Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 99 of 132
Found at i:30345417 original size:12 final size:15
Alignment explanation
Indices: 30345394--30345436 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
30345384 CCTCGTCAGT
*
30345394 TGCCACGTCATCACG
1 TGCCACATCATCACG
30345409 TGCCACATCATCACG
1 TGCCACATCATCACG
30345424 TGCCACATCATCA
1 TGCCACATCATCA
30345437 AGTCCACGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.21
Consensus pattern (15 bp):
TGCCACATCATCACG
Found at i:30364639 original size:25 final size:24
Alignment explanation
Indices: 30364582--30364653 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
30364572 ATTCATCTTC
*
30364582 TAATTTTTAATTAATTTAACTTAT
1 TAATTTTTAATTAATTTAAATTAT
* *
30364606 TAACTTTTTAATTTATTTAAATTGT
1 TAA-TTTTTAATTAATTTAAATTAT
*
30364631 TAATATTTTATACTAA-TTAAATT
1 TAAT-TTTTA-ATTAATTTAAATT
30364654 TTAGAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.10
25 33 0.82
26 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (24 bp):
TAATTTTTAATTAATTTAAATTAT
Found at i:30365539 original size:18 final size:18
Alignment explanation
Indices: 30365516--30365594 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
30365506 GCTGAAGAAG
*
30365516 AAGAAGAACAAGATCCTA
1 AAGAAGAAGAAGATCCTA
* * *
30365534 AAGAAGAAGAGGATCTTG
1 AAGAAGAAGAAGATCCTA
* *
30365552 AATAAGAAGAAGATCTTA
1 AAGAAGAAGAAGATCCTA
* *
30365570 AAGAAGAAGAGGATCCTG
1 AAGAAGAAGAAGATCCTA
30365588 AAGAAGA
1 AAGAAGA
30365595 TCCTGTGGAG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.52, C:0.09, G:0.25, T:0.14
Consensus pattern (18 bp):
AAGAAGAAGAAGATCCTA
Found at i:30365566 original size:36 final size:36
Alignment explanation
Indices: 30365515--30365594 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
30365505 AGCTGAAGAA
*
30365515 GAAGAAGAACAAGATCCTAAAGAAGAAGAGGATCTT
1 GAAGAAGAACAAGATCCTAAAGAAGAAGAGGATCCT
* * *
30365551 GAATAAGAAGAAGATCTTAAAGAAGAAGAGGATCCT
1 GAAGAAGAACAAGATCCTAAAGAAGAAGAGGATCCT
30365587 GAAGAAGA
1 GAAGAAGA
30365595 TCCTGTGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.51, C:0.09, G:0.26, T:0.14
Consensus pattern (36 bp):
GAAGAAGAACAAGATCCTAAAGAAGAAGAGGATCCT
Found at i:30376416 original size:5 final size:5
Alignment explanation
Indices: 30376398--30376432 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
30376388 CACATATAAA
30376398 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAA
30376433 ATGAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30384361 original size:21 final size:21
Alignment explanation
Indices: 30384336--30384387 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30384326 AAATATAAGT
30384336 ATAAAAAATATAATT-AAGAAC
1 ATAAAAAATATAATTCAAG-AC
* *
30384357 ATAAATAACATAATTCAAGAC
1 ATAAAAAATATAATTCAAGAC
30384378 A-AAAAAATAT
1 ATAAAAAATAT
30384388 CACAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 16 0.62
22 3 0.12
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAAATATAATTCAAGAC
Found at i:30384934 original size:21 final size:22
Alignment explanation
Indices: 30384910--30384971 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
30384900 AAAAACGCAT
*
30384910 AAAAATAACATCC-AAACAAC-
1 AAAAATAACAACCAAAACAACG
*
30384930 AAAAATAAAAACCAAAACAACAG
1 AAAAATAACAACCAAAACAAC-G
*
30384953 TAAAAATAAC-AGCAAAACA
1 -AAAAATAACAACCAAAACA
30384972 CCATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.32
21 7 0.21
23 8 0.24
24 8 0.24
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.08
Consensus pattern (22 bp):
AAAAATAACAACCAAAACAACG
Found at i:30384935 original size:20 final size:21
Alignment explanation
Indices: 30384910--30384951 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30384900 AAAAACGCAT
* *
30384910 AAAAATAACATCC-AAACAAC
1 AAAAATAAAAACCAAAACAAC
30384930 AAAAATAAAAACCAAAACAAC
1 AAAAATAAAAACCAAAACAAC
30384951 A
1 A
30384952 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.71, C:0.21, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAACCAAAACAAC
Found at i:30384971 original size:44 final size:44
Alignment explanation
Indices: 30384908--30385042 Score: 110
Period size: 44 Copynumber: 2.9 Consensus size: 44
30384898 GTAAAAACGC
* *
30384908 ATAAAAATAACATCCAAACAACAAAAATAAAAACCAAAACAACA
1 ATAAAAATAACAGCAAAACAACAAAAATAAAAACCAAAACAACA
* * * * * * *
30384952 GTAAAAATAACAGCAAAACACCATTAAA-AACAACAAAAATAGCA
1 ATAAAAATAACAGCAAAACAACA-AAAATAAAAACCAAAACAACA
*
30384996 ACAAAAATAACAGCAAAAACAACCAAAACAATAAAAAAACCAAAACA
1 ATAAAAATAACAGC-AAAACAA-C-AAA-AAT--AAAAACCAAAACA
30385043 GTAAAAAACA
Statistics
Matches: 67, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
44 43 0.64
45 9 0.13
46 2 0.03
47 3 0.04
50 10 0.15
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (44 bp):
ATAAAAATAACAGCAAAACAACAAAAATAAAAACCAAAACAACA
Found at i:30384997 original size:12 final size:12
Alignment explanation
Indices: 30384980--30385014 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30384970 CACCATTAAA
30384980 AACAACAAAAAT
1 AACAACAAAAAT
*
30384992 AGCAACAAAAAT
1 AACAACAAAAAT
*
30385004 AACAGCAAAAA
1 AACAACAAAAA
30385015 CAACCAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:30385001 original size:21 final size:19
Alignment explanation
Indices: 30384977--30385071 Score: 59
Period size: 21 Copynumber: 4.8 Consensus size: 19
30384967 AAACACCATT
30384977 AAAAACAACAAAAATAGCAAC
1 AAAAACAACAAAAA-A-CAAC
*
30384998 AAAAATAACAGCAAAAACAAC
1 AAAAACAACA--AAAAACAAC
* *
30385019 CAAAACAA-TAAAAA-AAC
1 AAAAACAACAAAAAACAAC
* **
30385036 CAAAACAGTAAAAAACAACAC
1 AAAAACAACAAAAAAC-A-AC
*
30385057 AAAAACAATAAAAAA
1 AAAAACAACAAAAAA
30385072 ATAGCAACCA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
20 1 0.02
21 34 0.57
22 1 0.02
23 4 0.07
ACGTcount: A:0.74, C:0.18, G:0.03, T:0.05
Consensus pattern (19 bp):
AAAAACAACAAAAAACAAC
Found at i:30385036 original size:17 final size:18
Alignment explanation
Indices: 30385010--30385070 Score: 79
Period size: 17 Copynumber: 3.3 Consensus size: 18
30385000 AAATAACAGC
30385010 AAAAACAACCAAAACAAT
1 AAAAACAACCAAAACAAT
*
30385028 AAAAA-AACCAAAACAGT
1 AAAAACAACCAAAACAAT
30385045 AAAAAACAACACAAAAACAAT
1 -AAAAACAAC-C-AAAACAAT
30385066 AAAAA
1 AAAAA
30385071 AATAGCAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 11 0.30
18 10 0.27
19 3 0.08
20 6 0.16
21 7 0.19
ACGTcount: A:0.75, C:0.18, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAAACAACCAAAACAAT
Found at i:30385084 original size:23 final size:22
Alignment explanation
Indices: 30385033--30385094 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
30385023 ACAATAAAAA
30385033 AACCAAAACAGTAAAAAACAAC
1 AACCAAAACAGTAAAAAACAAC
* *
30385055 -ACAAAAACAATAAAAAA-ATAGC
1 AACCAAAACAGTAAAAAACA-A-C
30385077 AACCAAAACAGTAAAAAA
1 AACCAAAACAGTAAAAAA
30385095 GAACCAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.48
22 1 0.03
23 15 0.45
ACGTcount: A:0.71, C:0.18, G:0.05, T:0.06
Consensus pattern (22 bp):
AACCAAAACAGTAAAAAACAAC
Found at i:30387064 original size:15 final size:15
Alignment explanation
Indices: 30387046--30387142 Score: 124
Period size: 15 Copynumber: 6.5 Consensus size: 15
30387036 CCAAATGCTG
30387046 CCAAATGCTTG-GGTA
1 CCAAATG-TTGCGGTA
*
30387061 CCAAATGTTGCAGTA
1 CCAAATGTTGCGGTA
*
30387076 CCAAATGTTGCCGTA
1 CCAAATGTTGCGGTA
*
30387091 CCAAATGTTGCTGTA
1 CCAAATGTTGCGGTA
30387106 CCAAATGTTGCGGTA
1 CCAAATGTTGCGGTA
* **
30387121 CCAAATGCTGCTATA
1 CCAAATGTTGCGGTA
30387136 CCAAATG
1 CCAAATG
30387143 CGGATGATAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
14 3 0.04
15 71 0.96
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (15 bp):
CCAAATGTTGCGGTA
Found at i:30387143 original size:15 final size:15
Alignment explanation
Indices: 30387058--30387142 Score: 125
Period size: 15 Copynumber: 5.7 Consensus size: 15
30387048 AAATGCTTGG
*
30387058 GTACCAAATGTTGCA
1 GTACCAAATGTTGCT
*
30387073 GTACCAAATGTTGCC
1 GTACCAAATGTTGCT
30387088 GTACCAAATGTTGCT
1 GTACCAAATGTTGCT
*
30387103 GTACCAAATGTTGCG
1 GTACCAAATGTTGCT
*
30387118 GTACCAAATGCTGCT
1 GTACCAAATGTTGCT
*
30387133 ATACCAAATG
1 GTACCAAATG
30387143 CGGATGATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 64 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (15 bp):
