Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 130 of 313
Found at i:42084687 original size:16 final size:16
Alignment explanation
Indices: 42084668--42084712 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42084658 TTATTAAATT
*
42084668 ATATATTTAAATTATA
1 ATATATTTAAATAATA
42084684 ATATATTT-AATAATA
1 ATATATTTAAATAATA
*
42084699 ATTATGTTTAAATA
1 A-TATATTTAAATA
42084713 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATATTTAAATAATA
Found at i:42084882 original size:39 final size:42
Alignment explanation
Indices: 42084837--42084937 Score: 100
Period size: 44 Copynumber: 2.4 Consensus size: 42
42084827 TTCCATTATG
42084837 CTATTACACCTCTATTC-T-ATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCATAATTCAACCAAACACAAGATTTA
* * *** *
42084876 CTATTACGCCTTTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-CA-TA-ATTCAACCAAACACAAGATTTA
42084921 CTATTACACCTCTATTC
1 CTATTACACCTCTATTC
42084938 CATTACGCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
39 14 0.29
40 1 0.02
42 1 0.02
44 16 0.33
45 16 0.33
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.36
Consensus pattern (42 bp):
CTATTACACCTCTATTCATAATTCAACCAAACACAAGATTTA
Found at i:42084938 original size:45 final size:44
Alignment explanation
Indices: 42084835--42084943 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 44
42084825 TTTTCCATTA
42084835 TGCTATTACACCTCTATT-C--T--ATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * * ***
42084874 TACTATTACGCCTTTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
42084919 TGCTATTACACCTCTATTCCATTAC
1 TGCTATTACACCTCTATTCCATTAC
42084944 GCCTCTATTC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
42 1 0.02
44 15 0.27
45 23 0.42
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:42084948 original size:16 final size:16
Alignment explanation
Indices: 42084923--42084960 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42084913 TTGATTTGCT
42084923 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
42084939 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
42084955 AATACA
1 ATTACA
42084961 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:42085075 original size:15 final size:15
Alignment explanation
Indices: 42085057--42085085 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42085047 GTTTTTTTTA
42085057 TTTATGTTTTAACAT
1 TTTATGTTTTAACAT
42085072 TTTATGTTTTAACA
1 TTTATGTTTTAACA
42085086 GTCTTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTATGTTTTAACAT
Found at i:42087137 original size:38 final size:37
Alignment explanation
Indices: 42087094--42087170 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 37
42087084 ACTAAAAATT
* *
42087094 TATTTTAAAA-ATAAAAAAATAAAAAATGTATTTTCAAA
1 TATTTTAAAATA-AAAAAAATAAAAAA-ATATTTTAAAA
42087132 TATTTTAAAATAAAAAAAATAAAAAAATATTTTAAAA
1 TATTTTAAAATAAAAAAAATAAAAAAATATTTTAAAA
42087169 TA
1 TA
42087171 AAAAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 11 0.31
38 24 0.67
39 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (37 bp):
TATTTTAAAATAAAAAAAATAAAAAAATATTTTAAAA
Found at i:42087147 original size:37 final size:38
Alignment explanation
Indices: 42087094--42087205 Score: 113
Period size: 37 Copynumber: 2.9 Consensus size: 38
42087084 ACTAAAAATT
* *
42087094 TATTTTAAAAAT-AAAAAAATAAAAAATGTATTTTCAAA
1 TATTTTAAAAATAAAAAAAATAAAAAA-ATATTTTAAAA
42087132 TATTTT-AAAATAAAAAAAATAAAAAAATATTTTAAAA
1 TATTTTAAAAATAAAAAAAATAAAAAAATATTTTAAAA
*** *
42087169 TA-AAAAAAAATAAAAAAAAGTATTAAAAATATATTTA
1 TATTTTAAAAATAAAAAAAA-TA-AAAAAATAT-TTTA
42087206 TTATATTCAG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
37 29 0.46
38 22 0.35
39 8 0.13
40 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (38 bp):
TATTTTAAAAATAAAAAAAATAAAAAAATATTTTAAAA
Found at i:42087159 original size:27 final size:28
Alignment explanation
Indices: 42087129--42087186 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
42087119 ATGTATTTTC
42087129 AAATATTTTAAAAT-AAAAAAAATAAAA
1 AAATATTTTAAAATAAAAAAAAATAAAA
42087156 AAATATTTTAAAATAAAAAAAAATAAAA
1 AAATATTTTAAAATAAAAAAAAATAAAA
42087184 AAA
1 AAA
42087187 AGTATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (28 bp):
AAATATTTTAAAATAAAAAAAAATAAAA
Found at i:42087194 original size:28 final size:27
Alignment explanation
Indices: 42087129--42087196 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
42087119 ATGTATTTTC
*
42087129 AAATATTTTAAAATAAAAAAAATAAAA
1 AAATATATTAAAATAAAAAAAATAAAA
*
42087156 AAATATTTTAAAATAAAAAAAAATAAAA
1 AAATATATTAAAAT-AAAAAAAATAAAA
42087184 AAA-AGTATTAAAA
1 AAATA-TATTAAAA
42087197 ATATATTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 15 0.39
28 23 0.61
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (27 bp):
AAATATATTAAAATAAAAAAAATAAAA
Found at i:42093488 original size:3 final size:3
Alignment explanation
Indices: 42093482--42093521 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
42093472 AAAAAAGAGG
42093482 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
42093522 AGAATGCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42095075 original size:17 final size:18
Alignment explanation
Indices: 42095029--42095080 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
42095019 TAGTTAATTA
* *
42095029 AATATTAAAATAATTATT
1 AATATTTAAATAATTAAT
*
42095047 AATATTT-CATAATTAAT
1 AATATTTAAATAATTAAT
*
42095064 AAT-TTTAAATAAATAAT
1 AATATTTAAATAATTAAT
42095081 TTTATTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 3 0.11
17 19 0.68
18 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTTAAATAATTAAT
Found at i:42095777 original size:29 final size:29
Alignment explanation
Indices: 42095740--42095801 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
42095730 CTTCCTATAC
42095740 ATTTTTTGTTCTGTAACCATTGTTATAGA
1 ATTTTTTGTTCTGTAACCATTGTTATAGA
*
42095769 ATTTTTTGTTTTGTAACCATTGTTATAGA
1 ATTTTTTGTTCTGTAACCATTGTTATAGA
42095798 ATTT
1 ATTT
42095802 AAAAGTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (29 bp):
ATTTTTTGTTCTGTAACCATTGTTATAGA
Found at i:42099878 original size:45 final size:45
Alignment explanation
Indices: 42099809--42100091 Score: 281
Period size: 45 Copynumber: 6.3 Consensus size: 45
42099799 TACACGGTGG
* * * * *
42099809 ATCAACACATAGC-ACCACCCTTATAGTCAATAGTA-CTCGGTGAA
1 ATCAGCACATAGCAATCACCTTTATAATCAATGGTATC-CGGTGAA
* *
42099853 ATCAGCACATAGCAACCACCTTTATACTCAATGGTA-CCAGGTGAA
1 ATCAGCACATAGCAATCACCTTTATAATCAATGGTATCC-GGTGAA
* * *
42099898 TTCAGCACATAGCAATCA-CTTATATAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAATCACCTT-TATAATCAATGGTATCCGGTGAA
* *
42099943 ATCAGCACATAGCAATCACCCTTATACTCAATGGTA-CCGGGTGAA
1 ATCAGCACATAGCAATCACCTTTATAATCAATGGTATCC-GGTGAA
* * * *
42099988 TTCAGCACATAACAATCA-CTTATATAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAATCACCTT-TATAATCAATGGTATCCGGTGAA
** * ** *
42100033 ATCAGCACATAGCAATCACCTTTATTTTCATTAATATCCGGTGCA
1 ATCAGCACATAGCAATCACCTTTATAATCAATGGTATCCGGTGAA
42100078 ATCAGCACATAGCA
1 ATCAGCACATAGCA
42100092 TCCACCTATA
Statistics
Matches: 202, Mismatches: 28, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
44 20 0.10
45 173 0.86
46 9 0.04
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (45 bp):
ATCAGCACATAGCAATCACCTTTATAATCAATGGTATCCGGTGAA
Found at i:42100023 original size:135 final size:135
Alignment explanation
Indices: 42099809--42100097 Score: 347
Period size: 135 Copynumber: 2.1 Consensus size: 135
42099799 TACACGGTGG
* * *
42099809 ATCAACACATAGC-ACCACCCTTATAGTCAATAGTACTCGGTGAAATCAGCACATAGCAACCACC
1 ATCAGCACATAGCAACCACCCTTATACTCAATAGTACTCGGTGAAATCAGCACATAACAACCACC
* **
42099873 TTTATACTCAATGGTA-CCAGGTGAATTCAGCACATAGCAATCA-CTTATATAACCATTGGTATC
66 TTTATACTCAATGGTATCC-GGTGAAATCAGCACATAGCAATCACCTT-TATAACCATTAATATC
42099936 CGGTGAA
129 CGGTGAA
* * * *
42099943 ATCAGCACATAGCAATCACCCTTATACTCAATGGTAC-CGGGTGAATTCAGCACATAACAATCA-
1 ATCAGCACATAGCAACCACCCTTATACTCAATAGTACTC-GGTGAAATCAGCACATAACAACCAC
* ***
42100006 CTTATATAAC-CATTGGTATCCGGTGAAATCAGCACATAGCAATCACCTTTATTTTCATTAATAT
65 CTT-TAT-ACTCAATGGTATCCGGTGAAATCAGCACATAGCAATCACCTTTATAACCATTAATAT
*
42100070 CCGGTGCA
128 CCGGTGAA
*
42100078 ATCAGCACATAGCATCCACC
1 ATCAGCACATAGCAACCACC
42100098 TATATTTCCA
Statistics
Matches: 132, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
134 16 0.12
135 109 0.83
136 7 0.05
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (135 bp):
ATCAGCACATAGCAACCACCCTTATACTCAATAGTACTCGGTGAAATCAGCACATAACAACCACC
TTTATACTCAATGGTATCCGGTGAAATCAGCACATAGCAATCACCTTTATAACCATTAATATCCG
GTGAA
Found at i:42100117 original size:90 final size:90
