Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold46
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: 2524624
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 119418 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1880395 original size:19 final size:19
Alignment explanation
Indices: 1880367--1880416 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1880357 ATCGATACAT
1880367 TGTATCGATATAAAACTTA
1 TGTATCGATATAAAACTTA
* *
1880386 TGTATTGATACAAAACTTA
1 TGTATCGATATAAAACTTA
1880405 TGTATCGATATA
1 TGTATCGATATA
1880417 TTTACTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCGATATAAAACTTA
Found at i:1881331 original size:49 final size:49
Alignment explanation
Indices: 1881203--1881537 Score: 210
Period size: 49 Copynumber: 7.0 Consensus size: 49
1881193 TTGAAGATGA
* * * * *
1881203 GAAGAATGCTAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAGGAATGTT
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAGCAACA-TCGGACTTA--AA-GAT
* * * *
1881256 AAAGATGCCAATATGTTGATTCAAGGCTAGCAATATCGGACTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
* * * * *
1881305 GAAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
* ** **
1881354 GAAGATGCCAATATGTTGATTCAAGGCCAGTGACATTAGACTT-AA-A-
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
** * * *
1881400 G--G-TGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTT----AT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
* * * * *
1881442 G-A-ATGCCAATATGCTAATTTAAGGCCAACGATATCGGACTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
* * * * * *
1881489 GATGATGCCAATGTGCTGATTGAAGGCTAGCGACATTGGACTTAGAAGA
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTA-AAGA
1881538 GTTGCCACCG
Statistics
Matches: 229, Mismatches: 42, Indels: 25
0.77 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 66 0.29
44 1 0.00
46 1 0.00
47 4 0.02
48 2 0.01
49 112 0.49
50 6 0.03
51 3 0.01
52 29 0.13
53 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (49 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAGCAACATCGGACTTAAAGAT
Found at i:1881420 original size:43 final size:43
Alignment explanation
Indices: 1881306--1881532 Score: 161
Period size: 43 Copynumber: 5.0 Consensus size: 43
1881296 CTTAAAGATG
* * *
1881306 AAGGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTT-A
* *
1881350 AGATGAAGATGCCAATATGTTGATTCAAGGCCAGTGACATTAGACTTA
1 A-A-G--G-TGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTTA
* *
1881398 AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTTA
* * ** * *
1881441 TGAA--TGCCAATATGCTAATTTAAGGCCAACGATATCGGACTTAA
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTT-A
* * * *
1881485 AGATGATGATGCCAATGTGCTGATTGAAGGCTAGCGACATTGGACTTA
1 A-A-G--G-TGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTTA
1881533 GAAGAGTTGC
Statistics
Matches: 146, Mismatches: 22, Indels: 26
0.75 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
43 68 0.47
44 3 0.02
45 3 0.02
46 2 0.01
47 1 0.01
48 4 0.03
49 64 0.44
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (43 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGTGACATTGGACTTA
Found at i:1881664 original size:32 final size:32
Alignment explanation
Indices: 1881628--1881901 Score: 201
Period size: 27 Copynumber: 9.1 Consensus size: 32
1881618 TAGGCTTTTG
* *
1881628 AAAGGAAAAGGTACCATAGAGTTGTGGACTTA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881660 AAAGG---A--TGCCACGGAGTTATGGACTTGA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTT-A
* * *
1881688 AAA-GAAAATGTGCCACAGAGTTGTAGATTTA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881719 AAAGG---A--TGCCATAGAGTTGTGGACTTG
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881746 AAAGGAAAAGGTGTCACGGAGTTGTGGACTTA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881778 AAAGG----GGTGCCACGGAGTTGTGGGCTTA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881806 AAAGAAATAAGGTGCCACAGAGTTGTGGGCTTA
1 AAAGGAA-AAGGTGCCACAGAGTTGTGGACTTA
* * *
1881839 AAA-G----GGTGCCACAAAGTTGTGAACTTG
1 AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
* *
1881866 AAAGGAAAAGGTGCCACAGAGGTGTGGGCTTTA
1 AAAGGAAAAGGTGCCACAGAGTTGTGGAC-TTA
1881899 AAA
1 AAA
1881902 AGTGAGGAAT
Statistics
Matches: 189, Mismatches: 30, Indels: 45
0.72 0.11 0.17
Matches are distributed among these distances:
27 61 0.32
28 30 0.16
29 2 0.01
30 2 0.01
31 4 0.02
32 60 0.32
33 30 0.16
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.22
Consensus pattern (32 bp):
AAAGGAAAAGGTGCCACAGAGTTGTGGACTTA
Found at i:1881682 original size:27 final size:27
Alignment explanation
Indices: 1881646--1881809 Score: 130
Period size: 32 Copynumber: 5.7 Consensus size: 27
1881636 AGGTACCATA
1881646 GAGTTGTGGACTTAAAAGGATGCCACG
1 GAGTTGTGGACTTAAAAGGATGCCACG
* * *
1881673 GAGTTATGGACTTGAAAAGAAAATGTGCCACA
1 GAGTTGTGGACTT-AAAAG--GA--TGCCACG
* * **
1881705 GAGTTGTAGATTTAAAAGGATGCCATA
1 GAGTTGTGGACTTAAAAGGATGCCACG
* *
1881732 GAGTTGTGGACTTGAAAGGAAAAGGTGTCACG
1 GAGTTGTGGACTTAAAAGG---A--TGCCACG
*
1881764 GAGTTGTGGACTTAAAAGGGGTGCCACG
1 GAGTTGTGGACTTAAAA-GGATGCCACG
*
1881792 GAGTTGTGGGCTTAAAAG
1 GAGTTGTGGACTTAAAAG
1881810 AAATAAGGTG
Statistics
Matches: 108, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
27 35 0.32
28 27 0.25
29 1 0.01
30 2 0.02
31 5 0.05
32 36 0.33
33 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.33, T:0.24
Consensus pattern (27 bp):
GAGTTGTGGACTTAAAAGGATGCCACG
Found at i:1881720 original size:59 final size:59
Alignment explanation
Indices: 1881625--1881901 Score: 329
Period size: 59 Copynumber: 4.6 Consensus size: 59
1881615 GTGTAGGCTT
* * * *
1881625 TTGAAAGGAAAAGGTACCATAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGAC
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC
* * * * *
1881684 TTGAAAAGAAAATGTGCCACAGAGTTGTAGATTTAAAAGGATGCCATAGAGTTGTGGAC
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC
* * * * *
1881743 TTGAAAGGAAAAGGTGTCACGGAGTTGTGGACTTAAAAGGGGTGCCACGGAGTTGTGGGC
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAA-GGATGCCACAGAGTTGTGGAC
* * * * * *
1881803 TTAAAAGAAATAAGGTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACAAAGTTGTGAAC
1 TTGAAAGGAA-AAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC
* *
1881863 TTGAAAGGAAAAGGTGCCACAGAGGTGTGGGCTTTAAAA
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGAC-TTAAAA
1881902 AGTGAGGAAT
Statistics
Matches: 184, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
59 103 0.56
60 56 0.30
61 25 0.14
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (59 bp):
TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC
Found at i:1881867 original size:120 final size:118
Alignment explanation
Indices: 1881625--1881901 Score: 358
Period size: 120 Copynumber: 2.3 Consensus size: 118
1881615 GTGTAGGCTT
* *
1881625 TTGAAAGGAAAAGGTACCATAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTGAAA
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTGAAA
* * * * *
1881690 AGAAAATGTGCCACAGAGTTGTAGATTTAAAAGGATGCCATAGAGTTGTGGAC
66 AGAAAAGGTGCCACAGAGTTGTAGACTTAAAAGGATGCCACAAAGTTGTGAAC
* * * * *
1881743 TTGAAAGGAAAAGGTGTCACGGAGTTGTGGACTTAAAAGGGGTGCCACGGAGTTGTGGGCTT-AA
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAA-GGATGCCACGGAGTTATGGACTTGAA
* * *
1881807 AAGAAATAAGGTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACAAAGTTGTGAAC
65 AAG-AA-AAGGTGCCACAGAGTTGTAGACTTAAAAGGATGCCACAAAGTTGTGAAC
* *
1881863 TTGAAAGGAAAAGGTGCCACAGAGGTGTGGGCTTTAAAA
1 TTGAAAGGAAAAGGTGCCACAGAGTTGTGGAC-TTAAAA
1881902 AGTGAGGAAT
Statistics
Matches: 136, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
118 39 0.29
119 22 0.16
120 69 0.51
121 6 0.04
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (118 bp):
TTGAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTGAAA
AGAAAAGGTGCCACAGAGTTGTAGACTTAAAAGGATGCCACAAAGTTGTGAAC
Found at i:1883355 original size:27 final size:26
Alignment explanation
Indices: 1883317--1883374 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
1883307 ATCCGGACCC
*
1883317 TTTTTTTTTTGTTTTGTTTTT-TGTT
1 TTTTTTTTTTGTTTTGTTTTTCTATT
1883342 TTTTTTGTGTTTGTTTTGTTTTTCTATT
1 TTTTTT-T-TTTGTTTTGTTTTTCTATT
1883370 TTTTT
1 TTTTT
1883375 AAAGACGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.21
26 1 0.03
27 14 0.48
28 8 0.28
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (26 bp):
TTTTTTTTTTGTTTTGTTTTTCTATT
Found at i:1888359 original size:52 final size:52
Alignment explanation
Indices: 1888211--1888339 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1888201 TGAAATATGA
* * *
1888211 AAATTTGCCTGCATTTATTGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1888263 AAATTTGCCTGTATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1888315 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATATATCGATACA
1888340 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1888366 original size:13 final size:13
Alignment explanation
Indices: 1888348--1888372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1888338 CAAAGATCAG
1888348 TGTATCGATACAA
1 TGTATCGATACAA
1888361 TGTATCGATACA
1 TGTATCGATACA
1888373 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1888449 original size:19 final size:19
Alignment explanation
Indices: 1888425--1888489 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1888415 AGTGATACAT
1888425 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1888444 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1888457 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
1888476 TGTATCTATACAAA
1 TGTATCGATACAAA
