Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_pilon, whole genome shotgun sequence
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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:226 original size:18 final size:18
Alignment explanation
Indices: 200--235 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
190 TCGAAAGGAC
*
200 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
218 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
236 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1441 original size:24 final size:24
Alignment explanation
Indices: 1345--1453 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1335 GAATATTTTA
* *
1345 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1369 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
1393 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
1417 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
1441 TTTGATTTCTGAT
1 TCTGATATCTGAT
1454 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:3457 original size:13 final size:13
Alignment explanation
Indices: 3441--3528 Score: 70
Period size: 13 Copynumber: 6.2 Consensus size: 13
3431 CCGTTGACCA
*
3441 ACCCGACCCGTTT
1 ACCCGACCCGTTG
3454 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTT-----G
3472 ACCCGACCCGTTG
1 ACCCGACCCGTTG
3485 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
3498 ACCGTTGACCCGTTG
1 ACC--CGACCCGTTG
*
3513 ACCTTGA-CCGTTG
1 ACC-CGACCCGTTG
3526 ACC
1 ACC
3529 GGAGTTGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
13 38 0.58
14 4 0.06
15 12 0.18
18 12 0.18
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:3475 original size:18 final size:18
Alignment explanation
Indices: 3419--3494 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
3409 ACCGATCACA
3419 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
3437 A-CCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
3453 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3467 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3485 ACCCGACCCG
1 ACCCGACCCG
3495 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.24
17 14 0.28
18 24 0.48
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3479 original size:31 final size:31
Alignment explanation
Indices: 3423--3500 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
3413 ATCACAACCC
3423 GACCCGACCCGTTGA-CCAACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
* *
3453 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
3484 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
3501 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 14 0.32
31 30 0.68
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCAACCCGACCCGTT
Found at i:3504 original size:7 final size:7
Alignment explanation
Indices: 3492--3529 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
3482 TTGACCCGAC
3492 CCGTTGA
1 CCGTTGA
3499 CCGTTGA
1 CCGTTGA
3506 CCCGTTGA
1 -CCGTTGA
3514 CC-TTGA
1 CCGTTGA
3520 CCGTTGA
1 CCGTTGA
3527 CCG
1 CCG
3530 GAGTTGACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:3523 original size:28 final size:28
Alignment explanation
Indices: 3445--3529 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 28
3435 TGACCAACCC
* **
3445 GACCCGTTTACCCGACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCCGTTGA-CCG--TT
3476 GACCCGTTGACCCGACCCGTTGACCGTT
1 GACCCGTTGACCCGACCCGTTGACCGTT
*
3504 GACCCGTTGACCTTGA-CCGTTGACCG
1 GACCCGTTGACC-CGACCCGTTGACCG
3530 GAGTTGACCA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 22 0.45
29 2 0.04
30 3 0.06
31 22 0.45
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.20
Consensus pattern (28 bp):
GACCCGTTGACCCGACCCGTTGACCGTT
Found at i:4848 original size:18 final size:18
Alignment explanation
Indices: 4822--4857 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4812 TCGAAAGGAC
*
4822 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
4840 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
4858 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:6068 original size:24 final size:23
Alignment explanation
Indices: 5972--6075 Score: 77
Period size: 24 Copynumber: 4.4 Consensus size: 23
5962 ATATTTTATC
5972 TGATTCTGAT-TGAATTATGTTT
1 TGATTCTGATCTGAATTATGTTT
* * * *
5994 TGACATCCGATCTGAAATCTG-TT
1 TGA-TTCTGATCTGAATTATGTTT
* * * * *
6017 TGATTCCTAACCTGGATTCTGTTC
1 TGATT-CTGATCTGAATTATGTTT
6041 TGATATCTGATCTGAATTATGTTT
1 TGAT-TCTGATCTGAATTATGTTT
6065 TGATTTCTGAT
1 TGA-TTCTGAT
6076 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 16, Indels: 10
0.70 0.19 0.12
Matches are distributed among these distances:
22 4 0.07
23 20 0.33
24 34 0.57
25 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.46
Consensus pattern (23 bp):
TGATTCTGATCTGAATTATGTTT
Found at i:10013 original size:17 final size:17
Alignment explanation
Indices: 9993--10025 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9983 ATAGTGTATT
9993 TTTTAATATTT-TTTATC
1 TTTTAAT-TTTATTTATC
10010 TTTTAATTTTATTTAT
1 TTTTAATTTTATTTAT
10026 TATGTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTATTTATC
Found at i:12836 original size:22 final size:23
Alignment explanation
Indices: 12811--12854 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12801 TATATTCACA
12811 TGAAGATTA-AAATAAAAATGAG
1 TGAAGATTACAAATAAAAATGAG
* *
12833 TGAATATTACAAATTAAAATGA
1 TGAAGATTACAAATAAAAATGA
12855 AATGACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (23 bp):
TGAAGATTACAAATAAAAATGAG
Found at i:12980 original size:30 final size:30
Alignment explanation
Indices: 12876--12985 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 30
12866 ATAAGTATTT
* * *
12876 GAAA-TTACAAGGACTAAAATAGCAAATACA
1 GAAACTTA-AAGGACTAAAATAGAAAAAATA
* * *
12906 -ATAACTTAAAGGATTTAAATAACAAAAAATA
1 GA-AACTTAAAGGACTAAAAT-AGAAAAAATA
* *
12937 GAAACTT-AGGGACTAAAATAGTAAAAATA
1 GAAACTTAAAGGACTAAAATAGAAAAAATA
*
12966 GAAACTTAAAGGACTGAAAT
1 GAAACTTAAAGGACTAAAAT
12986 GGTATTAACA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
29 16 0.26
30 31 0.50
31 14 0.23
32 1 0.02
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (30 bp):
GAAACTTAAAGGACTAAAATAGAAAAAATA
Found at i:14437 original size:3 final size:3
Alignment explanation
Indices: 14424--14630 Score: 328