Alignment explanation
Indices: 42099846--42100057 Score: 388
Period size: 90 Copynumber: 2.4 Consensus size: 90
42099836 CAATAGTACT
*
42099846 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATGGTACCAGGTGAATTCAGCACATAGC
1 CGGTGAAATCAGCACATAGCAATCACCTTTATACTCAATGGTACCAGGTGAATTCAGCACATAGC
42099911 AATCACTTATATAACCATTGGTATC
66 AATCACTTATATAACCATTGGTATC
* * *
42099936 CGGTGAAATCAGCACATAGCAATCACCCTTATACTCAATGGTACCGGGTGAATTCAGCACATAAC
1 CGGTGAAATCAGCACATAGCAATCACCTTTATACTCAATGGTACCAGGTGAATTCAGCACATAGC
42100001 AATCACTTATATAACCATTGGTATC
66 AATCACTTATATAACCATTGGTATC
42100026 CGGTGAAATCAGCACATAGCAATCACCTTTAT
1 CGGTGAAATCAGCACATAGCAATCACCTTTAT
42100058 TTTCATTAAT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 117 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (90 bp):
CGGTGAAATCAGCACATAGCAATCACCTTTATACTCAATGGTACCAGGTGAATTCAGCACATAGC
AATCACTTATATAACCATTGGTATC
Found at i:42100565 original size:12 final size:12
Alignment explanation
Indices: 42100550--42100579 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42100540 AAATTTATTT
42100550 TAAAAATTAAAA
1 TAAAAATTAAAA
42100562 TAAAAATTAAAA
1 TAAAAATTAAAA
42100574 -AAAAAT
1 TAAAAAT
42100580 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:42100600 original size:10 final size:11
Alignment explanation
Indices: 42100574--42100599 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42100564 AAAATTAAAA
42100574 AAAAATATTTT
1 AAAAATATTTT
42100585 AAAAATATTTT
1 AAAAATATTTT
42100596 AAAA
1 AAAA
42100600 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:42100623 original size:40 final size:41
Alignment explanation
Indices: 42100545--42100671 Score: 177
Period size: 40 Copynumber: 3.0 Consensus size: 41
42100535 ACTAAAAATT
*
42100545 TATTTTAAAAATTAAAATAAAAATTAAAAAAAAATATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAAGTATTTTAAAAA
42100590 TATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
* *
42100630 AAATTT-AAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
42100670 TA
1 TA
42100672 AAAAAATAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
39 14 0.18
40 42 0.55
41 7 0.09
42 2 0.03
44 6 0.08
45 6 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
Found at i:42100657 original size:29 final size:29
Alignment explanation
Indices: 42100625--42100685 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
42100615 AAAGTATTTT
*
42100625 AAAAAAAATTT-AAATTAAAAAAATTAAAA
1 AAAAAAAATTTAAAAATAAAAAAA-TAAAA
** *
42100654 AAAAGTATTTTAAAAATAAAAAAATAAAA
1 AAAAAAAATTTAAAAATAAAAAAATAAAA
42100683 AAA
1 AAA
42100686 TTTATTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (29 bp):
AAAAAAAATTTAAAAATAAAAAAATAAAA
Found at i:42100684 original size:39 final size:39
Alignment explanation
Indices: 42100563--42100687 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 39
42100553 AAATTAAAAT
* **
42100563 AAAAATTAAAAAAAAATATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAAGTATTTTAAAAATA--AAAAAATTAA
*
42100604 AAAAATT-AAAAAAAGTATTTTAAAAA-AAATTTAAATTAA
1 AAAAATTAAAAAAAAGTATTTTAAAAATAAA--AAAATTAA
42100643 AAAAATTAAAAAAAAGTATTTTAAAAATAAAAAAA-TAA
1 AAAAATTAAAAAAAAGTATTTTAAAAATAAAAAAATTAA
42100681 AAAAATT
1 AAAAATT
42100688 TATTATTCGG
Statistics
Matches: 75, Mismatches: 5, Indels: 11
0.82 0.05 0.12
Matches are distributed among these distances:
38 10 0.13
39 18 0.24
40 37 0.49
41 10 0.13
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (39 bp):
AAAAATTAAAAAAAAGTATTTTAAAAATAAAAAAATTAA
Found at i:42100688 original size:25 final size:25
Alignment explanation
Indices: 42100623--42100688 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
42100613 AAAAAGTATT
* *
42100623 TTAAAAAAAATTTAAATTAAAAAAA
1 TTAAAAAAATTTTAAAATAAAAAAA
42100648 TTAAAAAAAAGTATTTTAAAAATAAAAAAA
1 TT--AAAAAA--ATTTT-AAAATAAAAAAA
42100678 -TAAAAAAATTT
1 TTAAAAAAATTT
42100689 ATTATTCGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
25 6 0.18
27 12 0.35
29 5 0.15
30 11 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
TTAAAAAAATTTTAAAATAAAAAAA
Found at i:42106241 original size:42 final size:42
Alignment explanation
Indices: 42106126--42106261 Score: 193
Period size: 43 Copynumber: 3.2 Consensus size: 42
42106116 ACGTCGCTAA
* *
42106126 CTTTTGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTT
1 CTTTAGCGGCGCTT-TCCCACAAATGCCGCTAAAGACCATGTT
*
42106169 CTTTAGCGGCGCTTTTCCCA-TAATCGCCGCTAAAGACCATGTT
1 CTTTAGCGGCGC-TTTCCCACAAAT-GCCGCTAAAGACCATGTT
* *
42106212 CTTTAGCGGCGCTTTCCCACAAATGCCGCTAAAGACTATGAT
1 CTTTAGCGGCGCTTTCCCACAAATGCCGCTAAAGACCATGTT
42106254 CTTTAGCG
1 CTTTAGCG
42106262 ACGCCTTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
42 33 0.39
43 49 0.58
44 2 0.02
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTCCCACAAATGCCGCTAAAGACCATGTT
Found at i:42106301 original size:85 final size:86
Alignment explanation
Indices: 42106126--42106330 Score: 229
Period size: 85 Copynumber: 2.4 Consensus size: 86
42106116 ACGTCGCTAA
* * *
42106126 CTTTTGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCATA
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGACGCTTTTCCCATA
* ***
42106191 ATCGCCGCTAAAGACCATGTT
66 ATCGCCGCTAAAGAACATAAC
* * *
42106212 CTTTAGCGGCGCTT-TCCCACAAATGCCGCTAAAGACTATGATCTTTAGCGACGCCTTTTATCTC
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGACG-C-TTT-TCCC
*
42106276 A-AA-CGCCGCTATAGAACA-AAC
63 ATAATCGCCGCTAAAGAACATAAC
* * *
42106297 CTTTAGCGACGCTTCTCGCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAA
42106331 AACATATCAT
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
85 48 0.48
86 43 0.43
87 5 0.05
88 4 0.04
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGACGCTTTTCCCATA
ATCGCCGCTAAAGAACATAAC
Found at i:42106401 original size:24 final size:22
Alignment explanation
Indices: 42106360--42106403 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
42106350 TTATTTTAAT
42106360 TAAATAATATTTATTTTTATGA
1 TAAATAATATTTATTTTTATGA
*
42106382 TAAATATTATATTATGTTTTAT
1 TAAATAATAT-TTAT-TTTTAT
42106404 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TAAATAATATTTATTTTTATGA
Found at i:42109958 original size:50 final size:50
Alignment explanation
Indices: 42109903--42110001 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
42109893 CACCAATTAA
* * *
42109903 TCCTAAACCCTAAATCGTAAAATAGAAACTCTAAACCCCTAACCCCTATC
1 TCCTAAACCCTAAATCATAAAACAAAAACTCTAAACCCCTAACCCCTATC
42109953 TCCTAAACCCTAAATCATAAAACAAAAACTCTAAACCCCTAACCCCTAT
1 TCCTAAACCCTAAATCATAAAACAAAAACTCTAAACCCCTAACCCCTAT
42110002 TTTACAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.34, G:0.02, T:0.21
Consensus pattern (50 bp):
TCCTAAACCCTAAATCATAAAACAAAAACTCTAAACCCCTAACCCCTATC
Found at i:42110121 original size:21 final size:21
Alignment explanation
Indices: 42110105--42110149 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
42110095 CACTAACTCT
*
42110105 TAACCTCTAACATCTAACCCC
1 TAACCCCTAACATCTAACCCC
42110126 TAACCCCTAAC-TACTAACCCC
1 TAACCCCTAACAT-CTAACCCC
42110147 TAA
1 TAA
42110150 ACCTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (21 bp):
TAACCCCTAACATCTAACCCC
Found at i:42110889 original size:15 final size:15
Alignment explanation
Indices: 42110869--42110900 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42110859 CATAAACGCT
42110869 AATCCATAATCCCTA
1 AATCCATAATCCCTA
*
42110884 AATCCATACTCCCTA
1 AATCCATAATCCCTA
42110899 AA
1 AA
42110901 CATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (15 bp):
AATCCATAATCCCTA
Found at i:42111526 original size:41 final size:41
Alignment explanation
Indices: 42111471--42111666 Score: 311
Period size: 41 Copynumber: 4.8 Consensus size: 41
42111461 ATAAAATGCT
*
42111471 TTTAGCGGCGCTTCTTAAAAAACGCCCCTAAAGACCAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
42111512 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGA
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
42111553 TTTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
* * * * *
42111594 ATTAGTGGCGCTTCATCAAAAACGCCGCTAAAGACTAGAGC
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
*
42111635 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
1 TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAA
42111667 TCGCTAAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 144 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.20
Consensus pattern (41 bp):
TTTAGCGGCGCTTCTTAAAAAACGCCGCTAAAGACCAGAGC
Found at i:42111777 original size:39 final size:40
Alignment explanation
Indices: 42111711--42111842 Score: 128
Period size: 40 Copynumber: 3.3 Consensus size: 40