1888490 TCGTTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1888459 original size:32 final size:32
Alignment explanation
Indices: 1888418--1888487 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1888408 GCTTCGTAGT
1888418 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
1888450 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
1888482 TATACA
1 GATACA
1888488 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:1888462 original size:13 final size:13
Alignment explanation
Indices: 1888444--1888468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1888434 ACAAAACTTA
1888444 TGTATCGATACAT
1 TGTATCGATACAT
1888457 TGTATCGATACA
1 TGTATCGATACA
1888469 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1889522 original size:49 final size:48
Alignment explanation
Indices: 1889433--1889619 Score: 150
Period size: 49 Copynumber: 3.9 Consensus size: 48
1889423 TATTGGGCTT
* * * ** * *
1889433 ATGCCAATGTGCTGATTCAAGGCCAGCAATATTAGTCTTAAAGATGCCG
1 ATGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATG-AG
* *
1889482 ATGCTAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAG--GTG
1 ATGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAG
* * ** *
1889528 -T-C-AATATGCTGATTCAAGGTCAGCGATATTGGGTTTTAAAGATATAG
1 ATGCTAATATGCTGATTCAAGGCCAGCGATA-TCGGACTTAAAGAT-GAG
* * *
1889575 GTGCTAATATGCTGGTTCAAGGCCAGTGATATCGGACTTAGAAGA
1 ATGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTA-AAGA
1889620 AGATGCCACC
Statistics
Matches: 109, Mismatches: 21, Indels: 15
0.75 0.14 0.10
Matches are distributed among these distances:
43 24 0.22
44 10 0.09
45 1 0.01
46 1 0.01
47 2 0.02
48 1 0.01
49 43 0.39
50 27 0.25
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (48 bp):
ATGCTAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAG
Found at i:1889585 original size:93 final size:86
Alignment explanation
Indices: 1889312--1889614 Score: 300
Period size: 87 Copynumber: 3.4 Consensus size: 86
1889302 TAAAGATGCC
* * * * *
1889312 AATATGCTGATTCACGACCAACGATATTGGACTTATGCTAATGTGCTAATTCAAGGCCAGCGACA
1 AATATGCTGATTCAAGGCCAACGATATCGGACTTATGC-AATGTGCTGATTCAAGGCCAGCGATA
* *
1889377 TTGGATTTAAAGATAAGGTGCC
65 TTGGTTTTAAAGATAAGGTGCT
* * * * * * *
1889399 AATACGCCGATTCAAAGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAATA
1 AATATGCTGATTCAAGGCCAACGATATCGGACTTATG-CAATGTGCTGATTCAAGGCCAGCGATA
* * ** *
1889464 TTAGTCTTAAAGATGCCGATGCT
65 TTGGTTTTAAAGAT-AAGGTGCT
* *
1889487 AATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGGTGTCAATATGCTGATTCAAGGTCAGC
1 AATATGCTGATTCAAGGCCAACGATATCGGACTT--A--TG-CAATGTGCTGATTCAAGGCCAGC
1889552 GATATTGGGTTTTAAAGATATAGGTGCT
61 GATATT-GGTTTTAAAGATA-AGGTGCT
* **
1889580 AATATGCTGGTTCAAGGCCAGTGATATCGGACTTA
1 AATATGCTGATTCAAGGCCAACGATATCGGACTTA
1889615 GAAGAAGATG
Statistics
Matches: 173, Mismatches: 35, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
87 64 0.37
88 33 0.19
90 1 0.01
91 1 0.01
92 28 0.16
93 46 0.27
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (86 bp):
AATATGCTGATTCAAGGCCAACGATATCGGACTTATGCAATGTGCTGATTCAAGGCCAGCGATAT
TGGTTTTAAAGATAAGGTGCT
Found at i:1889693 original size:28 final size:28
Alignment explanation
Indices: 1889621--1889762 Score: 137
Period size: 28 Copynumber: 5.0 Consensus size: 28
1889611 CTTAGAAGAA
*
1889621 GATGCCACCAACTTGTGTGGGCTTTTGAAAGG
1 GATGCCACTAAC-T-TGTGGGCTTTTG-AA-G
* *
1889653 GTTG-CA-TCAACTTGTGTGCTTTTGAAG
1 GATGCCACT-AACTTGTGGGCTTTTGAAG
*
1889680 GCTGCCACTAACTTGTGGGC-TTTGAAAG
1 GATGCCACTAACTTGTGGGCTTTTG-AAG
* *
1889708 GATACCACTGACTTGTGGGCTTTTGAAG
1 GATGCCACTAACTTGTGGGCTTTTGAAG
* *
1889736 GTTGCCACTGACTTGTGGGCTTTTGAA
1 GATGCCACTAACTTGTGGGCTTTTGAA
1889763 AAAGGTGCCA
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
27 8 0.08
28 62 0.65
29 16 0.17
30 1 0.01
31 5 0.05
32 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (28 bp):
GATGCCACTAACTTGTGGGCTTTTGAAG
Found at i:1889793 original size:85 final size:85
Alignment explanation
Indices: 1889636--1889794 Score: 193
Period size: 85 Copynumber: 1.9 Consensus size: 85
1889626 CACCAACTTG
*
1889636 TGTGGGCTTTTGAAAGGGTTGCATCAACTTGTGTGCTTTTGAAGGCTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGGTTGCATCAACTTGTGGGCTTTTGAAGGCTGCCACTAACTTGTGGGCT
*
1889701 TTGAAAGGATACCACTGACT
66 TTAAAAGGATACCACTGACT
* * *
1889721 TGTGGGCTTTTG-AA-GGTTGCCA-CTGACTTGTGGGCTTTTGAAAAAGG-TGCCACTGATTTGT
1 TGTGGGCTTTTGAAAGGGTTG-CATC-AACTTGTGGGCTTTTG---AAGGCTGCCACTAACTTGT
1889782 GGGC-TTAAAAGGA
61 GGGCTTTAAAAGGA
1889795 AAAAGAGTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
83 6 0.09
84 18 0.28
85 20 0.31
86 16 0.25
87 4 0.06
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (85 bp):
TGTGGGCTTTTGAAAGGGTTGCATCAACTTGTGGGCTTTTGAAGGCTGCCACTAACTTGTGGGCT
TTAAAAGGATACCACTGACT
Found at i:1889839 original size:35 final size:34
Alignment explanation
Indices: 1889760--1889867 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 34
1889750 GTGGGCTTTT
* * *
1889760 GAAAAAG-GTGCCACTGATTTGTGGGCTTAAAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAA
1889793 GAAAAAGAGTGCCACGGAGTTGTGGGCTTACAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTA-AAAA
* *
1889828 GAAAAGGAGTGCCACGGAGTTGTGGACTTAAAAAA
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAAAA
1889863 GAAAA
1 GAAAA
1889868 TGTACCAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
33 7 0.10
34 20 0.30
35 39 0.58
36 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.31, T:0.19
Consensus pattern (34 bp):
GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAA
Found at i:1889950 original size:32 final size:32
Alignment explanation
Indices: 1889908--1889993 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
1889898 TATTGGGCTT
*
1889908 AAAGGTGCCACA-ACGTTGTGGACATAAAAAGA
1 AAAGGCGCCACAGA-GTTGTGGACATAAAAAGA
* * *
1889940 AAAGGCGCCACAGAGTTGTGGGCTTAAAAGGA
1 AAAGGCGCCACAGAGTTGTGGACATAAAAAGA
** *
1889972 AAATGATGCCACAGACTTGTGG
1 AAA-GGCGCCACAGAGTTGTGG
1889994 GCTTTTGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.17
Consensus pattern (32 bp):
AAAGGCGCCACAGAGTTGTGGACATAAAAAGA
Found at i:1890042 original size:30 final size:29
Alignment explanation
Indices: 1889978--1890142 Score: 189
Period size: 30 Copynumber: 5.7 Consensus size: 29
1889968 AGGAAAATGA
*
1889978 TGCCACAGACTTGTGGGCTTTTG---AAGG
1 TGCCACTGACTTGTGGGC-TTTGAAAAAGG
*
1890005 TTGCCACTGATTTGTGGGCTTTGAAAAAAGG
1 -TGCCACTGACTTGTGGGCTTTG-AAAAAGG
*
1890036 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-GAAAAAGG
*
1890066 TGCCACTGATTTGTGGGCTTTG---AAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAGG
* *
1890092 TTGCCACTGACTTCTGGGCTTTGAAAAAGA
1 -TGCCACTGACTTGTGGGCTTTGAAAAAGG
1890122 TGCCACTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1890143 TGAAGGGTGA
Statistics
Matches: 118, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
26 3 0.03
27 24 0.20
28 16 0.14
29 21 0.18
30 49 0.42
31 5 0.04
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAGG
Found at i:1890110 original size:87 final size:87
Alignment explanation
Indices: 1889969--1890142 Score: 269
Period size: 87 Copynumber: 2.0 Consensus size: 87
1889959 GGGCTTAAAA
* * *
1889969 GGAAAATGATGCCACAGACTTGTGGGCTTTTGAAGGTTGCCACTGATTTGTGGGCTTTGAAAAAA
1 GGAAAAGGATGCCACAGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTCTGGGCTTTG-AAAAA
*
1890034 GGTGCCACTGACTTGTGGGCTTT
65 GATGCCACTGACTTGTGGGCTTT
* * *
1890057 GGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGGTTGCCACTGACTTCTGGGCTTTGAAAAAG
1 GGAAAAGGATGCCACAGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTCTGGGCTTTGAAAAAG
1890121 ATGCCACTGACTTGTGGGCTTT
66 ATGCCACTGACTTGTGGGCTTT
1890143 TGAAGGGTGA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 27 0.34
87 29 0.37
88 23 0.29
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (87 bp):
GGAAAAGGATGCCACAGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTCTGGGCTTTGAAAAAG
ATGCCACTGACTTGTGGGCTTT
Found at i:1890120 original size:57 final size:56
Alignment explanation
Indices: 1890001--1890148 Score: 190
Period size: 57 Copynumber: 2.6 Consensus size: 56
1889991 TGGGCTTTTG
* * *
1890001 AAGGTTGCCACTGATTTGTGGGCTTTGAAAAAAGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGATTTGTGGGCTTTG----AAGGTGCCACTGACTTCTGGGCTTTGAAA
*
1890061 AAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTCTGGGCTTTGAAA
1 AAGGATGCCACTGATTTGTGGGCTTTGAAGG-TGCCACTGACTTCTGGGCTTTGAAA
*
1890118 AA-GATGCCACTGACTTGTGGGCTTTTGAAGG
1 AAGGATGCCACTGATTTGTGGGC-TTTGAAGG
1890149 GTGAGGAATG
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
56 22 0.27
57 33 0.41
60 26 0.32
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (56 bp):
AAGGATGCCACTGATTTGTGGGCTTTGAAGGTGCCACTGACTTCTGGGCTTTGAAA
Found at i:1891607 original size:19 final size:18
Alignment explanation
Indices: 1891575--1891654 Score: 66
Period size: 16 Copynumber: 4.7 Consensus size: 18
1891565 ATCCGGACCC
*
1891575 TTTTTGTTGTTTTGTTTT
1 TTTTTCTTGTTTTGTTTT
1891593 TTTTTCTTGTGTTTG--TT
1 TTTTTCTTGT-TTTGTTTT
*
1891610 TTTTTCTT-TTCT-TTTT
1 TTTTTCTTGTTTTGTTTT
*
1891626 TTTGT-TTG-TTTGTTTT
1 TTTTTCTTGTTTTGTTTT
1891642 TTTCTTCTT-TTTT
1 TTT-TTCTTGTTTT
1891655 TCTTCTTTCG
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 6 0.12
16 14 0.29
17 11 0.22
18 14 0.29
19 4 0.08
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTTCTTGTTTTGTTTT
Found at i:1891611 original size:17 final size:16
Alignment explanation
Indices: 1891591--1891647 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 16
1891581 TTGTTTTGTT
1891591 TTTTTTTCTTGTGTTTG