GTACCAAATGTTGCT
Found at i:30390206 original size:15 final size:15
Alignment explanation
Indices: 30390186--30390333 Score: 172
Period size: 15 Copynumber: 9.9 Consensus size: 15
30390176 ACCTTATGCC
30390186 GCTGTACCAAATGTT
1 GCTGTACCAAATGTT
* * *
30390201 GTTGTACCGAATGCT
1 GCTGTACCAAATGTT
* *
30390216 GCAGTGCCAAAT-TCT
1 GCTGTACCAAATGT-T
30390231 GCTGTACCAAATGTT
1 GCTGTACCAAATGTT
*
30390246 GCAGTACCAAATGTT
1 GCTGTACCAAATGTT
*
30390261 GTTGTACCAAATGTT
1 GCTGTACCAAATGTT
* *
30390276 GCGGTACCAAATGCT
1 GCTGTACCAAATGTT
30390291 GCTGTACCAAATGTT
1 GCTGTACCAAATGTT
* *
30390306 GCGGTACCAAATGCT
1 GCTGTACCAAATGTT
*
30390321 ACTGTACCAAATG
1 GCTGTACCAAATG
30390334 CGGACGATAA
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
15 108 0.99
16 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (15 bp):
GCTGTACCAAATGTT
Found at i:30392407 original size:30 final size:29
Alignment explanation
Indices: 30392367--30392448 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
30392357 ACGTTAACAA
*
30392367 GACACCCCCACATTTTCAAGTGGTTCTAG
1 GACACCCCCACATTTCCAAGTGGTTCTAG
30392396 GACACCCCCCACATTTCCAAGTGGTTCT--
1 GACA-CCCCCACATTTCCAAGTGGTTCTAG
* *
30392424 G-C-CACCTACATTTCCAAGTGGTTCT
1 GACACCCCCACATTTCCAAGTGGTTCT
30392449 CTTGTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
25 21 0.43
27 1 0.02
28 1 0.02
29 4 0.08
30 22 0.45
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (29 bp):
GACACCCCCACATTTCCAAGTGGTTCTAG
Found at i:30400441 original size:11 final size:11
Alignment explanation
Indices: 30400421--30400460 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
30400411 AGCAACCATG
30400421 TTTTTT-TCTT
1 TTTTTTCTCTT
*
30400431 CTTTTTCTCTT
1 TTTTTTCTCTT
30400442 TTTTTTCTCTT
1 TTTTTTCTCTT
30400453 TTTTTTCT
1 TTTTTTCT
30400461 TTTCGAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 5 0.19
11 22 0.81
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:30400463 original size:20 final size:20
Alignment explanation
Indices: 30400421--30400463 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
30400411 AGCAACCATG
30400421 TTTTTTTCT-TCTTTTTCTCT
1 TTTTTTTCTCTCTTTTT-TCT
*
30400441 TTTTTTTCTCTTTTTTTTCT
1 TTTTTTTCTCTCTTTTTTCT
30400461 TTT
1 TTT
30400464 CGAACCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTTCTCTCTTTTTTCT
Found at i:30400483 original size:10 final size:9
Alignment explanation
Indices: 30400421--30400463 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 9
30400411 AGCAACCATG
30400421 TTTTTTTCT
1 TTTTTTTCT
30400430 TCTTTTTCTCTT
1 T-TTTTT-TC-T
30400442 TTTTTTCTCT
1 TTTTTT-TCT
30400452 TTTTTTTCT
1 TTTTTTTCT
30400461 TTT
1 TTT
30400464 CGAACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.23
10 12 0.39
11 10 0.32
12 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:30404515 original size:3 final size:3
Alignment explanation
Indices: 30404507--30404537 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30404497 ATGGATTAAT
30404507 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30404538 ATATGAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30410239 original size:16 final size:17
Alignment explanation
Indices: 30410208--30410242 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30410198 TGCATAGGAA
*
30410208 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30410225 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30410241 TT
1 TT
30410243 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30412461 original size:16 final size:17
Alignment explanation
Indices: 30412440--30412479 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
30412430 CATTGTCCCC
*
30412440 AATGCACTGACATTA-A
1 AATGCACTGACAATAGA
*
30412456 AATGCAATGACAATAGA
1 AATGCACTGACAATAGA
30412473 AATGCAC
1 AATGCAC
30412480 GATAATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (17 bp):
AATGCACTGACAATAGA
Found at i:30412631 original size:15 final size:15
Alignment explanation
Indices: 30412599--30412627 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30412589 TTGCATGATG
30412599 CTTTTTCTTCCTCCT
1 CTTTTTCTTCCTCCT
30412614 CTTTTTC-TCCTCCT
1 CTTTTTCTTCCTCCT
30412628 TCTTGCGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTTTTCTTCCTCCT
Found at i:30428972 original size:18 final size:18
Alignment explanation
Indices: 30428949--30429048 Score: 128
Period size: 18 Copynumber: 5.6 Consensus size: 18
30428939 CAACAGCAAG
30428949 CTGAAGAAGAAGAAGATC
1 CTGAAGAAGAAGAAGATC
*
30428967 CTGAAGAAGAACAAGATC
1 CTGAAGAAGAAGAAGATC
*
30428985 CTGAAGAAGAAGAGGATC
1 CTGAAGAAGAAGAAGATC
* *
30429003 TTGAATAAGAAGAAGATC
1 CTGAAGAAGAAGAAGATC
* * *
30429021 TTAAAGAAGAAGAGGATC
1 CTGAAGAAGAAGAAGATC
*
30429039 CTGAGGAAGA
1 CTGAAGAAGA
30429049 TCCTGTGGAG
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.14
Consensus pattern (18 bp):
CTGAAGAAGAAGAAGATC
Found at i:30432581 original size:16 final size:17
Alignment explanation
Indices: 30432550--30432584 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30432540 TGCATAGGAA
*
30432550 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30432567 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30432583 TT
1 TT
30432585 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30441441 original size:27 final size:27
Alignment explanation
Indices: 30441385--30441443 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
30441375 GATGAGGAGA
*
30441385 AAGAAGAAGGAAAAGAAAAAGAACGAG
1 AAGAAGAAGGAAAAGAAAAAGAAAGAG
* *
30441412 AAGAGGAAGGGAAAGAAGAAAGAAAG-G
1 AAGAAGAAGGAAAAGAA-AAAGAAAGAG
30441439 AAGAA
1 AAGAA
30441444 CCTACTGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (27 bp):
AAGAAGAAGGAAAAGAAAAAGAAAGAG
Found at i:30446700 original size:2 final size:2
Alignment explanation
Indices: 30446693--30446717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30446683 TTTATTATTC
30446693 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30446718 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30450442 original size:123 final size:122
Alignment explanation
Indices: 30450273--30450520 Score: 460
Period size: 123 Copynumber: 2.0 Consensus size: 122
30450263 TTACGGGCAC
30450273 AAAATAGATGTCTATATCTCAAGTTATTGTCAAAATATTGAAACTGTATTGTGTTAAAAGTTTAA
1 AAAATAGATGTCTATATCTCAAGTTATTGTCAAAATATTGAAACTGTATTGTGTTAAAAGTTTAA
30450338 ACAACAAAAACTTACAAAAAAAATAAAATTTAAACTCTTTTATCTCCAATTACTTCCT
66 ACAACAAAAACTTAC-AAAAAAATAAAATTTAAACTCTTTTATCTCCAATTACTTCCT
** *
30450396 AAAATAGATGTCTATATCTCAAGTTATTGTCAGCATATTGAAACTGTATTGTGTTGAAAGTTTAA
1 AAAATAGATGTCTATATCTCAAGTTATTGTCAAAATATTGAAACTGTATTGTGTTAAAAGTTTAA
30450461 ACAACAAAAACTTACAAAAAAATAAAATTTAAACTCTTTTATCTCCAATTACTTCCT
66 ACAACAAAAACTTACAAAAAAATAAAATTTAAACTCTTTTATCTCCAATTACTTCCT
30450518 AAA
1 AAA
30450521 TCAATAATAA
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
122 45 0.37
123 77 0.63
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (122 bp):
AAAATAGATGTCTATATCTCAAGTTATTGTCAAAATATTGAAACTGTATTGTGTTAAAAGTTTAA
ACAACAAAAACTTACAAAAAAATAAAATTTAAACTCTTTTATCTCCAATTACTTCCT
Found at i:30450569 original size:21 final size:21
Alignment explanation
Indices: 30450544--30450591 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30450534 AAATATAAGT
*
30450544 ATAAAAAATATAATT-AAGAAC
1 ATAAAAAACATAATTCAAG-AC
*
30450565 ATAAATAACATAATTCAAGAC
1 ATAAAAAACATAATTCAAGAC
30450586 A-AAAAA
1 ATAAAAA
30450592 TATCACCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 16 0.70
22 3 0.13
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (21 bp):
ATAAAAAACATAATTCAAGAC
Found at i:30451224 original size:19 final size:19
Alignment explanation
Indices: 30451202--30451265 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
30451192 AAAAAACAGC
30451202 AAAAACAACCAAAACAATA
1 AAAAACAACCAAAACAATA
*
30451221 AAAAA-ATACCAAAACAGTA
1 AAAAACA-ACCAAAACAATA
30451240 AAAAACAACACAAAAACAATA
1 AAAAACAAC-C-AAAACAATA
30451261 AAAAA
1 AAAAA
30451266 ATATCTACCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.03
19 23 0.59
20 2 0.05
21 13 0.33
ACGTcount: A:0.75, C:0.17, G:0.02, T:0.06
Consensus pattern (19 bp):
AAAAACAACCAAAACAATA
Found at i:30451287 original size:44 final size:38
Alignment explanation