42111701 TTAGGTTTTT
*
42111711 GCGGCGCTTTTTGT-AAAA-CGCCGCTAATGCTC-ATTTTTA
1 GCGGCG-TTTTT-TAAAAAGCGCCGCTAATGCTCGATCTTTA
* *
42111750 GTGGCG-TTTTTAGAAAAGCGCCGCTAATACTCGATCTTTA
1 GCGGCGTTTTTTA-AAAAGCGCCGCTAATGCTCGATCTTTA
* * * * *
42111790 GCGGCGTTTTTTATATAGCGCCGCTAATGATTGATTTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTTTA
*
42111830 GCGGTGTTTTTTA
1 GCGGCGTTTTTTA
42111843 TTCAAACGCC
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
36 1 0.01
37 4 0.05
38 4 0.05
39 18 0.23
40 44 0.57
41 6 0.08
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTTTA
Found at i:42115155 original size:21 final size:22
Alignment explanation
Indices: 42115120--42115168 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
42115110 GTAAATTAAG
42115120 GAGAAATAAAAAATTGGAAG-AA
1 GAGAAATAAAAAATT-GAAGAAA
*
42115142 GAGAAAT-CAAAATTGAAGAAA
1 GAGAAATAAAAAATTGAAGAAA
42115163 GAGAAA
1 GAGAAA
42115169 GAAGTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 14 0.56
22 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (22 bp):
GAGAAATAAAAAATTGAAGAAA
Found at i:42124946 original size:18 final size:17
Alignment explanation
Indices: 42124920--42124972 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 17
42124910 AAATGACCCA
*
42124920 TTCTTCTCCCATTTCCCC
1 TTCTCCTCCC-TTTCCCC
42124938 TTCTCCTCCCCTTTCCCC
1 TTCTCCT-CCCTTTCCCC
42124956 TTCTCCTTCCCTTTCCC
1 TTCTCC-TCCCTTTCCC
42124973 GTTTCGAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.02, C:0.55, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCTCCTCCCTTTCCCC
Found at i:42126150 original size:35 final size:34
Alignment explanation
Indices: 42126111--42126176 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
42126101 CAAACACCAG
*
42126111 AAAACATTTTCCAGTAAGTCATTTTACAGAAATGT
1 AAAACATTTTCCAG-AAATCATTTTACAGAAATGT
* *
42126146 AAAACATTTTCCAGAAATTATTTTACGGAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAA
42126177 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAATGT
Found at i:42128865 original size:10 final size:10
Alignment explanation
Indices: 42128850--42128881 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
42128840 ATTCTTGTGG
42128850 CTTTTATTTT
1 CTTTTATTTT
42128860 CTTTTATTTT
1 CTTTTATTTT
*
42128870 CTTTTCTTTT
1 CTTTTATTTT
42128880 CT
1 CT
42128882 GAAAATGGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (10 bp):
CTTTTATTTT
Found at i:42129429 original size:17 final size:17
Alignment explanation
Indices: 42129384--42129429 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
42129374 ATTTAGGACA
42129384 ATGGTGTTAACTTTTTC
1 ATGGTGTTAACTTTTTC
42129401 AT-GTCGTCTAACTTTTTC
1 ATGGT-GT-TAACTTTTTC
42129419 ATGGTGTTAAC
1 ATGGTGTTAAC
42129430 GGTAATGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
18 14 0.54
19 2 0.08
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (17 bp):
ATGGTGTTAACTTTTTC
Found at i:42129504 original size:17 final size:17
Alignment explanation
Indices: 42129482--42129515 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42129472 AAAATTGAAA
*
42129482 TAAAATATAAAATATAT
1 TAAAATATAAAAAATAT
*
42129499 TAAAATTTAAAAAATAT
1 TAAAATATAAAAAATAT
42129516 ATAATTGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATATAAAAAATAT
Found at i:42139153 original size:21 final size:20
Alignment explanation
Indices: 42139120--42139159 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42139110 ATTAAATCTA
* *
42139120 AAAATTGGGCCCAATAACAC
1 AAAATTGGACCCAAAAACAC
42139140 AAAATTGAGACCCAAAAACA
1 AAAATTG-GACCCAAAAACA
42139160 GGTCGAACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATTGGACCCAAAAACAC
Found at i:42139573 original size:26 final size:30
Alignment explanation
Indices: 42139544--42139610 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 30
42139534 AATTTTATCC
42139544 ATAAAA-AATTTGACGTGACATATATAATAA
1 ATAAAAGAATTTGACGTGACA-ATATAATAA
42139574 ATAAATAAGAATTTGACGTGACATATATAATAA
1 AT-AA-AAGAATTTGACGTGACA-ATATAATAA
42139607 ATAA
1 ATAA
42139611 GAATTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 2 0.06
31 2 0.06
32 4 0.12
33 26 0.76
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (30 bp):
ATAAAAGAATTTGACGTGACAATATAATAA
Found at i:42142519 original size:44 final size:43
Alignment explanation
Indices: 42142453--42142659 Score: 227
Period size: 44 Copynumber: 4.6 Consensus size: 43
42142443 TTTGAGTACT
42142453 TCTGATCAGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGT-GTAGCTTCAGCTACACTTA
* *
42142497 TCTGATCAGTGACAAGTTATAAGTGATAGCTTCAACTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTG-TAGCTTCAGCTACACTTA
* * *
42142541 TCTGATCAGTGACAAGTGACAAGTGGTAACTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGT-GTAGCTTCAGCTACACTTA
*
42142585 TCTGATCAATGACAAGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTA
1 TCTG----AT--C-AGTGACAAGTGATAAGT-GTAGCTTCAGCTACACTTA
* * *
42142635 TTTGACCAGGGACAAGTGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
42142660 ATCATACGTA
Statistics
Matches: 140, Mismatches: 14, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
42 1 0.01
43 16 0.11
44 82 0.59
45 1 0.01
46 1 0.01
48 2 0.01
50 15 0.11
51 22 0.16
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (43 bp):
TCTGATCAGTGACAAGTGATAAGTGTAGCTTCAGCTACACTTA
Found at i:42142649 original size:50 final size:51
Alignment explanation
Indices: 42142548--42142661 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 51
42142538 TTATCTGATC
* * *
42142548 AGTGACAAGTGACAAGTGGTAACTTTAGCTACACTTATCTGATCAATGACA
1 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGACCAAGGACA
* * * *
42142599 AGTGGCAAGTGATAAGTGGTAGC-TTAGCTACACTTATTTGACCAGGGACA
1 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGACCAAGGACA
*
42142649 AGTGATAAGTGAT
1 AGTGACAAGTGAT
42142662 CATACGTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 34 0.63
51 20 0.37
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGACCAAGGACA
Found at i:42144528 original size:19 final size:21
Alignment explanation
Indices: 42144504--42144550 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
42144494 AGATTATTAG
42144504 AAGAAAACAGGAAA-AA-AAA
1 AAGAAAACAGGAAATAATAAA
*
42144523 AAGAAACCAGGAAATAATAAA
1 AAGAAAACAGGAAATAATAAA
*
42144544 AACAAAA
1 AAGAAAA
42144551 TTAGAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.57
20 2 0.09
21 8 0.35
ACGTcount: A:0.74, C:0.09, G:0.13, T:0.04
Consensus pattern (21 bp):
AAGAAAACAGGAAATAATAAA
Found at i:42148451 original size:24 final size:24
Alignment explanation
Indices: 42148416--42148461 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42148406 TTGTGTAATT
*
42148416 TAGTTCTTCTTCTTTTTTTTTGGG
1 TAGTTCTTCTTCTTCTTTTTTGGG
42148440 TAGTT-TTGCTTCTTCTTTTTTG
1 TAGTTCTT-CTTCTTCTTTTTTG
42148462 TGGCATTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.67
Consensus pattern (24 bp):
TAGTTCTTCTTCTTCTTTTTTGGG
Found at i:42149334 original size:29 final size:31
Alignment explanation
Indices: 42149287--42149363 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
42149277 CGCTAATTGA
* *
42149287 ACTTAAAAAAAAAAC-TTAGCA-ACCT-AGTG
1 ACTT-AAATAAAAACTTTAGAATACCTCAGTG
**
42149316 ACTTAAATAAAAACTTTAGAATAGTTCAGTG
1 ACTTAAATAAAAACTTTAGAATACCTCAGTG
42149347 ACTTAAATAAAAACTTT
1 ACTTAAATAAAAACTTT
42149364 CAAATAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.22
29 9 0.22
30 2 0.05
31 21 0.51
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTAGAATACCTCAGTG
Found at i:42156505 original size:27 final size:26
Alignment explanation
Indices: 42156453--42156505 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
42156443 ATCACAAAAA
*
42156453 AGAAAATTAAAAGAAAAAAGTTGAAAT
1 AGAAAATTAAAAGAAAAAAG-AGAAAT
42156480 AGAAAATTAAAAAAGAAAAAA-AGAAA
1 AGAAAATT--AAAAGAAAAAAGAGAAA
42156506 AATTGGCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
29 11 0.48
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (26 bp):
AGAAAATTAAAAGAAAAAAGAGAAAT
Found at i:42156654 original size:16 final size:17
Alignment explanation
Indices: 42156619--42156664 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
42156609 ACAAGAAAAC
*
42156619 AAATTTGTTTATTTTATA
1 AAATTT-TTAATTTTATA
42156637 AAATTTTTAATTTT-TA
1 AAATTTTTAATTTTATA
42156653 AAATTTTTAATT
1 AAATTTTTAATT
42156665 AAAACTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 14 0.52
17 7 0.26
18 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
AAATTTTTAATTTTATA
Found at i:42161136 original size:5 final size:5
Alignment explanation
Indices: 42161116--42161166 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