1 TTTTTTTCTT-TGTTTG
*
1891608 TTTTTTTCTTT-TCT-
1 TTTTTTTCTTTGTTTG
*
1891622 TTTTTTTGTTTGTTTG
1 TTTTTTTCTTTGTTTG
1891638 TTTTTTTCTT
1 TTTTTTTCTT
1891648 CTTTTTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.29
15 4 0.12
16 10 0.29
17 10 0.29
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTGTTTG
Found at i:1891619 original size:22 final size:21
Alignment explanation
Indices: 1891589--1891642 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
1891579 TGTTGTTTTG
1891589 TTTTTTTTTCTTGTGTTTGTT
1 TTTTTTTTTCTTGTGTTTGTT
* *
1891610 TTTTTCTTTTCTTTTTTTTGTT
1 TTTTT-TTTTCTTGTGTTTGTT
1891632 TGTTTGTTTTT
1 T-TTT-TTTTT
1891643 TTCTTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 15 0.54
23 7 0.25
24 1 0.04
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTCTTGTGTTTGTT
Found at i:1891627 original size:30 final size:28
Alignment explanation
Indices: 1891577--1891658 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 28
1891567 CCGGACCCTT
* *
1891577 TTTGTTGTTTTGTT-TTTTTTTCTTGTG
1 TTTGTTTTTTTCTTCTTTTTTTCTTGTG
*
1891604 TTTGTTTTTTTCTTTTCTTTTTTT-TGTTTG
1 TTTGTTTTTTTC--TTCTTTTTTTCT-TGTG
1891634 TTTGTTTTTTTCTTCTTTTTTTCTT
1 TTTGTTTTTTTCTTCTTTTTTTCTT
1891659 CTTTCGTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
27 10 0.21
28 11 0.23
29 4 0.09
30 22 0.47
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (28 bp):
TTTGTTTTTTTCTTCTTTTTTTCTTGTG
Found at i:1891654 original size:11 final size:11
Alignment explanation
Indices: 1891638--1891676 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1891628 TGTTTGTTTG
1891638 TTTTTTTCTTC
1 TTTTTTTCTTC
1891649 TTTTTTTCTTC
1 TTTTTTTCTTC
**
1891660 -TTTCGTCTTC
1 TTTTTTTCTTC
1891670 TTTTTTT
1 TTTTTTT
1891677 TTTGCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:1891671 original size:49 final size:49
Alignment explanation
Indices: 1891575--1891677 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
1891565 ATCCGGACCC
* *
1891575 TTTTTGTTGTTTTGTTTTTTTTTCTTGTGTTTGTTTTTTTCTTTTCTTT
1 TTTTTGTTGTTTTGTTTTTTTTTCTTGTGTTTGTTTCTTTCTCTTCTTT
1891624 TTTTTGTT-TGTTTGTTTTTTTCTTCTT-T-TTT-TCTTCTTTCGTCTTCTTT
1 TTTTTGTTGT-TTTGTTTTTTT-TTCTTGTGTTTGT-TTCTTTC-TCTTCTTT
1891673 TTTTT
1 TTTTT
1891678 TTGCGCAGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
47 1 0.02
48 10 0.21
49 32 0.67
50 5 0.10
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (49 bp):
TTTTTGTTGTTTTGTTTTTTTTTCTTGTGTTTGTTTCTTTCTCTTCTTT
Found at i:1896215 original size:33 final size:33
Alignment explanation
Indices: 1896178--1896247 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1896168 TTCAAGGATT
1896178 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1896211 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1896244 TGTA
1 TGTA
1896248 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1896216 original size:13 final size:13
Alignment explanation
Indices: 1896198--1896222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1896188 CATAAAATGT
1896198 TGTATCGATACAA
1 TGTATCGATACAA
1896211 TGTATCGATACA
1 TGTATCGATACA
1896223 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1896305 original size:13 final size:13
Alignment explanation
Indices: 1896287--1896311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1896277 ATTACTCACA
1896287 TGTATCGATACAT
1 TGTATCGATACAT
1896300 TGTATCGATACA
1 TGTATCGATACA
1896312 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1896448 original size:52 final size:52
Alignment explanation
Indices: 1896320--1896440 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1896310 CACTGATCTT
*
1896320 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
* *
1896372 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
1896424 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1896441 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCACAGATGTATCGATACACTATAAAA
Found at i:1912175 original size:52 final size:52
Alignment explanation
Indices: 1912037--1912183 Score: 215
Period size: 52 Copynumber: 2.8 Consensus size: 52
1912027 CGAAATATGA
* *
1912037 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGAGC
* * *
1912089 AAATTTACCTGTATGTATCGATACATTTGATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGAGC
**
1912141 AAATTTGCCTGCATGTATCGATACA-AAGATTAGTGTATCGATA
1 AAATTTGCCTGCATGTATCGATACATTTGA-TAGTGTATCGATA
1912184 TAATGTATCG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGAGC
Found at i:1912275 original size:19 final size:19
Alignment explanation
Indices: 1912251--1912315 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1912241 AGTGATACAT
1912251 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1912270 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1912283 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1912302 TGTATCGATACAAA
1 TGTATCGATACAAA
1912316 TTGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1912285 original size:32 final size:32
Alignment explanation
Indices: 1912244--1912313 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1912234 GCTTCGTAGT
1912244 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
1912276 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
1912308 GATACA
1 GATACA
1912314 AATTGTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:1912288 original size:13 final size:13
Alignment explanation
Indices: 1912270--1912294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1912260 ACAAAACTTA
1912270 TGTATCGATACAT
1 TGTATCGATACAT
1912283 TGTATCGATACA
1 TGTATCGATACA
1912295 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1919458 original size:19 final size:19
Alignment explanation
Indices: 1919434--1919499 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1919424 TAGCCAAACT
1919434 TGTATCGATACATAAAATA
1 TGTATCGATACATAAAATA
1919453 TGTATCGATAC-----A-A
1 TGTATCGATACATAAAATA
*
1919466 TGTATCGATACACAAAAAATA
1 TGTATCGAT--ACATAAAATA
1919487 TGTATCGATACAT
1 TGTATCGATACAT
1919500 TGGCTTGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
19 14 0.37
20 1 0.03
21 10 0.26
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATAAAATA
Found at i:1919470 original size:13 final size:13
Alignment explanation
Indices: 1919452--1919477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1919442 TACATAAAAT
1919452 ATGTATCGATACA
1 ATGTATCGATACA
1919465 ATGTATCGATACA
1 ATGTATCGATACA
1919478 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1919475 original size:32 final size:33
Alignment explanation
Indices: 1919434--1919498 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
1919424 TAGCCAAACT
*
1919434 TGTATCGAT-ACATAAAATATGTATCGATACAA
1 TGTATCGATAACAAAAAATATGTATCGATACAA
1919466 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATA-ACAAAAAATATGTATCGATACA
1919499 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 9 0.30
34 21 0.70
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATAACAAAAAATATGTATCGATACAA
Found at i:1925674 original size:13 final size:13
Alignment explanation
Indices: 1925656--1925693 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1925646 CATTTTTCTT
1925656 TGTATCGATACAA
1 TGTATCGATACAA
*
1925669 TGTATCGATACAC
1 TGTATCGATACAA
1925682 TGTATCGATACA
1 TGTATCGATACA
1925694 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1925848 original size:20 final size:20
Alignment explanation
Indices: 1925805--1925850 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1925795 AAATCTTTTG
1925805 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1925826 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1925846 CAAAA
1 CAAAA
1925851 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1928258 original size:13 final size:13
Alignment explanation
Indices: 1928240--1928265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1928230 TACATAAAAT
1928240 ATGTATCGATACA
1 ATGTATCGATACA
1928253 ATGTATCGATACA
1 ATGTATCGATACA
1928266 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1928263 original size:32 final size:33
Alignment explanation
Indices: 1928222--1928286 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
1928212 TAGCCAAACT
* *
1928222 TGTATCGAT-ACATAAAATATGTATCGATACAA
1 TGTATCGATAACAAAAAATATATATCGATACAA
1928254 TGTATCGATACACAAAAAATATATATCGATACA
1 TGTATCGATA-ACAAAAAATATATATCGATACA
1928287 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.31
34 20 0.69
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (33 bp):
TGTATCGATAACAAAAAATATATATCGATACAA
Found at i:1930322 original size:25 final size:25
Alignment explanation
Indices: 1930281--1930356 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
1930271 TATAGAGACA
1930281 GGATTGAAAAAGTTCAACTTTATCTG
1 GGATTG-AAAAGTTCAACTTTATCTG
*
1930307 GGATTGAAAAGTTCAACTTTATTTG
1 GGATTGAAAAGTTCAACTTTATCTG
*
1930332 GGATGGATAAAGTT-ATACTTTATCT
1 GGATTGA-AAAGTTCA-ACTTTATCT
1930357 AGAACTGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
25 25 0.56
26 20 0.44
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (25 bp):
GGATTGAAAAGTTCAACTTTATCTG
Found at i:1930413 original size:26 final size:26
Alignment explanation
Indices: 1930281--1930414 Score: 119
Period size: 26 Copynumber: 5.2 Consensus size: 26
1930271 TATAGAGACA
* *
1930281 GGATTGAAAAAGTTCAACTTTATCTG
1 GGATTGATAAAGTTTAACTTTATCTG
* *
1930307 GGATTGA-AAAGTTCAACTTTATTTG
1 GGATTGATAAAGTTTAACTTTATCTG
* *
1930332 GGATGGATAAAG-TTATACTTTATCTA
1 GGATTGATAAAGTTTA-ACTTTATCTG
* * * ** *
1930358 GAACTGATAAAGTTTAGCTTTGCCTA
1 GGATTGATAAAGTTTAACTTTATCTG
* *
1930384 GGATTGATAAAGTTTAATTTTATTTG
1 GGATTGATAAAGTTTAACTTTATCTG
