Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 6 of 199
Found at i:1899663 original size:24 final size:26
Alignment explanation
Indices: 1899636--1899691 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1899626 TTCAATCAAA
1899636 ATCAAATTAAATTT-T-ATTTTTTAT
1 ATCAAATTAAATTTATAATTTTTTAT
**
1899660 ATC-AATTACTTTTATAATTTTTTAT
1 ATCAAATTAAATTTATAATTTTTTAT
*
1899685 ATAAAAT
1 ATCAAAT
1899692 GTTTTCACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 4 0.15
25 11 0.42
26 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
ATCAAATTAAATTTATAATTTTTTAT
Found at i:1900382 original size:16 final size:16
Alignment explanation
Indices: 1900361--1900446 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
1900351 TTATAAAAAT
1900361 ATTATTTAATATATTA
1 ATTATTTAATATATTA
*
1900377 ATTATTTAATGTATT-
1 ATTATTTAATATATTA
1900392 ATTATATTAA-ATTATTTA
1 ATTAT-TTAATA-TA-TTA
** *
1900410 AAAATATAATTATATTGA
1 ATTATTTAA-TATATT-A
1900428 ATTATTTAAATATAGTTA
1 ATTATTT-AATATA-TTA
1900446 A
1 A
1900447 CATTATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.09
16 20 0.38
17 7 0.13
18 16 0.30
19 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTATTTAATATATTA
Found at i:1900385 original size:8 final size:8
Alignment explanation
Indices: 1900361--1900436 Score: 50
Period size: 8 Copynumber: 9.1 Consensus size: 8
1900351 TTATAAAAAT
1900361 ATTATTTA
1 ATTATTTA
1900369 A-TATATTA
1 ATTAT-TTA
1900377 ATTATTTA
1 ATTATTTA
1900385 ATGTA-TT-
1 AT-TATTTA
1900392 ATTATATTAA
1 ATTAT-TT-A
1900402 ATTATTTA
1 ATTATTTA
** *
1900410 AAAATATA
1 ATTATTTA
1900418 ATTATATTGA
1 ATTAT-TT-A
1900428 ATTATTTA
1 ATTATTTA
1900436 A
1 A
1900437 ATATAGTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
6 2 0.04
7 5 0.09
8 25 0.47
9 10 0.19
10 11 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (8 bp):
ATTATTTA
Found at i:1900421 original size:26 final size:25
Alignment explanation
Indices: 1900370--1900437 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
1900360 TATTATTTAA
** *
1900370 TATATTAATTATTT-AATGTATTAT
1 TATATTAATTATTTAAAAATATAAT
1900394 TATATTAAATTATTTAAAAATATAAT
1 TATATT-AATTATTTAAAAATATAAT
1900420 TATATTGAATTATTTAAA
1 TATATT-AATTATTTAAA
1900438 TATAGTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 6 0.16
25 8 0.21
26 24 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
TATATTAATTATTTAAAAATATAAT
Found at i:1906227 original size:18 final size:18
Alignment explanation
Indices: 1906191--1906224 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1906181 AGTATTTTTT
1906191 TTTGTATTAGATTAATTA
1 TTTGTATTAGATTAATTA
*
1906209 TTTGT-TTATATTAATT
1 TTTGTATTAGATTAATT
1906225 TATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (18 bp):
TTTGTATTAGATTAATTA
Found at i:1909712 original size:19 final size:18
Alignment explanation
Indices: 1909674--1909711 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1909664 AAAATTATAA
1909674 TTAAGTTTAATTAAAATT
1 TTAAGTTTAATTAAAATT
*
1909692 TTAAGTATTTATT-AAATT
1 TTAAGT-TTAATTAAAATT
1909710 TT
1 TT
1909712 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTAAGTTTAATTAAAATT
Found at i:1918856 original size:31 final size:31
Alignment explanation
Indices: 1918819--1918889 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1918809 TTTATACAAT
*
1918819 TATACACATGAAACTTTGATCATGGTTCAAG
1 TATACACATGAAACTTTGATCATGATTCAAG
* * * *
1918850 TGTACACATGAAATTTTGATTATGATTCAAT
1 TATACACATGAAACTTTGATCATGATTCAAG
1918881 TATACACAT
1 TATACACAT
1918890 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (31 bp):
TATACACATGAAACTTTGATCATGATTCAAG
Found at i:1919189 original size:7 final size:7
Alignment explanation
Indices: 1919177--1919209 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1919167 TAGATCGTAT
1919177 TTAAAAA
1 TTAAAAA
1919184 TTAAAAA
1 TTAAAAA
1919191 TTAAAAA
1 TTAAAAA
1919198 TTAAAAA
1 TTAAAAA
1919205 TTAAA
1 TTAAA
1919210 TAAATAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:1919390 original size:4 final size:4
Alignment explanation
Indices: 1919383--1919414 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1919373 ACATCTATCT
1919383 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC
1919415 TGCTTGCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
ATCC
Found at i:1923899 original size:22 final size:24
Alignment explanation
Indices: 1923871--1923914 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1923861 TATGGCAAGA
1923871 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
1923893 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
1923915 AACCTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:1924309 original size:36 final size:37
Alignment explanation
Indices: 1924225--1924320 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
1924215 GAATATATGT
* *
1924225 GTGAAATTGAAATGAATAT-TGACTTGAAAATGGAAAA
1 GTGAAATTGAATTGAAT-TGTGACTTGAAAATGAAAAA
*
1924262 GTGAATTTTGAATTGAATTGTGA-TTGAAAATGAAAAA
1 GTGAA-ATTGAATTGAATTGTGACTTGAAAATGAAAAA
*
1924299 GTGAAATTGAATTGAAATGTGA
1 GTGAAATTGAATTGAATTGTGA
1924321 ATTTGGAGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 15 0.29
37 24 0.46
38 13 0.25
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (37 bp):
GTGAAATTGAATTGAATTGTGACTTGAAAATGAAAAA
Found at i:1930556 original size:59 final size:58
Alignment explanation
Indices: 1930486--1930600 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 58
1930476 CATATTTTAG
* * *
1930486 TTTCCATATCATATCTAAAATGGATATTTA-ACTTTTTTAATTTTTAATATCATATCAA
1 TTTCCATATCATATCTAAAATAGATATTTAGA-TCTTTTAATTTTCAATATCATATCAA
1930544 TTTCCGATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATC
1 TTTCC-ATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATC
1930601 TAAAATGAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 5 0.10
59 46 0.88
60 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (58 bp):
TTTCCATATCATATCTAAAATAGATATTTAGATCTTTTAATTTTCAATATCATATCAA
Found at i:1956368 original size:16 final size:17
Alignment explanation
Indices: 1956347--1956378 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1956337 TATCTGAAGA
1956347 AATGAAAAAG-AAATAT
1 AATGAAAAAGTAAATAT
1956363 AATGAAAAAGTAAATA
1 AATGAAAAAGTAAATA
1956379 GATGAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AATGAAAAAGTAAATAT
Found at i:1965423 original size:20 final size:20
Alignment explanation
Indices: 1965400--1965443 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1965390 TTGTTGCTAT
* *
1965400 TTTTTTTAATTTTAT-AACTA
1 TTTTTATAATGTTATGAAC-A
1965420 TTTTTATAATGTTATGAACA
1 TTTTTATAATGTTATGAACA
1965440 TTTT
1 TTTT
1965444 ATTATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTATAATGTTATGAACA
Found at i:1967015 original size:27 final size:29
Alignment explanation
Indices: 1966954--1967016 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1966944 AAGAAAATTA
* * *
1966954 AAATATTGAATAAATTTGTCAAGAAATAT
1 AAATATGGAATAAATTGGTCAAGAAATAG
*
1966983 ATATATGGAATAAATTGGTC-A-AAATAG
1 AAATATGGAATAAATTGGTCAAGAAATAG
1967010 AAATATG
1 AAATATG
1967017 TAATTCAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 17 0.59
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (29 bp):
AAATATGGAATAAATTGGTCAAGAAATAG
Found at i:1969239 original size:109 final size:107
Alignment explanation
Indices: 1969102--1969363 Score: 317
Period size: 101 Copynumber: 2.5 Consensus size: 107
1969092 AAAAAAAAAA
* * *
1969102 TTGGGTGCTGGCCTGTTAATGGCCGGCACCCAGTAAACATTAATTTTTTTTTTCTTTTTTTTCGT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGAACAGTAA-TTTTTTTTT-TTTTTTTTCGT
* * **
1969167 GTCAGAGTCAGATATAAAAATACGAAAAAAAT-TTAAAATTTTTT
64 GTCAGAATCAGATATAAAAATACGAAAAAAATAATAAAA-AATTT
*
1969211 TTGGGTGCTGGCCTGTCAATGGTCGGCACCCAGTGAACAGTAA--------TTTTTTTTTCGTGT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGAACAGTAATTTTTTTTTTTTTTTTTCGTGT
*
1969268 CAGAATCAGATATAAAAATAGGAAAAAAATAAAATAAAAAATTT
66 CAGAATCAGATATAAAAATACGAAAAAAAT--AATAAAAAATTT
* *
1969312 TTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTGAACAGTAAATTTTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGAACAGTAATTTTTTTTT
1969364 CGTGTCAGAA
Statistics
Matches: 131, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
99 41 0.31
100 1 0.01
101 44 0.34
102 5 0.04
109 40 0.31
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (107 bp):
TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGAACAGTAATTTTTTTTTTTTTTTTTCGTGT
CAGAATCAGATATAAAAATACGAAAAAAATAATAAAAAATTT
Found at i:1969263 original size:99 final size:97
Alignment explanation
Indices: 1969156--1969398 Score: 353
Period size: 101 Copynumber: 2.5 Consensus size: 97
1969146 TTTTTTTTTC
* **
1969156 TTTTTTTTCGTGTCAGAGTCAGATATAAAAATACGAAAAAAATTTAAAATTTTTTTTGGGTGCTG