Period size: 3 Copynumber: 68.0 Consensus size: 3
14414 CAAAATGTAT
14424 TAA TAAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
14471 TAA TAA TAA TAA TAA TAA TAA TAC TAA TACA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
14517 TAA TAA TAA TAC TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
14563 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
14609 TAA TAA -AA TTA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
14631 AAGACCCGGA
Statistics
Matches: 191, Mismatches: 6, Indels: 14
0.91 0.03 0.07
Matches are distributed among these distances:
2 3 0.02
3 173 0.91
4 15 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:15127 original size:130 final size:135
Alignment explanation
Indices: 14814--15132 Score: 440
Period size: 130 Copynumber: 2.4 Consensus size: 135
14804 GGTCTGGTCG
* *
14814 TCTAAGGGTGACAC-AGCTCCTACGTGATGA-GAGATCTGGTCGGGGGATGACAC-TGCTCATAC
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTGCTCATAC
* * *
14876 GTGATGAAGAGTTCTTGGCCATTTTTAGGTAGGGTGATAACTCGGTTCCTACGCGATGAGGACGA
65 GTGATGAAGAGTTCTTGGCCATCTTTAGGTA-GATGATAACACGGTTCCTACGCGATGAGGACGA
*
14941 CTGGTTA
129 CTGATTA
* * *
14948 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGACACGT-CTCATACG
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTGCTCATACG
*
15012 TGATGAAGAGTTC-TGGCCATCTTTAGG-A-ATGATAACACGGTTCCTACGTGATGAGGACGA-T
66 TGATGAAGAGTTCTTGGCCATCTTTAGGTAGATGATAACACGGTTCCTACGCGATGAGGACGACT
*
15073 ATATTA
131 -GATTA
*
15079 TCT-GGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACG
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACG
15133 GTTCCTACGC
Statistics
Matches: 166, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
130 48 0.29
131 35 0.21
133 1 0.01
134 40 0.24
135 41 0.25
136 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (135 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTGCTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGGTAGATGATAACACGGTTCCTACGCGATGAGGACGACT
GATTA
Found at i:15141 original size:40 final size:41
Alignment explanation
Indices: 15046--15150 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
15036 AGGAATGATA
*
15046 ACACGGTTCCTACGTGATGAGGACGATATATTATCTGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGATATA-TATCGGGGGTG
** * * *
15088 ACACGACTCCTACGTGATGAGGA-GGTCTA-GTCGGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGATATATATCGGGGG-TG
*
15128 ACACGGTTCCTACGCGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
15151 TGACATGCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 6 0.11
40 22 0.42
41 4 0.08
42 21 0.40
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGACGATATATATCGGGGGTG
Found at i:15168 original size:130 final size:131
Alignment explanation
Indices: 14814--15168 Score: 357
Period size: 130 Copynumber: 2.7 Consensus size: 131
14804 GGTCTGGTCG
* * * *
14814 TCTAAGGGTGACAC-AGCTCCTACGTGATGA-GAGATCTGGTCGGGGGATGACAC-TGCTCATAC
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTCTAGTCAGGGGATGACACGT-CTCATAC
* * ** * *
14876 GTGATGAAGAGTTCTTGGCCATTTTTAGGTAGGGTGATAACTCGGTTCCTACGCGATGAGGACGA
64 GCGATGAAGAGTAC-TGGCCATAGTTAGG-A--ATGATAACACGGTTCCTACGCGATGAGGACGA
*
14941 CTGGTTA
125 CTGATTA
* * * *
14948 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGACACGTCTCATACGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAGGGGATGACACGTCTCATACGC
* ** * *
15013 GATGAAGAGTTCTGGCCATCTTTAGGAATGATAACACGGTTCCTACGTGATGAGGACGA-TATAT
66 GATGAAGAGTACTGGCCATAGTTAGGAATGATAACACGGTTCCTACGCGATGAGGACGACT-GAT
15077 TA
130 TA
* *
15079 TCT-GGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACGGT-TCCTACG
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAGGGGATGACAC-GTCTCATACG
*
15142 CGATGAGGA-TGACAT-GCCATAGTTAGG
65 CGATGAAGAGT-AC-TGGCCATAGTTAGG
15169 GATAATGGTT
Statistics
Matches: 193, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
129 1 0.01
130 71 0.37
131 38 0.20
133 1 0.01
134 40 0.21
135 41 0.21
136 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (131 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTAGTCAGGGGATGACACGTCTCATACGC
GATGAAGAGTACTGGCCATAGTTAGGAATGATAACACGGTTCCTACGCGATGAGGACGACTGATT
A
Found at i:15314 original size:31 final size:31
Alignment explanation
Indices: 15255--15315 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
15245 AAGGAAAACG
15255 ACTCAAAGATAGTTTTGTTTCAAGAGAAACAT
1 ACTCAAAGATA-TTTTGTTTCAAGAGAAACAT
15287 ACTCAAAGAT-TTTGTGTTTCCAA-AGAAAC
1 ACTCAAAGATATTT-TGTTT-CAAGAGAAAC
15316 CACCTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 11 0.41
32 13 0.48
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATATTTTGTTTCAAGAGAAACAT
Found at i:17557 original size:40 final size:40
Alignment explanation
Indices: 17502--17703 Score: 368
Period size: 40 Copynumber: 5.0 Consensus size: 40
17492 TGCAGATTTA
17502 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
17542 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
17582 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
17622 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
17662 TAATACACTTCGGTGTATATGATGGACACGACCTTACGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
17702 TA
1 TA
17704 GCACTACGGT
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 157 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:18723 original size:27 final size:26
Alignment explanation
Indices: 18693--18763 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 26
18683 CCTCAAAGCT
18693 GATTTTGTTAAGAGAAACAAACTCAAA
1 GATTTT-TTAAGAGAAACAAACTCAAA
* * * *
18720 GATTTTTCAAAAGGAACAGACTCAAA
1 GATTTTTTAAGAGAAACAAACTCAAA
18746 GATTTATTTCAAGAGAAA
1 GATTT-TTT-AAGAGAAA
18764 TTGTCTCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 21 0.60
27 8 0.23
28 6 0.17
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.27
Consensus pattern (26 bp):
GATTTTTTAAGAGAAACAAACTCAAA
Found at i:19034 original size:36 final size:36
Alignment explanation
Indices: 18979--19077 Score: 135
Period size: 36 Copynumber: 2.8 Consensus size: 36
18969 TTGTATCTCA
* * * *
18979 GAGAAAAAATGTCTCAAGCGAGACGAAATTTGCTTT
1 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
*
19015 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGTTTT
1 GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
* *
19051 TAGAGAAATTGTCTTAAGAGAGACAAA
1 GAGAGAAATTGTCTTAAGCGAGACAAA
19078 GTTTATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (36 bp):
GAGAGAAATTGTCTTAAGCGAGACAAAATTTGCTTT
Found at i:19232 original size:37 final size:37
Alignment explanation
Indices: 19139--19235 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
19129 AACAAATTCG
* *
19139 AAATTTGTATCTT-AAAGGGAAAATGTCTCAAGCGAAACA
1 AAATTTGT-T-TTCAAA-GGAAACTGTCTCAAACGAAACA
** * *
19178 AAATTTGTTTTTGAAGGAAACTGTCTCAAATGAGACA
1 AAATTTGTTTTCAAAGGAAACTGTCTCAAACGAAACA
19215 AAATTT-TGTTTCAAAGGAAAC
1 AAATTTGT-TTTCAAAGGAAAC
19236 AAACTGTAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 1 0.02
37 37 0.76
38 3 0.06
39 8 0.16
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (37 bp):
AAATTTGTTTTCAAAGGAAACTGTCTCAAACGAAACA
Found at i:19431 original size:33 final size:33
Alignment explanation
Indices: 19391--19459 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
19381 GTTGAATCCC
* * *
19391 CAAAGATGCCCCAATGTTCGATGTTGATTTCTT
1 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
19424 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
1 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
19457 CAA
1 CAA
19460 CACTGATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (33 bp):
CAAAGATGCCCCAATATTCAATGTTGATTGCTT
Found at i:20517 original size:30 final size:28
Alignment explanation
Indices: 20483--20602 Score: 84
Period size: 29 Copynumber: 4.1 Consensus size: 28
20473 GTCTGTGCTC
*
20483 TTTGTCCTCTTTTTGTTTTTTTCTTTTTCT
1 TTTGT-CTCTTTTTCTTTTTTT-TTTTTCT
**
20513 TTTGT-TCTTTTTTCTTTGATTTTTTTCT
1 TTTGTCTC-TTTTTCTTTTTTTTTTTTCT
* *
20541 CTTTGTTTCTTTTTCTTTGTTTTTTTGTC-
1 -TTTGTCTCTTTTTCTTT-TTTTTTTTTCT
*
20570 TTTG-CTCTTTATTTTTCTTTGTTGTTTTTCT
1 TTTGTCTCTTT-TTCTT-TTT-TT-TTTTTCT
20601 TT
1 TT
20603 CTTTGTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
27 5 0.07
28 19 0.26
29 27 0.38
30 19 0.26
31 2 0.03
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (28 bp):
TTTGTCTCTTTTTCTTTTTTTTTTTTCT
Found at i:20529 original size:44 final size:42
Alignment explanation
Indices: 20481--20626 Score: 113
Period size: 44 Copynumber: 3.3 Consensus size: 42
20471 TTGTCTGTGC
*
20481 TCTTTGTCCTCTTTTTGTTTTTTTCTTTTTCTTTTGTTCTTTTT
1 TCTTTGT-CTCTTTTTCTTTTTTTCTTTTTCTTTTGTT-TTTTT
20525 TCTTTGAT-T-TTTTTCTCTTTGTTTCTTTTTC-TTTGTTTTTTT
1 TCTTTG-TCTCTTTTTCT-TTT-TTTCTTTTTCTTTTGTTTTTTT
* *
20567 GTCTTTG-CTCTTTATTTTTCTTTGTTGTTTTTCTTTCT-TTGTTTTT
1 -TCTTTGTCTCTTT-TTCTT-TTT-TTCTTTTTCTTT-TGTT-TTTTT
*
20613 TCTCTTTTCTCTTT
1 TCT-TTGTCTCTTT
20627 GTTTTTCTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
42 12 0.14
43 21 0.25
44 29 0.35
45 8 0.10
46 8 0.10
47 6 0.07
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (42 bp):
TCTTTGTCTCTTTTTCTTTTTTTCTTTTTCTTTTGTTTTTTT
Found at i:20590 original size:17 final size:14
Alignment explanation
Indices: 20492--20656 Score: 127
Period size: 15 Copynumber: 11.0 Consensus size: 14
20482 CTTTGTCCTC
*
20492 TTTTTGTTT-TTTT
1 TTTTTCTTTGTTTT
*
20505 CTTTTTCTTTTGTTCT
1 -TTTTTC-TTTGTTTT
20521 TTTTTCTTTGATTTT
1 TTTTTCTTTG-TTTT
* *
20536 TTTCTCTTTGTTTC
1 TTTTTCTTTGTTTT
20550 TTTTTCTTTGTTTT
1 TTTTTCTTTGTTTT
*
20564 TTTGTCTTTGCTCTTT
1 TTTTTCTTTG-T-TTT
20580 ATTTTTCTTTGTTGTTT
1 -TTTTTCTTTG-T-TTT
20597 TTCTTTCTTTGTTTT
1 TT-TTTCTTTGTTTT
* *
20612 TTCTCTT-TTCTCTTTG
1 TT-T-TTCTT-TGTTTT
20628 TTTTTCTTTGTTTCT
1 TTTTTCTTTGTTT-T
*
20643 TTTCTCTTTGTTTT
1 TTTTTCTTTGTTTT
20657 GATTTGGTCT
Statistics
Matches: 124, Mismatches: 16, Indels: 22
0.77 0.10 0.14
Matches are distributed among these distances:
14 40 0.32
15 46 0.37
16 17 0.14
17 21 0.17
ACGTcount: A:0.01, C:0.13, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTGTTTT
Found at i:20606 original size:34 final size:34
Alignment explanation
Indices: 20550--20636 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
20540 TCTTTGTTTC
*
20550 TTTTTCTTTG-T-TTTTT-TGTCTTTGCTCTTTA
1 TTTTTCTTTGTTGTTTTTCTTTCTTTGCTCTTTA
* * *
20581 TTTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTC
1 TTTTTCTTTGTTGTTTTTCTTTCTTTGCTCTTTA
*
20615 TCTTTTCTCT-TTGTTTTTCTTT
1 T-TTTTCTTTGTTGTTTTTCTTT
20637 GTTTCTTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 10 0.21
32 1 0.02
33 5 0.11
34 24 0.51
35 7 0.15
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (34 bp):
TTTTTCTTTGTTGTTTTTCTTTCTTTGCTCTTTA
Found at i:20613 original size:47 final size:47
Alignment explanation
Indices: 20534--20656 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 47
20524 TTCTTTGATT
* *
20534 TTTTTCTCT-TTGTTTCTT-TTTCTTTGTTTTTTTGTCTTTGCTCTTTA
1 TTTTTCTTTGTTGTTT-TTCTTTCTTTG-TTTTTTCTCTTTGCTCTTTA
* *
20581 TTTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTTCTCTTTG
1 TTTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTGCTCTTTA
20628 TTTTTCTTTGTT-TCTTTTC--TCTTTGTTTT
1 TTTTTCTTTGTTGT-TTTTCTTTCTTTGTTTT
20657 GATTTGGTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
45 10 0.14
46 1 0.01
47 44 0.64
48 14 0.20
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (47 bp):
TTTTTCTTTGTTGTTTTTCTTTCTTTGTTTTTTCTCTTTGCTCTTTA
Found at i:20644 original size:25 final size:25
Alignment explanation
Indices: 20574--20656 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 25
20564 TTTGTCTTTG
* *
20574 CTCTTTATTTTTCTTTG-TTGTTTT
1 CTCTTTGTTTTTCTTTGTTTCTTTT
* *
20598 -TCTTTCTTTGTT-TTT-TCTCTTTT
1 CTCTTTGTTT-TTCTTTGTTTCTTTT
20621 CTCTTTGTTTTTCTTTGTTTCTTTT
1 CTCTTTGTTTTTCTTTGTTTCTTTT
20646 CTCTTTGTTTT
1 CTCTTTGTTTT
20657 GATTTGGTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
23 18 0.37
24 13 0.27
25 18 0.37
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.76
Consensus pattern (25 bp):
CTCTTTGTTTTTCTTTGTTTCTTTT
Found at i:24382 original size:29 final size:29
Alignment explanation
Indices: 24267--24385 Score: 94
Period size: 30 Copynumber: 4.0 Consensus size: 29
24257 TTGAATTTAC
* * * *
24267 AAGGACCAAAATAGCAAATACAATAACTT
1 AAGGACTAAAATAGTAAAAACAAAAACTT
* ** *
24296 AAAGGACTTAAATAACAAAAAAATAGAAACTT
1 -AAGGACTAAAATAGTAAAAACA-A-AAACTT
*
24328 AGGGACTAAAATAGTAAAAACAAAAACTT
1 AAGGACTAAAATAGTAAAAACAAAAACTT
* **
24357 AAAGGACTAAAATGGTATTAACAAAAACT
1 -AAGGACTAAAATAGTAAAAACAAAAACT
24386 AGAAGAACCT