Indices: 30451194--30451288 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 38
30451184 GGCAACAAAA
*
30451194 AAAACAG-CAAAAACAACCAAAACAATAAAAAAATACC
1 AAAACAGTAAAAAACAACCAAAACAATAAAAAAATACC
30451231 AAAACAGTAAAAAACAACACAAAAACAATAAAAAAATATCTACC
1 AAAACAGTAAAAAACAAC-C-AAAACAAT-AAAAAA-A--TACC
30451275 AAAACAGTAAAAAA
1 AAAACAGTAAAAAA
30451289 AGAAATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
37 7 0.14
38 9 0.18
39 1 0.02
40 8 0.16
41 6 0.12
42 1 0.02
44 18 0.36
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (38 bp):
AAAACAGTAAAAAACAACCAAAACAATAAAAAAATACC
Found at i:30453316 original size:15 final size:15
Alignment explanation
Indices: 30453234--30453315 Score: 110
Period size: 15 Copynumber: 5.5 Consensus size: 15
30453224 TGCTAAAGTG
*
30453234 CCAAATGTTGCAGTA
1 CCAAATGTTGCTGTA
*
30453249 CCAAATGTTGCCGTA
1 CCAAATGTTGCTGTA
*
30453264 CCAAATGTTGTTGTA
1 CCAAATGTTGCTGTA
*
30453279 CCAAATGTTGCGGTA
1 CCAAATGTTGCTGTA
* *
30453294 CCAAATGCTGCTATA
1 CCAAATGTTGCTGTA
30453309 CCAAATG
1 CCAAATG
30453316 CGGACGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (15 bp):
CCAAATGTTGCTGTA
Found at i:30456357 original size:15 final size:15
Alignment explanation
Indices: 30456275--30456356 Score: 110
Period size: 15 Copynumber: 5.5 Consensus size: 15
30456265 TGCTAAAGTG
*
30456275 CCAAATGTTGCAGTA
1 CCAAATGTTGCTGTA
*
30456290 CCAAATGTTGCCGTA
1 CCAAATGTTGCTGTA
*
30456305 CCAAATGTTGTTGTA
1 CCAAATGTTGCTGTA
*
30456320 CCAAATGTTGCGGTA
1 CCAAATGTTGCTGTA
* *
30456335 CCAAATGCTGCTATA
1 CCAAATGTTGCTGTA
30456350 CCAAATG
1 CCAAATG
30456357 CGGACGATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (15 bp):
CCAAATGTTGCTGTA
Found at i:30459299 original size:15 final size:15
Alignment explanation
Indices: 30459274--30459456 Score: 206
Period size: 15 Copynumber: 12.2 Consensus size: 15
30459264 CCACTACCTT
*
30459274 ATGTCGCTGTACCAA
1 ATGTTGCTGTACCAA
* * *
30459289 ATGCTGTTGTACCGA
1 ATGTTGCTGTACCAA
* * *
30459304 ATGCTGCAGTTCCAA
1 ATGTTGCTGTACCAA
30459319 AT-TCTGCTGTACCAA
1 ATGT-TGCTGTACCAA
*
30459334 ATGTTGCAGTACCAA
1 ATGTTGCTGTACCAA
*
30459349 ATGTTGTTGTACCAA
1 ATGTTGCTGTACCAA
* *
30459364 ATGTTACGGTACCAA
1 ATGTTGCTGTACCAA
*
30459379 ATGTTGCTATACCAA
1 ATGTTGCTGTACCAA
*
30459394 ATGTTGCGGTACCAA
1 ATGTTGCTGTACCAA
*
30459409 ATGCTGCTGTACCAA
1 ATGTTGCTGTACCAA
*
30459424 ATGTTGCGGTACCAA
1 ATGTTGCTGTACCAA
*
30459439 ATGTTACTGTACCAA
1 ATGTTGCTGTACCAA
30459454 ATG
1 ATG
30459457 CGGACGATAA
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
15 137 0.99
16 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (15 bp):
ATGTTGCTGTACCAA
Found at i:30459803 original size:5 final size:6
Alignment explanation
Indices: 30459786--30459823 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30459776 GGTATATAAA
**
30459786 AAATTT AAATTT -AATTT AAATTT AAAAAT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
30459824 AATAAATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:30459824 original size:11 final size:12
Alignment explanation
Indices: 30459802--30459830 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30459792 AAATTTAATT
30459802 TAAATTTAAAAA
1 TAAATTTAAAAA
30459814 TAAATTTAAAAA
1 TAAATTTAAAAA
30459826 TAAAT
1 TAAAT
30459831 AACAAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:30465826 original size:11 final size:10
Alignment explanation
Indices: 30465800--30465843 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
30465790 AACAACCATG
30465800 TTTTTTT-TC
1 TTTTTTTCTC
30465809 TTCTTTTTCTCC
1 TT-TTTTTCT-C
30465821 TTTTTTTCTC
1 TTTTTTTCTC
30465831 TTTTTTTCT-
1 TTTTTTTCTC
30465840 TTTT
1 TTTT
30465844 GAACCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.19
10 15 0.47
11 8 0.25
12 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:30469907 original size:3 final size:3
Alignment explanation
Indices: 30469899--30469926 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30469889 ATGGATTAAT
30469899 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30469927 ATATGAATGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30470522 original size:3 final size:3
Alignment explanation
Indices: 30470514--30470548 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
30470504 CCCATTATAT
*
30470514 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30470549 CTTTTCTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30471486 original size:16 final size:17
Alignment explanation
Indices: 30471455--30471489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30471445 TGCATAGGAA
*
30471455 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30471472 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30471488 TT
1 TT
30471490 AAATTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30473702 original size:16 final size:17
Alignment explanation
Indices: 30473681--30473720 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
30473671 CATTGTCTCC
* *
30473681 AATGCACTGACATTA-A
1 AATGCAATGACAATAGA
30473697 AATGCAATGACAATAGA
1 AATGCAATGACAATAGA
30473714 AATGCAA
1 AATGCAA
30473721 CGATAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (17 bp):
AATGCAATGACAATAGA
Found at i:30479259 original size:23 final size:23
Alignment explanation
Indices: 30479233--30479279 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
30479223 TCATTACAGC
*
30479233 AGGTTTCATGTGACTAATTCCCA
1 AGGTTTCATGTGACCAATTCCCA
30479256 AGGTTTCATGTGACCAATTCCCA
1 AGGTTTCATGTGACCAATTCCCA
30479279 A
1 A
30479280 TTTTCTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (23 bp):
AGGTTTCATGTGACCAATTCCCA
Found at i:30490960 original size:17 final size:17
Alignment explanation
Indices: 30490918--30490961 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
30490908 TTCATCTTCT
*
30490918 AATTTTTAATTTATTTA
1 AATTATTAATTTATTTA
*
30490935 ACTTATTAATTTATTTA
1 AATTATTAATTTATTTA
*
30490952 AATTGTTAAT
1 AATTATTAAT
30490962 ATTTTATACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTATTAATTTATTTA
Found at i:30491891 original size:15 final size:15
Alignment explanation
Indices: 30491840--30491897 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
30491830 CAAGCTGAAG
* * *
30491840 AAGAACAAGATCCTG
1 AAGAAGAAGATCTTA
*
30491855 AAGAAGAGGATCTTGAA
1 AAGAAGAAGATCTT--A
30491872 TAAGAAGAAGATCTTA
1 -AAGAAGAAGATCTTA
30491888 AAGAAGAAGA
1 AAGAAGAAGA
30491898 GGATCCTGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 21 0.60
16 1 0.03
18 13 0.37
ACGTcount: A:0.52, C:0.09, G:0.24, T:0.16
Consensus pattern (15 bp):
AAGAAGAAGATCTTA
Found at i:30491911 original size:18 final size:18
Alignment explanation
Indices: 30491854--30491912 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
30491844 ACAAGATCCT
30491854 GAAGAAGAGGATCTTGAA
1 GAAGAAGAGGATCTTGAA
* * *
30491872 TAAGAAGAAGATCTTAAA
1 GAAGAAGAGGATCTTGAA
* *
30491890 GAAGAAGAGGATCCTGAG
1 GAAGAAGAGGATCTTGAA
30491908 GAAGA
1 GAAGA
30491913 TCCTGTGGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.31, T:0.15
Consensus pattern (18 bp):
GAAGAAGAGGATCTTGAA
Found at i:30495473 original size:16 final size:17
Alignment explanation
Indices: 30495442--30495476 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30495432 TGCATAGGAA
*
30495442 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30495459 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30495475 TT
1 TT
30495477 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30505418 original size:27 final size:27
Alignment explanation
Indices: 30505362--30505420 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
30505352 GATAAGGAGA
*
30505362 AAGAAGAAGGAAAAGAAAAAGAATGAG
1 AAGAAGAAGGAAAAGAAAAAGAAAGAG
* *
30505389 AAGAGGAAGGGAAAGAAGAAAGAAAG-G
1 AAGAAGAAGGAAAAGAA-AAAGAAAGAG
30505416 AAGAA
1 AAGAA
30505421 CCTACTGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (27 bp):
AAGAAGAAGGAAAAGAAAAAGAAAGAG
Found at i:30506525 original size:5 final size:5
Alignment explanation
Indices: 30506474--30506518 Score: 81
Period size: 5 Copynumber: 8.8 Consensus size: 5
30506464 CACATATAAA
30506474 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