42161106 ATATTTAAAT
* * * *
42161116 TTATA ATATT TTATA TTATA TTATG TTAT- TTTTA TATATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA
42161166 T
1 T
42161167 AATTTATAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
4 3 0.08
5 30 0.81
6 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:42161145 original size:20 final size:20
Alignment explanation
Indices: 42161124--42161164 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42161114 ATTTATAATA
*
42161124 TTTTATATTATATTATGTTAT
1 TTTTATA-TATATTATATTAT
42161145 TTTTATATATATTATATTAT
1 TTTTATATATATTATATTAT
42161165 ATAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATATATATTATATTAT
Found at i:42161336 original size:24 final size:24
Alignment explanation
Indices: 42161294--42161339 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42161284 TTATTAAATA
*
42161294 TTAAAATAAATAAATAAATATTTT
1 TTAAAATAAATAAAAAAATATTTT
42161318 TTAAAATAAA-AACAAAAATATT
1 TTAAAATAAATAA-AAAAATATT
42161340 GGAAGGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAATAAATAAAAAAATATTTT
Found at i:42165873 original size:566 final size:566
Alignment explanation
Indices: 42164801--42165932 Score: 2264
Period size: 566 Copynumber: 2.0 Consensus size: 566
42164791 AATGTCTTCC
42164801 ACACCATTGCATCAGGCTTAAATGGCATTGATTCAATTAAGGTTCTTGCCTCACCAAGTTGCCTA
1 ACACCATTGCATCAGGCTTAAATGGCATTGATTCAATTAAGGTTCTTGCCTCACCAAGTTGCCTA
42164866 GCTCGCCCCAATATATCAACTGCACAAGCATAGTGCTCCATACGTGGTGGGATTCCATAATCAGA
66 GCTCGCCCCAATATATCAACTGCACAAGCATAGTGCTCCATACGTGGTGGGATTCCATAATCAGA
42164931 TTCCATAGATTTCAGAAAATTTAAGCCTTCTTCCACAAGACCAATATGACTACATGCAGTAAGAA
131 TTCCATAGATTTCAGAAAATTTAAGCCTTCTTCCACAAGACCAATATGACTACATGCAGTAAGAA
42164996 CTGCAACAAACGTTATATGATCGAGCCTCACCTTTCTGTCTCTCATCAGGAAGAATAGGTCAAGG
196 CTGCAACAAACGTTATATGATCGAGCCTCACCTTTCTGTCTCTCATCAGGAAGAATAGGTCAAGG
42165061 GCAATACTGCCCTGCCCATTTTGTGCATAGCCGAAAATTAATGAATTCCAAGCAATTGAACTGTC
261 GCAATACTGCCCTGCCCATTTTGTGCATAGCCGAAAATTAATGAATTCCAAGCAATTGAACTGTC
42165126 ATTGGGAGTCTCTTCAAAGGATTTTCGAGCATCTTCGATTATCCCACACTTCGAGTACAAGAAAA
326 ATTGGGAGTCTCTTCAAAGGATTTTCGAGCATCTTCGATTATCCCACACTTCGAGTACAAGAAAA
42165191 TCAATGCACTTGCCACAAAATCATTAGTCTTGAAGCCCGACTTAATTGCCAAGACATGAACCTGC
391 TCAATGCACTTGCCACAAAATCATTAGTCTTGAAGCCCGACTTAATTGCCAAGACATGAACCTGC
42165256 CGACCTAATTGAAGTGTCGCTAAATCAGCGCAAGATCTAAGGACAGCAGAAAAGGCATAGTGGTC
456 CGACCTAATTGAAGTGTCGCTAAATCAGCGCAAGATCTAAGGACAGCAGAAAAGGCATAGTGGTC
42165321 AATCTCTACCATCAAAGATCTCATTTGACCAAAAAGTTTCAAGGCG
521 AATCTCTACCATCAAAGATCTCATTTGACCAAAAAGTTTCAAGGCG
42165367 ACACCATTGCATCAGGCTTAAATGGCATTGATTCAATTAAGGTTCTTGCCTCACCAAGTTGCCTA
1 ACACCATTGCATCAGGCTTAAATGGCATTGATTCAATTAAGGTTCTTGCCTCACCAAGTTGCCTA
42165432 GCTCGCCCCAATATATCAACTGCACAAGCATAGTGCTCCATACGTGGTGGGATTCCATAATCAGA
66 GCTCGCCCCAATATATCAACTGCACAAGCATAGTGCTCCATACGTGGTGGGATTCCATAATCAGA
42165497 TTCCATAGATTTCAGAAAATTTAAGCCTTCTTCCACAAGACCAATATGACTACATGCAGTAAGAA
131 TTCCATAGATTTCAGAAAATTTAAGCCTTCTTCCACAAGACCAATATGACTACATGCAGTAAGAA
42165562 CTGCAACAAACGTTATATGATCGAGCCTCACCTTTCTGTCTCTCATCAGGAAGAATAGGTCAAGG
196 CTGCAACAAACGTTATATGATCGAGCCTCACCTTTCTGTCTCTCATCAGGAAGAATAGGTCAAGG
42165627 GCAATACTGCCCTGCCCATTTTGTGCATAGCCGAAAATTAATGAATTCCAAGCAATTGAACTGTC
261 GCAATACTGCCCTGCCCATTTTGTGCATAGCCGAAAATTAATGAATTCCAAGCAATTGAACTGTC
42165692 ATTGGGAGTCTCTTCAAAGGATTTTCGAGCATCTTCGATTATCCCACACTTCGAGTACAAGAAAA
326 ATTGGGAGTCTCTTCAAAGGATTTTCGAGCATCTTCGATTATCCCACACTTCGAGTACAAGAAAA
42165757 TCAATGCACTTGCCACAAAATCATTAGTCTTGAAGCCCGACTTAATTGCCAAGACATGAACCTGC
391 TCAATGCACTTGCCACAAAATCATTAGTCTTGAAGCCCGACTTAATTGCCAAGACATGAACCTGC
42165822 CGACCTAATTGAAGTGTCGCTAAATCAGCGCAAGATCTAAGGACAGCAGAAAAGGCATAGTGGTC
456 CGACCTAATTGAAGTGTCGCTAAATCAGCGCAAGATCTAAGGACAGCAGAAAAGGCATAGTGGTC
42165887 AATCTCTACCATCAAAGATCTCATTTGACCAAAAAGTTTCAAGGCG
521 AATCTCTACCATCAAAGATCTCATTTGACCAAAAAGTTTCAAGGCG
42165933 TCTTCATTCA
Statistics
Matches: 566, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
566 566 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (566 bp):
ACACCATTGCATCAGGCTTAAATGGCATTGATTCAATTAAGGTTCTTGCCTCACCAAGTTGCCTA
GCTCGCCCCAATATATCAACTGCACAAGCATAGTGCTCCATACGTGGTGGGATTCCATAATCAGA
TTCCATAGATTTCAGAAAATTTAAGCCTTCTTCCACAAGACCAATATGACTACATGCAGTAAGAA
CTGCAACAAACGTTATATGATCGAGCCTCACCTTTCTGTCTCTCATCAGGAAGAATAGGTCAAGG
GCAATACTGCCCTGCCCATTTTGTGCATAGCCGAAAATTAATGAATTCCAAGCAATTGAACTGTC
ATTGGGAGTCTCTTCAAAGGATTTTCGAGCATCTTCGATTATCCCACACTTCGAGTACAAGAAAA
TCAATGCACTTGCCACAAAATCATTAGTCTTGAAGCCCGACTTAATTGCCAAGACATGAACCTGC
CGACCTAATTGAAGTGTCGCTAAATCAGCGCAAGATCTAAGGACAGCAGAAAAGGCATAGTGGTC
AATCTCTACCATCAAAGATCTCATTTGACCAAAAAGTTTCAAGGCG
Found at i:42167984 original size:39 final size:39
Alignment explanation
Indices: 42167899--42167984 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
42167889 TAGTATTAGG
* * * *
42167899 GAGCAATAGTTAAAGTCTCTTGTGGACATCTTTATAATC
1 GAGCAATGGTTAAAGTCTATTGTGGACACCTTTATAACC
*
42167938 GAGCAATGGTTAAAGTCTATTGTTGACACCTTTATAACC
1 GAGCAATGGTTAAAGTCTATTGTGGACACCTTTATAACC
42167977 GAGCAATG
1 GAGCAATG
42167985 ATTCTCTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (39 bp):
GAGCAATGGTTAAAGTCTATTGTGGACACCTTTATAACC
Found at i:42173968 original size:21 final size:21
Alignment explanation
Indices: 42173944--42173983 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42173934 ATCTTTTCTA
42173944 AAGTT-AAAAGTTAAAACCATT
1 AAGTTAAAAAG-TAAAACCATT
42173965 AAGTTAAAAAGTAAAACCA
1 AAGTTAAAAAGTAAAACCA
42173984 CATCGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAAGTAAAACCATT
Found at i:42183231 original size:16 final size:16
Alignment explanation
Indices: 42183195--42183234 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
42183185 ATTATATTTC
42183195 TTAATTACTATTTTGA
1 TTAATTACTATTTTGA
*
42183211 ATAATT-CTATTTTGTA
1 TTAATTACTATTTTG-A
42183227 TTAATTAC
1 TTAATTAC
42183235 ATAAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (16 bp):
TTAATTACTATTTTGA
Found at i:42193136 original size:19 final size:20
Alignment explanation
Indices: 42193114--42193154 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
42193104 TAATATTTAT
*
42193114 TTATTTTAGATTTTT-ATAA
1 TTATTTCAGATTTTTCATAA
*
42193133 TTATTTCATATTTTTCATAA
1 TTATTTCAGATTTTTCATAA
42193153 TT
1 TT
42193155 TACTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATTTCAGATTTTTCATAA
Found at i:42193147 original size:27 final size:26
Alignment explanation
Indices: 42193088--42193147 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
42193078 GACCGCATCA
42193088 ATTTTTAAATTTTTAATAATATTTAT
1 ATTTTTAAATTTTTAATAATATTTAT
* *
42193114 TTATTTTAGATTTTT-ATAATTATTTCAT
1 AT-TTTTAAATTTTTAATAA-TATTT-AT
42193142 ATTTTT
1 ATTTTT
42193148 CATAATTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.18
27 20 0.71
28 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTTTAAATTTTTAATAATATTTAT
Found at i:42193267 original size:20 final size:21
Alignment explanation
Indices: 42193229--42193279 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
42193219 TTTTTTCCAC
*
42193229 ATTTTTATAATCTATTAATAA
1 ATTTTTATAATATATTAATAA
*
42193250 ATTTTTATAATATA-TAATAT
1 ATTTTTATAATATATTAATAA
42193270 ATTTTTATAA
1 ATTTTTATAA
42193280 AATTTTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTATAATATATTAATAA
Found at i:42193462 original size:21 final size:21
Alignment explanation
Indices: 42193433--42193473 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42193423 ATATTTTTTG
*
42193433 ATGTCAAATGTCATGTCAACA
1 ATGTCAAATGCCATGTCAACA
*
42193454 ATGTGAAATGCCATGTCAAC
1 ATGTCAAATGCCATGTCAAC
42193474 TATCACACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (21 bp):
ATGTCAAATGCCATGTCAACA
Found at i:42193690 original size:20 final size:21
Alignment explanation
Indices: 42193652--42193702 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
42193642 TTTTTTCCAC
*
42193652 ATTTTTATAATCTATTAATAA
1 ATTTTTATAATATATTAATAA
*
42193673 ATTTTTATAATATA-TAATAT
1 ATTTTTATAATATATTAATAA
42193693 ATTTTTATAA
1 ATTTTTATAA
42193703 AATTTTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTATAATATATTAATAA
Found at i:42193815 original size:20 final size:19
Alignment explanation
Indices: 42193790--42193833 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
42193780 TAATTTTCTC
42193790 TTAAATAAATAAAAAATCAA
1 TTAAATAAATAAAAAAT-AA
* * *
42193810 TTAAATTATTATAAAATAA
1 TTAAATAAATAAAAAATAA
42193829 TTAAA
1 TTAAA
42193834 CCATTAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAATAAATAAAAAATAA
Found at i:42193839 original size:19 final size:20
Alignment explanation