1930410 GGATT
1 GGATT
1930415 CTAAATAAGG
Statistics
Matches: 86, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
25 25 0.29
26 58 0.67
27 3 0.03
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (26 bp):
GGATTGATAAAGTTTAACTTTATCTG
Found at i:1937070 original size:20 final size:20
Alignment explanation
Indices: 1937028--1937081 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1937018 TTCAACAAAT
*
1937028 TGTATCGATATAATAAGGTAA
1 TGTATCGATA-CATAAGGTAA
1937049 TGTATCGATACATAA-GTAAA
1 TGTATCGATACATAAGGT-AA
*
1937069 TGTATCAATACAT
1 TGTATCGATACAT
1937082 GTCTGAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 18 0.60
21 10 0.33
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGGTAA
Found at i:1937260 original size:105 final size:104
Alignment explanation
Indices: 1937143--1937353 Score: 386
Period size: 105 Copynumber: 2.0 Consensus size: 104
1937133 AATTTCATTG
1937143 TATCGATGCATTCTAGGTTTTGACCTAAATATATCGATACATTCTTCAATGTATCGATACATACA
1 TATCGATGCATTCTAGGTTTTGACCTAAATATATCGATACATTCTTCAATGTATCGATACATACA
*
1937208 GGCAAATTTGTACATTTTGTAACATTTTCTTCTTTTACCA
66 AG-AAATTTGTACATTTTGTAACATTTTCTTCTTTTACCA
* *
1937248 TATCGATGCATTCTAGGTTTTGACTTAAATATATTGATACATTCTTCAATGTATCGATACATACA
1 TATCGATGCATTCTAGGTTTTGACCTAAATATATCGATACATTCTTCAATGTATCGATACATACA
1937313 AGAAATTTGTACATTTTGTAACATTTTCTTCTTTTACCA
66 AGAAATTTGTACATTTTGTAACATTTTCTTCTTTTACCA
1937352 TA
1 TA
1937354 CCACATTCAA
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 39 0.38
105 64 0.62
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (104 bp):
TATCGATGCATTCTAGGTTTTGACCTAAATATATCGATACATTCTTCAATGTATCGATACATACA
AGAAATTTGTACATTTTGTAACATTTTCTTCTTTTACCA
Found at i:1946727 original size:30 final size:30
Alignment explanation
Indices: 1946662--1946777 Score: 119
Period size: 29 Copynumber: 3.9 Consensus size: 30
1946652 TCTTTTTCCA
* *
1946662 AAAGTCCAAAACTCAATGGCACC-ATTCTT
1 AAAGTCCACAACTCAATGGCACCTCTTCTT
* *
1946691 AAAGTCCATAACTCAATGGCACCTCTTCTC
1 AAAGTCCACAACTCAATGGCACCTCTTCTT
* ** *
1946721 AAAGTCCACGACTCCGTGGCA-CTCTTTTT
1 AAAGTCCACAACTCAATGGCACCTCTTCTT
* *
1946750 AAAGTCCACAACTCTATAGCACCCTCTT
1 AAAGTCCACAACTCAATGGCA-CCTCTT
1946778 TTCTTTTTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
29 45 0.63
30 21 0.30
31 5 0.07
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (30 bp):
AAAGTCCACAACTCAATGGCACCTCTTCTT
Found at i:1946728 original size:59 final size:60
Alignment explanation
Indices: 1946662--1946777 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 60
1946652 TCTTTTTCCA
* *
1946662 AAAGTCCAAAACTCAATGGCAC-CATTCTTAAAGTCCATAACTCAATGGCA-CCTCTTCTC
1 AAAGTCCAAAACTCAATGGCACTC-TTCTTAAAGTCCACAACTCAATAGCACCCTCTTCTC
** ** * *
1946721 AAAGTCCACGACTCCGTGGCACTCTTTTTAAAGTCCACAACTCTATAGCACCCTCTT
1 AAAGTCCAAAACTCAATGGCACTCTTCTTAAAGTCCACAACTCAATAGCACCCTCTT
1946778 TTCTTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 40 0.85
60 7 0.15
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (60 bp):
AAAGTCCAAAACTCAATGGCACTCTTCTTAAAGTCCACAACTCAATAGCACCCTCTTCTC
Found at i:1946824 original size:33 final size:34
Alignment explanation
Indices: 1946746--1946835 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
1946736 GTGGCACTCT
* * *
1946746 TTTTAAAGTCCACAACTCTATAGCACCCTCTTTTCT
1 TTTT-AAGTCCACAACTCTGT-GCACCCTCTTGTCC
1946782 TTTTAAGTCCACAACTCTGTGTCA-CCT-TTGTCC
1 TTTTAAGTCCACAACTCTGTG-CACCCTCTTGTCC
*
1946815 TTTTAAGTCCATAACTCTGTG
1 TTTTAAGTCCACAACTCTGTG
1946836 GTGCCTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.49
34 4 0.08
35 17 0.35
36 4 0.08
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (34 bp):
TTTTAAGTCCACAACTCTGTGCACCCTCTTGTCC
Found at i:1946951 original size:31 final size:31
Alignment explanation
Indices: 1946908--1947315 Score: 420
Period size: 31 Copynumber: 12.8 Consensus size: 31
1946898 AGTACCCTTC
* *
1946908 TCTAAAGTCCACACAAGTTGGTGGCAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1946939 TCTAAAGCCCACATAAGTCAGTGGCAACCAT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* * ** *
1946970 TTTAAAGCCTACACAAGTTAGTAGCAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1947001 TCTAAAGCCTAGACAAGTCGATGGCAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* ** *
1947032 TCTATAGCCCACACAAGTCAATGGCAACCATT
1 TCTAAAGCCCACACAAGTCGGTGGCAACC-CT
* * *
1947064 CTCTAAAGCCCACACAAATAGGTGGCAACCCC
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1947096 TCTAAAGCCTACACAAGTCGATGGCAACTCTT
1 TCTAAAGCCCACACAAGTCGGTGGCAAC-CCT
* *
1947128 CTCTAAAGCCCACACAAGTAGGTGACAACCCT
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCT
*
1947160 TCTAAAGCCCACACAAGCCGGTGGCAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* **
1947191 TCTTTAAAGCTCACACAAGTCGGTGGCAACTTT
1 TC--TAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1947224 CTCTAAAGCTCACACAAATCGATGGCAACCCT
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCT
* *
1947256 TCTAAAGCCCACACAAGTCGGTTGTAACCCT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCT
1947287 TCTCAAAAGCCCACACAAAGTCGGTGGCA
1 TCT--AAAGCCCACAC-AAGTCGGTGGCA
1947316 TCTCTTTCTA
Statistics
Matches: 309, Mismatches: 58, Indels: 17
0.80 0.15 0.04
Matches are distributed among these distances:
31 184 0.60
32 29 0.09
33 84 0.27
34 12 0.04
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.20
Consensus pattern (31 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCT
Found at i:1947091 original size:64 final size:63
Alignment explanation
Indices: 1946908--1947315 Score: 385
Period size: 64 Copynumber: 6.4 Consensus size: 63
1946898 AGTACCCTTC
* * * * * *
1946908 TCTAAAGTCCACACAAGTTGGTGGCAACCCT-TCTAAAGCCCACATAAGTCA-GTGGCAACCAT
1 TCTAAAGCCCACACAAGTCGATGGCAACCTTCTCTAAAGCCCACACAAGT-AGGTGGCAACCCT
* * * * * * * * *
1946970 TTTAAAGCCTACACAAGT-TAGTAGCAACCCT-TCTAAAGCCTAGACAAGTCGATGGCAACCCT
1 TCTAAAGCCCACACAAGTCGA-TGGCAACCTTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
* * * *
1947032 TCTATAGCCCACACAAGTCAATGGCAACCATTCTCTAAAGCCCACACAAATAGGTGGCAACCCC
1 TCTAAAGCCCACACAAGTCGATGGCAACC-TTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
* *
1947096 TCTAAAGCCTACACAAGTCGATGGCAACTCTTCTCTAAAGCCCACACAAGTAGGTGACAACCCT
1 TCTAAAGCCCACACAAGTCGATGGCAAC-CTTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
* * * * * **
1947160 TCTAAAGCCCACACAAGCCGGTGGCAACCCTTCTTTAAAGCTCACACAAGTCGGTGGCAACTTT
1 TCTAAAGCCCACACAAGTCGATGGCAA-CCTTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
* * * * * *
1947224 CTCTAAAGCTCACACAAATCGATGGCAACCCT-TCTAAAGCCCACACAAGTCGGTTGTAACCCT
1 -TCTAAAGCCCACACAAGTCGATGGCAACCTTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
*
1947287 TCTCAAAAGCCCACACAAAGTCGGTGGCA
1 TCT--AAAGCCCACAC-AAGTCGATGGCA
1947316 TCTCTTTCTA
Statistics
Matches: 282, Mismatches: 53, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
62 73 0.26
63 27 0.10
64 147 0.52
65 35 0.12
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.20
Consensus pattern (63 bp):
TCTAAAGCCCACACAAGTCGATGGCAACCTTCTCTAAAGCCCACACAAGTAGGTGGCAACCCT
Found at i:1947115 original size:95 final size:94
Alignment explanation
Indices: 1946907--1947271 Score: 373
Period size: 95 Copynumber: 3.9 Consensus size: 94
1946897 TAGTACCCTT
* * * * *
1946907 CTCTAAAGTCC-ACACAAGTTGGTGGCAACCCT-TCTAAAGCCCACATAAGTCAGTGGCAACCAT
1 CTCTAAAG-CCTACACAAGTCGATGGCAACCCTCTCTAAAGCCCACACAAGTCAATGGCAACCCT
* * * *
1946970 TTTAAAGCCTACACAAGTTA-GTAGCAACCC
65 TCTAAAGCCCACACAA-ATAGGTGGCAACCC
* * * *
1947000 TTCTAAAGCCTAGACAAGTCGATGGCAACCCT-TCTATAGCCCACACAAGTCAATGGCAACCATT
1 CTCTAAAGCCTACACAAGTCGATGGCAACCCTCTCTAAAGCCCACACAAGTCAATGGCAACC-CT
1947064 CTCTAAAGCCCACACAAATAGGTGGCAACCC
65 -TCTAAAGCCCACACAAATAGGTGGCAACCC
* * *
1947095 CTCTAAAGCCTACACAAGTCGATGGCAACTCTTCTCTAAAGCCCACACAAGT-AGGTGACAACCC
1 CTCTAAAGCCTACACAAGTCGATGGCAAC-CCTCTCTAAAGCCCACACAAGTCA-ATGGCAACCC
***
1947159 TTCTAAAGCCCACACAAGCCGGTGGCAACCC
64 TTCTAAAGCCCACACAAATAGGTGGCAACCC
* * ** * * *
1947190 TTCTTTAAAG-CTCACACAAGTCGGTGGCAACTTTCTCTAAAGCTCACACAAATCGATGGCAACC
1 --CTCTAAAGCCT-ACACAAGTCGATGGCAACCCTCTCTAAAGCCCACACAAGTCAATGGCAACC
1947254 CTTCTAAAGCCCACACAA
63 CTTCTAAAGCCCACACAA
1947272 GTCGGTTGTA
Statistics
Matches: 231, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
92 2 0.01
93 51 0.22
94 3 0.01
95 77 0.33
96 50 0.22
97 48 0.21
ACGTcount: A:0.33, C:0.32, G:0.16, T:0.20
Consensus pattern (94 bp):
CTCTAAAGCCTACACAAGTCGATGGCAACCCTCTCTAAAGCCCACACAAGTCAATGGCAACCCTT
CTAAAGCCCACACAAATAGGTGGCAACCC
Found at i:1947453 original size:52 final size:52
Alignment explanation
Indices: 1947383--1947521 Score: 197
Period size: 52 Copynumber: 2.7 Consensus size: 52
1947373 CATCTCTTTC
* * * *
1947383 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATTTTTTTCTTTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTTATCATCTT
* * * *
1947435 TAAGTCAAATATCACTGGCCTTGAATTAGCATATTGGCATCTTTATCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTTATCATCTT
*
1947487 TAAGTCCAATATCGCTGGCCTTAAATCAACATATT
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATT
1947522 AGCGTTGTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (52 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTTATCATCTT
Found at i:1947789 original size:113 final size:113
Alignment explanation
Indices: 1947530--1947789 Score: 304
Period size: 113 Copynumber: 2.3 Consensus size: 113
1947520 TTAGCGTTGT
* * * * * * * * *
1947530 TGGCCTTGGATCAACATATTGACGCCTTTGTCATCTTTAAGTCCAATATTGCTGGCCTTGAATTA
1 TGGCCTTGAATCAACATATTGGCACCTTTATTATCTTTAAGCCCAATATCGCTAGCCTTGAATCA
* * * * *
1947595 GCATATCGGTACTTTTATCATTCTTCTCATCTTCAAGTCCAATGTCGC
