAAAACAC
TATTAGATGATCACTTAAAGTGC
Found at i:51414484 original size:125 final size:125
Alignment explanation
Indices: 51414270--51414551 Score: 399
Period size: 125 Copynumber: 2.3 Consensus size: 125
51414260 TTATTTTGAG
**
51414270 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTTTACCAAGATGCTATCAAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAAGATGCTATCAAAGAAGAAATTGT
* * * *
51414334 GAAATCGTGCCCTCGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAATAATT-TTTT
65 AAAATCGCGCCCTCGAGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
* *
51414394 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAAGATGCTATCA-AAGAAGAAATTG
* *
51414458 TAAAATCGCGCCCTCGAGGATGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TAAAATCGCGCCCTCGAGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
* * *
51414520 TTGACATTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
51414552 GCCCTCGTGG
Statistics
Matches: 141, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
124 7 0.05
125 124 0.88
126 10 0.07
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAAGATGCTATCAAAGAAGAAATTGTA
AAATCGCGCCCTCGAGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:51417785 original size:29 final size:29
Alignment explanation
Indices: 51417747--51418805 Score: 1398
Period size: 29 Copynumber: 36.4 Consensus size: 29
51417737 TAAAATGGGC
** *
51417747 TTTTAATTAAATTAGTTTAGGGTTAGGGC
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* ***
51417776 TTTTAATTAAAATGGGTTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
** *
51417805 TTTTAATTAAATTAGGTTACGGTTTAGGG-
1 TTTTAATTAAATTAAATTA-GGGTTAGGGT
*
51417834 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* **
51417863 TTTTAATTAACTTAGGTTAGGGTTAGGG-
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
51417891 TTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51417920 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* **
51417949 TTTTCATTAAATTAGGTTAGGGTTTAGGG-
1 TTTTAATTAAATTAAATTAGGG-TTAGGGT
*
51417978 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418007 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418036 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
**
51418065 TTTTAATTAAATTAGGTTAGGGTTTAGGG-
1 TTTTAATTAAATTAAATTAGGG-TTAGGGT
*
51418094 TTTTAATTAAATTAAATTAAGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
**
51418123 TTTTAATTAAATTAGGTTAGGGTTTAGGG-
1 TTTTAATTAAATTAAATTAGGG-TTAGGGT
*
51418152 TTTTAATTAAATTAAATTAGGGTTAAGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418181 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
** *
51418210 TTTTAATTAAATTAGGTTAAGGTTTAGGG-
1 TTTTAATTAAATTAAATT-AGGGTTAGGGT
*
51418239 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* *
51418268 TTTTAATTAAATTAAACTAGGGCTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* **
51418297 TTTTATTTAAATTAGGTTAGGGTTTAGGG-
1 TTTTAATTAAATTAAATTAGGG-TTAGGGT
*
51418326 TTTTAATTAAATTAAATTAAGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418355 TTTTAATTAAATTAAACTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* *** *
51418384 TTTTAATTAAAATGGGTTAGGGTTATGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
51418413 TTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* *
51418442 TTTTAATTAAATTAAATTAGGGTTAGAGA
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* **
51418471 TTTTAATTAAATTAAACTAGGGTTAAAGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* *** *
51418500 TTTTAATTAAAATGGGTTAAGGTTAGGGTTT
1 TTTTAATTAAATTAAATTAGGGTTAGGG--T
51418531 TTAATTAAATTAAATTAAATTAGGGTTAGGGT
1 TT--TT-AATTAAATTAAATTAGGGTTAGGGT
51418563 TTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418592 TTTTAAATAAATTAAATTAGGGTTAGGGTT
1 TTTTAATTAAATTAAATTAGGGTTAGGG-T
51418622 TTTTAA-TAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
51418650 TTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
* ***
51418679 TTTTAATTAAAATGGGTTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418708 TTTTAATTAAATTAAATTAGAGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
51418737 TTTTAATTAAATTAAATTAGGGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
51418766 TTTTAATTAAATTAAATTA-GGTTAGGGT
1 TTTTAATTAAATTAAATTAGGGTTAGGGT
*
51418794 TTTTAATCAAAT
1 TTTTAATTAAAT
51418806 AATATCAAAA
Statistics
Matches: 908, Mismatches: 102, Indels: 41
0.86 0.10 0.04
Matches are distributed among these distances:
28 92 0.10
29 740 0.81
30 49 0.05
31 3 0.00
32 3 0.00
33 2 0.00
34 19 0.02
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (29 bp):
TTTTAATTAAATTAAATTAGGGTTAGGGT
Found at i:51419116 original size:24 final size:24
Alignment explanation
Indices: 51419084--51419139 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
51419074 TGTATGTGGA
51419084 GGTGTTTGCATCATGAACGGCAAC
1 GGTGTTTGCATCATGAACGGCAAC
*
51419108 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCAAC
51419132 GGTGTTTG
1 GGTGTTTG
51419140 AAAGCCATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGGCAAC
Found at i:51420001 original size:7 final size:7
Alignment explanation
Indices: 51419991--51420022 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
51419981 TTATATACAT
51419991 AATACTA
1 AATACTA
51419998 AATACTA
1 AATACTA
51420005 AATACTA
1 AATACTA
51420012 AATACTA
1 AATACTA
51420019 AATA
1 AATA
51420023 TCAATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:51420995 original size:14 final size:15
Alignment explanation
Indices: 51420978--51421011 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51420968 AATAATTATC
51420978 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
51420992 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
51421007 TAAAA
1 TAAAA
51421012 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Done.