Indices: 42193802--42193839 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
42193792 AAATAAATAA
**
42193802 AAAATCAATTAAATTATTAT
1 AAAATCAATTAAACCATTAT
42193822 AAAAT-AATTAAACCATTA
1 AAAATCAATTAAACCATTA
42193840 ACACCAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCAATTAAACCATTAT
Found at i:42193870 original size:423 final size:424
Alignment explanation
Indices: 42193083--42193937 Score: 1606
Period size: 423 Copynumber: 2.0 Consensus size: 424
42193073 TCAACGACCG
*
42193083 CATCAATTTTTAAATTTTTAATAATATTTATTTATTTTAGATTTTTATAATTATTTCATATTTTT
1 CATCAATTTTTAAATTTTTAATAATATTTATTTATTTTAGATCTTTATAATTATTTCATATTTTT
*
42193148 CATAATTTACTAATAATGTTTTATAATATTTATAAATTCAATACATTTTTATACATTTTCTATAT
66 CATAATTTACTAATAATATTTTATAATATTTATAAATTCAATACATTTTTATACATTTTCTATAT
42193213 TTTTATTTTTTTCCACATTTTTATAATCTATTAATAAATTTTTATAATATATAATATATTTTTAT
131 TTTTATTTTTTTCCACATTTTTATAATCTATTAATAAATTTTTATAATATATAATATATTTTTAT
*
42193278 AAAATTTTCCTAAATATTTATAAATTTTTTAGTATCATTTAATGATTTTTATAGTTTTTTAAACT
196 AAAATTTTCCTAAATATTTATAAATTTTTTAGTATCATTTAATGATTTTTATAATTTTTTAAACT
*
42193343 TTTATAATATTCCAATAGTTTCTCTTAAATAAATAAAAAATCAATTAAATTATTGTAAAATAATT
261 TTTATAATATTCCAATAGTTTCTCTTAAATAAATAAAAAATCAATTAAATTATTATAAAATAATT
*
42193408 AAACCATTAACGCCAATATTTTTTGATGTCAAATGTCATGTCAACAATGTGAAATGCCATGTCAA
326 AAACCATTAACACCAATATTTTTTGATGTCAAATGTCATGTCAACAATGTGAAATGCCATGTCAA
42193473 CTATCACACCATCATTTTTCCACATTGGCTACTA
391 CTATCACACCATCATTTTTCCACATTGGCTACTA
42193507 CATCAATTTTTAAATTTTTAATAATATTTATTTATTTTAGATCTTTATAATTATTTCATATTTTT
1 CATCAATTTTTAAATTTTTAATAATATTTATTTATTTTAGATCTTTATAATTATTTCATATTTTT
*
42193572 CATAATTTACTAATAATATTTTATAATATTTATAAATTCAATACCTTTTTATACATTTTCTATAT
66 CATAATTTACTAATAATATTTTATAATATTTATAAATTCAATACATTTTTATACATTTTCTATAT
42193637 TTTTA-TTTTTTCCACATTTTTATAATCTATTAATAAATTTTTATAATATATAATATATTTTTAT
131 TTTTATTTTTTTCCACATTTTTATAATCTATTAATAAATTTTTATAATATATAATATATTTTTAT
42193701 AAAATTTTCCTAAATATTTAT-AATTTTTTAGTATCATTTAATGATTTTTATAATTTTTTAAACT
196 AAAATTTTCCTAAATATTTATAAATTTTTTAGTATCATTTAATGATTTTTATAATTTTTTAAACT
* *
42193765 TTTATAATATTCTAATAATTTTCTCTTAAATAAATAAAAAATCAATTAAATTATTATAAAATAAT
261 TTTATAATATTCCAAT-AGTTTCTCTTAAATAAATAAAAAATCAATTAAATTATTATAAAATAAT
42193830 TAAACCATTAACACCAATATTTTTTGATGTCAAATGTCATGTCAACAATGTGAAATGCCATGTCA
325 TAAACCATTAACACCAATATTTTTTGATGTCAAATGTCATGTCAACAATGTGAAATGCCATGTCA
*
42193895 GCTATCACACCATCATTTTTCCACATTGGCTACTA
390 ACTATCACACCATCATTTTTCCACATTGGCTACTA
42193930 CATCAATT
1 CATCAATT
42193938 GCTATGTCAT
Statistics
Matches: 421, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
422 57 0.14
423 232 0.55
424 132 0.31
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (424 bp):
CATCAATTTTTAAATTTTTAATAATATTTATTTATTTTAGATCTTTATAATTATTTCATATTTTT
CATAATTTACTAATAATATTTTATAATATTTATAAATTCAATACATTTTTATACATTTTCTATAT
TTTTATTTTTTTCCACATTTTTATAATCTATTAATAAATTTTTATAATATATAATATATTTTTAT
AAAATTTTCCTAAATATTTATAAATTTTTTAGTATCATTTAATGATTTTTATAATTTTTTAAACT
TTTATAATATTCCAATAGTTTCTCTTAAATAAATAAAAAATCAATTAAATTATTATAAAATAATT
AAACCATTAACACCAATATTTTTTGATGTCAAATGTCATGTCAACAATGTGAAATGCCATGTCAA
CTATCACACCATCATTTTTCCACATTGGCTACTA
Found at i:42197093 original size:15 final size:15
Alignment explanation
Indices: 42197058--42197099 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42197048 TTAAGAATTT
*
42197058 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42197072 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42197086 TATTTAATAATAAT
1 TATTTAATTATAAT
42197100 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42197246 original size:19 final size:19
Alignment explanation
Indices: 42197222--42197260 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42197212 TCATTTTAGT
42197222 TTTTTCCATTATGCTATTA
1 TTTTTCCATTATGCTATTA
42197241 TTTTTCCATTATGCTATTA
1 TTTTTCCATTATGCTATTA
42197260 T
1 T
42197261 ACCTCTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTCCATTATGCTATTA
Found at i:42197361 original size:16 final size:16
Alignment explanation
Indices: 42197340--42197391 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
42197330 TTGATTTGAT
42197340 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
42197356 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
42197372 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
42197388 ATTA
1 ATTA
42197392 AACAAAGCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:42197516 original size:15 final size:15
Alignment explanation
Indices: 42197491--42197530 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
42197481 GACCCATGCA
42197491 GAAAA-TTAAGTTCT
1 GAAAATTTAAGTTCT
42197505 GAAAATTTAAGTTCT
1 GAAAATTTAAGTTCT
42197520 G--AATTTAAGTT
1 GAAAATTTAAGTT
42197531 ATAAAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.40
14 5 0.20
15 10 0.40
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (15 bp):
GAAAATTTAAGTTCT
Found at i:42197526 original size:13 final size:14
Alignment explanation
Indices: 42197491--42197530 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
42197481 GACCCATGCA
*
42197491 GAAAATTAAGTTCT
1 GAAATTTAAGTTCT
42197505 GAAAATTTAAGTTCT
1 G-AAATTTAAGTTCT
42197520 G-AATTTAAGTT
1 GAAATTTAAGTT
42197531 ATAAAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 13 0.54
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (14 bp):
GAAATTTAAGTTCT
Found at i:42199557 original size:24 final size:25
Alignment explanation
Indices: 42199510--42199557 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
42199500 TCTAAAACCC
***
42199510 ACAAAACCCTAACCTTACTTAAAAA
1 ACAAAACCCTAACCTTAAAAAAAAA
42199535 ACAAAA-CCTAACCTTAAAAAAAA
1 ACAAAACCCTAACCTTAAAAAAAA
42199558 TGCTTCTAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (25 bp):
ACAAAACCCTAACCTTAAAAAAAAA
Found at i:42200052 original size:21 final size:20
Alignment explanation
Indices: 42200028--42200067 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42200018 AATCAATTAA
*
42200028 TTAATTAATTAAAATATAAAT
1 TTAAATAATTAAAA-ATAAAT
*
42200049 TTAAATAGTTAAAAATAAA
1 TTAAATAATTAAAAATAAA
42200068 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAATAATTAAAAATAAAT
Found at i:42200308 original size:24 final size:24
Alignment explanation
Indices: 42200274--42200321 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
42200264 TTTTATTAGC
42200274 TTATTAATTTAATAAAAGTATAAA
1 TTATTAATTTAATAAAAGTATAAA
*
42200298 TTATTAGTTTAATAAAAGTATAAA
1 TTATTAATTTAATAAAAGTATAAA
42200322 GAGTAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TTATTAATTTAATAAAAGTATAAA
Found at i:42207502 original size:15 final size:14
Alignment explanation
Indices: 42207438--42207507 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
42207428 ATAGAAATTT
*
42207438 ATTTAAA-ATAAAA
1 ATTTAAATATTAAA
42207451 ATATT-AA-ATTAAA
1 AT-TTAAATATTAAA
*
42207464 ATTAAAATA-TAAGA
1 ATTTAAATATTAA-A
42207478 ATTTATAATATTAAA
1 ATTTA-AATATTAAA
42207493 TATTTAAATA-TAAA
1 -ATTTAAATATTAAA
42207507 A
1 A
42207508 AACATTACTG
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
12 1 0.02
13 17 0.36
14 12 0.26
15 9 0.19
16 8 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (14 bp):
ATTTAAATATTAAA
Found at i:42207736 original size:21 final size:19
Alignment explanation
Indices: 42207712--42207757 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
42207702 TATAAAAAAA
* *
42207712 ATATTTTTCTAGATTTTAT
1 ATATTTTTCTAAATTTTTT
*
42207731 ATATATTTCTAAATTTTTT
1 ATATTTTTCTAAATTTTTT
42207750 ATATTTTT
1 ATATTTTT
42207758 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATTTTTCTAAATTTTTT
Found at i:42209719 original size:31 final size:31
Alignment explanation
Indices: 42209681--42209743 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42209671 GTTAACACCA
42209681 AAACAAAATCGGGGTTTCATTTATTTTATTT
1 AAACAAAATCGGGGTTTCATTTATTTTATTT
42209712 AAACAAAATCGGGGTTTCATTTATTTTATTT
1 AAACAAAATCGGGGTTTCATTTATTTTATTT
42209743 A
1 A
42209744 GTCTAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (31 bp):
AAACAAAATCGGGGTTTCATTTATTTTATTT
Found at i:42227735 original size:22 final size:23
Alignment explanation
Indices: 42227696--42227741 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
42227686 TCATGATAAA
* *
42227696 TAAATTGATAATTGTAATATATT
1 TAAATTGATAATTATAATACATT
*
42227719 TAAATTTA-AATTATAATACATT
1 TAAATTGATAATTATAATACATT
42227741 T
1 T
42227742 GAACAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAATTGATAATTATAATACATT
Found at i:42228680 original size:22 final size:22
Alignment explanation
Indices: 42228644--42228713 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
42228634 AACTGCTATT
* *