30506519 AAGAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30510725 original size:2 final size:2
Alignment explanation
Indices: 30510718--30510742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30510708 TTTATTATTC
30510718 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30510743 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30513022 original size:7 final size:7
Alignment explanation
Indices: 30513007--30513040 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
30512997 AGTACTTCTT
*
30513007 TAAACCC
1 TAAATCC
30513014 TAAATCC
1 TAAATCC
30513021 TAAATCC
1 TAAATCC
*
30513028 TAAACCC
1 TAAATCC
30513035 TAAATC
1 TAAATC
30513041 TTAATACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAATCC
Found at i:30515064 original size:21 final size:21
Alignment explanation
Indices: 30515027--30515143 Score: 71
Period size: 21 Copynumber: 5.5 Consensus size: 21
30515017 AAAACGCATA
*
30515027 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
30515047 AAAAATAACAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
* *
30515068 AGTAAAAATAAC-AGCAAAACACC
1 ---AAAAATAACAACCAAAACAAC
* * * *
30515091 ATTAAA-AACAACAAAAATAGC
1 A-AAAATAACAACCAAAACAAC
* *
30515112 AGCAAA-AACAACCAAAACAAT
1 A-AAAATAACAACCAAAACAAC
*
30515133 AAAAAAAACAA
1 AAAAATAACAA
30515144 AAACAACAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
20 19 0.25
21 38 0.51
23 9 0.12
24 9 0.12
ACGTcount: A:0.68, C:0.21, G:0.03, T:0.08
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:30515119 original size:44 final size:41
Alignment explanation
Indices: 30515027--30515151 Score: 110
Period size: 44 Copynumber: 3.0 Consensus size: 41
30515017 AAAACGCATA
* * * *
30515027 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAACAGT
1 AAAAATAACA-CAAAAC-ACATAAA-AACAACAAAAACAACAGC
* *
30515071 AAAAATAACAGCAAAACACCATTAAAAACAACAAAAATAGCAGC
1 AAAAATAACA-CAAAACA-CA-TAAAAACAACAAAAACAACAGC
* *
30515115 AAAAACAAC-CAAAACA-ATAAAAAAAACAAAAACAACA
1 AAAAATAACACAAAACACATAAAAACAACAAAAACAACA
30515152 ATATAATTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
39 17 0.25
40 1 0.01
42 7 0.10
43 1 0.01
44 39 0.57
45 3 0.04
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (41 bp):
AAAAATAACACAAAACACATAAAAACAACAAAAACAACAGC
Found at i:30515130 original size:9 final size:9
Alignment explanation
Indices: 30515094--30515152 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
30515084 AAACACCATT
30515094 AAAAACAAC
1 AAAAACAAC
*
30515103 AAAAATAGCAGC
1 -AAAA-A-CAAC
30515115 AAAAACAAC
1 AAAAACAAC
* *
30515124 CAAAACAAT
1 AAAAACAAC
*
30515133 AAAAAAAAC
1 AAAAACAAC
30515142 AAAAACAAC
1 AAAAACAAC
30515151 AA
1 AA
30515153 TATAATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 26 0.67
10 5 0.13
11 5 0.13
12 3 0.08
ACGTcount: A:0.75, C:0.19, G:0.03, T:0.03
Consensus pattern (9 bp):
AAAAACAAC
Found at i:30515139 original size:32 final size:31
Alignment explanation
Indices: 30515053--30515139 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
30515043 CAACAAAAAT
*
30515053 AACAACCAAAACAACAGTAAAAATAACAGCAA
1 AACAACCAAAACAACA-AAAAAATAACAGCAA
*
30515085 AAC-ACCATTAAA-AACAACAAAAATAGCAGCAAA
1 AACAACCA--AAACAACAA-AAAAATAACAGC-AA
*
30515118 AACAACCAAAACAATAAAAAAA
1 AACAACCAAAACAACAAAAAAA
30515140 ACAAAAACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
31 4 0.09
32 26 0.57
33 12 0.26
34 4 0.09
ACGTcount: A:0.68, C:0.21, G:0.05, T:0.07
Consensus pattern (31 bp):
AACAACCAAAACAACAAAAAAATAACAGCAA
Found at i:30515151 original size:21 final size:21
Alignment explanation
Indices: 30515040--30515154 Score: 76
Period size: 21 Copynumber: 5.5 Consensus size: 21
30515030 AATAACATCC
*
30515040 AAACAACAA-AAATAACAACCA
1 AAACAACAATAAA-AACAACAA
* *
30515061 AAACAACAGTAAAAATAACAGCA
1 AAACAACAATAAAAACAACA--A
* *
30515084 AAACACCATTAAAAACAACAA
1 AAACAACAATAAAAACAACAA
* * **
30515105 AAATAGCAGCAAAAACAAC--
1 AAACAACAATAAAAACAACAA
* *
30515124 CAA-AACAATAAAAAAAACAA
1 AAACAACAATAAAAACAACAA
30515144 AAACAACAATA
1 AAACAACAATA
30515155 TAATTTTTTT
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
18 11 0.15
19 2 0.03
20 2 0.03
21 36 0.50
22 3 0.04
23 18 0.25
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (21 bp):
AAACAACAATAAAAACAACAA
Found at i:30516335 original size:2 final size:2
Alignment explanation
Indices: 30516328--30516355 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30516318 AAAATGATTA
30516328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30516356 GGCAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30517081 original size:30 final size:30
Alignment explanation
Indices: 30517044--30517188 Score: 148
Period size: 30 Copynumber: 4.8 Consensus size: 30
30517034 TTATGCCGCT
* * *
30517044 GTACCAAATACTGTTGTACCAAATGCTGAA
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
* *
30517074 GTGCCAAATGCTAG-GGTACCAAATGTTGCA
1 GTACCAAATGCT-GTTGTACCAAATGTTGCA
* ** *
30517104 GTACCAAATGTTGCAGTACCAAATGTTGCT
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
* *
30517134 GTACCAAATGTTGTTGTACCAAATGTTGCG
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
* * *
30517164 GTTCCAAATGCTGCTATACCAAATG
1 GTACCAAATGCTGTTGTACCAAATG
30517189 CGGACGATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 1 0.01
30 95 0.98
31 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (30 bp):
GTACCAAATGCTGTTGTACCAAATGTTGCA
Found at i:30517095 original size:15 final size:15
Alignment explanation
Indices: 30517044--30517189 Score: 80
Period size: 15 Copynumber: 9.7 Consensus size: 15
30517034 TTATGCCGCT
* **
30517044 GTACCAAATACTGTT
1 GTACCAAATGCTGAA
30517059 GTACCAAATGCTGAA
1 GTACCAAATGCTGAA
* *
30517074 GTGCCAAATGCT-AGG
1 GTACCAAATGCTGA-A
* *
30517089 GTACCAAATGTTGCA
1 GTACCAAATGCTGAA
* *
30517104 GTACCAAATGTTGCA
1 GTACCAAATGCTGAA
* **
30517119 GTACCAAATGTTGCT
1 GTACCAAATGCTGAA
* **
30517134 GTACCAAATGTTGTT
1 GTACCAAATGCTGAA
* **
30517149 GTACCAAATGTTGCG
1 GTACCAAATGCTGAA
* *
30517164 GTTCCAAATGCTGCTA
1 GTACCAAATGCTG-AA
30517180 -TACCAAATGC
1 GTACCAAATGC
30517190 GGACGATAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
14 1 0.01
15 109 0.99
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (15 bp):
GTACCAAATGCTGAA
Found at i:30517159 original size:45 final size:45
Alignment explanation
Indices: 30517041--30517188 Score: 163
Period size: 45 Copynumber: 3.3 Consensus size: 45
30517031 ACCTTATGCC
** * * * *
30517041 GCTGTACCAAATACTGTTGTACCAAATGCTGAAGTGCCAAATGCTA
1 GCTGTACCAAATGTTGTTGTACCAAATGTTGCAGTACCAAATG-TT
* **
30517087 G-GGTACCAAATGTTGCAGTACCAAATGTTGCAGTACCAAATGTT
1 GCTGTACCAAATGTTGTTGTACCAAATGTTGCAGTACCAAATGTT
* * *
30517131 GCTGTACCAAATGTTGTTGTACCAAATGTTGCGGTTCCAAATGCT
1 GCTGTACCAAATGTTGTTGTACCAAATGTTGCAGTACCAAATGTT
*
30517176 GCTATACCAAATG
1 GCTGTACCAAATG
30517189 CGGACGATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.02
45 82 0.96
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (45 bp):
GCTGTACCAAATGTTGTTGTACCAAATGTTGCAGTACCAAATGTT
Found at i:30520107 original size:15 final size:15
Alignment explanation
Indices: 30520087--30520235 Score: 145
Period size: 15 Copynumber: 9.9 Consensus size: 15
30520077 ACCTTATGTC
30520087 GCTGTACCAAATGCT
1 GCTGTACCAAATGCT
* *
30520102 GTTGTACCGAATGCT
1 GCTGTACCAAATGCT
* * *
30520117 GCAGTTCCAAATTCT
1 GCTGTACCAAATGCT
*
30520132 GCTGTACCAAATGTT
1 GCTGTACCAAATGCT
* *
30520147 GCAGTACCAAATGTT
1 GCTGTACCAAATGCT
* *
30520162 GTTGTACCAAATGTT
1 GCTGTACCAAATGCT
*
30520177 GCGGTACCAAATGCT
1 GCTGTACCAAATGCT
* *
30520192 GCTATACCAAATGTT
1 GCTGTACCAAATGCT
* *
30520207 GCGGTACCAAATGTT
1 GCTGTACCAAATGCT
* *
30520222 ACTATACCAAATGC
1 GCTGTACCAAATGC
30520236 GGACGATAAA
Statistics
Matches: 108, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 108 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (15 bp):
GCTGTACCAAATGCT
Found at i:30520127 original size:30 final size:30
Alignment explanation
Indices: 30520090--30520234 Score: 173
Period size: 30 Copynumber: 4.8 Consensus size: 30
30520080 TTATGTCGCT
* * *
30520090 GTACCAAATGCTGTTGTACCGAATGCTGCA
1 GTACCAAATGCTGCTGTACCAAATGTTGCA
* *
30520120 GTTCCAAATTCTGCTGTACCAAATGTTGCA
1 GTACCAAATGCTGCTGTACCAAATGTTGCA
* * *
30520150 GTACCAAATGTTGTTGTACCAAATGTTGCG