1 TTTTTTTTCGTGTCAGAATCAGATATAAAAATA-GAAAAAAATTTAAAA-AATTTTTGGGTGCTG
* * *
1969221 GCCTGTCAATGGTCGGCACCCAGTGAACAGTAAT
64 GCCTATCAATGGCCGGCACCCAGTGAACAGTAAA
*
1969255 TTTTTTTTCGTGTCAGAATCAGATATAAAAATAGGAAAAAAATAAAATAAAAAATTTTTGGGTGC
1 TTTTTTTTCGTGTCAGAATCAGATATAAAAATA-GAAAAAAAT---TTAAAAAATTTTTGGGTGC
1969320 TGGCCTATCAATGGCCGGCACCCAGTGAACAGTAAA
62 TGGCCTATCAATGGCCGGCACCCAGTGAACAGTAAA
*
1969356 TTTTTTTTCGTGTCAGAATTAGATATAAAAATA-AAAAAAATTT
1 TTTTTTTTCGTGTCAGAATCAGATATAAAAATAGAAAAAAATTT
1969399 CTATTTCCTC
Statistics
Matches: 131, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
96 1 0.01
99 49 0.37
101 76 0.58
102 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (97 bp):
TTTTTTTTCGTGTCAGAATCAGATATAAAAATAGAAAAAAATTTAAAAAATTTTTGGGTGCTGGC
CTATCAATGGCCGGCACCCAGTGAACAGTAAA
Found at i:1969698 original size:100 final size:100
Alignment explanation
Indices: 1969519--1969925 Score: 576
Period size: 100 Copynumber: 4.1 Consensus size: 100
1969509 TTTTTTTTTA
****
1969519 TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAG--AATTTTTTTTACTGTGT-AC
1 TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTTTACTGT-TCAC
*
1969581 TGGGTGCCGACCATTGACAGGCCAGCACCCAAATTT
65 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
*
1969617 TTTTTTTCGTATTTTTATATCTGATTCTTACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACT
1 TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACT
* *
1969682 GGGTGCCGGCCATTGACAGGCCTGCA-CCAATTTGTTTT
66 GGGTGCCGGCCATTGACAGGCCAGCACCCAA----ATTT
* *
1969720 ATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA-AGAAAAAAA-TTCATTGTTCA
1 -TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGA-AAAAAAATTTTACTGTTCA
*
1969783 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
64 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
* *
1969820 TTTTTTT-GTATTTTTATATCTGACTCTGACACGAAAAAAAAGAAAAAAAAATTTTACTGTTTAC
1 TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAG-AAAAAAAATTTTACTGTTCAC
1969884 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
65 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
1969920 TTTTTT
1 TTTTTT
1969926 CTTTTTCGTA
Statistics
Matches: 277, Mismatches: 19, Indels: 24
0.87 0.06 0.08
Matches are distributed among these distances:
98 75 0.27
99 19 0.07
100 91 0.33
103 40 0.14
104 52 0.19
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (100 bp):
TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACT
GGGTGCCGGCCATTGACAGGCCAGCACCCAAATTT
Found at i:1969895 original size:203 final size:203
Alignment explanation
Indices: 1969511--1969936 Score: 655
Period size: 203 Copynumber: 2.1 Consensus size: 203
1969501 CTATAAATTT
***** *
1969511 TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTACTG
1 TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTCACTG
*
1969576 TGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAATTTTTTTTTTCGTATTTTTATATCTGA
66 TGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTTCGTATTTTTATATCTGA
* * *
1969641 TTCTTACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCTG
131 CTCTGACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAG
1969706 CA-CC-AA
196 CACCCAAA
*
1969712 TTTGTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTCAT
1 TTT-TTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACG-AAAAAAAAGAAAAAAATTCAC
*
1969777 TGT-TCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT-GTATTTTTATATC
64 TGTGT-ACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTTCGTATTTTTATATC
*
1969840 TGACTCTGACACGAAAAAAAAGAAAAAAAAATTTTACTGTTTACTGGGTGCCGGCCATTGACAGG
128 TGACTCTGACACGAAAAAAAAG-AAAAAAAATTTTACTGTTCACTGGGTGCCGGCCATTGACAGG
1969905 CCAGCACCCAAA
192 CCAGCACCCAAA
1969917 TTTTTTT-TTCTTTTTCGTAT
1 TTTTTTTATT-TTTTTCGTAT
1969937 ATCAGTATTA
Statistics
Matches: 205, Mismatches: 13, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
201 3 0.01
202 73 0.36
203 108 0.53
204 16 0.08
205 5 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (203 bp):
TTTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAGAAAAAAATTCACTG
TGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTTCGTATTTTTATATCTGA
CTCTGACACGAAAAAAAAGAAAAAAAATTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAG
CACCCAAA
Found at i:1975519 original size:34 final size:35
Alignment explanation
Indices: 1975481--1975547 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1975471 CAGTAAAATA
*
1975481 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
1975515 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
1975548 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1979214 original size:13 final size:14
Alignment explanation
Indices: 1979196--1979224 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1979186 TAAAAATTCA
1979196 AAATATAA-TTCTT
1 AAATATAACTTCTT
1979209 AAATATAACTTCTT
1 AAATATAACTTCTT
1979223 AA
1 AA
1979225 GAGTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATAACTTCTT
Found at i:1981297 original size:31 final size:29
Alignment explanation
Indices: 1981227--1981300 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1981217 GGCTCAGGTT
* *
1981227 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
1981256 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
1981287 ACATTTTAGTCACT
1 ACATTTTAGTCACT
1981301 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:1981862 original size:31 final size:29
Alignment explanation
Indices: 1981827--1981925 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 29
1981817 TTAACGACTC
* *
1981827 AGTGACTAAAATGTTACAATACGATAACGTA
1 AGTGACTAAAATGTAACAATAC-A-AACATA
* * *
1981858 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAATACAAACATA
* *
1981887 AGTGACTAAAATGTAACCTAAGACAAACAAA
1 AGTGACTAAAATGTAA-C-AATACAAACATA
1981918 AGTGACTA
1 AGTGACTA
1981926 TTTTGATAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.36
30 2 0.04
31 34 0.61
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAATACAAACATA
Found at i:1984440 original size:16 final size:17
Alignment explanation
Indices: 1984408--1984440 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1984398 CAAATAATTC
*
1984408 AATTAAATTCAATTTTT
1 AATTAAATTCAAGTTTT
1984425 AATTAAA-TCAAGTTTT
1 AATTAAATTCAAGTTTT
1984441 GCTTAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTAAATTCAAGTTTT
Found at i:1985150 original size:24 final size:24
Alignment explanation
Indices: 1985121--1985171 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1985111 TCTTTCTAGA
**
1985121 ATATTTAGTATTTATGAGAATAAT
1 ATATTTAACATTTATGAGAATAAT
* *
1985145 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTTATGAGAATAAT
1985169 ATA
1 ATA
1985172 CTTGACTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (24 bp):
ATATTTAACATTTATGAGAATAAT
Found at i:1988215 original size:26 final size:26
Alignment explanation
Indices: 1988186--1988237 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1988176 AGTTTTCTGA
1988186 ATGTGGTTGAAAAGTTATATGTATGT
1 ATGTGGTTGAAAAGTTATATGTATGT
1988212 ATGTGGTTGAAAAGTTATATGTATGT
1 ATGTGGTTGAAAAGTTATATGTATGT
1988238 GTTTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (26 bp):
ATGTGGTTGAAAAGTTATATGTATGT
Found at i:1993797 original size:20 final size:20
Alignment explanation
Indices: 1993774--1993815 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1993764 TCGATCATAG
1993774 ATGATAGATTTTGAGGACCC
1 ATGATAGATTTTGAGGACCC
1993794 ATGATAGATTTTGAGGACCC
1 ATGATAGATTTTGAGGACCC
1993814 AT
1 AT
1993816 TGGTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
ATGATAGATTTTGAGGACCC
Found at i:1998563 original size:19 final size:17
Alignment explanation
Indices: 1998531--1998565 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1998521 TTATTTATTG
1998531 TATATTATTTTTAAATA
1 TATATTATTTTTAAATA
1998548 TATATCTATATTTTAAAT
1 TATAT-TAT-TTTTAAAT
1998566 TATCACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTATTTTTAAATA
Found at i:2002988 original size:9 final size:9
Alignment explanation
Indices: 2002971--2003001 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2002961 TCGAGTTGAT
2002971 TCGAATAAC
1 TCGAATAAC
*
2002980 TCGATTAAC
1 TCGAATAAC
2002989 TCGAATAAC
1 TCGAATAAC
2002998 TCGA
1 TCGA
2003002 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:2004207 original size:26 final size:27
Alignment explanation
Indices: 2004168--2004229 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
2004158 TTTAAAATAC
* *
2004168 TTTTAAAATAATTTTTTTATTTTTTAT
1 TTTTAAAATAATTTTTTTAATGTTTAT
2004195 TTTTAAAAT-ATTTTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTTAATGTTTAT
*
2004221 TTTAAAAAT
1 TTTTAAAAT
2004230 GGGTCGGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTTAATGTTTAT
Found at i:2014830 original size:23 final size:25
Alignment explanation
Indices: 2014786--2014833 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2014776 AACGTACGTT
* *
2014786 TATATTTTTGTTAATTTGAAATTTA
1 TATATATTTGTTAAGTTGAAATTTA
2014811 TATATATTT-TTAAGTT-AAATTTA
1 TATATATTTGTTAAGTTGAAATTTA
2014834 GTCATTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TATATATTTGTTAAGTTGAAATTTA
Found at i:2015184 original size:17 final size:19
Alignment explanation
Indices: 2015155--2015195 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
2015145 TTATTTTTAG
2015155 TATTTAGTATTATA-TAAT
1 TATTTAGTATTATATTAAT
2015173 TATTTA-TATTATATTAAT
1 TATTTAGTATTATATTAAT
2015191 T-TTTA
1 TATTTA
2015196 CAAGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTAGTATTATATTAAT
Found at i:2017449 original size:31 final size:32
Alignment explanation
Indices: 2017397--2017488 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 32
2017387 ACAAAAGAAA
* ** *
2017397 ATTAGATACCAAATTGTGAAAATAA-GTCAAG
1 ATTACATACCAAATTAAGAAAAAAATGTCAAG
2017428 ATTACATACCAAATTAAGAAAAAAATGTCAAG
1 ATTACATACCAAATTAAGAAAAAAATGTCAAG
* *
2017460 -TT-CAAGTACCAAATT-AGATAAAAGTGTCA
1 ATTAC-A-TACCAAATTAAGAAAAAAATGTCA
2017489 TATTCAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.02
31 36 0.69
32 15 0.29
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (32 bp):
ATTACATACCAAATTAAGAAAAAAATGTCAAG
Found at i:2017495 original size:31 final size:32
Alignment explanation
Indices: 2017434--2017504 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
2017424 CAAGATTACA
2017434 TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
1 TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
* *
2017466 TACCAAATT-AGATAAAAGTGTCATA-TTCAAG
1 TACCAAATTAAGAAAAAAATGTCA-AGTTCAAG
*
2017497 TATCAAAT
1 TACCAAAT
2017505 GTTATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (32 bp):
TACCAAATTAAGAAAAAAATGTCAAGTTCAAG
Found at i:2023976 original size:10 final size:10
Alignment explanation
Indices: 2023963--2023991 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2023953 TCCATTTATA
2023963 TATATATATG
1 TATATATATG
2023973 TATATATATG
1 TATATATATG
2023983 TATATATAT
1 TATATATAT
2023992 CTATTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:2029036 original size:19 final size:18
Alignment explanation
Indices: 2028993--2029040 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2028983 GTTTTGGATT
2028993 TTAAA-TTTTAAATTTTA
1 TTAAATTTTTAAATTTTA
*
2029010 -TATGATTTTTAGAATTTTA
1 TTA-AATTTTTA-AATTTTA
2029029 TTAAATTTTTAA
1 TTAAATTTTTAA
2029041 TATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 6 0.24
19 14 0.56
20 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TTAAATTTTTAAATTTTA
Found at i:2037348 original size:3 final size:3
Alignment explanation
Indices: 2037340--2037368 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2037330 TTGTATTTGA
2037340 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2037369 ATTTTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2046169 original size:194 final size:193
Alignment explanation
Indices: 2045835--2046222 Score: 749
Period size: 194 Copynumber: 2.0 Consensus size: 193
2045825 AACTCACAAG
2045835 TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
1 TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
2045900 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
66 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
2045965 ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
131 ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
*
2046028 TTGGTAAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATGAATTATTGTTTTCTATTC
1 TTGGT-AAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTC
2046093 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
65 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
*
2046158 TATAAGATATTTAGGCATATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
130 TATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
2046222 T
1 T
2046223 GCCACCATTT
Statistics
Matches: 192, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
193 5 0.03
194 187 0.97
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (193 bp):
TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
ATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
Found at i:2076894 original size:15 final size:15
Alignment explanation
Indices: 2076874--2076904 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2076864 GCACCAACTA
*
2076874 ATAACATAGTGACAC
1 ATAACATAATGACAC
2076889 ATAACATAATGACAC
1 ATAACATAATGACAC
2076904 A
1 A
2076905 ACCTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (15 bp):
ATAACATAATGACAC
Found at i:2079054 original size:16 final size:18
Alignment explanation
Indices: 2079035--2079072 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2079025 TATATTATAC
2079035 AAAAACTAT-AA-AAAAT
1 AAAAACTATAAATAAAAT
*
2079051 AAAAATTATAAATAAAAT
1 AAAAACTATAAATAAAAT
2079069 AAAA
1 AAAA
2079073 TAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAACTATAAATAAAAT
Found at i:2079086 original size:66 final size:70
Alignment explanation
Indices: 2079013--2079176 Score: 248
Period size: 73 Copynumber: 2.4 Consensus size: 70
2079003 TTATGTATAA
*
2079013 AATATTTATTTTTATATTATACAAAAA-C-T-ATA-AAAAATAAAAATTATAAATAAAATAAAAT
1 AATATTTATTTTTATATTATACAAAAACCATAAAAGAAAAATAAAAATTATAAATAAAATAAAAT
2079074 AAAAT
66 AAAAT
2079079 AATATTTATTTTTATATTATACAAAAACCATAAAAAAGTAAAAATAAAAATTATAAATAAAATAA
1 AATATTTATTTTTATATTATACAAAAACCAT--AAAAG-AAAAATAAAAATTATAAATAAAATAA
2079144 AATAAAAT
63 AATAAAAT
*
2079152 AATATTTATTTTTATACTATA-AAAA
1 AATATTTATTTTTATATTATACAAAA
2079177 TCAAATTTAA
Statistics
Matches: 89, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
66 27 0.30
67 1 0.01
68 1 0.01
71 2 0.02
72 4 0.04
73 54 0.61
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (70 bp):
AATATTTATTTTTATATTATACAAAAACCATAAAAGAAAAATAAAAATTATAAATAAAATAAAAT
AAAAT
Found at i:2094808 original size:83 final size:83
Alignment explanation
Indices: 2094669--2094834 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
2094659 TTAAAAATTC
2094669 CCATTATAATTGCCACAGATCTTCTCTCCCTTTTTTAAAAATTTTAAGATTTTATATTGCTTAAC
1 CCATTATAATTGCCACAGATCTTCTCTCCCTTTTTTAAAAATTTTAAGATTTTATATTGCTTAAC
2094734 AAAAAACAACAATTTTAT
66 AAAAAACAACAATTTTAT
2094752 CCATTATAATTGCCACAGATCTTCTCTCCCTTTTTTAAAAATTTTAAGATTTTATATTGCTTAAC
1 CCATTATAATTGCCACAGATCTTCTCTCCCTTTTTTAAAAATTTTAAGATTTTATATTGCTTAAC
2094817 AAAAAACAACAATTTTAT
66 AAAAAACAACAATTTTAT
2094835 TTTATGAACT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (83 bp):
CCATTATAATTGCCACAGATCTTCTCTCCCTTTTTTAAAAATTTTAAGATTTTATATTGCTTAAC
AAAAAACAACAATTTTAT
Found at i:2105916 original size:24 final size:23
Alignment explanation
Indices: 2105889--2105941 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
2105879 ATTTTTAGAA
2105889 TTTAAAAAATTCAAAAAATTATTT
1 TTTAAAAAATT-AAAAAATTATTT
*
2105913 TTTAAAAAAATTATAAAATTATTT
1 TTT-AAAAAATTAAAAAATTATTT
2105937 TTTAA
1 TTTAA
2105942 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.07
24 17 0.63
25 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAAATTAAAAAATTATTT
Found at i:2106871 original size:24 final size:24
Alignment explanation
Indices: 2106806--2106859 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2106796 TCTTTCTAGA
* * *
2106806 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
2106830 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
2106854 ATATTT
1 ATATTT
2106860 GACTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:2109735 original size:35 final size:35
Alignment explanation
Indices: 2109695--2109768 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
2109685 TTTAATAAAA
2109695 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
1 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
*
2109730 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAT
1 TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
2109765 TAAA
1 TAAA
2109769 AGCAGTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (35 bp):
TAAACCATATAAAATAAAAATTTTAAAGTCCAAAC
Found at i:2111463 original size:19 final size:19
Alignment explanation
Indices: 2111411--2111466 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2111401 TTAATTTTTT
*
2111411 AAAATT-TTAAAAATGTCAA
1 AAAATTATTAAAAATAT-AA
*
2111430 AAAA-TA--AAAATTATAA
1 AAAATTATTAAAAATATAA
2111446 AAAATTATTAAAAATATAA
1 AAAATTATTAAAAATATAA
2111465 AA
1 AA
2111467 TAATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 1 0.03
19 15 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATTATTAAAAATATAA
Found at i:2111921 original size:16 final size:18
Alignment explanation