42228644 TTTTTTTGCTATTTTCTTACTA
1 TTTTTTTACTGTTTTCTTACTA
*
42228666 TTTTTTTACTGTTTTGC-TATTA
1 TTTTTTTACTGTTTT-CTTACTA
* * **
42228688 TTTTCTTATTGTTTTCTCGCTA
1 TTTTTTTACTGTTTTCTTACTA
42228710 TTTT
1 TTTT
42228714 ACTATTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.11, C:0.13, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTTTTACTGTTTTCTTACTA
Found at i:42231278 original size:19 final size:19
Alignment explanation
Indices: 42231211--42231279 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
42231201 CAGTCATGTG
* *
42231211 TAATATA-TTTAATTATTA
1 TAATATATTTTATTTAATA
42231229 TAAT-TAATTTTATTT-A-A
1 TAATAT-ATTTTATTTAATA
* *
42231246 -AATTTATATTATTTAATA
1 TAATATATTTTATTTAATA
42231264 TAATATATTTTATTTA
1 TAATATATTTTATTTA
42231280 GTTCCTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
16 11 0.28
17 4 0.10
18 6 0.15
19 19 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATATATTTTATTTAATA
Found at i:42231645 original size:15 final size:15
Alignment explanation
Indices: 42231610--42231653 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42231600 TCAAGTTTAA
* *
42231610 GATTTTTTGAATTTG
1 GATTTTTTGAGTTAG
*
42231625 GGTTTTTTGAGTTAG
1 GATTTTTTGAGTTAG
42231640 GATTTTTTTGAGTT
1 GA-TTTTTTGAGTT
42231654 TAAATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (15 bp):
GATTTTTTGAGTTAG
Found at i:42231711 original size:15 final size:16
Alignment explanation
Indices: 42231691--42231723 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42231681 GAGTTCAATC
42231691 TTATTT-GAATTCAAG
1 TTATTTCGAATTCAAG
*
42231706 TTATTTCGATTTCAAG
1 TTATTTCGAATTCAAG
42231722 TT
1 TT
42231724 CAAGCAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (16 bp):
TTATTTCGAATTCAAG
Found at i:42238751 original size:105 final size:105
Alignment explanation
Indices: 42238600--42238865 Score: 383
Period size: 105 Copynumber: 2.5 Consensus size: 105
42238590 AATGTTTAAA
*
42238600 TGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTGGGTTATGATATC-TTG
1 TGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTGGGTTATGACA-CATTG
* * **
42238664 AACTTAATA-TCATGGTTAGACCATGGCAGTATAGATACATG
65 AACGTAAGACT-ATGGTTAGACCATAACAGTATAGATACATG
* *
42238705 TGTAAGACCATAGCTGAGCTATGGCATTTTAATAAAAAGATCATAACTGGGTTATGACACATTGA
1 TGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTGGGTTATGACACATTGA
*
42238770 ACGTAAGACTATGGTTGGACCATAACAGTATAGATACATG
66 ACGTAAGACTATGGTTAGACCATAACAGTATAGATACATG
* * * * *
42238810 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATG
1 TGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTGGGTTATG
42238866 GCACTACAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 142 0.99
106 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTGGGTTATGACACATTGA
ACGTAAGACTATGGTTAGACCATAACAGTATAGATACATG
Found at i:42238882 original size:33 final size:32
Alignment explanation
Indices: 42238810--42238886 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
42238800 TAGATACATG
* * **
42238810 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
42238842 TGATAAGACCATAACTGGGCTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
42238876 TGTAAGACCAT
1 TGTAAGACCAT
42238887 GGCAGGGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 32 0.82
34 5 0.13
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:42239915 original size:42 final size:42
Alignment explanation
Indices: 42239831--42239926 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
42239821 ACGGCCTAAG
* **
42239831 ACACGGGTATGTCTCCTAGCCGTGTGAGCCACACGGCAGGCC
1 ACACGGGCATGTCTCCTAGCCGTGTGAGCCACACACCAGGCC
* * * * *
42239873 ACACGGGCGTGTCTCCTGGCCGTGTGAGTCACATACCCGGCC
1 ACACGGGCATGTCTCCTAGCCGTGTGAGCCACACACCAGGCC
*
42239915 ACATGGGCATGT
1 ACACGGGCATGT
42239927 GTCTTCTGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.18, C:0.32, G:0.31, T:0.19
Consensus pattern (42 bp):
ACACGGGCATGTCTCCTAGCCGTGTGAGCCACACACCAGGCC
Found at i:42240262 original size:21 final size:21
Alignment explanation
Indices: 42240223--42240262 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42240213 AAACACCCCT
*
42240223 TTGGTGAGTGAGAACGGCCCA
1 TTGGTGAGTGAAAACGGCCCA
* *
42240244 TTGGTGGGTGAAAATGGCC
1 TTGGTGAGTGAAAACGGCC
42240263 TTTGGCAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.23
Consensus pattern (21 bp):
TTGGTGAGTGAAAACGGCCCA
Found at i:42240296 original size:21 final size:20
Alignment explanation
Indices: 42240258--42240305 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
42240248 TGGGTGAAAA
*
42240258 TGGCCTTTGGCAGAAGAGAG
1 TGGCCCTTGGCAGAAGAGAG
*
42240278 TGGTCCCTTGGCA-AGAGAGGG
1 TGG-CCCTTGGCAGA-AGAGAG
42240299 TGGCCCT
1 TGGCCCT
42240306 CTTTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.21
Consensus pattern (20 bp):
TGGCCCTTGGCAGAAGAGAG
Found at i:42241565 original size:18 final size:17
Alignment explanation
Indices: 42241533--42241567 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42241523 TAATTCTTAA
*
42241533 AAAAATCAAAAATAAAT
1 AAAAATAAAAAATAAAT
42241550 AAAAATAAAAAGATAAAT
1 AAAAATAAAAA-ATAAAT
42241568 TGGTTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAATAAAAAATAAAT
Found at i:42243499 original size:50 final size:50
Alignment explanation
Indices: 42243375--42243623 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
42243365 GATAATAACA
* * ** * *
42243375 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
42243426 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
42243476 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
42243526 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
42243581 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
42243624 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:42243553 original size:100 final size:104
Alignment explanation
Indices: 42243374--42243623 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
42243364 TGATAATAAC
**
42243374 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
42243439 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
42243476 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
42243539 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
42243581 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42243624 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:42243739 original size:13 final size:13
Alignment explanation
Indices: 42243718--42243749 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42243708 GCTTGGATCA
*
42243718 TCATCAAATAAAT
1 TCATAAAATAAAT
42243731 TCATAAAATAAAT
1 TCATAAAATAAAT
42243744 TCATAA
1 TCATAA
42243750 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:42243996 original size:30 final size:30
Alignment explanation
Indices: 42243961--42244018 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42243951 CCTCGACTCT
*
42243961 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
42243991 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
42244019 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:42252569 original size:9 final size:9
Alignment explanation
Indices: 42252555--42252671 Score: 162
Period size: 9 Copynumber: 12.6 Consensus size: 9
42252545 TTTGGTTAAA
42252555 AATTACCCG
1 AATTACCCG
42252564 AATTACCCG
1 AATTACCCG
*
42252573 ACTTACCCG
1 AATTACCCG
*
42252582 ACTTACCCG
1 AATTACCCG
42252591 AATTACCCG
1 AATTACCCG
*
42252600 ACTTACCCG
1 AATTACCCG
42252609 AATTACCCG
1 AATTACCCG
42252618 AATTACCCG
1 AATTACCCG
*
42252627 AAAATTACCCA
1 --AATTACCCG
42252638 AATTACCCG
1 AATTACCCG
42252647 AAAATTACCCG
1 --AATTACCCG
42252658 AATTACCCG
1 AATTACCCG
42252667 AATTA
1 AATTA
42252672 AATCACTACA
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
9 81 0.83
11 17 0.17
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:42252700 original size:17 final size:17
Alignment explanation
Indices: 42252678--42252738 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
42252668 ATTAAATCAC
42252678 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
42252695 TACATAAATCTTTGAATCAC
1 TACAT-AA--TTAAAAACAT
*
42252715 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
42252732 TACATAA
1 TACATAA
42252739 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:42252720 original size:20 final size:20
Alignment explanation
Indices: 42252695--42252758 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
42252685 TTAAAAACAT
42252695 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
42252715 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
42252732 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
42252752 TACATAA
1 TACATAA