1 GTACCAAATGCTGCTGTACCAAATGTTGCA
* *
30520180 GTACCAAATGCTGCTATACCAAATGTTGCG
1 GTACCAAATGCTGCTGTACCAAATGTTGCA
* * *
30520210 GTACCAAATGTTACTATACCAAATG
1 GTACCAAATGCTGCTGTACCAAATG
30520235 CGGACGATAA
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (30 bp):
GTACCAAATGCTGCTGTACCAAATGTTGCA
Found at i:30520580 original size:11 final size:11
Alignment explanation
Indices: 30520564--30520588 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30520554 GTATATAAAA
30520564 AATTTAAATTT
1 AATTTAAATTT
30520575 AATTTAAATTT
1 AATTTAAATTT
30520586 AAT
1 AAT
30520589 AATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:30526537 original size:11 final size:11
Alignment explanation
Indices: 30526517--30526557 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
30526507 AGCAACCATG
30526517 TTTTTT-TCTT
1 TTTTTTCTCTT
*
30526527 CTTTTTCTCTTT
1 TTTTTTCTC-TT
30526539 TTTTTTCTCTT
1 TTTTTTCTCTT
30526550 TTTTTTCT
1 TTTTTTCT
30526558 TTTCGAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 5 0.19
11 12 0.44
12 10 0.37
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:30526543 original size:12 final size:12
Alignment explanation
Indices: 30526528--30526555 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30526518 TTTTTTCTTC
30526528 TTTTTCTCTTTT
1 TTTTTCTCTTTT
30526540 TTTTTCTCTTTT
1 TTTTTCTCTTTT
30526552 TTTT
1 TTTT
30526556 CTTTTCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:30526553 original size:9 final size:10
Alignment explanation
Indices: 30526518--30526560 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
30526508 GCAACCATGT
30526518 TTTTTTCTTC
1 TTTTTTCTTC
*
30526528 TTTTTCTCTTT
1 TTTTT-TCTTC
30526539 TTTTTTC-TC
1 TTTTTTCTTC
30526548 TTTTTT-TTC
1 TTTTTTCTTC
30526557 TTTT
1 TTTT
30526561 CGAACCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 13 0.45
10 7 0.24
11 9 0.31
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:30530656 original size:3 final size:3
Alignment explanation
Indices: 30530648--30530675 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30530638 ATGGATTAAT
30530648 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30530676 ATATGAATGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30532222 original size:16 final size:17
Alignment explanation
Indices: 30532191--30532225 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30532181 TGCATAGGAA
*
30532191 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30532208 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30532224 TT
1 TT
30532226 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30534446 original size:16 final size:17
Alignment explanation
Indices: 30534425--30534464 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
30534415 CATTGTCTCC
* *
30534425 AATGCACTGACATTA-A
1 AATGCAATGACAATAGA
30534441 AATGCAATGACAATAGA
1 AATGCAATGACAATAGA
30534458 AATGCAA
1 AATGCAA
30534465 CGATAATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (17 bp):
AATGCAATGACAATAGA
Found at i:30534617 original size:15 final size:15
Alignment explanation
Indices: 30534585--30534613 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30534575 CTGCATGATG
30534585 CTTTTTCTTCCTCCT
1 CTTTTTCTTCCTCCT
30534600 CTTTTTC-TCCTCCT
1 CTTTTTCTTCCTCCT
30534614 TCTTGCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTTTTCTTCCTCCT
Found at i:30551219 original size:22 final size:22
Alignment explanation
Indices: 30551177--30551229 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
30551167 TTATCAAAAG
* *
30551177 TTTAAATTAGAATTTTTTTTAA
1 TTTAAATTAAAATTTTGTTTAA
30551199 TTTAAA-TAAAATTTGTGTTTAA
1 TTTAAATTAAAATTT-TGTTTAA
*
30551221 GTTGAAATT
1 -TTTAAATT
30551230 GGACTTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 5 0.20
24 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TTTAAATTAAAATTTTGTTTAA
Found at i:30551830 original size:16 final size:17
Alignment explanation
Indices: 30551791--30551831 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
30551781 ATTCATCTTC
*
30551791 TAATTT-TTAATTTATT
1 TAATTTATTAACTTATT
*
30551807 TAACTTATTAACTT-TT
1 TAATTTATTAACTTATT
30551823 TAATTTATT
1 TAATTTATT
30551832 TAAATTGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATTTATTAACTTATT
Found at i:30551848 original size:25 final size:24
Alignment explanation
Indices: 30551791--30551849 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
30551781 ATTCATCTTC
*
30551791 TAATTTTTAATTTATTTAACTTAT
1 TAATTTTTAATTTATTTAAATTAT
*
30551815 TAACTTTTTAATTTATTTAAATTGT
1 TAA-TTTTTAATTTATTTAAATTAT
30551840 TAATATTTTA
1 TAAT-TTTTA
30551850 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:30552743 original size:21 final size:21
Alignment explanation
Indices: 30552719--30552788 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
30552709 CAGCAAGCTG
*
30552719 AAGAAGAAGAACAAGATCCTA
1 AAGAAGAAGAAGAAGATCCTA
*
30552740 AAGAAGAAGAAGAGGAT-CT-
1 AAGAAGAAGAAGAAGATCCTA
* * *
30552759 -TGAATAAGAAGAAGATCTTA
1 AAGAAGAAGAAGAAGATCCTA
30552779 AAGAAGAAGA
1 AAGAAGAAGA
30552789 GGATCCTGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 13 0.34
19 1 0.03
20 2 0.05
21 22 0.58
ACGTcount: A:0.56, C:0.07, G:0.24, T:0.13
Consensus pattern (21 bp):
AAGAAGAAGAAGAAGATCCTA
Found at i:30552802 original size:18 final size:18
Alignment explanation
Indices: 30552742--30552803 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
30552732 AGATCCTAAA
30552742 GAAGAAGAAGAGGATCTT
1 GAAGAAGAAGAGGATCTT
* *
30552760 GAATAAGAAGAAGATCTT
1 GAAGAAGAAGAGGATCTT
* *
30552778 AAAGAAGAAGAGGATCCT
1 GAAGAAGAAGAGGATCTT
*
30552796 GAGGAAGA
1 GAAGAAGA
30552804 TCCTATGGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.48, C:0.06, G:0.31, T:0.15
Consensus pattern (18 bp):
GAAGAAGAAGAGGATCTT
Found at i:30556376 original size:16 final size:17
Alignment explanation
Indices: 30556345--30556379 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30556335 TGCATAGGAA
*
30556345 TTTAACTTAGATTTAAT
1 TTTAACTTAGACTTAAT
30556362 TTTAACTTAG-CTTAAT
1 TTTAACTTAGACTTAAT
30556378 TT
1 TT
30556380 AATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAACTTAGACTTAAT
Found at i:30559474 original size:135 final size:137
Alignment explanation
Indices: 30559262--30559535 Score: 475
Period size: 135 Copynumber: 2.0 Consensus size: 137
30559252 TTGTGGCTGT
30559262 ATCGAAGGGATAGGATTTTGTGGTGGCAATGGAGGTATGACTGCATCATTTCTAGGCAAAGCCAT
1 ATCGAAGGGATAGGATTTTGTGGTGGCAATGGAGGTATGACTGCATCATTTCTAGGCAAAGCCAT
*
30559327 ATTTCTTTGTTCTTGTCTTCTCCTTCTAATAGTTCATTCG-TTTTTCTGATCTAAGCCAACAACA
66 ATTTCTTTGTTCTTGTCTTCTCCTTCTAATAGTTCATTCGATTTTT-GGATCTAAGCCAACAACA
30559391 ATTTCAGA
130 ATTTCAGA
*
30559399 ATCGAAGGGATAGGATTTAT-T-GTGGCAATGGAGGTATGACTGCATCA-TTCTAGGTAAAGCCA
1 ATCGAAGGGATAGGATTT-TGTGGTGGCAATGGAGGTATGACTGCATCATTTCTAGGCAAAGCCA
*
30559461 TATTTCTTTGTTCTTGTCTTCTCCTTCTAATAGTTCATTCGATTTTTGGATCTAAGCCAACAATA
65 TATTTCTTTGTTCTTGTCTTCTCCTTCTAATAGTTCATTCGATTTTTGGATCTAAGCCAACAACA
30559526 ATTTCAGA
130 ATTTCAGA
30559534 AT
1 AT
30559536 TGCTCCTGGT
Statistics
Matches: 132, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
135 81 0.61
136 31 0.23
137 19 0.14
138 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (137 bp):
ATCGAAGGGATAGGATTTTGTGGTGGCAATGGAGGTATGACTGCATCATTTCTAGGCAAAGCCAT
ATTTCTTTGTTCTTGTCTTCTCCTTCTAATAGTTCATTCGATTTTTGGATCTAAGCCAACAACAA
TTTCAGA
Found at i:30566533 original size:27 final size:27
Alignment explanation
Indices: 30566477--30566535 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
30566467 GATGAGGAGA
*
30566477 AAGAAGAAGGAAAAGAAAAAGAACGAG
1 AAGAAGAAGGAAAAGAAAAAGAAAGAG
* *
30566504 AAGAGGAAGGGAAAGAAGAAAGAAAG-G
1 AAGAAGAAGGAAAAGAA-AAAGAAAGAG
30566531 AAGAA
1 AAGAA
30566536 CCTACTGTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (27 bp):
AAGAAGAAGGAAAAGAAAAAGAAAGAG
Found at i:30571719 original size:2 final size:2
Alignment explanation
Indices: 30571712--30571746 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30571702 TTTATTATTC
30571712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30571747 TCTTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30575468 original size:21 final size:21
Alignment explanation