Indices: 2111900--2111939 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2111890 TTTTTTAATT
2111900 TAAAAA-TATCAAAAA-A
1 TAAAAATTATCAAAAATA
*
2111916 TAAAAATTATTAAAAATA
1 TAAAAATTATCAAAAATA
2111934 TAAAAA
1 TAAAAA
2111940 ATATTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAATTATCAAAAATA
Found at i:2111929 original size:10 final size:9
Alignment explanation
Indices: 2111899--2111945 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
2111889 TTTTTTTAAT
2111899 TTAAAAATA
1 TTAAAAATA
*
2111908 TCAAAAA-A
1 TTAAAAATA
2111916 -TAAAAATTA
1 TTAAAAA-TA
2111925 TTAAAAATA
1 TTAAAAATA
*
2111934 TAAAAAATA
1 TTAAAAATA
2111943 TTA
1 TTA
2111946 TTTGCTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
7 5 0.16
8 1 0.03
9 19 0.61
10 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAATA
Found at i:2111936 original size:18 final size:16
Alignment explanation
Indices: 2111900--2111945 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
2111890 TTTTTTAATT
*
2111900 TAAAAATATCAAAAAA
1 TAAAAATATTAAAAAA
2111916 TAAAAATTATTAAAAATA
1 TAAAAA-TATTAAAAA-A
2111934 TAAAAAATATTA
1 T-AAAAATATTA
2111946 TTTGCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 7 0.27
19 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATATTAAAAAA
Found at i:2112246 original size:13 final size:13
Alignment explanation
Indices: 2112228--2112254 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2112218 ACTCTTGTTT
2112228 TCTTTAAACTTAA
1 TCTTTAAACTTAA
2112241 TCTTTAAACTTAA
1 TCTTTAAACTTAA
2112254 T
1 T
2112255 AATTATTTTA
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:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTTTAAACTTAA
Found at i:2113956 original size:17 final size:17
Alignment explanation
Indices: 2113936--2113974 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2113926 TTTAAAACAC
*
2113936 TAAAAATTGT-AAATTTT
1 TAAAAATT-TAAAATTAT
2113953 TAAAAATTTAAAATTAT
1 TAAAAATTTAAAATTAT
2113970 TAAAA
1 TAAAA
2113975 TAAAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAAATTTAAAATTAT
Found at i:2113975 original size:16 final size:16
Alignment explanation
Indices: 2113936--2113998 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
2113926 TTTAAAACAC
* *
2113936 TAAAAATTGTAAATTTT
1 TAAAAATT-TAAAATTA
2113953 TAAAAATTTAAAATTA
1 TAAAAATTTAAAATTA
* ** *
2113969 TTAAAATAAAAAATTG
1 TAAAAATTTAAAATTA
2113985 TAAAAATATTAAAA
1 TAAAAAT-TTAAAA
2113999 AAGTGTTCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TAAAAATTTAAAATTA
Found at i:2114243 original size:39 final size:40
Alignment explanation
Indices: 2114200--2114276 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
2114190 AAAGTTGTTG
* *
2114200 AAAAATTATAAAAATGTAAAAAG-TATTAAAAATATATTT
1 AAAAATTATAAAAATATAAAAAGTTATAAAAAATATATTT
* * *
2114239 AAAAATTGTAAAATTATTAAAAGTTATAAAAAATATAT
1 AAAAATTATAAAAATATAAAAAGTTATAAAAAATATAT
2114277 AATTTTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (40 bp):
AAAAATTATAAAAATATAAAAAGTTATAAAAAATATATTT
Found at i:2114434 original size:11 final size:10
Alignment explanation
Indices: 2114418--2114483 Score: 57
Period size: 11 Copynumber: 6.6 Consensus size: 10
2114408 TAAAAAAATC
2114418 ATTTTTAGTAA
1 ATTTTTA-TAA
*
2114429 ATTTTTACAA
1 ATTTTTATAA
2114439 ATTTTTAATAA
1 ATTTTT-ATAA
*
2114450 A-TTTTA-CA
1 ATTTTTATAA
2114458 ATTTTCTATAA
1 ATTTT-TATAA
*
2114469 ATTTTAAT-A
1 ATTTTTATAA
2114478 ATTTTT
1 ATTTTT
2114484 CCAACTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.04
9 10 0.22
10 16 0.36
11 17 0.38
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:2114462 original size:19 final size:20
Alignment explanation
Indices: 2114418--2114483 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 20
2114408 TAAAAAAATC
*
2114418 ATTTTTAGTAAATTTTTACAA
1 ATTTTTAATAAA-TTTTACAA
2114439 ATTTTTAATAAATTTTAC-A
1 ATTTTTAATAAATTTTACAA
2114458 ATTTTCT-ATAAATTTTA-ATA
1 ATTTT-TAATAAATTTTACA-A
2114478 ATTTTT
1 ATTTTT
2114484 CCAACTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 17 0.41
20 13 0.32
21 11 0.27
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTTAATAAATTTTACAA
Found at i:2114688 original size:20 final size:17
Alignment explanation
Indices: 2114661--2114718 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 17
2114651 TTGGTATTAC
2114661 TTAGAAATTTGGATATCA
1 TTAGAAATTT-GATATCA
2114679 TGTGAGAAATATTGATATTCA
1 T-T-AGAAAT-TTGATA-TCA
*
2114700 TTATAAATTTTGATATCA
1 TTAGAAA-TTTGATATCA
2114718 T
1 T
2114719 ATTAGAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.15
19 11 0.32
20 12 0.35
21 6 0.18
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (17 bp):
TTAGAAATTTGATATCA
Found at i:2114712 original size:19 final size:19
Alignment explanation
Indices: 2114641--2114715 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
2114631 TTTTGTATGT
* *
2114641 ATTAAAAATTTTGGTATT-
1 ATTAGAAATTTTGATATTC
*
2114659 ACTTAGAAATTTGGATA-TC
1 A-TTAGAAATTTTGATATTC
*
2114678 ATGTGAGAAATATTGATATTC
1 AT-T-AGAAATTTTGATATTC
*
2114699 ATTATAAATTTTGATAT
1 ATTAGAAATTTTGATAT
2114716 CATATTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.07
19 26 0.58
20 12 0.27
21 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (19 bp):
ATTAGAAATTTTGATATTC
Found at i:2115971 original size:5 final size:5
Alignment explanation
Indices: 2115961--2115990 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2115951 GTATATCCAT
2115961 AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
2115991 TATTGGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:2116105 original size:6 final size:6
Alignment explanation
Indices: 2116094--2116120 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2116084 TTTAGTAAAT
2116094 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
2116121 AAAGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:2119737 original size:23 final size:23
Alignment explanation
Indices: 2119671--2119756 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
2119661 CCTGATCAGT
*
2119671 ATACAACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
* *
2119692 A-ACGACACA-AGAGGTG-CT-TG
1 ATACGACACATA-AAGTGCCTGAG
* *
2119712 ATATGACCCATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
2119735 ATACGGCACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2119757 TAGGCAAAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
20 10 0.21
21 15 0.31
22 3 0.06
23 20 0.42
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:2120863 original size:22 final size:21
Alignment explanation
Indices: 2120838--2120887 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2120828 CTTCCCCTGT
2120838 TTTCGTCTCTT-TCTCTGTTTC
1 TTTCGTCTCTTCTCT-TGTTTC
2120859 GTTTCTGT-TCTTCTCTTGTTTC
1 -TTTC-GTCTCTTCTCTTGTTTC
2120881 TTT-GTCT
1 TTTCGTCT
2120888 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 3 0.12
22 14 0.56
23 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (21 bp):
TTTCGTCTCTTCTCTTGTTTC
Found at i:2125332 original size:28 final size:28
Alignment explanation
Indices: 2125300--2125357 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2125290 GGTAAATTTG
*
2125300 TTTACCTGTTTTAGGCTCAGGGACTAAA
1 TTTACCTGTTTTAGGCTCAGGGACCAAA
*
2125328 TTTACCTGTTTTAGGTTCAGGGACCAAA
1 TTTACCTGTTTTAGGCTCAGGGACCAAA
2125356 TT
1 TT
2125358 ACATGAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (28 bp):
TTTACCTGTTTTAGGCTCAGGGACCAAA
Found at i:2127598 original size:25 final size:26
Alignment explanation
Indices: 2127547--2127608 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
2127537 TAAAAAAATA
2127547 ATCAAAATATTATAACTTTTTTTATTT
1 ATCAAAATATTATAAC-TTTTTTATTT
2127574 ATCAAAATATTATAA-TTTTTTATTT
1 ATCAAAATATTATAACTTTTTTATTT
*
2127599 ATTAAAATAT
1 ATCAAAATAT
2127609 ACCAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 19 0.56
27 15 0.44
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
ATCAAAATATTATAACTTTTTTATTT
Found at i:2128275 original size:23 final size:23
Alignment explanation
Indices: 2128249--2128320 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2128239 ACTCTATTTT
2128249 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
* * * **
2128272 AA-TTACTTAAA-AACTCT-ATTTT
1 AATTTA-ATAAACTATTCTCA-TCA
2128294 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
2128317 AATT
1 AATT
2128321 ACCAAAATAG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 18 0.53
24 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:2128348 original size:15 final size:15
Alignment explanation
Indices: 2128328--2128377 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
2128318 ATTACCAAAA
2128328 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
2128343 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