42252759 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:42252778 original size:37 final size:37
Alignment explanation
Indices: 42252672--42252784 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
42252662 ACCCGAATTA
* *
42252672 AATCACTACATAATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
42252709 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
42252746 AATCACTACATAATTAAAAATATTACACAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
42252782 AAT
1 AAT
42252785 TAAAACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:42252852 original size:24 final size:24
Alignment explanation
Indices: 42252825--42252883 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
42252815 ATTCTCCATT
*
42252825 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
42252849 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
42252873 TATCTCCATTT
1 TATATCCATTT
42252884 GCATTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:42255931 original size:9 final size:9
Alignment explanation
Indices: 42255917--42255942 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42255907 GAGTGTGAAA
42255917 GTGAAATTT
1 GTGAAATTT
42255926 GTGAAATTT
1 GTGAAATTT
42255935 GTGAAATT
1 GTGAAATT
42255943 AGGGAGGAGA
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:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (9 bp):
GTGAAATTT
Found at i:42257136 original size:14 final size:14
Alignment explanation
Indices: 42257117--42257151 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42257107 CAAATTACAT
42257117 GTTAGAATAGTATC
1 GTTAGAATAGTATC
42257131 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
42257145 ATTAGAA
1 GTTAGAA
42257152 AAAAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:42258596 original size:15 final size:15
Alignment explanation
Indices: 42258566--42258603 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42258556 ATTCATTGCT
*
42258566 TTTAGGG-TTTAGGG
1 TTTAGGGTTTTAAGG
*
42258580 TTTATGGTTTTAAGG
1 TTTAGGGTTTTAAGG
42258595 TTTAGGGTT
1 TTTAGGGTT
42258604 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTTAAGG
Found at i:42258873 original size:26 final size:28
Alignment explanation
Indices: 42258823--42258887 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
42258813 ATAAACACCA
42258823 AAAAAAATATTTTAAAAATAAAAAGAAT
1 AAAAAAATATTTTAAAAATAAAAAGAAT
*
42258851 AAAAAAATATTTT-AAAAT-TAAAGAAT
1 AAAAAAATATTTTAAAAATAAAAAGAAT
42258877 -AAAAAATATTT
1 AAAAAAATATTT
42258888 ATTTATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 11 0.31
26 7 0.19
27 5 0.14
28 13 0.36
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAAAATATTTTAAAAATAAAAAGAAT
Found at i:42262789 original size:21 final size:21
Alignment explanation
Indices: 42262765--42262816 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
42262755 TTGTCCAGCT
* *
42262765 TCCGGAGGGGGTTGTGGTTTA
1 TCCGGAGGGGATTATGGTTTA
* *
42262786 TCCGGTGGGGATTATGGTTTT
1 TCCGGAGGGGATTATGGTTTA
42262807 TCCGGTAGGG
1 TCCGG-AGGG
42262817 TATCTAGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.10, C:0.12, G:0.44, T:0.35
Consensus pattern (21 bp):
TCCGGAGGGGATTATGGTTTA
Found at i:42263095 original size:16 final size:17
Alignment explanation
Indices: 42263074--42263108 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
42263064 AAAAGGAAAC
42263074 ATAT-AAGGGTTAGGAT
1 ATATAAAGGGTTAGGAT
42263090 ATATAAAAGGGTTAGGAT
1 ATAT-AAAGGGTTAGGAT
42263108 A
1 A
42263109 CGCACCTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
ATATAAAGGGTTAGGAT
Found at i:42263420 original size:63 final size:63
Alignment explanation
Indices: 42263342--42263466 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
42263332 TCCTTTGCCG
*
42263342 ACAGTAAATACGGCTTGTCATGGATCCTAAACTATGGCATGTCTTCTAGCACGCACGCTAACA
1 ACAGTAAATACGGCTTGTCATGGATCCTAAACTATGGCATGTCTTCCAGCACGCACGCTAACA
42263405 ACAGTAAATACGGCTTGTCATGGATCCTAAACTATGGCATGTCTTCCAGCACGCACGCTAAC
1 ACAGTAAATACGGCTTGTCATGGATCCTAAACTATGGCATGTCTTCCAGCACGCACGCTAAC
42263467 TCCAGAACGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (63 bp):
ACAGTAAATACGGCTTGTCATGGATCCTAAACTATGGCATGTCTTCCAGCACGCACGCTAACA
Found at i:42264788 original size:22 final size:21
Alignment explanation
Indices: 42264763--42264824 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
42264753 ATATATGGAT
42264763 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAA-TTGAG-AGGAAA
*
42264785 TTGATAGCAAATTGAGAGGAAA
1 TTGAGAG-AAATTGAGAGGAAA
42264807 TTGAGAGAATAATTGAGA
1 TTGAGAG-A-AATTGAGA
42264825 AAGGATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (21 bp):
TTGAGAGAAATTGAGAGGAAA
Found at i:42264822 original size:12 final size:11
Alignment explanation
Indices: 42264763--42264824 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
42264753 ATATATGGAT
*
42264763 TTGAGAGAAAT
1 TTGAGAGAAAA
*
42264774 TTG-GAAGGAAA
1 TTGAG-AGAAAA
* *
42264785 TTGATAGCAAA
1 TTGAGAGAAAA
*
42264796 TTGAGAGGAAA
1 TTGAGAGAAAA
42264807 TTGAGAGAATAA
1 TTGAGAGAA-AA
42264819 TTGAGA
1 TTGAGA
42264825 AAGGATTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
10 1 0.02
11 32 0.78
12 8 0.20
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:42266590 original size:22 final size:22
Alignment explanation
Indices: 42266559--42266600 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42266549 CCGCCCTCTC
42266559 TTTCTCCTTC-TTCTTCTCTTCT
1 TTTCTCCTTCTTTC-TCTCTTCT
*
42266581 TTTCTTCTTCTTTCTCTCTT
1 TTTCTCCTTCTTTCTCTCTT
42266601 TCGATTGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTCCTTCTTTCTCTCTTCT
Found at i:42272808 original size:12 final size:12
Alignment explanation
Indices: 42272791--42272820 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42272781 AAGTTATAAT
42272791 TTATTTTAATTA
1 TTATTTTAATTA
42272803 TTATTTTAATTA
1 TTATTTTAATTA
*
42272815 ATATTT
1 TTATTT
42272821 GAGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:42279448 original size:23 final size:23
Alignment explanation
Indices: 42279350--42279460 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
42279340 ACCTGATCAG
*
42279350 TATACGACACAT-AAGTGCCTGA
1 TATACGACACATGAGGTGCCTGA
*
42279372 -A-ACGACACACGAGGTGCCTG-
1 TATACGACACATGAGGTGCCTGA
*
42279392 -ATACGACACACGAGGTGCCTGA
1 TATACGACACATGAGGTGCCTGA
42279414 TATACGACACATGAGGTGCCTGA
1 TATACGACACATGAGGTGCCTGA
* *
42279437 TATACGACACATAAAGTGCCTGA
1 TATACGACACATGAGGTGCCTGA
42279460 T
1 T
42279461 CGGCAAAGCC
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
20 9 0.11
21 28 0.35
23 43 0.54
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.19
Consensus pattern (23 bp):
TATACGACACATGAGGTGCCTGA
Found at i:42280631 original size:3 final size:3
Alignment explanation
Indices: 42280623--42280648 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42280613 TATTCCTAGT
42280623 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
42280649 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42280810 original size:17 final size:17
Alignment explanation
Indices: 42280778--42280826 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
42280768 TATTTAAAAT
42280778 ATAATAATAA-TT--TA
1 ATAATAATAATTTAATA
*
42280792 ATAATACTAATTTAATA
1 ATAATAATAATTTAATA
42280809 ATAATAATAATTTAATA
1 ATAATAATAATTTAATA
42280826 A
1 A
42280827 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
17 19 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATAATTTAATA
Found at i:42280826 original size:14 final size:14
Alignment explanation
Indices: 42280778--42280816 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
42280768 TATTTAAAAT
42280778 ATAATAATAATTTA
1 ATAATAATAATTTA
*
42280792 ATAATACTAATTTA
1 ATAATAATAATTTA
42280806 ATAATAATAAT
1 ATAATAATAAT
42280817 AATTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:42280837 original size:31 final size:31
Alignment explanation
Indices: 42280769--42280828 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
42280759 TTATTTATTT
* *
42280769 ATTTAAAATATAATAATAATTTAATAATACTA
1 ATTTAATA-ATAATAATAATTTAATAACACTA
42280801 ATTTAATAATAATAATAATTTAATAACA
1 ATTTAATAATAATAATAATTTAATAACA
42280829 TTTTTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTAATAATAATAATAATTTAATAACACTA
Found at i:42292310 original size:9 final size:9
Alignment explanation
Indices: 42292296--42292456 Score: 84
Period size: 9 Copynumber: 17.8 Consensus size: 9
42292286 ATATTTTCTC
42292296 ATAAAAATT
1 ATAAAAATT
42292305 ATAAAAAATT
1 AT-AAAAATT
*
42292315 ATAAATA-T
1 ATAAAAATT
*
42292323 ATTAAAATT
1 ATAAAAATT
*
42292332 GA-ATAAACTT
1 -ATA-AAAATT
42292342 ATAAAAATT
1 ATAAAAATT
* *
42292351 ATAACAATA