66 GCATATCGGCACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCAC
* * **
1947643 TGGCCTTGAATCAACACATTAGCACCTACATTATCTTTAAGCCCAATATCGCTAGCCTTGAATCA
1 TGGCCTTGAATCAACATATTGGCACCTTTATTATCTTTAAGCCCAATATCGCTAGCCTTGAATCA
* * * *
1947708 GTATATTGGCACCTTTATCATTTTTCTCATCTTGAAGCCCAATATCAC
66 GCATATCGGCACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCAC
* *
1947756 TGGCCGTGAATCAGCATATTGGCACCTTTATTAT
1 TGGCCTTGAATCAACATATTGGCACCTTTATTAT
1947790 TTTTCACATC
Statistics
Matches: 119, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
113 119 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (113 bp):
TGGCCTTGAATCAACATATTGGCACCTTTATTATCTTTAAGCCCAATATCGCTAGCCTTGAATCA
GCATATCGGCACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCAC
Found at i:1947827 original size:61 final size:61
Alignment explanation
Indices: 1947675--1947850 Score: 219
Period size: 61 Copynumber: 2.9 Consensus size: 61
1947665 CACCTACATT
* *
1947675 ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGTATATTGGCACCTTTATCATTTTTCTC
1 ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTCAC
* * * * *
1947736 ATCTTGAAGCCCAATATCACTGGCCGTGAATCAGCATATTGGCACCTTTATTATTTTTCAC
1 ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTCAC
* * * * * *
1947797 ATCTTTAAGTCCAATGTCGGTAACCTTGAATCAACACATTGGCACTCTTT-TCAT
1 ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCAC-CTTTATCAT
1947851 CCTTATCATC
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
61 92 0.96
62 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (61 bp):
ATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCATTTTTCAC
Found at i:1958814 original size:2 final size:2
Alignment explanation
Indices: 1958809--1958836 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1958799 TATATATATA
1958809 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1958837 CATATTTTAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1964969 original size:16 final size:15
Alignment explanation
Indices: 1964948--1964982 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1964938 AAATATTTTA
1964948 TATTAATATTTATATC
1 TATTAATA-TTATATC
*
1964964 TATTAATATTATATT
1 TATTAATATTATATC
1964979 TATT
1 TATT
1964983 TATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATATTATATC
Found at i:1964990 original size:16 final size:15
Alignment explanation
Indices: 1964948--1964996 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1964938 AAATATTTTA
*
1964948 TATTAATATTTATATC
1 TATTAATA-TTATATT
1964964 TATTAATATTATATT
1 TATTAATATTATATT
* *
1964979 TATTTATAATTAAATT
1 TATTAAT-ATTATATT
1964995 TA
1 TA
1964997 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAATATTATATT
Found at i:1968926 original size:20 final size:20
Alignment explanation
Indices: 1968901--1968954 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1968891 ATTTGAGTCA
1968901 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATGTGC--C
1968921 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1968941 ATGTATCGATACAA
1 ATGTATCGATACAA
1968955 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:1969657 original size:24 final size:24
Alignment explanation
Indices: 1969625--1969677 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1969615 AAAAAGTTCT
*
1969625 TTTTATTTCTCCTCCTTTGTCAAG
1 TTTTCTTTCTCCTCCTTTGTCAAG
1969649 TTTTCTTTCTCCTCCTTTGTCAAG
1 TTTTCTTTCTCCTCCTTTGTCAAG
1969673 TTTTC
1 TTTTC
1969678 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.09, C:0.26, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTCTTTCTCCTCCTTTGTCAAG
Found at i:1978853 original size:13 final size:13
Alignment explanation
Indices: 1978835--1978862 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1978825 CTAATGCTTA
1978835 ATTATGATTTATT
1 ATTATGATTTATT
1978848 ATTATGATTTATT
1 ATTATGATTTATT
1978861 AT
1 AT
1978863 GTTATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
ATTATGATTTATT
Found at i:1987055 original size:20 final size:20
Alignment explanation
Indices: 1987030--1987068 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1987020 AAAATATTTT
1987030 TTATTTATTCTTAAAAATTG
1 TTATTTATTCTTAAAAATTG
*
1987050 TTATTTATTTTTAAAAATT
1 TTATTTATTCTTAAAAATT
1987069 ATCATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTATTTATTCTTAAAAATTG
Found at i:1987245 original size:24 final size:23
Alignment explanation
Indices: 1987187--1987245 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
1987177 ATAATATTAT
* *
1987187 ATATTTTTATAATTTTAAATATA
1 ATATTCTTAAAATTTTAAATATA
* * **
1987210 TTATGCAAAAAATTATTAAATATA
1 ATATTCTTAAAATT-TTAAATATA
1987234 ATATTCTTAAAA
1 ATATTCTTAAAA
1987246 ATATATTTAA
Statistics
Matches: 25, Mismatches: 10, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTCTTAAAATTTTAAATATA
Found at i:1987246 original size:27 final size:25
Alignment explanation
Indices: 1987216--1987303 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 25
1987206 TATATTATGC
1987216 AAAAAATTATTAAATATAATATTCTTA
1 AAAAAATTATTAAATA-AATATT-TTA
* * *
1987243 AAAATA-TATTTAAATACATAATATTA
1 AAAAAATTA-TTAAATAAAT-ATTTTA
1987269 AAAAAATTAATT-AATAAATATTTATA
1 AAAAAATT-ATTAAATAAATATTT-TA
1987295 AAAATAATT
1 AAAA-AATT
1987304 TAAAATTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 3 0.06
26 24 0.49
27 21 0.43
28 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAAAATTATTAAATAAATATTTTA
Found at i:1987255 original size:51 final size:49
Alignment explanation
Indices: 1987195--1987315 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 49
1987185 ATATATTTTT
*
1987195 ATAATTTTAAATATATTATGCAAAAAATT-ATTAAATATAATATTCT-TAAAA
1 ATAA-TTTAAATATATTATGAAAAAAATTAATT-AATA-AATATT-TATAAAA
* *
1987246 ATATATTTAAATACATAATATTAAAAAAATTAATTAATAAATATTTATAAAA
1 ATA-ATTTAAAT--ATATTATGAAAAAAATTAATTAATAAATATTTATAAAA
1987298 ATAATTTAAA-ATTATTAT
1 ATAATTTAAATA-TATTAT
1987316 ATTTTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
48 1 0.02
49 5 0.08
51 18 0.30
52 15 0.25
53 18 0.30
54 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (49 bp):
ATAATTTAAATATATTATGAAAAAAATTAATTAATAAATATTTATAAAA
Found at i:1987284 original size:26 final size:27
Alignment explanation
Indices: 1987216--1987284 Score: 63
Period size: 29 Copynumber: 2.6 Consensus size: 27
1987206 TATATTATGC
* *
1987216 AAAAAATT-ATTAA-ATATAATATTCT
1 AAAAAATTAATTAATACATAATATTCA
* *
1987241 TAAAAATATATTTAAATACATAATATT-A
1 AAAAAAT-TAATT-AATACATAATATTCA
1987269 AAAAAATTAATTAATA
1 AAAAAATTAATTAATA
1987285 AATATTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 6 0.18
28 8 0.24
29 9 0.26
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAAATTAATTAATACATAATATTCA
Found at i:1987947 original size:16 final size:16
Alignment explanation
Indices: 1987922--1987956 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1987912 TTCGAAACTA
1987922 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
*
1987938 AAAATGATTTAAATTT
1 AAAATAATTTAAATTT
1987954 AAA
1 AAA
1987957 TTTTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:1988413 original size:18 final size:19
Alignment explanation
Indices: 1988373--1988414 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1988363 CAAAATTTAA
* *
1988373 AATAATTTTTTAAATATAT
1 AATAATCTTTTAAATACAT
1988392 AATAATCTTTTAAA-ACAT
1 AATAATCTTTTAAATACAT
1988410 AATAA
1 AATAA
1988415 AATGTTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATCTTTTAAATACAT
Found at i:1991490 original size:41 final size:40
Alignment explanation
Indices: 1991441--1991523 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
1991431 TTAAGTTCAA
* ** * *
1991441 ATTTAATTTAAATTATTATTTAATTAT-TAAAAATATTTTT
1 ATTTAATTT-AATTATAACATAATAATATAAAAATAATTTT
1991481 ATTTAAATTTAATTATAACATAATAATATAAAAATAATTTT
1 ATTT-AATTTAATTATAACATAATAATATAAAAATAATTTT
1991522 AT
1 AT
1991524 AATATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 17 0.47
41 19 0.53
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTTAATTTAATTATAACATAATAATATAAAAATAATTTT
Found at i:1992355 original size:31 final size:31
Alignment explanation
Indices: 1992320--1992399 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
1992310 CAAAAATATA
*
1992320 ATATAATATAAATA-TAGATATTTTAAAATTT
1 ATATAATATAAATATTA-ATATATTAAAATTT
* *
1992351 ATATAATATAATTATTAATGTATTAAAATTT
1 ATATAATATAAATATTAATATATTAAAATTT
1992382 ATATAAATATAAAGTATT
1 ATAT-AATATAAA-TATT
1992400 TTAAATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 29 0.69
32 9 0.21
33 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (31 bp):
ATATAATATAAATATTAATATATTAAAATTT
Found at i:1992422 original size:16 final size:16
Alignment explanation
Indices: 1992316--1992432 Score: 55
Period size: 17 Copynumber: 7.3 Consensus size: 16
1992306 ATAACAAAAA
*
1992316 TATAATATAATATAAA
1 TATAATATAATATAAT
** *
1992332 TATAGATATTTTAAAAT
1 TATA-ATATAATATAAT
1992349 T-T-ATATAATATAAT
1 TATAATATAATATAAT
* * *
1992363 TATTAATGTATTAAAAT
1 TA-TAATATAATATAAT
*
1992380 T-T-ATATAAATATAAAG
1 TATAATAT-AATAT-AAT
**
1992396 TATTTTA-AATATAAT
1 TATAATATAATATAAT
*
1992411 TATAATATAATAAAAT
1 TATAATATAATATAAT
1992427 ATATAA
1 -TATAA
1992433 ATTATTAAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 19
0.65 0.17 0.17
Matches are distributed among these distances:
14 13 0.18
15 11 0.15
16 21 0.29
17 25 0.35
18 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TATAATATAATATAAT
Found at i:1993049 original size:13 final size:14
Alignment explanation
Indices: 1993031--1993061 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1993021 ATTAATTAGG
1993031 TTTAAT-AACATAT
1 TTTAATGAACATAT