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
29 6 0.08
30 42 0.59
31 18 0.25
32 5 0.07
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (29 bp):
AAGGACTAAAATAGTAAAAACAAAAACTT
Found at i:25799 original size:3 final size:3
Alignment explanation
Indices: 25785--25842 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
25775 CAAAATGTAT
* * *
25785 TAA TAA -AA TAA TAA TAA TAC TAA TATA TAT TAA TAA TAA -AA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
25829 -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
25843 AAGACCAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25837 original size:19 final size:18
Alignment explanation
Indices: 25790--25844 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
25780 TGTATTAATA
*
25790 AAATAATAATAATACTAAT
1 AAATAATAATAATA-AAAT
* *
25809 ATATATTAATAATAAAATT
1 AAATAATAATAATAAAA-T
25828 AAATAATAATAATAAAA
1 AAATAATAATAATAAAA
25845 GACCAGGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 2 0.07
19 28 0.93
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAATAATAAAAT
Found at i:26850 original size:21 final size:21
Alignment explanation
Indices: 26826--26871 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
26816 ATACAGGGCG
26826 GACTATAGGGTATGCTAAATT
1 GACTATAGGGTATGCTAAATT
26847 GACTATAGGGTATGCTAAATT
1 GACTATAGGGTATGCTAAATT
26868 GACT
1 GACT
26872 GTAAAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (21 bp):
GACTATAGGGTATGCTAAATT
Found at i:32745 original size:23 final size:23
Alignment explanation
Indices: 32719--32762 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
32709 ACCACATTTT
*
32719 TTTGCACCAAAGTGTCACATAGG
1 TTTGCACCAAAGTGCCACATAGG
* *
32742 TTTGCATCGAAGTGCCACATA
1 TTTGCACCAAAGTGCCACATA
32763 ATTGTCCCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (23 bp):
TTTGCACCAAAGTGCCACATAGG
Found at i:38358 original size:21 final size:21
Alignment explanation
Indices: 38334--38383 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
38324 TGTGATTCCT
*
38334 TTGCTTTAAGCTCATGAATTC
1 TTGCTTCAAGCTCATGAATTC
38355 TTGCTTCAAGCTCATGAATTC
1 TTGCTTCAAGCTCATGAATTC
38376 TTGCTTCA
1 TTGCTTCA
38384 TCTGACGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (21 bp):
TTGCTTCAAGCTCATGAATTC
Found at i:39721 original size:23 final size:23
Alignment explanation
Indices: 39691--39743 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
39681 TCCTGAATGA
39691 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
*
39714 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
39737 CCACATA
1 CCACATA
39744 ATTGTCCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:53538 original size:23 final size:23
Alignment explanation
Indices: 53501--53544 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53491 TAATATCTAT
*
53501 ATATTTTTTATTTTATAAATAAA
1 ATATTTTTTATTTTAGAAATAAA
53524 ATATTTATTTA-TTTAGAAATA
1 ATATTT-TTTATTTTAGAAATA
53545 TCAGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTTTTTATTTTAGAAATAAA
Found at i:53835 original size:130 final size:130
Alignment explanation
Indices: 53512--53858 Score: 411
Period size: 130 Copynumber: 2.6 Consensus size: 130
53502 TATTTTTTAT
* * *
53512 TTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAT
1 TTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAA
* *
53577 CTCATTTCTTAATATTAAAAACATATATTAATAAAACATTTCTCTAAAAATAATTAAAATTAATA
66 C-AATTTCTTAATATTAAAAACATATATAAATAAAACATTTCTC----AATAATTAAAATTAATA
53642 TATAA
126 TATAA
* *
53647 TTTATAAA-AATAGGATATTTATTTATTTAAGAATATCAGAAAAGAACTTCTAGGTGCTTTAAGA
1 TTTATAAATAA-A--ATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGA
* *
53711 CAGACAATTTCTTAATATTAATAA-ATGA-ATAAATAAAAACATTT-TC-CTAA-TAAAATTAAT
63 CA-ACAATTTCTTAATATTAAAAACAT-ATATAAAT-AAAACATTTCTCAATAATTAAAATTAAT
53771 ATATAA
125 ATATAA
* *
53777 TTTATGAAAGTAAAATATTTATTT-TCTTAAAAATATCAGAAAAGGACTTGTAGTTGCTTTAAGA
1 TTTAT-AAA-TAAAATATTTATTTAT-TTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGA
53841 CAATCAATTTCTTAATAT
63 CAA-CAATTTCTTAATAT
53859 CGAAAAATAA
Statistics
Matches: 188, Mismatches: 13, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
129 2 0.01
130 81 0.43
131 6 0.03
132 1 0.01
133 2 0.01
134 2 0.01
135 9 0.05
136 9 0.05
137 75 0.40
138 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (130 bp):
TTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAA
CAATTTCTTAATATTAAAAACATATATAAATAAAACATTTCTCAATAATTAAAATTAATATATAA
Found at i:55021 original size:72 final size:73
Alignment explanation
Indices: 54904--55049 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
54894 TGGTGGTGAC
54904 TCACCATAGAGCTGCAACGTAGGTGATTTCGTGGCGTTCTGGAGACTTCGGTTGGGACGT-GCAA
1 TCACCATAGAGCTGCAACGTAGGTGATTTCGTGGCGTTCTGGAGACTTCGGTTGGGACGTGGCAA
54968 TAGCTGGT
66 TAGCTGGT
54976 TCACCATAGAGCTGCAACGTAGGTGATTTCGTGGCGTTCTGGAGACTTCGGTTGGGACGTGGCAA
1 TCACCATAGAGCTGCAACGTAGGTGATTTCGTGGCGTTCTGGAGACTTCGGTTGGGACGTGGCAA
55041 TAGCTGGT
66 TAGCTGGT
55049 T
1 T
55050 GAGGCGGTGG
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 60 0.82
73 13 0.18
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (73 bp):
TCACCATAGAGCTGCAACGTAGGTGATTTCGTGGCGTTCTGGAGACTTCGGTTGGGACGTGGCAA
TAGCTGGT
Found at i:55340 original size:3 final size:3
Alignment explanation
Indices: 55332--55418 Score: 83
Period size: 3 Copynumber: 30.0 Consensus size: 3
55322 TTTGGGCATG
* *
55332 TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAG T-A TAAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* * * *
55375 TAA -AA TGA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55419 AGAACAAATG
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
2 6 0.09
3 59 0.88
4 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:56045 original size:122 final size:122
Alignment explanation
Indices: 55784--56216 Score: 572
Period size: 122 Copynumber: 3.6 Consensus size: 122
55774 TTAAGGCAAT
*
55784 GTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * *
55848 ACTCTTT-TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAG
66 ACT-TTTCTGGAAAAGTTAATGCTGATCTATCTCCTTCTGTAATAGAGTCATGCAAAG
55905 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
55969 ACTTTCTCTGGAAAAGTTAATGCTGATCTATCTCCTTCTGTAATAGAGTCATGCAAAG
66 ACTTT-TCTGGAAAAGTTAATGCTGATCTATCTCCTTCTGTAATAGAGTCATGCAAAG