2128358 GAGAATCGTTTATTAAAT
1 TAG-A--GTTTATTAAAT
2128376 TA
1 TA
2128378 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
16 1 0.03
18 12 0.40
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:2132920 original size:42 final size:42
Alignment explanation
Indices: 2132854--2132934 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
2132844 TATTTATCCA
* *
2132854 ATGATGCACTTACATATCAGTATATTTTCTTCAGTATATCGT
1 ATGATGCACTTACATACCAGTATATTTGCTTCAGTATATCGT
* * *
2132896 ATGATGCACTTACATGCCATTATATTTGCTTCGGTATAT
1 ATGATGCACTTACATACCAGTATATTTGCTTCAGTATAT
2132935 ACTGGCATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (42 bp):
ATGATGCACTTACATACCAGTATATTTGCTTCAGTATATCGT
Found at i:2133855 original size:21 final size:22
Alignment explanation
Indices: 2133831--2133871 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2133821 GTTTTAATAT
*
2133831 TAAAATCT-AATTTTGAAAAAA
1 TAAAATCTCAAATTTGAAAAAA
2133852 TAAAATCTCAAATTTGAAAA
1 TAAAATCTCAAATTTGAAAA
2133872 GTAAATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (22 bp):
TAAAATCTCAAATTTGAAAAAA
Found at i:2138204 original size:20 final size:20
Alignment explanation
Indices: 2138179--2138226 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2138169 ATTTTCTCTT
2138179 TTCATCAAGAATATCAATAA
1 TTCATCAAGAATATCAATAA
* *
2138199 TTCATCATGAATATCAATAC
1 TTCATCAAGAATATCAATAA
2138219 TTCATCAA
1 TTCATCAA
2138227 TTATCATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (20 bp):
TTCATCAAGAATATCAATAA
Found at i:2139937 original size:12 final size:13
Alignment explanation
Indices: 2139905--2139941 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2139895 AATCGGTAAA
2139905 ATTTTTC-TATCG
1 ATTTTTCATATCG
2139917 ATATTTTCATA-CG
1 AT-TTTTCATATCG
2139930 ATTTTTCATATC
1 ATTTTTCATATC
2139942 ATATCAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.45
13 10 0.45
14 2 0.09
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (13 bp):
ATTTTTCATATCG
Found at i:2140817 original size:13 final size:13
Alignment explanation
Indices: 2140788--2140835 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2140778 GCATAAATTT
2140788 AAATAAAATAAGT-
1 AAATAAAATAA-TA
*
2140801 AAATAAAATACTA
1 AAATAAAATAATA
*
2140814 AAATAAAAATAAAA
1 AAAT-AAAATAATA
2140828 AAATAAAA
1 AAATAAAA
2140836 AAGACACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.03
13 18 0.60
14 11 0.37
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:2141606 original size:31 final size:31
Alignment explanation
Indices: 2141570--2141629 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
2141560 TGGACGGTTG
*
2141570 TTTATTATTTATTATTTT-TATTTTGGTTTTA
1 TTTATTATTTATT-TTTTGTATTTGGGTTTTA
2141601 TTTATTATTTATTTTTTGTATTTGGGTTT
1 TTTATTATTTATTTTTTGTATTTGGGTTT
2141630 CTGTTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (31 bp):
TTTATTATTTATTTTTTGTATTTGGGTTTTA
Found at i:2141947 original size:90 final size:92
Alignment explanation
Indices: 2141789--2142019 Score: 251
Period size: 90 Copynumber: 2.5 Consensus size: 92
2141779 TTAGGGGCGT
* * * * *
2141789 AAAAAGCCCTT-AAACTTTTTTAAAAAAAGTAATTAAG-TCTGTGTTTTGTTTTTTTGTACTCAT
1 AAAAAG-CCTTCAAAC-TTTTTCAAAAAAGCAATTAAGCCCTCTGTTTTGTTTTTTTGCACTCAT
*
2141852 ATGGGTACTTGAACTTTCAAAATGCAT-A
64 ATGGGTACTTGAACTTTCAAAATACATCA
2141880 AAAAAGCCTTCAAACTTTTTCAAAAAAGCAATTAAGCCCTACT-TTTT-TTTTTTTGCACTCA-A
1 AAAAAGCCTTCAAACTTTTTCAAAAAAGCAATTAAGCCCT-CTGTTTTGTTTTTTTGCACTCATA
*
2141942 TTGGGTACTTGAATTTTCAAAATACATCA
65 -TGGGTACTTGAACTTTCAAAATACATCA
* * * *
2141971 AAAAAACCCTCAAATTTTTTCAAAAAAAAACAATTAAGCCC-CTGCTTTT
1 AAAAAGCCTTCAAACTTTTTC--AAAAAAGCAATTAAGCCCTCTG-TTTT
2142020 ATTAAAAATT
Statistics
Matches: 120, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
89 1 0.01
90 60 0.50
91 37 0.31
92 1 0.01
93 21 0.17
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (92 bp):
AAAAAGCCTTCAAACTTTTTCAAAAAAGCAATTAAGCCCTCTGTTTTGTTTTTTTGCACTCATAT
GGGTACTTGAACTTTCAAAATACATCA
Found at i:2142046 original size:11 final size:10
Alignment explanation
Indices: 2142018--2142184 Score: 73
Period size: 10 Copynumber: 16.8 Consensus size: 10
2142008 GCCCCTGCTT
*
2142018 TTATTAAAAA
1 TTATAAAAAA
2142028 TTATAAAAAA
1 TTATAAAAAA
2142038 TTATAAAAAA
1 TTATAAAAAA
2142048 TT-TAAAATAA
1 TTATAAAA-AA
*
2142058 --AT-AAAAT
1 TTATAAAAAA
* *
2142065 TTAT-ATATA
1 TTATAAAAAA
* **
2142074 TTATTAAATT
1 TTATAAAAAA
2142084 TTAATAAAAAA
1 TT-ATAAAAAA
*
2142095 TTCAAATATTAAAATT
1 TT---ATA--AAAA-A
*
2142111 TTATTAAAAA
1 TTATAAAAAA
2142121 TTA-AAAAAA
1 TTATAAAAAA
*
2142130 TTGTAAAAAA
1 TTATAAAAAA
2142140 -TATAAAAAA
1 TTATAAAAAA
* **
2142149 -TGTAAAATT
1 TTATAAAAAA
2142158 TTATAAAAAA
1 TTATAAAAAA
*
2142168 -TGTAAAAAA
1 TTATAAAAAA
2142177 TTATAAAA
1 TTATAAAA
2142185 TATATAGAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
7 1 0.01
8 3 0.03
9 43 0.36
10 49 0.41
11 11 0.09
13 6 0.05
15 4 0.03
16 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:2142046 original size:19 final size:19
Alignment explanation
Indices: 2142022--2142203 Score: 82
Period size: 19 Copynumber: 9.8 Consensus size: 19
2142012 CTGCTTTTAT
2142022 TAAAAATTATAAAAAATTA
1 TAAAAATTATAAAAAATTA
2142041 TAAAAAATT-TAAAATAA--A
1 T-AAAAATTATAAAA-AATTA
* * *
2142059 TAAAATTTAT-ATATATTA
1 TAAAAATTATAAAAAATTA
**
2142077 TTAAATTTTAATAAAAAATT-
1 -TAAAAATT-ATAAAAAATTA
* * **
2142097 CAAATA-T-TAAAATTTTA
1 TAAAAATTATAAAAAATTA
*
2142114 TTAAAAATTA-AAAAAATTG
1 -TAAAAATTATAAAAAATTA
*
2142133 TAAAAAATATAAAAAATGTA
1 TAAAAATTATAAAAAAT-TA
**
2142153 -AAATTTTATAAAAAATGTA
1 TAAAAATTATAAAAAAT-TA
*
2142172 -AAAAATTATAAAATA-TA
1 TAAAAATTATAAAAAATTA
*
2142189 TAGAAA-TATAAAAAA
1 TAAAAATTATAAAAAA
2142204 AAATATGAAA
Statistics
Matches: 123, Mismatches: 25, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
16 8 0.07
17 18 0.15
18 21 0.17
19 59 0.48
20 12 0.10
21 5 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAATTATAAAAAATTA
Found at i:2142068 original size:47 final size:47
Alignment explanation
Indices: 2142017--2142184 Score: 150
Period size: 46 Copynumber: 3.6 Consensus size: 47
2142007 AGCCCCTGCT
2142017 TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
1 TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
* * * ** * *
2142064 TTTA-TATATATTATTAAATTTTAATAAAAAA-TTCAAAT-ATTAAAA
1 TTTATTAAAAATTATAAAAAATT-ATAAAAAATTTAAAATAAATAAAA
* * *
2142109 TTTTATTAAAAATTA-AAAAAATTGTAAAAAATATAAAA-AATGTAAAA
1 -TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAA-ATAAAA
* *
2142156 TTT-TATAAAAAATGTAAAAAATTATAAAA
1 TTTAT-TAAAAATTATAAAAAATTATAAAA
2142185 TATATAGAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
45 14 0.15
46 43 0.46
47 37 0.39
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (47 bp):
TTTATTAAAAATTATAAAAAATTATAAAAAATTTAAAATAAATAAAA
Found at i:2144587 original size:14 final size:11
Alignment explanation
Indices: 2144565--2144607 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2144555 TAAAATATAG
2144565 CAAAACAACAA
1 CAAAACAACAA
* *
2144576 CATACCAACAA
1 CAAAACAACAA
2144587 CAAAACAACAA
1 CAAAACAACAA
2144598 C-AAACAACAA
1 CAAAACAACAA
2144608 TAGGGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.02
Consensus pattern (11 bp):
CAAAACAACAA
Found at i:2144593 original size:22 final size:21
Alignment explanation
Indices: 2144565--2144607 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2144555 TAAAATATAG
*
2144565 CAAAACAACAACATACCAACAA
1 CAAAACAACAACA-AACAACAA
2144587 CAAAACAACAACAAACAACAA
1 CAAAACAACAACAAACAACAA
2144608 TAGGGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.02
Consensus pattern (21 bp):
CAAAACAACAACAAACAACAA
Found at i:2144715 original size:19 final size:18
Alignment explanation
Indices: 2144680--2144719 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2144670 GAAAATGAAT
* *
2144680 TTTATTTTTTTGTCTAAA
1 TTTATTTTTTAGCCTAAA
2144698 TTTATTTTTTGAGCCTAAA
1 TTTATTTTTT-AGCCTAAA
2144717 TTT
1 TTT
2144720 TTACCTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.62
Consensus pattern (18 bp):
TTTATTTTTTAGCCTAAA
Found at i:2145290 original size:34 final size:34
Alignment explanation
Indices: 2145247--2145315 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2145237 TAAAATAAAA
2145247 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
2145281 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
2145315 T
1 T
2145316 TATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (34 bp):
TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
Found at i:2145428 original size:29 final size:29
Alignment explanation
Indices: 2145402--2145470 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
2145392 AATTCTCAGT
2145402 GAACAAGTTCTTCATTGCGAACTCTCAAC
1 GAACAAGTTCTTCATTGCGAACTCTCAAC