1993044 TTTAATGAACATAT
1 TTTAATGAACATAT
1993058 TTTA
1 TTTA
1993062 TATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTAATGAACATAT
Found at i:1993447 original size:15 final size:15
Alignment explanation
Indices: 1993427--1993460 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1993417 ATCTTGCAAA
1993427 TATCTCTTACTGGAT
1 TATCTCTTACTGGAT
1993442 TATCTCTTACTGGAT
1 TATCTCTTACTGGAT
1993457 TATC
1 TATC
1993461 ATAAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (15 bp):
TATCTCTTACTGGAT
Found at i:1999796 original size:22 final size:21
Alignment explanation
Indices: 1999755--1999796 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1999745 TTAAGTATAA
*
1999755 ATATTTTTCAAGCTATAAATC
1 ATATTTTTCAAGCTAAAAATC
1999776 ATATATTTTCAAAG-TAAAAAT
1 ATAT-TTTTC-AAGCTAAAAAT
1999797 AATCCAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATC
Found at i:2001614 original size:13 final size:13
Alignment explanation
Indices: 2001596--2001620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2001586 CATTATGCTT
2001596 TGTATCGATACAA
1 TGTATCGATACAA
2001609 TGTATCGATACA
1 TGTATCGATACA
2001621 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2001617 original size:33 final size:32
Alignment explanation
Indices: 2001575--2001639 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2001565 ACACACCCAG
*
2001575 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
2001608 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
2001640 TGAAAAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:2001651 original size:20 final size:20
Alignment explanation
Indices: 2001626--2001664 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2001616 ATACATGTTC
2001626 ATTGTATCGATACATGAAAA
1 ATTGTATCGATACATGAAAA
2001646 ATTGTATCGATACATGAAA
1 ATTGTATCGATACATGAAA
2001665 CTGGTAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
ATTGTATCGATACATGAAAA
Found at i:2001715 original size:20 final size:19
Alignment explanation
Indices: 2001690--2001763 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
2001680 CTACCATTGT
2001690 TTGTATCGATACATGGCTTA
1 TTGTATCGATACAT-GCTTA
2001710 TTGTATCGATACAT-C--A
1 TTGTATCGATACATGCTTA
* *
2001726 -TGTATCGATACATGATGAA
1 TTGTATCGATACATGCT-TA
2001745 TTGTATCGATACATTGCTT
1 TTGTATCGATACA-TGCTT
2001764 TAAACAGCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.29
16 1 0.02
18 1 0.02
19 1 0.02
20 26 0.58
21 3 0.07
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGCTTA
Found at i:2001737 original size:35 final size:35
Alignment explanation
Indices: 2001691--2001758 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
2001681 TACCATTGTT
* *
2001691 TGTATCGATACATGGCT-TATTGTATCGATACATCA
1 TGTATCGATACAT-GATGAATTGTATCGATACATCA
2001726 TGTATCGATACATGATGAATTGTATCGATACAT
1 TGTATCGATACATGATGAATTGTATCGATACAT
2001759 TGCTTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (35 bp):
TGTATCGATACATGATGAATTGTATCGATACATCA
Found at i:2007849 original size:13 final size:13
Alignment explanation
Indices: 2007831--2007856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2007821 ACAATATTCT
2007831 TTGTATCGATACA
1 TTGTATCGATACA
2007844 TTGTATCGATACA
1 TTGTATCGATACA
2007857 AGGGTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2009811 original size:28 final size:30
Alignment explanation
Indices: 2009726--2009798 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
2009716 AATAAATTTT
2009726 TTATCAAGGGAGAGAAAATCTTTTTAACCAA
1 TTATCAAGGG-GAGAAAATCTTTTTAACCAA
2009757 TTATCAAGGGGAGAAAATCTTTTTAACCAA
1 TTATCAAGGGGAGAAAATCTTTTTAACCAA
2009787 TTATCAAGGGGA
1 TTATCAAGGGGA
2009799 AATTTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 32 0.76
31 10 0.24
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (30 bp):
TTATCAAGGGGAGAAAATCTTTTTAACCAA
Found at i:2010378 original size:13 final size:13
Alignment explanation
Indices: 2010360--2010384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2010350 CATTATGCTT
2010360 TGTATCGATACAA
1 TGTATCGATACAA
2010373 TGTATCGATACA
1 TGTATCGATACA
2010385 TGAAACTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2010450 original size:13 final size:13
Alignment explanation
Indices: 2010432--2010483 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
2010422 GATACATGGC
2010432 ACATTGTATCGAT
1 ACATTGTATCGAT
*
2010445 ACATTGTATCCAT
1 ACATTGTATCGAT
2010458 ACA-TG-AT-G--
1 ACATTGTATCGAT
2010466 A-ATTGTATCGAT
1 ACATTGTATCGAT
2010478 ACATTG
1 ACATTG
2010484 CTTCAAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
7 1 0.03
8 3 0.10
9 2 0.06
10 1 0.03
11 2 0.06
12 3 0.10
13 19 0.61
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2022663 original size:36 final size:35
Alignment explanation
Indices: 2022623--2022709 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 35
2022613 AAATTGCATA
*
2022623 TTTTAATTATTTAAATTTAATTCTTTTAAAAATGAT
1 TTTTAATTATTTAAATTTAAAT-TTTTAAAAATGAT
** * * *
2022659 TTTTAACAAATTAAATTTTAAATTTTTATAAATTAT
1 TTTTAATTATTTAAA-TTTAAATTTTTAAAAATGAT
2022695 TTTT-ATT-TTTAAATT
1 TTTTAATTATTTAAATT
2022710 ACGATATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 1 0.02
36 27 0.66
37 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTTAATTATTTAAATTTAAATTTTTAAAAATGAT
Found at i:2023783 original size:39 final size:39
Alignment explanation
Indices: 2023676--2023786 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
2023666 TAGGGTTAAC
* ** *
2023676 TAGAATCTAAAAGATATGATTAATGTATGGATTTTTTAT
1 TAGAATCTAAAAGATATGACTAATGTATAAATTATTTAT
* * * * * *
2023715 TGGATTTTGAAAGATATTAGTAATGTATAAATTATTTAT
1 TAGAATCTAAAAGATATGACTAATGTATAAATTATTTAT
* *
2023754 TAGAATCTAAAATATATGACTAATATATAAATT
1 TAGAATCTAAAAGATATGACTAATGTATAAATT
2023787 TTTTGTTAAA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (39 bp):
TAGAATCTAAAAGATATGACTAATGTATAAATTATTTAT
Found at i:2024061 original size:165 final size:165
Alignment explanation
Indices: 2023837--2024246 Score: 513
Period size: 165 Copynumber: 2.5 Consensus size: 165
2023827 TGTTTTTGGA
* * * * *
2023837 AAATATGATAAATACATAAATTTTTAATCGAAAATCAGATTCTTTCTGATATGAAAGAAGTTGAT
1 AAATATGATAAATGCATAAATTCTTAATAG-GAATCAGATT-TTTCTGATATAAAAGAAGTTGAT
* * * * * *
2023902 AAGATTAATGCATGGATTGTAAATATTAGACTGTAAGGAATAGACTAATGA-ATGGATT-AAATT
64 AAGACTAATGCATGGATTATAAATATCAAACTGCAAAGAATAGACTAAT-ACATGGATTGAAA-T
* *
2023965 TCGAAAGATGGGACTAATGCATGGATTCTATTTTTAAAT
127 TAGAAAGATGGGACTAATGCATGGATTCTATTTTGAAAT
* *
2024004 AAATATGAGAAATGCATAAATTCTTAATAGGAATAAGATTTTTCTGATATAAAAGAAGTTGATAA
1 AAATATGATAAATGCATAAATTCTTAATAGGAATCAGATTTTTCTGATATAAAAGAAGTTGATAA
* * * *
2024069 GACTAATGTATGGATTATAAATATCAAATTGCAAAGAATAGACTTATACATGGATTGGAATTAGA
66 GACTAATGCATGGATTATAAATATCAAACTGCAAAGAATAGACTAATACATGGATTGAAATTAGA
2024134 AAGATGGGACTAATGCATGGATTCTATTTTGAAAT
131 AAGATGGGACTAATGCATGGATTCTATTTTGAAAT
* * * * *
2024169 AAATGTGATTAATGCATAAATTGC--AGATGGGAATCCGATTTCTTCTGATATAAAAAAAGTTGA
1 AAATATGATAAATGCATAAATT-CTTA-ATAGGAATCAGATTT-TTCTGATATAAAAGAAGTTGA
2024232 TAAGACTAATGCATG
63 TAAGACTAATGCATG
2024247 ATGCATAGAT
Statistics
Matches: 211, Mismatches: 27, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
164 2 0.01
165 138 0.65
166 45 0.21
167 26 0.12
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.33
Consensus pattern (165 bp):
AAATATGATAAATGCATAAATTCTTAATAGGAATCAGATTTTTCTGATATAAAAGAAGTTGATAA
GACTAATGCATGGATTATAAATATCAAACTGCAAAGAATAGACTAATACATGGATTGAAATTAGA
AAGATGGGACTAATGCATGGATTCTATTTTGAAAT
Found at i:2024494 original size:22 final size:22
Alignment explanation
Indices: 2024426--2024494 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
2024416 GACTGTAAAG
2024426 ATTAGACTAATGCATGAATTGT
1 ATTAGACTAATGCATGAATTGT
* *
2024448 ATAAGACTAAAGCATGAATTGT
1 ATTAGACTAATGCATGAATTGT
* *
2024470 ATTAGACTAATGCATGGATTAT
1 ATTAGACTAATGCATGAATTGT
2024492 ATT
1 ATT
2024495 TGAGAATCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
ATTAGACTAATGCATGAATTGT
Found at i:2027951 original size:28 final size:28
Alignment explanation
Indices: 2027919--2027982 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
2027909 TCATCTCTAA
*
2027919 GGATACTCTAAGCCCACCATCACTGT-GG
1 GGATACTCTAACCCCACCATCACT-TAGG
*
2027947 GGATACTCTAACCCCACCATCTCTTAGG
1 GGATACTCTAACCCCACCATCACTTAGG
2027975 GGATACTC
1 GGATACTC
2027983 CAACTCCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (28 bp):
GGATACTCTAACCCCACCATCACTTAGG
Found at i:2028158 original size:79 final size:80
Alignment explanation
Indices: 2027948--2028304 Score: 396
Period size: 80 Copynumber: 4.5 Consensus size: 80
2027938 TCACTGTGGG
** * * *
2027948 GATACTCTAACCCCACCATCTCTTAGGGGATACTCCAACTCCATTTTTACTTCCAAAACACTGAA
1 GATACTCTAACCCCACCATCTCCGAGGGGATACTCCAACACTATTTTTACTTCCAAAACACCGAA
* *
2028013 TTTTTCATCTTTGGG
66 TTTTTCATCTCTGGA
* * * ** *
2028028 GATACTCTAACCTCACCATCTCCAAGGGGATACTCCAACCAC-ATTTCTACTTCCAAAATGCCAA
1 GATACTCTAACCCCACCATCTCCGAGGGGATACTCCAA-CACTATTTTTACTTCCAAAACACCGA
2028092 ATTTTTCATCTCT-GA
65 ATTTTTCATCTCTGGA
** **
2028107 GATACTCTAACCCCACCATCTCCGAGGGGGCACTCCAACACTATTTTTACTTCCAAAACGTCGAA
1 GATACTCTAACCCCACCATCTCCGAGGGGATACTCCAACACTATTTTTACTTCCAAAACACCGAA
2028172 TTTTTCATCTCTGGA
66 TTTTTCATCTCTGGA
* * * * * * * *
2028187 GATA-TTTCAACCCCACTATCTTCGAAGGGATACTCTAACTCTATTTTTTACTTCCACAATACCG
1 GATACTCT-AACCCCACCATCTCCGAGGGGATACTCCAACACTA-TTTTTACTTCCAAAACACCG
* * *
2028251 AATTCTTCATCTTTGGG
64 AATTTTTCATCTCTGGA
* *
2028268 GATACTCTAACCCCACCATCTTCGAGGGAATACTCCA
1 GATACTCTAACCCCACCATCTCCGAGGGGATACTCCA
2028305 TCCCCGGTTT
Statistics
Matches: 232, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