*
56027 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTTAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * *** ** * *
56091 ACTTTTTTTGG---A---AATGCTGATCCATCGAGTGATG-AATTCGAG-C--G-AAAT
66 AC-TTTTCTGGAAAAGTTAATGCTGATCTATCTCCTTCTGTAA-TAGAGTCATGCAAAG
* *
56139 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
*
56204 ACTCTTCTGGAAA
66 ACTTTTCTGGAAA
56217 TGTTGAAAAC
Statistics
Matches: 284, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
112 45 0.16
113 28 0.10
115 3 0.01
116 20 0.07
119 1 0.00
120 2 0.01
121 63 0.22
122 119 0.42
123 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (122 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTTTTCTGGAAAAGTTAATGCTGATCTATCTCCTTCTGTAATAGAGTCATGCAAAG
Found at i:57061 original size:22 final size:22
Alignment explanation
Indices: 57036--57109 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
57026 AAAGCTTTCC
57036 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
57058 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
* * *
57080 TCTTTGAGATGAGAATCTATTA
1 TCTTTGAAAAGAGAATCTATCA
57102 TCTTTGAA
1 TCTTTGAA
57110 GAATGTAGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:63849 original size:42 final size:41
Alignment explanation
Indices: 63802--63884 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 41
63792 TTAGTCTTGT
* * * * *
63802 CATTTGCTCCTTTGACTCACCTTGGATTTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGA-ATTTTTTACTTGATC
*
63844 CATTTGTTCATTTGAATCACCCTGGAATTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAATTTTTTACTTGATC
63885 AATCATCTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (41 bp):
CATTTGCTCATTTGAATCACCCTGGAATTTTTTACTTGATC
Found at i:64876 original size:36 final size:36
Alignment explanation
Indices: 64814--64882 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
64804 CTTACCGTAA
* **
64814 ACTACTTTTGATATCAATCTGGCAGGATATTTGTGT
1 ACTACTTTTGATATCAATATAACAGGATATTTGTGT
* *
64850 ACTACTTTTGATATTAATATAACAGGATCTTTG
1 ACTACTTTTGATATCAATATAACAGGATATTTG
64883 CGTGTATAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (36 bp):
ACTACTTTTGATATCAATATAACAGGATATTTGTGT
Found at i:66323 original size:23 final size:21
Alignment explanation
Indices: 66283--66324 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
66273 ATATATATAT
*
66283 ATATTTATTTTTATAAATAAG
1 ATATTTATTTTTAGAAATAAG
66304 ATATTTATTTACTTAGAAATA
1 ATATTTATTT--TTAGAAATA
66325 TCAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAG
Found at i:66602 original size:3 final size:3
Alignment explanation
Indices: 66594--66677 Score: 86
Period size: 3 Copynumber: 29.0 Consensus size: 3
66584 TTTGGGCCTG
*
66594 TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAG T-A TAAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* * * *
66637 TAA -AA TGA TAA TAA TAA TAT TAA TAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66678 AGAACAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
2 7 0.11
3 57 0.86
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:72081 original size:21 final size:20
Alignment explanation
Indices: 72057--72095 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
72047 GTAGTTTAGG
72057 GCTACTATGGTTATATTCTGT
1 GCTACTATGGTTAT-TTCTGT
* *
72078 GCTAGTCTGGTTATTTCT
1 GCTACTATGGTTATTTCT
72096 TGTCATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (20 bp):
GCTACTATGGTTATTTCTGT
Found at i:76043 original size:12 final size:12
Alignment explanation
Indices: 76026--76056 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
76016 ATTCGTGCAC
76026 TTTTTAAAAATA
1 TTTTTAAAAATA
76038 TTTTTAAAAATA
1 TTTTTAAAAATA
76050 TCTTTTA
1 T-TTTTA
76057 TAACACTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTTAAAAATA
Found at i:102639 original size:13 final size:12
Alignment explanation
Indices: 102608--102699 Score: 73
Period size: 13 Copynumber: 7.4 Consensus size: 12
102598 ATTTAAAGAG
*
102608 AAAACAAAT-AA
1 AAAAAAAATGAA
*
102619 AAAGAAAATGAGA
1 AAAAAAAATGA-A
102632 AAAAAAAAT--A
1 AAAAAAAATGAA
102642 AAAAAAAATGAGA
1 AAAAAAAATGA-A
102655 AAAATGAAAATGAA
1 AAAA--AAAATGAA
*
102669 AAGAGAAAATGAA
1 AA-AAAAAATGAA
*
102682 AAGAGAAAATGAA
1 AA-AAAAAATGAA
102695 AAAAA
1 AAAAA
102700 TGAAAAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.15
11 7 0.10
12 3 0.04
13 37 0.54
14 3 0.04
15 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.09
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:102709 original size:13 final size:13
Alignment explanation
Indices: 102617--102698 Score: 91
Period size: 13 Copynumber: 6.4 Consensus size: 13
102607 GAAAACAAAT
102617 AAAAAGAAAATGA
1 AAAAAGAAAATGA
102630 GAAAAA-AAAAT--
1 -AAAAAGAAAATGA
102641 AAAAA-AAAATGA
1 AAAAAGAAAATGA
102653 GAAAAATGAAAATGA
1 -AAAAA-GAAAATGA
*
102668 AAAGAGAAAATGA
1 AAAAAGAAAATGA
*
102681 AAAGAGAAAATGA
1 AAAAAGAAAATGA
102694 AAAAA
1 AAAAA
102699 ATGAAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.16
13 35 0.57
14 9 0.15
15 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:102709 original size:26 final size:26
Alignment explanation
Indices: 102643--102716 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
102633 AAAAAAATAA
* *
102643 AAAAAAATG-AGAAAAA-TGAAAATG
1 AAAAAAATGAAAAAAAAGAGAAAATG
*
102667 -AAAAGA-GAAAATGAAAAGAGAAAATG
1 AAAAAAATGAAAA--AAAAGAGAAAATG
102693 AAAAAAATGAAAAAAAAGAAGAAA
1 AAAAAAATGAAAAAAAAG-AGAAA
102717 GGGAAAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
22 1 0.03
23 7 0.18
25 4 0.10
26 12 0.31
27 10 0.26
28 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAAAAATGAAAAAAAAGAGAAAATG
Found at i:102739 original size:6 final size:6
Alignment explanation
Indices: 102617--102747 Score: 56
Period size: 6 Copynumber: 20.7 Consensus size: 6
102607 GAAAACAAAT
* * *
102617 AAAAAG AAAATG AGAAAA- AAAAAT AAAAA- AAAATGAG AAAAATG AAAATG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAA--AG AAAAA-G AAAAAG
* *
102667 AAAAGAG AAAATG AAAAGAG AAAATG AAAAA- AATGAAA- AAAAAG AAGAAAGGG
1 AAAA-AG AAAAAG AAAA-AG AAAAAG AAAAAG AA--AAAG AAAAAG AA-AAA--G
* *
102720 AAAAATG -AAGAG AAAAAG AAATAG AAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAA
102748 TAAAAGGGGG
Statistics
Matches: 97, Mismatches: 13, Indels: 30
0.69 0.09 0.21