Indices: 30575444--30575495 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30575434 AAATATAAGT
30575444 ATAAAAAATATAATT-AAGAAC
1 ATAAAAAATATAATTCAAG-AC
* *
30575465 ATAAATAACATAATTCAAGAC
1 ATAAAAAATATAATTCAAGAC
30575486 A-AAAAAATAT
1 ATAAAAAATAT
30575496 TACAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.27
21 16 0.62
22 3 0.12
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAAATATAATTCAAGAC
Found at i:30576043 original size:20 final size:21
Alignment explanation
Indices: 30576018--30576131 Score: 72
Period size: 21 Copynumber: 5.2 Consensus size: 21
30576008 AAAAACGCAT
*
30576018 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
30576038 AAAAATAACAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
* *
30576059 AGTAAAAATAAC-AGCAAAACACC
1 ---AAAAATAACAACCAAAACAAC
* *
30576082 ATTAAA-AACAACAAAAATAGCAAC
1 A-AAAATAACAAC-CAAA-A-CAAC
* *
30576106 AAAAATAACAGCAAAAACAAC
1 AAAAATAACAACCAAAACAAC
*
30576127 CAAAA
1 AAAAA
30576132 CAATAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
20 16 0.22
21 19 0.26
22 4 0.05
23 17 0.23
24 18 0.24
ACGTcount: A:0.68, C:0.21, G:0.04, T:0.08
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:30576049 original size:12 final size:12
Alignment explanation
Indices: 30576032--30576122 Score: 57
Period size: 12 Copynumber: 7.9 Consensus size: 12
30576022 ATAACATCCA
30576032 AACAACAAAAAT
1 AACAACAAAAAT
* *
30576044 AACAACCAAAAC
1 AACAACAAAAAT
**
30576056 AACAGTAAAAAT
1 AACAACAAAAAT
*
30576068 AACAGC---AA-
1 AACAACAAAAAT
* *
30576076 AACACCATTAAA-
1 AACAACA-AAAAT
30576088 AACAACAAAAAT
1 AACAACAAAAAT
*
30576100 AGCAACAAAAAT
1 AACAACAAAAAT
*
30576112 AACAGCAAAAA
1 AACAACAAAAA
30576123 CAACCAAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
11 3 0.05
12 51 0.84
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:30576079 original size:44 final size:43
Alignment explanation
Indices: 30576016--30576131 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 43
30576006 GTAAAAACGC
* * *
30576016 ATAAAAATAACATCCAAACAACAAAAATAACAACCAAAACAACA
1 ATAAAAATAACAGCAAAACAACAAAAA-AACAACAAAAACAACA
* * * * *
30576060 GTAAAAATAACAGCAAAACACCATTAAAAACAACAAAAATAGCA
1 ATAAAAATAACAGCAAAACAACA-AAAAAACAACAAAAACAACA
* *
30576104 ACAAAAATAACAGCAAAAACAACCAAAA
1 ATAAAAATAACAGC-AAAACAACAAAAA
30576132 CAATAAAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
44 47 0.82
45 10 0.18
ACGTcount: A:0.67, C:0.21, G:0.03, T:0.09
Consensus pattern (43 bp):
ATAAAAATAACAGCAAAACAACAAAAAAACAACAAAAACAACA
Found at i:30576109 original size:21 final size:19
Alignment explanation
Indices: 30576085--30576181 Score: 61
Period size: 21 Copynumber: 4.8 Consensus size: 19
30576075 AAACACCATT
30576085 AAAAACAACAAAAATAGCAAC
1 AAAAACAACAAAAA-A-CAAC
*
30576106 AAAAATAACAGCAAAAACAAC
1 AAAAACAACA--AAAAACAAC
* *
30576127 CAAAACAATAAAAAA-ATAC
1 AAAAACAACAAAAAACA-AC
* **
30576146 CAAAACAGTAAAAAACAACAC
1 AAAAACAACAAAAAAC-A-AC
*
30576167 AAAAACAATAAAAAA
1 AAAAACAACAAAAAA
30576182 TAGCAACCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.02
19 21 0.33
21 36 0.57
22 1 0.02
23 4 0.06
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.06
Consensus pattern (19 bp):
AAAAACAACAAAAAACAAC
Found at i:30576147 original size:19 final size:19
Alignment explanation
Indices: 30576118--30576216 Score: 92
Period size: 19 Copynumber: 4.9 Consensus size: 19
30576108 AAATAACAGC
30576118 AAAAACAACCAAAACAATA
1 AAAAACAACCAAAACAATA
*
30576137 AAAAA-ATACCAAAACAGTA
1 AAAAACA-ACCAAAACAATA
30576156 AAAAACAACACAAAAACAATAA
1 AAAAACAAC-C-AAAACAAT-A
* *
30576178 AAAATAGCAACCAAAATAGTAA
1 AAAA-A-CAACCAAAACAAT-A
*
30576200 AAAAAGAACCAAAACAA
1 AAAAACAACCAAAACAA
30576217 CAATATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 23 0.35
20 11 0.17
21 8 0.12
22 17 0.26
23 2 0.03
24 4 0.06
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.07
Consensus pattern (19 bp):
AAAAACAACCAAAACAATA
Found at i:30576201 original size:43 final size:42
Alignment explanation
Indices: 30576085--30576213 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 42
30576075 AAACACCATT
* * **
30576085 AAAAACAA-CAAAAATAGCAACAAAAATAACAGCAAAAACAACC
1 AAAAACAATAAAAAATAGCAACCAAAATAGTA--AAAAACAACC
* *
30576128 -AAAACAATAAAAAA-A--TACCAAAACAGTAAAAAACAACAC
1 AAAAACAATAAAAAATAGCAACCAAAATAGTAAAAAACAAC-C
*
30576167 AAAAACAATAAAAAATAGCAACCAAAATAGTAAAAAAAGAACC
1 AAAAACAATAAAAAATAGCAACCAAAATAGT-AAAAAACAACC
30576210 AAAA
1 AAAA
30576214 CAACAATATA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
38 9 0.13
39 1 0.01
40 22 0.31
41 1 0.01
42 8 0.11
43 20 0.29
44 9 0.13
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (42 bp):
AAAAACAATAAAAAATAGCAACCAAAATAGTAAAAAACAACC
Found at i:30578127 original size:15 final size:15
Alignment explanation
Indices: 30578121--30578220 Score: 146
Period size: 15 Copynumber: 6.7 Consensus size: 15
30578111 AAATGCTGGG
30578121 GTACCAAATGTTGCT
1 GTACCAAATGTTGCT
*
30578136 GTACCAAATGTTGCA
1 GTACCAAATGTTGCT
* *
30578151 GTACCAAATATTGCC
1 GTACCAAATGTTGCT
30578166 GTACCAAATGTTGCT
1 GTACCAAATGTTGCT
*
30578181 GTACCAAATGTTGCG
1 GTACCAAATGTTGCT
*
30578196 GTACCAAATGCTGCT
1 GTACCAAATGTTGCT
*
30578211 ATACCAAATG
1 GTACCAAATG
30578221 CGAACGATAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 76 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (15 bp):
GTACCAAATGTTGCT
Found at i:30578145 original size:45 final size:45
Alignment explanation
Indices: 30578090--30578220 Score: 163
Period size: 45 Copynumber: 2.9 Consensus size: 45
30578080 CAAATACTGT
* * * * **
30578090 TGTACAAAATGCTGAAGTGCCAAATGCTGGGGTACCAAATGTTGC
1 TGTACCAAATGTTGCAGTACCAAATGCTGCCGTACCAAATGTTGC
**
30578135 TGTACCAAATGTTGCAGTACCAAATATTGCCGTACCAAATGTTGC
1 TGTACCAAATGTTGCAGTACCAAATGCTGCCGTACCAAATGTTGC
* **
30578180 TGTACCAAATGTTGCGGTACCAAATGCTGCTATACCAAATG
1 TGTACCAAATGTTGCAGTACCAAATGCTGCCGTACCAAATG
30578221 CGAACGATAA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (45 bp):
TGTACCAAATGTTGCAGTACCAAATGCTGCCGTACCAAATGTTGC
Found at i:30578221 original size:15 final size:15
Alignment explanation
Indices: 30578077--30578221 Score: 128
Period size: 15 Copynumber: 9.7 Consensus size: 15
30578067 TATGCCGCTA
* *
30578077 TACCAAATACTGTTG
1 TACCAAATGCTGCTG
* **
30578092 TACAAAATGCTGAAG
1 TACCAAATGCTGCTG
* **
30578107 TGCCAAATGCTGGGG
1 TACCAAATGCTGCTG
*
30578122 TACCAAATGTTGCTG
1 TACCAAATGCTGCTG
* *
30578137 TACCAAATGTTGCAG
1 TACCAAATGCTGCTG
** *
30578152 TACCAAATATTGCCG
1 TACCAAATGCTGCTG
*
30578167 TACCAAATGTTGCTG
1 TACCAAATGCTGCTG
* *
30578182 TACCAAATGTTGCGG
1 TACCAAATGCTGCTG
*
30578197 TACCAAATGCTGCTA
1 TACCAAATGCTGCTG
30578212 TACCAAATGC
1 TACCAAATGC
30578222 GAACGATAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 109 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (15 bp):
TACCAAATGCTGCTG
Found at i:30581283 original size:15 final size:15
Alignment explanation
Indices: 30581265--30581418 Score: 123
Period size: 15 Copynumber: 10.3 Consensus size: 15
30581255 CCGCTACCTT
*
30581265 ATGCGGCTGTACCAA
1 ATGCTGCTGTACCAA
* * *
30581280 ATGCTGTTGTATCGA
1 ATGCTGCTGTACCAA
* * *
30581295 ATGTTGCAGTGCCAA
1 ATGCTGCTGTACCAA
*
30581310 ATTCTGCTGTACCAA
1 ATGCTGCTGTACCAA
*
30581325 ATGTTG-TAGTACCAA
1 ATGCTGCT-GTACCAA
* *
30581340 ATGTTGTTGTACCAA
1 ATGCTGCTGTACCAA
* *
30581355 ATGTTGCGGTACCAA
1 ATGCTGCTGTACCAA
*
30581370 ATGCTGTTGTACCAA
1 ATGCTGCTGTACCAA
**
30581385 ATG-TAGAGGTACCAA
1 ATGCT-GCTGTACCAA
*
30581400 ATGCTACTGTACCAA
1 ATGCTGCTGTACCAA
30581415 ATGC
1 ATGC
30581419 GGACGATAAA
Statistics
Matches: 109, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
14 2 0.02
15 105 0.96
16 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (15 bp):
ATGCTGCTGTACCAA
Found at i:30581320 original size:45 final size:44
Alignment explanation
Indices: 30581270--30581418 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 44
30581260 ACCTTATGCG
* * *
30581270 GCTGTACCAAATGCTGTTGTATCGAATGTTGCAGTGCCAAATTCT
1 GCTGTACCAAATGCTGTTGTACCAAATGTTG-AGTACCAAATTCT
* * *
30581315 GCTGTACCAAATGTTGTAGTACCAAATGTTGTTGTACCAAATGT-T
1 GCTGTACCAAATGCTGTTGTACCAAATGTTG-AGTACCAAAT-TCT
* * *
30581360 GCGGTACCAAATGCTGTTGTACCAAATGTAGAGGTACCAAATGCT
1 GCTGTACCAAATGCTGTTGTACCAAATGTTGA-GTACCAAATTCT