78 3 0.01
79 68 0.29
80 98 0.42
81 61 0.26
82 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.31
Consensus pattern (80 bp):
GATACTCTAACCCCACCATCTCCGAGGGGATACTCCAACACTATTTTTACTTCCAAAACACCGAA
TTTTTCATCTCTGGA
Found at i:2032490 original size:14 final size:14
Alignment explanation
Indices: 2032453--2032499 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
2032443 CTCTCCTTCA
*
2032453 TTCTTATTTTTCCT
1 TTCTTTTTTTTCCT
*
2032467 TTTTTCTTTTTTCCT
1 TTCTT-TTTTTTCCT
*
2032482 TTCTTTTTTTCCCT
1 TTCTTTTTTTTCCT
2032496 TTCT
1 TTCT
2032500 CCTTCCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTTTTTTCCT
Found at i:2032616 original size:21 final size:21
Alignment explanation
Indices: 2032562--2032616 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
2032552 TTAAACCAAA
** *
2032562 AAATAAATCTTAAATTTCTGC
1 AAATAAAAATTAAATTTCTCC
2032583 AAATAAAAA-TAAATTTCTCC
1 AAATAAAAATTAAATTTCTCC
2032603 ATAA-AAAAATTAAA
1 A-AATAAAAATTAAA
2032617 CACATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATAAAAATTAAATTTCTCC
Found at i:2033794 original size:26 final size:21
Alignment explanation
Indices: 2033765--2033814 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 21
2033755 TATTTAAAGC
2033765 TAAATACATATATACTTATTTAATAT
1 TAAA-ACA-ATATA-TT-TTTAAT-T
2033791 TAAAACAATATATTTTTAATT
1 TAAAACAATATATTTTTAATT
2033812 TAA
1 TAA
2033815 TCAAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.17
22 6 0.25
23 2 0.08
24 5 0.21
25 3 0.12
26 4 0.17
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAACAATATATTTTTAATT
Found at i:2037773 original size:23 final size:22
Alignment explanation
Indices: 2037717--2037774 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
2037707 ATCCAAAAGC
2037717 ATTATATTTTT-T-TCTTTAAA
1 ATTATATTTTTATCTCTTTAAA
** *
2037737 AAAATATCTATTATCTCTTTAAA
1 ATTATAT-TTTTATCTCTTTAAA
2037760 ATTATATTTCTTATC
1 ATTATATTT-TTATC
2037775 ATAGTTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.18
21 3 0.11
22 2 0.07
23 18 0.64
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATATTTTTATCTCTTTAAA
Found at i:2040584 original size:18 final size:17
Alignment explanation
Indices: 2040561--2040625 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
2040551 ATTTTAAATA
2040561 TAAATATAATATATGTAT
1 TAAATATAATATAT-TAT
*
2040579 TAAATATATTATATTAT
1 TAAATATAATATATTAT
**
2040596 T-TTTATTAATCATA-T-T
1 TAAATA-TAAT-ATATTAT
2040612 TAAATATAATATAT
1 TAAATATAATATAT
2040626 CATATTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 3 0.08
16 8 0.22
17 10 0.27
18 16 0.43
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAATATAATATATTAT
Found at i:2041785 original size:16 final size:16
Alignment explanation
Indices: 2041764--2041799 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2041754 CATTTTTAGG
2041764 TTTGGGTAATTTCGAA
1 TTTGGGTAATTTCGAA
**
2041780 TTTGGGTTGTTTCGAA
1 TTTGGGTAATTTCGAA
2041796 TTTG
1 TTTG
2041800 AGTCAATGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTGGGTAATTTCGAA
Found at i:2042671 original size:16 final size:16
Alignment explanation
Indices: 2042650--2042726 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
2042640 ATTATTCAGG
2042650 TCATTTCGGGTTCGGA
1 TCATTTCGGGTTCGGA
* *
2042666 TCATTTTGGGTTCTGA
1 TCATTTCGGGTTCGGA
*
2042682 TCATTTCGGGTTC-AA
1 TCATTTCGGGTTCGGA
**
2042697 GTCATTTTAGGTTCGGA
1 -TCATTTCGGGTTCGGA
*
2042714 TCATTTCGTGTTC
1 TCATTTCGGGTTC
2042727 AGGTTATTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
15 1 0.02
16 47 0.96
17 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.25, T:0.44
Consensus pattern (16 bp):
TCATTTCGGGTTCGGA
Found at i:2042686 original size:32 final size:32
Alignment explanation
Indices: 2042650--2042742 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
2042640 ATTATTCAGG
* * *
2042650 TCATTTCGGGTTC-GGATCATTTTGGGTTCTGA
1 TCATTTCGGGTTCAAG-TCATTTTAGGTTCGGA
2042682 TCATTTCGGGTTCAAGTCATTTTAGGTTCGGA
1 TCATTTCGGGTTCAAGTCATTTTAGGTTCGGA
* * *
2042714 TCATTTCGTGTTCAGGTTATTTTCAGGTT
1 TCATTTCGGGTTCAAGTCATTTT-AGGTT
2042743 TGTATTTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 47 0.89
33 6 0.11
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (32 bp):
TCATTTCGGGTTCAAGTCATTTTAGGTTCGGA
Found at i:2043525 original size:9 final size:9
Alignment explanation
Indices: 2043511--2043550 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
2043501 ATAAATTAAT
2043511 AAAAAAATC
1 AAAAAAATC
2043520 AAAAAAATC
1 AAAAAAATC
2043529 AAAAAAATC
1 AAAAAAATC
2043538 --AAAAATC
1 AAAAAAATC
2043545 AAAAAA
1 AAAAAA
2043551 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.24
9 22 0.76
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:2043541 original size:16 final size:17
Alignment explanation
Indices: 2043511--2043550 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
2043501 ATAAATTAAT
2043511 AAAAAAATCAAAAAAATC
1 AAAAAAATC-AAAAAATC
2043529 AAAAAAATC-AAAAATC
1 AAAAAAATCAAAAAATC
2043545 AAAAAA
1 AAAAAA
2043551 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (17 bp):
AAAAAAATCAAAAAATC
Found at i:2043581 original size:55 final size:54
Alignment explanation
Indices: 2043475--2043602 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 54
2043465 TAATAATAAT
*
2043475 ATAAAAATAAAAAATAAAAAATAATAATAAATTAATAAAAAAATCAAAAAAATCA
1 ATAAAAATAAAAAATAAAAAATAATAATAAATTAATAAAAAAACCAAAAAAAT-A
*
2043530 A-AAAAATCAAAAATCAAAAAATAATAAT-AA-TAA-AAAAAATGACCAATAAAAATA
1 ATAAAAATAAAAAAT-AAAAAATAATAATAAATTAATAAAAAA--ACCAA-AAAAATA
*
2043584 ATAAAAAT-AATAATAAAAA
1 ATAAAAATAAAAAATAAAAA
2043603 GAGAGGGGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
52 6 0.09
53 8 0.12
54 25 0.38
55 26 0.40
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.19
Consensus pattern (54 bp):
ATAAAAATAAAAAATAAAAAATAATAATAAATTAATAAAAAAACCAAAAAAATA
Found at i:2044214 original size:44 final size:44
Alignment explanation
Indices: 2044151--2044240 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
2044141 CAATAGAGAT
*
2044151 GCTGCAGCAAATTAACAAATGGCAACAATGATGGATGAGCACCA
1 GCTGCAGCAAATTAACAAATGGCAACAACGATGGATGAGCACCA
**
2044195 GCTGCAGCAAATTAACAAATGGCAGTAACGATGGATGAGCACCA
1 GCTGCAGCAAATTAACAAATGGCAACAACGATGGATGAGCACCA
2044239 GC
1 GC
2044241 AGCACGTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (44 bp):
GCTGCAGCAAATTAACAAATGGCAACAACGATGGATGAGCACCA
Found at i:2044281 original size:13 final size:13
Alignment explanation
Indices: 2044263--2044296 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2044253 CTGGAATGAA
2044263 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
2044276 AAAATAATAAAAT
1 AAAATAAAAAAAT
2044289 AAAATAAA
1 AAAATAAA
2044297 TAATATTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:2057652 original size:22 final size:22
Alignment explanation
Indices: 2057618--2057676 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 22
2057608 TGGAATCCCC
**
2057618 AAAATGAGTAAATCAAG-CTATA
1 AAAATGAACAAATCAAGAC-ATA
2057640 AAAATGAACAAAT-AAGACATA
1 AAAATGAACAAATCAAGACATA
*
2057661 GAAA-GAATCAAATCAA
1 AAAATGAA-CAAATCAA
2057677 ATCATGAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 14 0.45
22 14 0.45
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (22 bp):
AAAATGAACAAATCAAGACATA
Found at i:2057946 original size:42 final size:43
Alignment explanation
Indices: 2057899--2058333 Score: 291
Period size: 42 Copynumber: 10.3 Consensus size: 43
2057889 ATTAAACCCC
** *
2057899 TGGAGATTTTCCT-TTTCTAAGTCTTCCTATCGGCTTTGACCT
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * *
2057941 TGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACTT
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * * *
2057984 TGGAGACTTTT-TTA-CCCTCAGTCTGCCTGTCGACTTTGACCC
1 TGGAGA-TTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * * * *
2058026 TAGAGACTTTT-TTA-CCCTCAGTCTGCCTGTCGACTTTGACCC
1 TGGAGA-TTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * *
2058068 TGGAGACTTTT-CTA-CCCTCAGTCTACCTATCGGCCTTGACCT
1 TGGAGA-TTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * *
2058110 TAGAGACTTTT-CTA-CCCTCAGTCTGCCTGTCGGCTTTGACCC
1 TGGAGA-TTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * * * *
2058152 TAGAGACTTTCCT-TCCCTTAGTCTGCTTGTCGGCTTTGACCC
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * * * * *
2058194 TGGAGACTTT-ATTTCCCTTAGTCTGCCTGTCGGCTTTGGCCC
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * ** *
2058236 TGGAGACTTTCCT-TCTCTAAGTCTGCCTGTCACCTTTGACCC
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
* * * * * *
2058278 TGTAGACTTTCCTATCCCTTAGTCTGCTTGTCGGCTTTGACCC
1 TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
2058321 TGGAGACTTTTCC
1 TGGAGA-TTTTCC
2058334 ACCTTTTTGT
Statistics
Matches: 339, Mismatches: 46, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
41 4 0.01
42 266 0.78
43 61 0.18
44 8 0.02
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (43 bp):
TGGAGATTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCT
Found at i:2058072 original size:84 final size:83
Alignment explanation
Indices: 2057918--2058331 Score: 463
Period size: 84 Copynumber: 4.9 Consensus size: 83
2057908 TCCTTTTCTA
* * * * * *
2057918 AGTCTTCCTATCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTGACC
*
2057983 TTGGAGACTTTTTTACCCTC
65 CTGGAGACTTTTTT-CCCTC
* * *
2058003 AGTCTGCCTGTCGACTTTGACCCTAGAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCC
*
2058068 TGGAGACTTTTCTACCCTC
66 TGGAGACTTTT-TTCCCTC
* * * *
2058087 AGTCTACCTATCGGCCTTGACCTTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCC
* * *
2058152 TAGAGACTTTCCTTCCCTT
66 TGGAGACTTT-TTTCCCTC
* * * * *
2058171 AGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTAT-TTCCCTTAGTCTGCCTGTCGGCTTTGGCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTT-TCTACCCTCAGTCTGCCTGTCGGCTTTGACC
* * *
2058235 CTGGAGACTTTCCTTCTCTA
65 CTGGAGACTTT-TTTCCCTC
** * * *
2058255 AGTCTGCCTGTCACCTTTGACCCT-GTAGACTTTCCTATCCCTTAGTCTGCTTGTCGGCTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTGAC
2058319 CCTGGAGACTTTT
64 CCTGGAGACTTTT
2058332 CCACCTTTTT
Statistics
Matches: 281, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.00
84 212 0.75
85 68 0.24
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.37
Consensus pattern (83 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCC
TGGAGACTTTTTTCCCTC
Found at i:2058119 original size:126 final size:126
Alignment explanation
Indices: 2057918--2058332 Score: 516
Period size: 126 Copynumber: 3.3 Consensus size: 126
2057908 TCCTTTTCTA
* * * * *
2057918 AGTCTTCCTATCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTGACC
* *
2057983 TTGGAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTTTTACCCTC
65 TTGGAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCTTACCCTT
* * * *
2058045 AGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCTACCCTCAGTCTACCTATCGGCCTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCT
* * *
2058110 TAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTT-CCCTT
66 TGGAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTTT-CTTACCCTT
* * * *
2058171 AGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTAT-TTCCCTTAGTCTGCCTGTCGGCTTTGGCC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-TCTACCCTCAGTCTGCCTGTCGGCTTTGACC
* * * * *
2058235 CTGGAGACTTTCCTT-CTCTAAGTCTGCCTGTC-ACCTTTGACCCT-GTAGACTTTCCTATCCCT
65 TTGGAGACTTT-TTTACCCTCAGTCTGCCTGTCGA-CTTTGACCCTAG-AGACTTTCTTA-CCCT
2058297 T
126 T
*
2058298 AGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
2058333 CACCTTTTTG
Statistics
Matches: 250, Mismatches: 30, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
125 3 0.01
126 173 0.69
127 74 0.30
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.37
Consensus pattern (126 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCT
TGGAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCTTACCCTT
Found at i:2058903 original size:24 final size:23
Alignment explanation
Indices: 2058812--2058925 Score: 101
Period size: 24 Copynumber: 5.0 Consensus size: 23
2058802 TTTCAACATA
*
2058812 AAAAAATAATAATAATATAAAAAT
1 AAAAAATAATAATAATA-ATAAAT
*
2058836 AAAAAATAATAAT-A-AATTAAT
1 AAAAAATAATAATAATAATAAAT
*
2058857 AAAAAATCAA-AAAAATCAA-AAAT
1 AAAAAAT-AATAATAAT-AATAAAT
2058880 CAAAAAATAATAATAATAATAAAT
1 -AAAAAATAATAATAATAATAAAT
* ** *
2058904 GACCAATAAAAATAATAATAAA
1 AAAAAATAATAATAATAATAAA
2058926 AAGAGAGGGG
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
21 13 0.18
22 4 0.05
23 26 0.35
24 31 0.42
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (23 bp):
AAAAAATAATAATAATAATAAAT
Found at i:2060065 original size:79 final size:79
Alignment explanation
Indices: 2059965--2060166 Score: 228
Period size: 79 Copynumber: 2.6 Consensus size: 79
2059955 AATAACAGGG
* * * * *
2059965 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
2060028 GAAAAAAAAATCGGGA
64 GAAAAAAAAACCGGGA
* * *
2060044 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
2060109 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* * *
2060123 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
2060167 GAAATAACGA
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 97 0.93
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:2060158 original size:28 final size:28
Alignment explanation
Indices: 2060118--2060189 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2060108 GGAATAAAGC
** *
2060118 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2060146 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2060174 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2060190 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2060247 original size:52 final size:52
Alignment explanation
Indices: 2060178--2060514 Score: 194
Period size: 52 Copynumber: 6.4 Consensus size: 52
2060168 AAATAACGAG
*
2060178 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
2060230 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
2060283 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
2060334 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAAT-GGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
2060389 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
2060443 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
2060494 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
2060515 GAGAATTGAT
Statistics
Matches: 214, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.17
52 79 0.37
53 34 0.16
54 27 0.13
55 17 0.08
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2060374 original size:28 final size:27
Alignment explanation
Indices: 2060334--2060404 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
2060324 TAAAACCGGA
**
2060334 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* * *
2060362 GTTGGAGTATCCCCGATGATTAATGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
2060389 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
2060405 TTGTGAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:2060417 original size:107 final size:106
Alignment explanation
Indices: 2060064--2060456 Score: 334
Period size: 107 Copynumber: 3.7 Consensus size: 106
2060054 CCTTCGAAAA
* * * * * * * *
2060064 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
2060129 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
2060171 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
2060236 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
2060273 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
2060337 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * * *
2060382 TAATGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
2060447 GAGTATCCCC
63 GAGTATCCCC
2060457 GATTATAGAA
Statistics
Matches: 219, Mismatches: 49, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 46 0.21
105 20 0.09
106 18 0.08
107 71 0.32
108 32 0.15
109 27 0.12
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (106 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:2060470 original size:212 final size:212
Alignment explanation
Indices: 2060111--2060516 Score: 629
Period size: 212 Copynumber: 1.9 Consensus size: 212
2060101 TATTTTGGGA
* * *
2060111 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2060176 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* *
2060241 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
2060305 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
* *
2060323 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAATG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2060387 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
2060452 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
2060516 A
194 A
2060517 GAATTGATAA
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 106 0.60
213 39 0.22
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:2060489 original size:51 final size:53
Alignment explanation
Indices: 2060393--2060511 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
2060383 AATGGGGTTG
* * *
2060393 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
2060447 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
2060498 GAATATCCTCGATT
1 GAGTATCCCCGATT
2060512 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:2062891 original size:13 final size:13
Alignment explanation
Indices: 2062873--2062898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2062863 ACAGAGATCC
2062873 ATGTATCGATACA
1 ATGTATCGATACA
2062886 ATGTATCGATACA
1 ATGTATCGATACA
2062899 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2062894 original size:33 final size:33
Alignment explanation
Indices: 2062852--2062918 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2062842 AAAATTTCCA
* ***
2062852 AATGTATCGATACAGAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
2062885 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTATCGATAC
2062918 A
1 A
2062919 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACACAGAAAAATGTATCGATAC
Found at i:2062962 original size:19 final size:18
Alignment explanation
Indices: 2062938--2063005 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2062928 CAGTAGCTAA
2062938 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2062957 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2062972 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2062989 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2063006 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2062978 original size:13 final size:13
Alignment explanation
Indices: 2062960--2062984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2062950 ACAATACTTA
2062960 TGTATCGATACAT
1 TGTATCGATACAT
2062973 TGTATCGATACA
1 TGTATCGATACA
2062985 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2062982 original size:32 final size:32
Alignment explanation
Indices: 2062941--2063003 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2062931 TAGCTAATTA
*
2062941 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2062973 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2063004 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.