Matches are distributed among these distances:
5 14 0.14
6 45 0.46
7 28 0.29
8 7 0.07
9 3 0.03
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (6 bp):
AAAAAG
Found at i:102746 original size:24 final size:25
Alignment explanation
Indices: 102695--102747 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
102685 AGAAAATGAA
*
102695 AAAAATGAAAAAAAAGAAGAAAGGG
1 AAAAATGAAAAAAAAGAAGAAAGAG
* * *
102720 AAAAATGAAGAGAAA-AAGAAATAG
1 AAAAATGAAAAAAAAGAAGAAAGAG
102744 AAAA
1 AAAA
102748 TAAAAGGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAAATGAAAAAAAAGAAGAAAGAG
Found at i:102747 original size:64 final size:63
Alignment explanation
Indices: 102613--102740 Score: 149
Period size: 64 Copynumber: 2.0 Consensus size: 63
102603 AAGAGAAAAC
*
102613 AAAT-AAAAAGAAAATGAGAAAAAAAAATAAAAAAAAATGAGAAAAATGAAAATGAAAAGAGA
1 AAATGAAAAAGAAAATGAGAAAAAAAAATAAAAAAAAAAGAGAAAAATGAAAATGAAAAGAGA
* *
102675 AAATGAAAAGAGAAAATGA-AAAAAATGAAA-AAAAAGAAGAAAGGGAAAAATGAAGA-GAAAA-
1 AAATGAAAA-AGAAAATGAGAAAAAA--AAATAAAAA-AA-AAAGAGAAAAATGAAAATGAAAAG
102736 AGA
61 AGA
102739 AA
1 AA
102741 TAGAAAATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
62 4 0.07
63 10 0.18
64 19 0.33
65 10 0.18
66 14 0.25
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (63 bp):
AAATGAAAAAGAAAATGAGAAAAAAAAATAAAAAAAAAAGAGAAAAATGAAAATGAAAAGAGA
Found at i:104108 original size:37 final size:37
Alignment explanation
Indices: 104022--104131 Score: 141
Period size: 37 Copynumber: 2.9 Consensus size: 37
104012 TCGAAACAAG
* * * *
104022 TCAATCTTAAGCCTTCACGAAAAAAATAGTGAAGCAAT
1 TCAATCTTAAGCCTTCAC-AGAAGAGTAGTGAAGCAAA
104060 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
**
104097 TC-ATCTATAAGCCTTCATGGAAGAGTAGTGAAGCA
1 TCAATCT-TAAGCCTTCACAGAAGAGTAGTGAAGCA
104132 TACTCATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 4 0.06
37 43 0.66
38 18 0.28
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
Found at i:104230 original size:55 final size:55
Alignment explanation
Indices: 104156--104785 Score: 536
Period size: 55 Copynumber: 11.5 Consensus size: 55
104146 AGATCTATTC
* * *
104156 CTATACTCTCTGAAGGAATAAGGAGAAGACACGTTTTCAGAAGATTGTTCGAGTT
1 CTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTT
* * * * * ** * *
104211 CTATACTCCTTGAATGAATAAGAAGCAAAC-CTGTTTTTGGAAGATTGTTTGAGTC
1 CTATACTCCCTGAAGGAATAGGGAGCAGACAC-GTTTTCAGAAGATTGTTCGAGTT
* * *
104266 CTATACTCTCTGAAGGAATAGGGAGCAGACATGATTGTT--GAAGATT-TTCGAGTC
1 CTATACTCCCTGAAGGAATAGGGAGCAGACACG-TT-TTCAGAAGATTGTTCGAGTT
* * *
104320 CTATACTCTCTGAAGGAA-AGGGAGCGGACACGTTTGTTA-AAGATTGTTCGAGTT
1 CTATACTCCCTGAAGGAATAGGGAGCAGACACGTTT-TCAGAAGATTGTTCGAGTT
* * * * *
104374 CTATACTCCCTGAATGAATAAGGAGC-GAACCCGTTTT-ATGAAAATTGTTCGAGTA
1 CTATACTCCCTGAAGGAATAGGGAGCAG-ACACGTTTTCA-GAAGATTGTTCGAGTT
* * * * * *
104429 CTATACTCCCTGAACGAATAGGGAG-TGAACCCATTTGCTAG-AGATTGTTGGAG-T
1 CTATACTCCCTGAAGGAATAGGGAGCAG-ACACGTTTTC-AGAAGATTGTTCGAGTT
* * * *
104483 CTTATACTCCCTGAATGAATAGGGAGTAGACACGTTTGCCA-AAGATTGTTCGAGTC
1 C-TATACTCCCTGAAGGAATAGGGAGCAGACACGTTT-TCAGAAGATTGTTCGAGTT
* **
104539 CTATACTCCCTGAAGGAATAGGGAGCGGACACGTTTTGTTGAAGATTGTTCGAG-T
1 CTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTT-CAGAAGATTGTTCGAGTT
* * *
104594 CTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCGAG-T
1 C-TATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTT
* * ** * * *
104649 CTTATTCTCCCTGAATGAATAGGGAGTGGATACGTTTGCTGAAGATTGTTCGAG-T
1 C-TATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTT
** * * * * *
104704 CTTATACTCCCTGAAAAAATAAGGAGTAGACACATTTGCTGAAGATTGTTCGAG-T
1 C-TATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTT
104759 CTTATACTCCCTGAAGGAATAGGGAGC
1 C-TATACTCCCTGAAGGAATAGGGAGC
104786 GCCATTCGAA
Statistics
Matches: 484, Mismatches: 68, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
51 1 0.00
52 3 0.01
53 19 0.04
54 52 0.11
55 354 0.73
56 52 0.11
57 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (55 bp):
CTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTT
Found at i:104296 original size:110 final size:109
Alignment explanation
Indices: 104154--104786 Score: 606
Period size: 110 Copynumber: 5.8 Consensus size: 109
104144 AAAGATCTAT
* *
104154 TCCTATACTCTCTGAAGGAATAAGGAGAAGACACGTTTTCAGAAGATTGTTCGAGTTCTATACTC
1 TCCTATACTCCCTGAAGGAATAAGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTTCTATACTC
* * * * * *
104219 CTTGAATGAATAAGAAGCAAACCTGTTT-TTGGAAGATTGTTTGAG
66 CCTGAAGGAATAGGGAGCGAACC-GTTTGTT-GAAGATTGTTCGAG
* * * *
104264 TCCTATACTCTCTGAAGGAATAGGGAGCAGACATGATTGTT--GAAGATT-TTCGAGTCCTATAC
1 TCCTATACTCCCTGAAGGAATAAGGAGCAGACACG-TT-TTCAGAAGATTGTTCGAGTTCTATAC
* * *
104326 TCTCTGAAGGAA-AGGGAGCGGACACGTTTGTTAAAGATTGTTCGAG
64 TCCCTGAAGGAATAGGGAGCGAAC-CGTTTGTTGAAGATTGTTCGAG
* * * * *
104372 TTCTATACTCCCTGAATGAATAAGGAGC-GAACCCGTTTT-ATGAAAATTGTTCGAGTACTATAC
1 TCCTATACTCCCTGAAGGAATAAGGAGCAG-ACACGTTTTCA-GAAGATTGTTCGAGTTCTATAC
* * * * *
104435 TCCCTGAACGAATAGGGAGTGAACCCATTTGCT-AGAGATTGTTGGAG
64 TCCCTGAAGGAATAGGGAGCGAA-CCGTTTGTTGA-AGATTGTTCGAG
* * * * * *
104482 TCTTATACTCCCTGAATGAATAGGGAGTAGACACGTTTGCCA-AAGATTGTTCGAGTCCTATACT
1 TCCTATACTCCCTGAAGGAATAAGGAGCAGACACGTTT-TCAGAAGATTGTTCGAGTTCTATACT
*
104546 CCCTGAAGGAATAGGGAGCGGACACGTTTTGTTGAAGATTGTTCGAG
65 CCCTGAAGGAATAGGGAGCGAAC-CG-TTTGTTGAAGATTGTTCGAG
* * * * * *
104593 TCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCGAG-TCTTATTCT
1 TCCTATACTCCCTGAAGGAATAAGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTTC-TATACT
* * *
104657 CCCTGAATGAATAGGGAGTGGATA-CGTTTGCTGAAGATTGTTCGAG
65 CCCTGAAGGAATAGGGAG-CGA-ACCGTTTGTTGAAGATTGTTCGAG
* ** * * * *
104703 TCTTATACTCCCTGAAAAAATAAGGAGTAGACACATTTGCTGAAGATTGTTCGAG-TCTTATACT
1 TCCTATACTCCCTGAAGGAATAAGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTTC-TATACT
104767 CCCTGAAGGAATAGGGAGCG
65 CCCTGAAGGAATAGGGAGCG
104787 CCATTCGAAG
Statistics
Matches: 442, Mismatches: 60, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
106 2 0.00
107 3 0.01
108 56 0.13
109 51 0.12
110 231 0.52
111 93 0.21
112 5 0.01
113 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (109 bp):
TCCTATACTCCCTGAAGGAATAAGGAGCAGACACGTTTTCAGAAGATTGTTCGAGTTCTATACTC
CCTGAAGGAATAGGGAGCGAACCGTTTGTTGAAGATTGTTCGAG
Found at i:104645 original size:221 final size:219