*
30581405 ACTGTACCAAATGC
1 GCTGTACCAAATGC
30581419 GGACGATAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
45 85 0.99
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
GCTGTACCAAATGCTGTTGTACCAAATGTTGAGTACCAAATTCT
Found at i:30581328 original size:30 final size:30
Alignment explanation
Indices: 30581273--30581417 Score: 175
Period size: 30 Copynumber: 4.8 Consensus size: 30
30581263 TTATGCGGCT
* *
30581273 GTACCAAATGCTGTTGTATCGAATGTTGCA
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
* * * *
30581303 GTGCCAAATTCTGCTGTACCAAATGTTGTA
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
* *
30581333 GTACCAAATGTTGTTGTACCAAATGTTGCG
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
*
30581363 GTACCAAATGCTGTTGTACCAAATGTAG-A
1 GTACCAAATGCTGTTGTACCAAATGTTGCA
**
30581392 GGTACCAAATGCTACTGTACCAAATG
1 -GTACCAAATGCTGTTGTACCAAATG
30581418 CGGACGATAA
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
GTACCAAATGCTGTTGTACCAAATGTTGCA
Found at i:30581764 original size:11 final size:11
Alignment explanation
Indices: 30581748--30581783 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
30581738 GTATATAAAA
30581748 AATTTAAATTT
1 AATTTAAATTT
30581759 AATTTAAATTT
1 AATTTAAATTT
*
30581770 AATAATAAATTT
1 AAT-TTAAATTT
30581782 AA
1 AA
30581784 AAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:30581780 original size:12 final size:12
Alignment explanation
Indices: 30581752--30581791 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
30581742 ATAAAAAATT
*
30581752 TAAATTTAAT-T
1 TAAATTTAATAA
30581763 TAAATTTAATAA
1 TAAATTTAATAA
*
30581775 TAAATTTAAAAA
1 TAAATTTAATAA
30581787 TAAAT
1 TAAAT
30581792 AACAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATTTAATAA
Found at i:30583516 original size:30 final size:29
Alignment explanation
Indices: 30583462--30583520 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
30583452 TTACGTTAAC
* * *
30583462 AGGACACCCTCATATTTTCAAGTGGTTCT
1 AGGACACCCCCACATTTCCAAGTGGTTCT
30583491 AGGACACCCCCCACATTTCCAAGTGGTTCT
1 AGGACA-CCCCCACATTTCCAAGTGGTTCT
30583521 CTTGTCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (29 bp):
AGGACACCCCCACATTTCCAAGTGGTTCT
Found at i:30591569 original size:9 final size:9
Alignment explanation
Indices: 30591498--30591590 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 9
30591488 AGCAACCATG
30591498 TTTTTTTCT
1 TTTTTTTCT
30591507 TCTTTTTCTCCT
1 T-TTTTT-T-CT
30591519 TTTTTTCTCT
1 TTTTTT-TCT
30591529 TTTTTTTCT
1 TTTTTTTCT
***
30591538 TTTTGAAC-
1 TTTTTTTCT
* *
30591546 -CTTTTGCT
1 TTTTTTTCT
30591554 TTTTTTTCT
1 TTTTTTTCT
*
30591563 TTTTTTTGT
1 TTTTTTTCT
* *
30591572 TGTTCTT-T
1 TTTTTTTCT
30591580 TTTTTTTCT
1 TTTTTTTCT
30591589 TT
1 TT
30591591 ATTCGAGCTC
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.05
8 6 0.09
9 31 0.48
10 13 0.20
11 8 0.12
12 3 0.05
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.78
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:30595633 original size:3 final size:3
Alignment explanation
Indices: 30595625--30595655 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30595615 ATGGATTAAT
30595625 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30595656 ATATGAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30596247 original size:3 final size:3
Alignment explanation
Indices: 30596239--30596282 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
30596229 CCTATTATAT
30596239 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30596283 CTTTTTTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30597966 original size:58 final size:58
Alignment explanation
Indices: 30597856--30597968 Score: 131
Period size: 58 Copynumber: 1.9 Consensus size: 58
30597846 TGCTATATCA
** * *
30597856 GTTTTGAATAAAGTTACCTTTTGATCTTTGTTTAACCAAAGAAAGAAAGTCAAAATTT
1 GTTTTGAATAAAGCCACCTTTTGATCTTTGTTCAACCAAAAAAAGAAAGTCAAAATTT
* * *
30597914 GTTTCTGAATAAAGCCA-CTTTTCGATC-TTGTTCAACTAAAAAAAGGAGGTCAAAA
1 GTTT-TGAATAAAGCCACCTTTT-GATCTTTGTTCAACCAAAAAAAGAAAGTCAAAA
30597969 CCCGTTTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 32 0.70
59 14 0.30
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (58 bp):
GTTTTGAATAAAGCCACCTTTTGATCTTTGTTCAACCAAAAAAAGAAAGTCAAAATTT
Found at i:30599181 original size:14 final size:11
Alignment explanation
Indices: 30599151--30599178 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30599141 TCTAGGAATG
30599151 AGAGAATAAGA
1 AGAGAATAAGA
30599162 AGAGAATAAGA
1 AGAGAATAAGA
30599173 AGAGAA
1 AGAGAA
30599179 GAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (11 bp):
AGAGAATAAGA
Found at i:30600113 original size:16 final size:16
Alignment explanation
Indices: 30600093--30600130 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
30600083 TCAAGTTCAG
*
30600093 ATTTTCTCGAGTTT-A
1 ATTTTTTCGAGTTTGA
*
30600108 ATTTTTTTGAGTTTGA
1 ATTTTTTCGAGTTTGA
30600124 ATTTTTT
1 ATTTTTT
30600131 TAAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (16 bp):
ATTTTTTCGAGTTTGA
Found at i:30600119 original size:15 final size:16
Alignment explanation
Indices: 30600101--30600131 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30600091 AGATTTTCTC
30600101 GAGTTT-AATTTTTTT
1 GAGTTTGAATTTTTTT
30600116 GAGTTTGAATTTTTTT
1 GAGTTTGAATTTTTTT
30600132 AAATTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (16 bp):
GAGTTTGAATTTTTTT
Found at i:30603409 original size:18 final size:18
Alignment explanation
Indices: 30603386--30603437 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
30603376 TTTTCAGTTG
30603386 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
30603404 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
30603422 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
30603438 CTCATCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:30606004 original size:31 final size:31
Alignment explanation
Indices: 30605946--30606005 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
30605936 AAATCAAACA
**
30605946 TGAAAATGCAACTTTTCAAGGGCTTTAATGG
1 TGAAAATGCAACTTTTCAAGAACTTTAATGG
*
30605977 TGAAAATGCAACTTTTCAAGAATTTTAAT
1 TGAAAATGCAACTTTTCAAGAACTTTAAT
30606006 CAATACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (31 bp):
TGAAAATGCAACTTTTCAAGAACTTTAATGG
Found at i:30607434 original size:16 final size:16
Alignment explanation
Indices: 30607394--30607437 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
30607384 TGTAATTATT
*
30607394 TTAAAATTTTCAATTAA
1 TTAAAATTTT-ATTTAA
30607411 TT--AATTTTATTTAA
1 TTAAAATTTTATTTAA
30607425 TTAAAATTTTATT
1 TTAAAATTTTATT
30607438 CCCATTCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 9 0.38
17 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAAATTTTATTTAA
Found at i:30616457 original size:23 final size:24
Alignment explanation
Indices: 30616423--30616470 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
30616413 AATGTATTAT
30616423 ATATATTT-AAAAATTATATAAAA
1 ATATATTTAAAAAATTATATAAAA
30616446 ATAT-TTTCAAAAAAATTATATAAAA
1 ATATATTT--AAAAAATTATATAAAA
30616471 CTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.14
23 4 0.18
25 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATTTAAAAAATTATATAAAA
Found at i:30616482 original size:25 final size:25
Alignment explanation
Indices: 30616431--30616482 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
30616421 ATATATATTT
* * *
30616431 AAAAATTATATAAAAATATTTTCAA
1 AAAAATTATATAAAAATAATATAAA
*
30616456 AAAAATTATATAAAACTAATATAAA
1 AAAAATTATATAAAAATAATATAAA
30616481 AA
1 AA
30616483 TTGTAATACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAATTATATAAAAATAATATAAA
Found at i:30616720 original size:31 final size:31
Alignment explanation
Indices: 30616678--30616736 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
30616668 ATCAAATGAC
*
30616678 TTAAATAAAAACTTTTGAATAGTTTAGTAAT
1 TTAAATAAAAACCTTTGAATAGTTTAGTAAT
*
30616709 TTAAATGAAAACCTTTGAATAGTTTAGT
1 TTAAATAAAAACCTTTGAATAGTTTAGT
30616737 GATCATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (31 bp):
TTAAATAAAAACCTTTGAATAGTTTAGTAAT
Found at i:30628183 original size:13 final size:13
Alignment explanation
Indices: 30628165--30628195 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