2145431 GAACAAGTTCTTCATTGCGAACTCTCAAC
1 GAACAAGTTCTTCATTGCGAACTCTCAAC
2145460 GAACAAGTTCT
1 GAACAAGTTCT
2145471 CCACCTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (29 bp):
GAACAAGTTCTTCATTGCGAACTCTCAAC
Found at i:2150958 original size:10 final size:10
Alignment explanation
Indices: 2150927--2150964 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2150917 TGCAGGTAAC
2150927 ATATATAAAGT
1 ATATATAAA-T
*
2150938 ATACA-AAAT
1 ATATATAAAT
2150947 ATATATAAAT
1 ATATATAAAT
2150957 ATATATAA
1 ATATATAA
2150965 TTTAGGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 5 0.21
10 15 0.62
11 4 0.17
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (10 bp):
ATATATAAAT
Found at i:2152631 original size:8 final size:8
Alignment explanation
Indices: 2152618--2152666 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
2152608 TAGCAAATCA
2152618 TATATTTT
1 TATATTTT
2152626 TATATTTT
1 TATATTTT
2152634 TAATAATTTT
1 T-AT-ATTTT
2152644 TAT-TTTT
1 TATATTTT
2152651 TGATATTTT
1 T-ATATTTT
*
2152660 TAAATTT
1 TATATTT
2152667 AAAAAAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 5 0.14
8 16 0.44
9 9 0.25
10 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
TATATTTT
Found at i:2152644 original size:18 final size:17
Alignment explanation
Indices: 2152619--2152666 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
2152609 AGCAAATCAT
2152619 ATATTTTTATATTTTTA
1 ATATTTTTATATTTTTA
*
2152636 ATAATTTTTAT-TTTTTG
1 AT-ATTTTTATATTTTTA
*
2152653 ATATTTTTAAATTT
1 ATATTTTTATATTT
2152667 AAAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 12 0.44
18 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATATTTTTATATTTTTA
Found at i:2153113 original size:18 final size:18
Alignment explanation
Indices: 2153090--2153133 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2153080 AACTAATAAA
2153090 ATATTATTTTATATTTTT
1 ATATTATTTTATATTTTT
*
2153108 ATATTATTTAATATTTTT
1 ATATTATTTTATATTTTT
2153126 -TATT-TTTT
1 ATATTATTTT
2153134 TGACATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 4 0.17
18 17 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATATTATTTTATATTTTT
Found at i:2153863 original size:29 final size:29
Alignment explanation
Indices: 2153804--2153865 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2153794 ACCCATTTCC
* ***
2153804 AACATTATTTACAGAAATGGGCCACTTAA
1 AACATTATTTACAGAAATGGGACAAAAAA
2153833 AACATTATTTACCAG-AATGGGACAAAAAA
1 AACATTATTTA-CAGAAATGGGACAAAAAA
2153862 AACA
1 AACA
2153866 AAACGCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (29 bp):
AACATTATTTACAGAAATGGGACAAAAAA
Found at i:2154140 original size:29 final size:28
Alignment explanation
Indices: 2154078--2154140 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2154068 CAATAAACCT
**
2154078 TAAACCCTAATTTATTTTAAAAAAATTT
1 TAAACCCTAATTTATTTTAAAAAAATCA
**
2154106 TAAACCCTAATTTATTTTCCCAAAAATCA
1 TAAACCCTAATTTATTTT-AAAAAAATCA
2154135 TAAACC
1 TAAACC
2154141 ATAAAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAACCCTAATTTATTTTAAAAAAATCA
Found at i:2155382 original size:28 final size:30
Alignment explanation
Indices: 2155335--2155390 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
2155325 AGGTTTTTGA
2155335 AAAAATAAACAATAAACCCTAATTTATTTT
1 AAAAATAAACAATAAACCCTAATTTATTTT
2155365 AAAAA-AAAC-ATAAACCCTAATTTATT
1 AAAAATAAACAATAAACCCTAATTTATT
2155391 CTTCCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 17 0.65
29 4 0.15
30 5 0.19
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAAATAAACAATAAACCCTAATTTATTTT
Found at i:2155957 original size:19 final size:18
Alignment explanation
Indices: 2155933--2155991 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
2155923 TTATTAAAAT
* *
2155933 ATTATAAAATGTATTTTAA
1 ATTATAAAAT-TATATGAA
2155952 ATTATAAAATTATATGAA
1 ATTATAAAATTATATGAA
* *
2155970 AATATAAAATAATTATGAA
1 ATTATAAAATTA-TATGAA
2155989 ATT
1 ATT
2155992 GTAAGTGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTATAAAATTATATGAA
Found at i:2155977 original size:18 final size:18
Alignment explanation
Indices: 2155935--2155989 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2155925 ATTAAAATAT
* * *
2155935 TATAAAATGTATTTTAAAT
1 TATAAAAT-TATATGAAAA
2155954 TATAAAATTATATGAAAA
1 TATAAAATTATATGAAAA
*
2155972 TATAAAATAATTATGAAA
1 TATAAAATTA-TATGAAA
2155990 TTGTAAGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
TATAAAATTATATGAAAA
Found at i:2166093 original size:22 final size:21
Alignment explanation
Indices: 2166051--2166096 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2166041 ATTATGCTTC
2166051 AATATAATATAGATTTAATTT
1 AATATAATATAGATTTAATTT
* *
2166072 AATATAATTATAGTTTTGATTT
1 AATATAA-TATAGATTTAATTT
2166094 AAT
1 AAT
2166097 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
AATATAATATAGATTTAATTT
Found at i:2167868 original size:2 final size:2
Alignment explanation
Indices: 2167851--2167894 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2167841 GTTTATAAAT
* *
2167851 AG AG GG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2167893 AG
1 AG
2167895 TAGGAGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2168272 original size:2 final size:2
Alignment explanation
Indices: 2168265--2168318 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2168255 AGGTATGTAA
2168265 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2168307 TC TC TC TC TC TC
1 TC TC TC TC TC TC
2168319 CTTTCAGCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2178384 original size:44 final size:44
Alignment explanation
Indices: 2178333--2178421 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
2178323 ATAATTGTAA
**
2178333 ATTAAATTATAATTATTTTTAAATGTGTAATTATCAC-AACTTCT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAA-TTCT
2178377 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
2178421 A
1 A
2178422 CTTTGCCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.46
Consensus pattern (44 bp):
ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
Found at i:2192765 original size:40 final size:41
Alignment explanation
Indices: 2192708--2192867 Score: 250
Period size: 40 Copynumber: 3.8 Consensus size: 41
2192698 CAGCGTTTAC
2192708 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
1 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
*
2192749 -AAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTT
1 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
2192789 AGAAAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
1 ---AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
* *
2192833 AGAAAAAAACGCCGCTAAAGATCATGTTTTTTAGC
1 A-AAAAAAACGCCGCTAAAGACCATGTTCTTTAGC
2192868 AGCGTTTTTG
Statistics
Matches: 110, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
40 39 0.35
41 1 0.01
42 31 0.28
44 39 0.35
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (41 bp):
AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT
Found at i:2192806 original size:84 final size:85
Alignment explanation
Indices: 2192708--2192867 Score: 277
Period size: 84 Copynumber: 1.9 Consensus size: 85
2192698 CAGCGTTTAC
*
2192708 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-AAAAAAACGCCTCTAAAGACCAT
1 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGACCAT
2192772 GTTCTTTAGCGGCGCTTAGA
66 GTTCTTTAGCGGCGCTTAGA
*
2192792 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCA
1 AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AAAAAAACGCCGCTAAAGACCA
*
2192857 TGTTTTTTAGC
65 TGTTCTTTAGC
2192868 AGCGTTTTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
84 41 0.58
86 30 0.42
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (85 bp):
AAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAAAAAACGCCGCTAAAGACCAT
GTTCTTTAGCGGCGCTTAGA
Found at i:2192812 original size:44 final size:42
Alignment explanation
Indices: 2192709--2192867 Score: 259
Period size: 44 Copynumber: 3.8 Consensus size: 42
2192699 AGCGTTTACA
2192709 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT--
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
2192749 AAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
2192791 AAAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 --AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
2192835 AAAAAAACGCCGCTAAAGATCATGTTTTTTAGC
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGC
2192868 AGCGTTTTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
40 39 0.35
42 31 0.28
44 41 0.37
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:2200044 original size:114 final size:114
Alignment explanation
Indices: 2199839--2200055 Score: 249
Period size: 114 Copynumber: 1.9 Consensus size: 114
2199829 ATTAAGTTTC
* * *
2199839 TTGCGGCGTTTTAATCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTCCAAATAAGCGCCA
1 TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
* * ** *
2199904 CTAATGAATCTATACGTGTAGTCGAAACGATGCGTTTCCCTAAGAAATT
66 CTAAAGAAGCTATACGTCAAGACGAAACGATGCGTTTCCCTAAGAAATT
* * **
2199953 TTGCGGCG-CTTAAGCATAAGCGCCACTAAAAGCTGATATTTAGCGGCGTTTACGGATAAGCGCC
1 TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATA-TCAGCGGCGTTTACAAATAAGCGCC
* ** * *
2200017 AGTAAAGGCGCTATA-GCTCAAGACGAAACGTTGTGTTTC
65 ACTAAAGAAGCTATACG-TCAAGACGAAACGATGCGTTTC
2200056 GGCTTCACAT
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
113 28 0.33
114 56 0.67
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (114 bp):
TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
CTAAAGAAGCTATACGTCAAGACGAAACGATGCGTTTCCCTAAGAAATT
Found at i:2200595 original size:114 final size:114
Alignment explanation
Indices: 2200221--2201237 Score: 1638
Period size: 114 Copynumber: 8.9 Consensus size: 114
2200211 AATGTGCTTT
*
2200221 AGCGGCGTTTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* *
2200286 TAACATTTTTTTGTGGCGCTTACAAACAAACGCCGTTAATGATCCACTTC
66 TAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* *
2200336 AGCGGCGTTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* * *
2200401 TAACATTTTTTTGCGGCGCTTACAAACAAACACCGCTATTTATCCACTTC
66 TAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* * *
2200451 GGCGGCATTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* * *
2200516 TAACATTTTTTGCGGCGCTTGCAAGCAAACGCTGCTAATGATCCACTTC
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* * *
2200565 AGTGGCGTTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* * *
2200630 TAACATTTTTTTGCGGCGCTTACAAACAAACACCGCTATTTATCCACTTC
66 TAACA-TTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* * *
2200680 GGCGGCATTTTTACAGAAACGCCACTAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* * * *
2200745 TAACATTTTTTGCGGCACTTGCAAGCAAACGCTGCTAATGATCCACTTC
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* * * *
2200794 AGTGGCGTTTTGACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGCTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* * * *
2200859 TAACATTTTTTGCGGCGCTTACAAATAAATGCCACTAATGATACACTTC
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
2200908 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* *
2200973 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTC
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
2201022 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
2201087 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
* *
2201136 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTTTACCTCAATCTTGTACGTTGCGTTTTGTT
1 AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
* *
2201201 TAACATTGTTTGCGGCGCTTACAAACAAATGCCGCTA
66 TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTA
2201238 CTGCCACTAT
Statistics
Matches: 829, Mismatches: 72, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
114 553 0.67
115 276 0.33
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (114 bp):
AGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTT
TAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTC
Found at i:2201667 original size:19 final size:19
Alignment explanation
Indices: 2201643--2201685 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2201633 GATTAAGGTT
*
2201643 ATTAAAATTTCGATTATCA
1 ATTAAAATTTCAATTATCA
* *
2201662 ATTAAAATTTTAATTATTA
1 ATTAAAATTTCAATTATCA
2201681 ATTAA
1 ATTAA
2201686 TTCGGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTAAAATTTCAATTATCA
Found at i:2225894 original size:30 final size:30
Alignment explanation
Indices: 2225860--2225920 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2225850 TATTATTTTG
2225860 TATGAGTCATAAAAGTAAATTTGTTTGTTA
1 TATGAGTCATAAAAGTAAATTTGTTTGTTA
*
2225890 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAATTTGTTTGTTA
2225920 T
1 T
2225921 GTAAAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (30 bp):
TATGAGTCATAAAAGTAAATTTGTTTGTTA
Found at i:2230838 original size:22 final size:23
Alignment explanation
Indices: 2230780--2230840 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2230770 GAAATTTTAA
*
2230780 AAATATTAATTCTATAAAATAGT
1 AAATGTTAATTCTATAAAATAGT
* *
2230803 AAATGATATTTTCTA-AAAATAGT
1 AAATGTTA-ATTCTATAAAATAGT
*
2230826 AAGTGTTAATTCTAT
1 AAATGTTAATTCTAT
2230841 TTCAATTTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 5 0.17
23 20 0.67
24 5 0.17
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (23 bp):
AAATGTTAATTCTATAAAATAGT
Found at i:2234025 original size:51 final size:51
Alignment explanation
Indices: 2233961--2234061 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
2233951 ACGGATACCC
*
2233961 AGTGGCCTACACATGGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
1 AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
*
2234012 AGTGGCCTGCACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACA
1 AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACA
2234062 TAGTACCACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.24
Consensus pattern (51 bp):
AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
Found at i:2234062 original size:37 final size:38
Alignment explanation
Indices: 2234021--2234099 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
2234011 AAGTGGCCTG
*
2234021 CACATAGTACCACCCTTGT-AGCCAAAGCTA-CCTTCTT
1 CACATAGTACCACACTTGTGA-CCAAAGCTATCCTTCTT
*
2234058 CACATAGTACCACACTTGTGACCAAAGCTATCTTTCTT
1 CACATAGTACCACACTTGTGACCAAAGCTATCCTTCTT
2234096 CACA
1 CACA
2234100 AAGTGGCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 27 0.71
38 11 0.29
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.28
Consensus pattern (38 bp):
CACATAGTACCACACTTGTGACCAAAGCTATCCTTCTT
Found at i:2236017 original size:11 final size:11
Alignment explanation
Indices: 2236003--2236029 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2235993 AATATTAAAA
2236003 ATATATAGAAC
1 ATATATAGAAC
2236014 ATATATAGAAC
1 ATATATAGAAC
2236025 ATATA
1 ATATA
2236030 CAATACGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATATAGAAC
Found at i:2236458 original size:126 final size:123
Alignment explanation
Indices: 2236325--2236571 Score: 302
Period size: 126 Copynumber: 2.0 Consensus size: 123
2236315 AAAAAGTAAA
** * *
2236325 TATAATAAAATGATATTAAAATAAAGTCATTAAAAACAGTAATATATGTATATATACAT-CTAAT
1 TATAATAAAAAAATATTAAAATAAAGT-AATAAAAACAGTAATACA--TATATATACATAC--AT
* * *
2236389 -AAGAATATATAGTAATGT-TAATGATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
61 GAAG-ATATACACTAATGTATAATAATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
* *
2236451 TATAATAAAAAAATATTAAAATAAAGTAATAAAAACATTACTACATATATATACATACATGAAGA
1 TATAATAAAAAAATATTAAAATAAAGTAATAAAAACAGTAATACATATATATACATACATGAAGA
*
2236516 TATACACTAATGTACAATAATAATAATAATAATAATAATAATATTGAAATACAAAA
66 TATACACTAATGT---ATAATAATAATAATAAAAATAATAATATTGAAATACAAAA
2236572 AATGTAATAT
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
122 14 0.13
123 14 0.13
124 1 0.01
125 14 0.13
126 62 0.59
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (123 bp):
TATAATAAAAAAATATTAAAATAAAGTAATAAAAACAGTAATACATATATATACATACATGAAGA
TATACACTAATGTATAATAATAATAATAAAAATAATAATATTGAAATACAAAAGCTAT
Found at i:2236539 original size:3 final size:3
Alignment explanation
Indices: 2236531--2236558 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2236521 ACTAATGTAC
2236531 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2236559 TTGAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2237182 original size:18 final size:18
Alignment explanation
Indices: 2237155--2237190 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2237145 AAGGTAAAAA
*
2237155 TTTATATTTTTTTATTTT
1 TTTATATTTTTGTATTTT
*
2237173 TTTATTTTTTTGTATTTT
1 TTTATATTTTTGTATTTT
2237191 CTTTTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTATATTTTTGTATTTT
Found at i:2237190 original size:8 final size:8
Alignment explanation
Indices: 2237159--2237183 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2237149 TAAAAATTTA
2237159 TATTTTTT
1 TATTTTTT
2237167 TATTTTTT
1 TATTTTTT
2237175 TATTTTTT
1 TATTTTTT
2237183 T
1 T
2237184 GTATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:2238545 original size:72 final size:72
Alignment explanation
Indices: 2238309--2238561 Score: 400
Period size: 73 Copynumber: 3.5 Consensus size: 72
2238299 ACATGTGAAC
* *
2238309 TGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
* *
2238373 CAGCGTGTCC
63 CAACGTGTCT
*
2238383 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCA
2238448 ACGTGTCT
65 ACGTGTCT
2238456 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