1 ATAAAAATT
*
42292360 ATAATAACTT
1 ATAA-AAATT
**
42292370 ATAAGTATT
1 ATAAAAATT
*
42292379 ATAAAAAAT
1 ATAAAAATT
*
42292388 CTAAAAA-T
1 ATAAAAATT
*
42292396 AT--ATATT
1 ATAAAAATT
*
42292403 A-AAAAATA
1 ATAAAAATT
42292411 AT-AAAATT
1 ATAAAAATT
42292419 AATAAAATATAT
1 -ATAAAA-AT-T
*
42292431 TTAAAAATTT
1 ATAAAAA-TT
42292441 ATAAAAATT
1 ATAAAAATT
42292450 ATAAAAA
1 ATAAAAA
42292457 ATCTAATAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 17 0.15
9 49 0.44
10 33 0.29
11 8 0.07
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:42292313 original size:10 final size:10
Alignment explanation
Indices: 42292298--42292458 Score: 58
Period size: 10 Copynumber: 16.6 Consensus size: 10
42292288 ATTTTCTCAT
42292298 AAAAATTATA
1 AAAAATTATA
42292308 AAAAATTAT-
1 AAAAATTATA
*
42292317 AAATA-TAT-
1 AAAAATTATA
*
42292325 TAAAATTGA-A
1 AAAAATT-ATA
* *
42292335 TAAACTTAT-
1 AAAAATTATA
42292344 AAAAATTAT-
1 AAAAATTATA
* *
42292353 AACAATAATA
1 AAAAATTATA
* *
42292363 ATAACTTAT-
1 AAAAATTATA
**
42292372 AAGTATTATA
1 AAAAATTATA
42292382 AAAAATCTA-A
1 AAAAAT-TATA
*
42292392 AAATATATATTA
1 AAAAAT-TA-TA
42292404 AAAAA-TA-A
1 AAAAATTATA
*
42292412 TAAAATTAATA
1 AAAAATT-ATA
42292423 AAATATATT-TA
1 AAA-A-ATTATA
*
42292434 AAAATTTAT-
1 AAAAATTATA
42292443 AAAAATTATA
1 AAAAATTATA
42292453 AAAAAT
1 AAAAAT
42292459 CTAATAAAAT
Statistics
Matches: 110, Mismatches: 25, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
8 11 0.10
9 36 0.33
10 44 0.40
11 10 0.09
12 6 0.05
13 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAAATTATA
Found at i:42292409 original size:14 final size:14
Alignment explanation
Indices: 42292390--42292437 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
42292380 TAAAAAATCT
42292390 AAAAATATATATTA
1 AAAAATATATATTA
*
42292404 AAAAATAATAAAATTA
1 AAAAAT-AT-ATATTA
42292420 ATAAAATATAT-TTA
1 A-AAAATATATATTA
42292434 AAAA
1 AAAA
42292438 TTTATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 3 0.10
14 10 0.34
15 3 0.10
16 8 0.28
17 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATATATATTA
Found at i:42292411 original size:29 final size:29
Alignment explanation
Indices: 42292379--42292492 Score: 80
Period size: 30 Copynumber: 4.0 Consensus size: 29
42292369 TATAAGTATT
42292379 ATAA-AAAATCTAA-AAATATATATTAAAAA
1 ATAATAAAAT-TAATAAA-ATATATTAAAAA
42292408 ATAATAAAATTAATAAAATATATTTAAAAA
1 ATAATAAAATTAATAAAATATA-TTAAAAA
* * *
42292438 TTTATAAAAATT-ATAAAA-A-ATCT-AATA
1 ATAAT-AAAATTAATAAAATATAT-TAAAAA
* * *
42292465 A-AATCAAATCAATAAAATATATTTAAAA
1 ATAATAAAATTAATAAAATATATTAAAAA
42292493 TTTTTATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
25 4 0.06
26 8 0.12
27 6 0.09
28 7 0.10
29 13 0.19
30 24 0.35
31 6 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (29 bp):
ATAATAAAATTAATAAAATATATTAAAAA
Found at i:42292429 original size:31 final size:30
Alignment explanation
Indices: 42292382--42292455 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
42292372 AAGTATTATA
42292382 AAAAATCTA-AAAATATATATTAAAAAATAAT
1 AAAAAT-TATAAAATATAT-TTAAAAAATAAT
* *
42292413 -AAAATTAATAAAATATATTTAAAAATTTAT
1 AAAAATT-ATAAAATATATTTAAAAAATAAT
42292443 AAAAATTATAAAA
1 AAAAATTATAAAA
42292456 AATCTAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 1 0.03
30 22 0.58
31 15 0.39
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAAATTATAAAATATATTTAAAAAATAAT
Found at i:42292438 original size:21 final size:21
Alignment explanation
Indices: 42292408--42292468 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
42292398 ATATTAAAAA
42292408 ATAATAAAATTAATAAAATA-T
1 ATAA-AAAATTAATAAAATATT
* *
42292429 ATTTAAAAATTTATAAAA-ATT
1 A-TAAAAAATTAATAAAATATT
42292450 ATAAAAAATCTAATAAAAT
1 ATAAAAAAT-TAATAAAAT
42292469 CAAATCAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAAAATTAATAAAATATT
Found at i:42292456 original size:19 final size:18
Alignment explanation
Indices: 42292296--42292456 Score: 84
Period size: 19 Copynumber: 8.9 Consensus size: 18
42292286 ATATTTTCTC
42292296 ATAAAAATTATAAAAAATT
1 ATAAAAATTAT-AAAAATT
* *
42292315 ATAAATA-TATTAAAATT
1 ATAAAAATTATAAAAATT
*
42292332 GA-ATAAACTTATAAAAATT
1 -ATA-AAAATTATAAAAATT
* * *
42292351 ATAACAATAATAATAACTT
1 ATAAAAATTATAA-AAATT
** *
42292370 ATAAGTATTATAAAAAAT
1 ATAAAAATTATAAAAATT
* *
42292388 CTAAAAA-TAT--ATATT
1 ATAAAAATTATAAAAATT
*
42292403 A-AAAAATAAT-AAAATT
1 ATAAAAATTATAAAAATT
*
42292419 AATAAAATATATTTAAAAATTT
1 -ATAAAA-AT-TATAAAAA-TT
42292441 ATAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
42292457 ATCTAATAAA
Statistics
Matches: 104, Mismatches: 25, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
14 5 0.05
15 5 0.05
16 4 0.04
17 11 0.11
18 25 0.24
19 39 0.38
20 3 0.03
21 10 0.10
22 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (18 bp):
ATAAAAATTATAAAAATT
Found at i:42292925 original size:13 final size:14
Alignment explanation
Indices: 42292889--42292926 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42292879 AACTATTAGC
42292889 ATATCTTTAAATAAA
1 ATAT-TTTAAATAAA
*
42292904 ATATTTTAACTAAA
1 ATATTTTAAATAAA
42292918 AT-TTTTAAA
1 ATATTTTAAA
42292927 ATCAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTTTAAATAAA
Found at i:42302796 original size:15 final size:15
Alignment explanation
Indices: 42302752--42302799 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 15
42302742 AAATCATTTT
42302752 AATATATATTTTATTA
1 AATATAT-TTTTATTA
*
42302768 ATAAATTAGTTTTTATTA
1 A-ATA-TA-TTTTTATTA
42302786 AATATATTTTTATT
1 AATATATTTTTATT
42302800 TCCAATTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 4 0.15
18 11 0.41
19 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
AATATATTTTTATTA
Found at i:42303657 original size:4 final size:4
Alignment explanation
Indices: 42303648--42303688 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
42303638 CCTCTCCCTC
42303648 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
42303689 ACCTTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:42307667 original size:22 final size:23
Alignment explanation
Indices: 42307642--42307702 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
42307632 GTTTTCTCAT
42307642 AAATAATTTTA-ACTTT-TAATTA
1 AAATAATTTTATA-TTTATAATTA
*
42307664 AAATATTTTTATATTTATAATT-
1 AAATAATTTTATATTTATAATTA
*
42307686 -AATTATTTTAT-TTTATA
1 AAATAATTTTATATTTATA
42307703 GATTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 13 0.38
23 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATAATTTTATATTTATAATTA
Found at i:42311807 original size:27 final size:27
Alignment explanation
Indices: 42311777--42311829 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
42311767 GACTGAAACT
42311777 ATAACATATTATGTGCTTTCTATTCAA
1 ATAACATATTATGTGCTTTCTATTCAA
* * *
42311804 ATAAGATATTCTGTGTTTTCTATTCA
1 ATAACATATTATGTGCTTTCTATTCA
42311830 CTTCTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (27 bp):
ATAACATATTATGTGCTTTCTATTCAA
Found at i:42314392 original size:146 final size:146
Alignment explanation
Indices: 42314128--42314414 Score: 513
Period size: 146 Copynumber: 2.0 Consensus size: 146
42314118 GAATTAAGTA
* *
42314128 AAGAAGCTCAACGAAAAATAGCCACAATTGTTTCCCAAGCTGATCACAACAATTATCATCAAGAG
1 AAGAAGCTCAACGAAAAATAGCCACAATTGTTACCCAAGCTGAGCACAACAATTATCATCAAGAG
42314193 GAAGAATATGTGTTGAGCAGTGTATTGGTACACCATGAAACTTATTTCACTATGCAACTGCGTAT
66 GAAGAATATGTGTTGAGCAGTGTATTGGTACACCATGAAACTTATTTCACTATGCAACTGCGTAT
*
42314258 GGATTTAAATTGGGTG
131 GGATTCAAATTGGGTG
* *
42314274 AAGAAGCTCAAC-AAAGAATAGCCACAATTGTTACCCAAGTTGAGCACAACAATTATCATGAAGA
1 AAGAAGCTCAACGAAA-AATAGCCACAATTGTTACCCAAGCTGAGCACAACAATTATCATCAAGA
42314338 GGAAGAATATGTGTTGAGCAGTGTATTGGTACACCATGAAACTTATTTCACTATGCAACTGCGTA
65 GGAAGAATATGTGTTGAGCAGTGTATTGGTACACCATGAAACTTATTTCACTATGCAACTGCGTA
42314403 TGGATTCAAATT
130 TGGATTCAAATT
42314415 ATGCAGGTCA
Statistics
Matches: 135, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
145 3 0.02
146 132 0.98
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (146 bp):
AAGAAGCTCAACGAAAAATAGCCACAATTGTTACCCAAGCTGAGCACAACAATTATCATCAAGAG
GAAGAATATGTGTTGAGCAGTGTATTGGTACACCATGAAACTTATTTCACTATGCAACTGCGTAT
GGATTCAAATTGGGTG
Found at i:42316107 original size:21 final size:21
Alignment explanation
Indices: 42316083--42316135 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42316073 CATTGTTTCT
*
42316083 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* * *
42316104 AATCTCACTGCTACTGTAACT
1 AATCTCACCGCTACAGTAACC
42316125 AATCTCACCGC
1 AATCTCACCGC
42316136 CTCAGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Done.