30628155 AGCACCGAAT
30628165 TCTCTCTCATAAA
1 TCTCTCTCATAAA
30628178 TCTCTCTCATAAA
1 TCTCTCTCATAAA
30628191 TCTCT
1 TCTCT
30628196 AAACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (13 bp):
TCTCTCTCATAAA
Found at i:30630138 original size:31 final size:31
Alignment explanation
Indices: 30630080--30630148 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
30630070 ACTTAATATC
* * *
30630080 TCAATGACTTAAATAAAAACTTCCAAATAGT
1 TCAATAACTTAAATAAAAACATCCAAATAAT
*
30630111 TCAATAACTTAAATGAAAACCAT-CAAATAAT
1 TCAATAACTTAAAT-AAAAACATCCAAATAAT
*
30630142 TTAATAA
1 TCAATAA
30630149 TCATTTTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.29
Consensus pattern (31 bp):
TCAATAACTTAAATAAAAACATCCAAATAAT
Found at i:30633923 original size:21 final size:21
Alignment explanation
Indices: 30633899--30633947 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
30633889 TTTAAACCAA
*
30633899 TGATTTAGTAAAAATGAAGGT
1 TGATTTAGTAAAAATGAAGGC
*
30633920 TGATTTTGGTAAAAATGAAGGC
1 TGA-TTTAGTAAAAATGAAGGC
30633942 TGATTT
1 TGATTT
30633948 TGATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (21 bp):
TGATTTAGTAAAAATGAAGGC
Found at i:30633934 original size:22 final size:22
Alignment explanation
Indices: 30633906--30633949 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30633896 CAATGATTTA
*
30633906 GTAAAAATGAAGGTTGATTTTG
1 GTAAAAATGAAGGCTGATTTTG
30633928 GTAAAAATGAAGGCTGATTTTG
1 GTAAAAATGAAGGCTGATTTTG
30633950 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (22 bp):
GTAAAAATGAAGGCTGATTTTG
Found at i:30634652 original size:2 final size:2
Alignment explanation
Indices: 30634645--30634694 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
30634635 TCATCTTCTG
* * *
30634645 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT TT AT -T AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
30634687 AT AT AT AT
1 AT AT AT AT
30634695 TTGTAAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:30635623 original size:60 final size:59
Alignment explanation
Indices: 30635554--30635970 Score: 335
Period size: 60 Copynumber: 7.0 Consensus size: 59
30635544 ATATTTTGAC
* *
30635554 CCCTTAACTTCTCTAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
1 CCCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
* * * * * *
30635613 CCCTTAAACTTTTCCAGAATCACATTTTAACCCTTAAACTTTTTTAAAATTATAATTTAA
1 CCC-TAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
* * * **
30635673 CCTCTAAACTTTTCCAAAATTACATTTCAACCCCTAAACTTCTCCAAAATTACATTTTAA
1 CC-CTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
* * * * * ** *
30635733 -CCTCAACTTCTCCAAAATTATATTTTGACCC-TAAACTTCTTCAAAATCATGTTTTGAC
1 CCCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTT-AA
* * ** * * *
30635791 CCCTAAACCTAT-TCCAAAATCA-AGTTTTGACCCTT-AACTTTCCCTGAAATCACATTTTGA
1 CCCTAAA-CT-TCTCCAAAATTACA-TTTTAACCCTTAAAC-TTCTTTAAAATTACATTTTAA
* * * ** *
30635851 CCCTAAATTTCTCCAAAATCACATTTTAACCC-CAAACTTCTCCAAAATCACATTTTAA
1 CCCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
* * * * * **
30635909 CCCCAAA-TTTTCCTAAAATTACATTTTTACCCCTAAACTTTTTTTAAAATTATGTTTTAA
1 CCCTAAACTTCTCC-AAAATTACATTTTAACCCTTAAAC-TTCTTTAAAATTACATTTTAA
30635969 CC
1 CC
30635971 TCGTATTCTC
Statistics
Matches: 288, Mismatches: 55, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
57 25 0.09
58 66 0.23
59 36 0.12
60 145 0.50
61 16 0.06
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (59 bp):
CCCTAAACTTCTCCAAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAA
Found at i:30635779 original size:29 final size:29
Alignment explanation
Indices: 30635554--30635948 Score: 275
Period size: 30 Copynumber: 13.3 Consensus size: 29
30635544 ATATTTTGAC
*
30635554 CCCTTAACTTC-TCTAAAATTACATTTTAA
1 CCCTAAACTTCTTC-AAAATTACATTTTAA
*
30635583 CCCTTAAACTTCTTTAAAATTACATTTTAA
1 CCC-TAAACTTCTTCAAAATTACATTTTAA
* *
30635613 CCCTTAAACTT-TTCCAGAATCACATTTTAA
1 CCC-TAAACTTCTT-CAAAATTACATTTTAA
* * * *
30635643 CCCTTAAACTTTTTTAAAATTATAATTTAA
1 CCC-TAAACTTCTTCAAAATTACATTTTAA
*
30635673 CCTCTAAACTT-TTCCAAAATTACATTTCAA
1 CC-CTAAACTTCTT-CAAAATTACATTTTAA
*
30635703 CCCCTAAACTTCTCCAAAATTACATTTTAA
1 -CCCTAAACTTCTTCAAAATTACATTTTAA
* * * *
30635733 -CCTCAACTTCTCCAAAATTATATTTTGA
1 CCCTAAACTTCTTCAAAATTACATTTTAA
* ** *
30635761 CCCTAAACTTCTTCAAAATCATGTTTTGAC
1 CCCTAAACTTCTTCAAAATTACATTTT-AA
* * * *
30635791 CCCTAAACCTATTCCAAAATCA-AGTTTTGA
1 CCCTAAACTTCTT-CAAAATTACA-TTTTAA
* * * * *
30635821 CCCTTAACTT-TCCCTGAAATCACATTTTGA
1 CCCTAAACTTCT-TC-AAAATTACATTTTAA
* * *
30635851 CCCTAAATTTCTCCAAAATCACATTTTAA
1 CCCTAAACTTCTTCAAAATTACATTTTAA
* * *
30635880 CCCCAAACTTCTCCAAAATCACATTTTAA
1 CCCTAAACTTCTTCAAAATTACATTTTAA
* *
30635909 CCCCAAA-TT-TTCCTAAAATTACATTTTTAC
1 CCCTAAACTTCTT-C-AAAATTACA-TTTTAA
30635939 CCCTAAACTT
1 CCCTAAACTT
30635949 TTTTTAAAAT
Statistics
Matches: 302, Mismatches: 44, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.00
28 28 0.09
29 86 0.28
30 164 0.54
31 23 0.08
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCTTCAAAATTACATTTTAA
Found at i:30635812 original size:31 final size:31
Alignment explanation
Indices: 30635743--30635823 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
30635733 CCTCAACTTC
* * * *
30635743 TCCAAAATTATATTTTGA-CCCTAAACTTCT
1 TCCAAAATCATGTTTTGACCCCTAAACCTAT
30635773 T-CAAAATCATGTTTTGACCCCTAAACCTAT
1 TCCAAAATCATGTTTTGACCCCTAAACCTAT
*
30635803 TCCAAAATCAAGTTTTGACCC
1 TCCAAAATCATGTTTTGACCC
30635824 TTAACTTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 14 0.32
30 12 0.27
31 18 0.41
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (31 bp):
TCCAAAATCATGTTTTGACCCCTAAACCTAT
Found at i:30640773 original size:7 final size:7
Alignment explanation
Indices: 30640750--30640835 Score: 77
Period size: 7 Copynumber: 11.9 Consensus size: 7
30640740 TTCGATGAAG
30640750 AAAAAAT
1 AAAAAAT
30640757 AAATAAAAT
1 -AA-AAAAT
30640766 AAAAAAT
1 AAAAAAT
30640773 AAAATAAAAT
1 --AA-AAAAT
30640783 AAAAAAT
1 AAAAAAT
30640790 AAAAAA-
1 AAAAAAT
* *
30640796 AGAGAA-
1 AAAAAAT
* *
30640802 GAAAAAG
1 AAAAAAT
30640809 AAAAAAT
1 AAAAAAT
30640816 AAAAAAT
1 AAAAAAT
30640823 AAAAAAT
1 AAAAAAT
30640830 AAAAAA
1 AAAAAA
30640836 AGAGAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
6 7 0.11
7 41 0.62
8 6 0.09
9 7 0.11
10 5 0.08
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:30640792 original size:33 final size:31
Alignment explanation
Indices: 30640750--30640845 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 31
30640740 TTCGATGAAG
30640750 AAAAAATAAATAAAATAAAAAATAA-AATAAAAT
1 AAAAAATAAA-AAAATAAAAAA-AAGAA-AAAAT
*
30640783 AAAAAATAAAAAAAGAGAAGAAAAAGAAAAAAT
1 AAAAAATAAAAAAATA-AA-AAAAAGAAAAAAT
30640816 AAAAAAT-AAAAAATAAAAAAAGAGAAAAAA
1 AAAAAATAAAAAAATAAAAAAA-AGAAAAAA
30640846 GGAAAAAGAG
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.07
31 10 0.18
32 12 0.21
33 26 0.46
34 5 0.09
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.10
Consensus pattern (31 bp):
AAAAAATAAAAAAATAAAAAAAAGAAAAAAT
Found at i:30640833 original size:12 final size:12
Alignment explanation
Indices: 30640757--30640826 Score: 72
Period size: 12 Copynumber: 5.7 Consensus size: 12
30640747 AAGAAAAAAT
30640757 AAATAAAATAAA
1 AAATAAAATAAA
30640769 AAATAAAATAAA
1 AAATAAAATAAA
30640781 ATAA-AAAATAAA
1 A-AATAAAATAAA
*
30640793 AAA-AGAGAAGAAA
1 AAATA-A-AATAAA
*
30640806 AAGAAAAAATAAA
1 AA-ATAAAATAAA
30640819 AAATAAAA
1 AAATAAAA
30640827 AATAAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 3 0.06
12 28 0.56
13 16 0.32
14 2 0.04
15 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:30640845 original size:17 final size:16
Alignment explanation
Indices: 30640750--30640828 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
30640740 TTCGATGAAG
*
30640750 AAAAAATAAATAAAAT
1 AAAAAATAAAAAAAAT
30640766 AAAAAATAAAATAAAAT
1 AAAAAATAAAA-AAAAT
*
30640783 AAAAAATAAAAAAAGAG
1 AAAAAATAAAAAAA-AT
*
30640800 AAGAAAA-AGAAAAAAT
1 AA-AAAATAAAAAAAAT
30640816 AAAAAATAAAAAA
1 AAAAAATAAAAAA
30640829 TAAAAAAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
15 4 0.07
16 21 0.39
17 25 0.46
18 4 0.07
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Done.