*
2238521 TGTGTCT
66 CGTGTCT
*
2238528 TGAGGCTCAACTCATTTCTCGCAATAGGAGTTGA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
2238562 TTCTTTCAAA
Statistics
Matches: 169, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
72 67 0.40
73 72 0.43
74 30 0.18
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (72 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAA
CGTGTCT
Found at i:2239987 original size:46 final size:44
Alignment explanation
Indices: 2239884--2239991 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
2239874 TGTCTTTGAC
** * * **
2239884 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAACCATATATAAT
*
2239928 ATGGACTTACATGGCTCAATCCTGTCTCCAAAACCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAACCATA--TATAAT
2239974 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2239992 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAACCATATATAAT
Found at i:2241389 original size:72 final size:73
Alignment explanation
Indices: 2241169--2241497 Score: 417
Period size: 75 Copynumber: 4.4 Consensus size: 73
2241159 AATCTGAAGA
*
2241169 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCATGT
* *
2241234 GAACCGAGGC
66 -CA-TGAGGC
* * * *
2241244 TCAACTCACCTCTCGCAATATTAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACCTTAACGT
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAACAGAAATTGAAAATACCTCAGCAT
2241309 GTCATGAGGC
64 GTCATGAGGC
** * * *
2241319 TCAACTCATTTCTCGCAATATAAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCATGT
*
2241383 CCTGAGGC
66 CATGAGGC
** * * * *
2241391 TCAACTCATTTCTTGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAA-AACAGAAATTGAAAATACCTCAGCAT
2241456 GTCATGAGGC
64 GTCATGAGGC
*
2241466 TCAACTCACCTCTAGCAATATGAGTTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
2241498 GAAAAACAAA
Statistics
Matches: 224, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
72 64 0.29
74 10 0.04
75 116 0.52
76 1 0.00
77 33 0.15
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCATGT
CATGAGGC
Found at i:2241421 original size:147 final size:147
Alignment explanation
Indices: 2241169--2241515 Score: 477
Period size: 147 Copynumber: 2.3 Consensus size: 147
2241159 AATCTGAAGA
* *
2241169 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGT
1 TCAACTCACCTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAAATACCTCAGCATGT
*
2241234 GAACCGAGGCTCAACTCACCTCTCGCAATATTAGTTGATTTTTTTTGAA-AACAGAAATTGAAAA
65 --ACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT-AACAACAGAAATTGAAAA
*
2241298 TACCTTAACGTGTCATGAGGC
127 TACCTCAACGTGTCATGAGGC
** * *
2241319 TCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT-
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAGCATGTA
** * *
2241383 CCTGAGGCTCAACTCATTTCTTGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTAC
66 CC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATAC
*
2241448 CTCAGCGTGTCATGAGGC
130 CTCAACGTGTCATGAGGC
* *
2241466 TCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT-AAAA
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAA
2241516 GGCTTAACTC
Statistics
Matches: 175, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
146 13 0.07
147 104 0.59
149 33 0.19
150 25 0.14
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (147 bp):
TCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAGCATGTA
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATACC
TCAACGTGTCATGAGGC
Found at i:2241663 original size:71 final size:70
Alignment explanation
Indices: 2241515--2241690 Score: 194
Period size: 71 Copynumber: 2.5 Consensus size: 70
2241505 AAAAATTAAA
* * * * * * ** *
2241515 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCTGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTA
2241579 CCCCG
66 CCCCG
*
2241584 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT
* **
2241649 ATCTTG
65 ACCCCG
*
2241655 AGGCTCAACTCA-TCTCTCGCATTATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
2241691 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
69 26 0.29
70 6 0.07
71 58 0.64
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTA
CCCCG
Found at i:2251048 original size:262 final size:262
Alignment explanation
Indices: 2250583--2251110 Score: 1011
Period size: 262 Copynumber: 2.0 Consensus size: 262
2250573 TCATTGTCAG
* *
2250583 TGAGTAAAAAGAATGTCATCTGGGTCATTGTCGATCGACTCACAAAGTCAGTTCATTTTATAGCA
1 TGAGTAAAAAGAATGTCATCTGGGTAATTGTCGATCGACTCACAAAGTCAGCTCATTTTATAGCA
* * *
2250648 GTTAGAACCGATTGGTCACTACAGAAGCTTGCCGAGGTTTATATCCGGAAAATTGTTAGATTACA
66 GTTAGAACCGACTGGTCAATACAGAAGCTTGCCGAGGTTTATATCCGAAAAATTGTTAGATTACA
2250713 CGGTATTTCAGTATCGATAATTTCAGATCGGGATCCTTGATTTACATCAAGATTTTGGAAGCAGT
131 CGGTATTTCAGTATCGATAATTTCAGATCGGGATCCTTGATTTACATCAAGATTTTGGAAGCAGT
2250778 TACATGAGTCATTGGGTACGTGACTTAATTTTAGCACTGCATTTCATCTGCAAACCGACAGATAG
196 TACATGAGTCATTGGGTACGTGACTTAATTTTAGCACTGCATTTCATCTGCAAACCGACAGATAG
2250843 TT
261 TT
2250845 TGAGTAAAAAGAATGTCATCTGGGTAATTGTCGATCGACTCACAAAGTCAGCTCATTTTATAGCA
1 TGAGTAAAAAGAATGTCATCTGGGTAATTGTCGATCGACTCACAAAGTCAGCTCATTTTATAGCA
2250910 GTTAGAACCGACTGGTCAATACAGAAGCTTGCCGAGGTTTATATCCGAAAAATTGTTAGATTACA
66 GTTAGAACCGACTGGTCAATACAGAAGCTTGCCGAGGTTTATATCCGAAAAATTGTTAGATTACA
2250975 CGGTATTTCAGTATCGATAATTTCAGATCGGGATCCTTGATTTACATCAAGATTTTGGAAGCAGT
131 CGGTATTTCAGTATCGATAATTTCAGATCGGGATCCTTGATTTACATCAAGATTTTGGAAGCAGT
2251040 TACATGAGTCATTGGGTACGTGACTTAATTTTAGCACTGCATTTCATCTGCAAACCGACAGATAG
196 TACATGAGTCATTGGGTACGTGACTTAATTTTAGCACTGCATTTCATCTGCAAACCGACAGATAG
2251105 TT
261 TT
2251107 TGAG
1 TGAG
2251111 CGAGTAATTC
Statistics
Matches: 261, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
262 261 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (262 bp):
TGAGTAAAAAGAATGTCATCTGGGTAATTGTCGATCGACTCACAAAGTCAGCTCATTTTATAGCA
GTTAGAACCGACTGGTCAATACAGAAGCTTGCCGAGGTTTATATCCGAAAAATTGTTAGATTACA
CGGTATTTCAGTATCGATAATTTCAGATCGGGATCCTTGATTTACATCAAGATTTTGGAAGCAGT
TACATGAGTCATTGGGTACGTGACTTAATTTTAGCACTGCATTTCATCTGCAAACCGACAGATAG
TT
Found at i:2252525 original size:30 final size:28
Alignment explanation
Indices: 2252470--2252531 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
2252460 ATTATTTAAC
*
2252470 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAAGATCTTTTACTTAATAATAAA
*
2252498 TAATAAAGATCTATTTACTTAAATAATAAG
1 TAATAAAGATCT-TTTACTT-AATAATAAA
2252528 TAAT
1 TAAT
2252532 TTAAATCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 7 0.23
30 12 0.40
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (28 bp):
TAATAAAGATCTTTTACTTAATAATAAA
Found at i:2252793 original size:11 final size:11
Alignment explanation
Indices: 2252779--2252826 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
2252769 TTTTTTATTG
2252779 TTTTGCTATAA
1 TTTTGCTATAA
*
2252790 TTTTACTATAA
1 TTTTGCTATAA
* *
2252801 TTTCGCTATTA
1 TTTTGCTATAA
* *
2252812 TATTGCTATTA
1 TTTTGCTATAA
2252823 TTTT
1 TTTT
2252827 ATTTTTATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.58
Consensus pattern (11 bp):
TTTTGCTATAA
Found at i:2262091 original size:14 final size:14
Alignment explanation
Indices: 2262072--2262101 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2262062 TTTCATGCTT
2262072 AAATCTAACTGTTA
1 AAATCTAACTGTTA
*
2262086 AAATCTAATTGTTA
1 AAATCTAACTGTTA
2262100 AA
1 AA
2262102 TTTATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AAATCTAACTGTTA
Found at i:2262102 original size:13 final size:13
Alignment explanation
Indices: 2262070--2262114 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2262060 CTTTTCATGC
*
2262070 TTAAATCTAACTG
1 TTAAATCTAATTG
2262083 TTAAAATCTAATTG
1 TT-AAATCTAATTG
* *
2262097 TTAAATTTATTTG
1 TTAAATCTAATTG
2262110 TTAAA
1 TTAAA
2262115 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (13 bp):
TTAAATCTAATTG
Found at i:2262116 original size:14 final size:14
Alignment explanation
Indices: 2262081--2262120 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2262071 TAAATCTAAC
*
2262081 TGTTAAAATCTAAT
1 TGTTAAAATTTAAT
*
2262095 TGTT-AAATTTATT
1 TGTTAAAATTTAAT
2262108 TGTTAAAATTTAA
1 TGTTAAAATTTAA
2262121 AAATTTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (14 bp):
TGTTAAAATTTAAT
Found at i:2269109 original size:22 final size:23
Alignment explanation
Indices: 2269055--2269110 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
2269045 ACTCTTTTTG
2269055 AAATATTAATAATCAAATTTAACAA
1 AAATA-TAA-AATCAAATTTAACAA
* **
2269080 AAAAATAAAATCAAA-TTAATTA
1 AAATATAAAATCAAATTTAACAA
2269102 AAATATAAA
1 AAATATAAA
2269111 CATTAAGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.48
23 7 0.26
24 3 0.11
25 4 0.15
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAAAATCAAATTTAACAA
Done.