Alignment explanation
Indices: 104156--104786 Score: 779
Period size: 221 Copynumber: 2.9 Consensus size: 219
104146 AGATCTATTC
* * * * *
104156 CTATACTCTCTGAAGGAATAAGGAGAAGACACGTTTTCAGAAGATTGTTCGAGTTCTATACTCCT
1 CTATACTCCCTGAACGAATAAGGAGCAGACACGTTTTCTGAAGATTGTTCGAG-TCTATACTCCC
* * ** * * * * * *
104221 TGAATGAATAAGAAGCAAACCTGTTT-TTGGAAGATTGTTTGAGTCCTATACTCTCTGAAGGAAT
65 TGAATGAATAGGGAGTGAACCCGTTTGCT-GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAT
* * * * *
104285 AGGGAGCAGACATGATTGTTGAAGATT-TTCGAGTCCTATACTCTCTGAAGGAA-AGGGAGCGGA
129 AGGGAGTAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGA
104348 CACGTTTGTTAAAGATTGTTCGAGTT
194 CACGTTTGTTAAAGATTGTTCGAGTT
* * * *
104374 CTATACTCCCTGAATGAATAAGGAGC-GAACCCGTTTTATGAAAATTGTTCGAGTACTATACTCC
1 CTATACTCCCTGAACGAATAAGGAGCAG-ACACGTTTTCTGAAGATTGTTCGAGT-CTATACTCC
* * * *
104438 CTGAACGAATAGGGAGTGAACCCATTTGCT-AGAGATTGTTGGAGTCTTATACTCCCTGAATGAA
64 CTGAATGAATAGGGAGTGAACCCGTTTGCTGA-AGATTGTTCGAGTCTTATACTCCCTGAAAGAA
**
104502 TAGGGAGTAGACACGTTTGCCAAAGATTGTTCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGG
128 TAGGGAGTAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGG
*
104567 ACACGTTTTGTTGAAGATTGTTCGAG-T
193 ACACG-TTTGTTAAAGATTGTTCGAGTT
* * *
104594 CTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCGAGTCTTATTCTCC
1 C-TATACTCCCTGAACGAATAAGGAGCAGACACGTTTTCTGAAGATTGTTCGAGTC-TATACTCC
* ** *
104659 CTGAATGAATAGGGAGTGGATACGTTTGCTGAAGATTGTTCGAGTCTTATACTCCCTGAAAAAAT
64 CTGAATGAATAGGGAGTGAACCCGTTTGCTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAT
* * *
104724 AAGGAGTAGACACATTTGCTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCG
129 AGGGAGTAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGAAGGAATAGGGAGCG
104787 CCATTCGAAG
Statistics
Matches: 354, Mismatches: 48, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
217 3 0.01
218 122 0.34
219 26 0.07
220 17 0.05
221 184 0.52
222 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (219 bp):
CTATACTCCCTGAACGAATAAGGAGCAGACACGTTTTCTGAAGATTGTTCGAGTCTATACTCCCT
GAATGAATAGGGAGTGAACCCGTTTGCTGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAG
GGAGTAGACACGTTTGCTGAAGATTGTTCGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACA
CGTTTGTTAAAGATTGTTCGAGTT
Found at i:106082 original size:28 final size:28
Alignment explanation
Indices: 106050--106133 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
106040 TTAGCTTTTA
*
106050 TATTAAATGTTTATTGAAAGTTCACGTG
1 TATTAAATGTTTATTGAAAGTTCACATG
** ***
106078 TATT--A-GTTTA-AAATAAGTT-TTTTG
1 TATTAAATGTTTATTGA-AAGTTCACATG
106102 TATTAAATGTTTATTGAAAGTTCACATG
1 TATTAAATGTTTATTGAAAGTTCACATG
106130 TATT
1 TATT
106134 TATGCTTTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
24 7 0.17
25 10 0.25
26 2 0.05
27 10 0.25
28 11 0.28
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (28 bp):
TATTAAATGTTTATTGAAAGTTCACATG
Found at i:110400 original size:3 final size:3
Alignment explanation
Indices: 110392--110437 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
110382 CTCCAAGTCA
110392 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
110438 GTTGGGATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:111121 original size:20 final size:20
Alignment explanation
Indices: 111092--111184 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
111082 GCAGCCTTCG
*
111092 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
111112 TGCATCGATGCACAGCATGA
1 TGCATCGATGCACAGCAGGA
* *
111132 TGCATCGATGCATATCAGGA
1 TGCATCGATGCACAGCAGGA
* *
111152 TGCATCAATACACAGCAGGA
1 TGCATCGATGCACAGCAGGA
111172 TGCATCGATGCAC
1 TGCATCGATGCAC
111185 TAAGTGTATT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:111237 original size:21 final size:21
Alignment explanation
Indices: 111211--111260 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
111201 AGAGTGCATG
*
111211 GATGCAGTGCAGGGGTACATA
1 GATGCACTGCAGGGGTACATA
* *
111232 GATGCACTGCAGGGGTGCATG
1 GATGCACTGCAGGGGTACATA
111253 GATGCACT
1 GATGCACT
111261 TTGACGCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.20
Consensus pattern (21 bp):
GATGCACTGCAGGGGTACATA
Found at i:116888 original size:19 final size:19
Alignment explanation
Indices: 116864--116917 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
116854 AAAGCGGGGA
116864 AAAAAGAAAAAAAAAGAAG
1 AAAAAGAAAAAAAAAGAAG
*
116883 AAAAAGAAGAGAAAAGAGAAG
1 AAAAAGAA-A-AAAAAAGAAG
116904 AAAGAAGAAAAAAA
1 AAA-AAGAAAAAAA
116918 GGGAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 8 0.26
20 5 0.16
21 13 0.42
22 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAGAAG
Found at i:116892 original size:12 final size:11
Alignment explanation
Indices: 116863--116918 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 11
116853 CAAAGCGGGG
116863 AAAAAAGAA-A
1 AAAAAAGAAGA
116873 AAAAAAGAAG-
1 AAAAAAGAAGA
116883 -AAAAAGAAG-
1 AAAAAAGAAGA
*
116892 AGAAAAG-AG-
1 AAAAAAGAAGA
*
116901 AAGAAAGAAGA
1 AAAAAAGAAGA
116912 AAAAAAG
1 AAAAAAG
116919 GGAAATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 16 0.42
10 16 0.42
11 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:121923 original size:18 final size:18
Alignment explanation
Indices: 121900--121937 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
121890 GCGCATCTCC
121900 TGGAGAATTTCCAATTGT
1 TGGAGAATTTCCAATTGT
*
121918 TGGAGAATTTCTAATTGT
1 TGGAGAATTTCCAATTGT
121936 TG
1 TG
121938 AGCTCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (18 bp):
TGGAGAATTTCCAATTGT
Found at i:123727 original size:23 final size:21
Alignment explanation
Indices: 123668--123733 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
123658 ATAATCAGAA
123668 CCCT-CAGGGGGTATCGATTC
1 CCCTACAGGGGGTATCGATTC
* *
123688 CCCTACAGGGGGAATCGGTTC
1 CCCTACAGGGGGTATCGATTC
*
123709 CCCTTCAAGGGGGGTATCGATTC
1 CCCTAC-A-GGGGGTATCGATTC
123732 CC
1 CC
123734 TATGCACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 4 0.11
21 19 0.50
22 1 0.03
23 14 0.37
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (21 bp):
CCCTACAGGGGGTATCGATTC
Found at i:128702 original size:17 final size:17
Alignment explanation
Indices: 128657--128704 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
128647 AGAAAGAAAG
128657 AAAA-AAATGAAAAAAA
1 AAAACAAATGAAAAAAA
* * *
128673 AAAAGAAAAGAAAAGAA
1 AAAACAAATGAAAAAAA
*
128690 AAATCAAATGAAAAA
1 AAAACAAATGAAAAA
128705 TGATAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.06
Consensus pattern (17 bp):
AAAACAAATGAAAAAAA
Found at i:130498 original size:113 final size:112
Alignment explanation
Indices: 130293--130585 Score: 410
Period size: 113 Copynumber: 2.6 Consensus size: 112
130283 TCCGGAAGAG
* *
130293 TTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGAAGAACTTTTTCAAC
** * * *
130358 CTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAGAA
66 CTTTCACTTGAATTCATCACTTAATGGATCAACATTGCCAAGTAGAA
* * * *
130405 TTCATGATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTTTTCAA
1 TTCATAATGAGAAGAACTCATCTGAA-AAAGAAGAAGAAATTCATAATGAGAAGAACTTTTTCAA
** *
130470 CCTTTCACTTGAATTCATCA-TTCAATGGATCAACATTTTCAAGTAGAG
65 CCTTTCACTTGAATTCATCACTT-AATGGATCAACATTGCCAAGTAGAA
* *
130518 TTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGTTCATAATGAGAAGAGC-TTTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGAAGAACTTTTTCAAC
130582 CTTT
66 CTTT
130586 GTTTGATTCT
Statistics
Matches: 159, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
111 12 0.08
112 52 0.33
113 95 0.60
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (112 bp):
TTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAATTCATAATGAGAAGAACTTTTTCAAC
CTTTCACTTGAATTCATCACTTAATGGATCAACATTGCCAAGTAGAA
Found at i:130778 original size:122 final size:122
Alignment explanation
Indices: 130498--130831 Score: 413
Period size: 122 Copynumber: 2.7 Consensus size: 122
130488 CATTCAATGG
* * * *
130498 ATCAACATTTTCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAGAAGAAGTTCATA
1 ATCAACA-TTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* ** * * * * *
130563 ATGAGAAGAGCTT-TTCAACC-TTTGTTTGATTCTATCATAGAATGAGATAGATCAGC
65 ATGAGAAAAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
* * * * * *
130619 AGCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
130684 ATGAGAAAAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
65 ATGAGAAAAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
* * *
130742 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCAAAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* *
130807 TGA-AAAGAACTTGTTCAATCTTTTG
66 TGAGAAA-AGCTTGTTCAACCTTTTG
130832 TTACATTACA
Statistics
Matches: 180, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
120 6 0.03
121 63 0.35
122 70 0.39
123 41 0.23
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAAAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
Found at i:131121 original size:3 final size:3
Alignment explanation
Indices: 131049--131103 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
131039 ATTTTTTGAT
* *
131049 TTA TTA TAA TTA TT- TTA TTA TTA -TA TTA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
131095 TTA TTA TTA
1 TTA TTA TTA
131104 AATAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:131662 original size:27 final size:27
Alignment explanation
Indices: 131624--131679 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
131614 AAAGAAAAAG
131624 GAGAGAAGCTTACCGATAGGAATACGC
1 GAGAGAAGCTTACCGATAGGAATACGC
*
131651 GAGAGAAGCTTACCGATAGGAATATGC
1 GAGAGAAGCTTACCGATAGGAATACGC
131678 GA
1 GA
131680 TCATCGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (27 bp):
GAGAGAAGCTTACCGATAGGAATACGC
Found at i:132607 original size:2 final size:2
Alignment explanation
Indices: 132594--132623 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
132584 TTACTTAGTC
*
132594 AT AT AG 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 AT
132624 TAAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:134484 original size:60 final size:60
Alignment explanation
Indices: 134416--134537 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
134406 GACCATAGAT
134416 AGCAGTGAATAAGAAAGATGTCGAGACAGAACTAGTAGCGATCCTGACATGAATGAATTG
1 AGCAGTGAATAAGAAAGATGTCGAGACAGAACTAGTAGCGATCCTGACATGAATGAATTG
134476 AGCAGTGAATAAGAAAGATGTCGAGACAGAACTAGTAGCGATCCTGACATGAATGAATTG
1 AGCAGTGAATAAGAAAGATGTCGAGACAGAACTAGTAGCGATCCTGACATGAATGAATTG
134536 AG
1 AG
134538 GATGGATAGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (60 bp):
AGCAGTGAATAAGAAAGATGTCGAGACAGAACTAGTAGCGATCCTGACATGAATGAATTG
Found at i:142549 original size:3 final size:3
Alignment explanation
Indices: 142541--142664 Score: 248
Period size: 3 Copynumber: 41.3 Consensus size: 3
142531 TCTTTTATTG
142541 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
142589 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
142637 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
142665 CGCAGCAGCT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:143640 original size:2 final size:2
Alignment explanation
Indices: 143629--143671 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
143619 TTGAAACATT
143629 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
143669 TA T
1 TA T
143672 TATTTATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:143841 original size:11 final size:12
Alignment explanation
Indices: 143827--143905 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 12
143817 ATGCATCTGT
143827 TATACT-TATAA
1 TATACTATATAA
143838 TATA-TATATAA
1 TATACTATATAA
*
143849 TATTTATGTATATAA
1 TA--TA-CTATATAA
*
143864 TATACT-TATGCA
1 TATACTATAT-AA
*
143876 TATATTAATATAA
1 TATACT-ATATAA
143889 TATA-TATATAA
1 TATACTATATAA
143900 TATACT
1 TATACT
143906 TATGTAATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
10 1 0.02
11 24 0.44
12 9 0.16
13 9 0.16
14 3 0.05
15 9 0.16
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (12 bp):
TATACTATATAA
Found at i:143897 original size:36 final size:36
Alignment explanation
Indices: 143839--143909 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
143829 TACTTATAAT
* *
143839 ATATATATAATATTTATGTATATAATATACTTATGC
1 ATATATATAATATATATATATATAATATACTTATGC
143875 ATATAT-TAATATAATATATATATAATATACTTATG
1 ATATATATAATAT-ATATATATATAATATACTTATG
143910 TAATTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATATATATATAATATACTTATGC
Found at i:144024 original size:19 final size:19
Alignment explanation
Indices: 143985--144070 Score: 61
Period size: 19 Copynumber: 4.5 Consensus size: 19
143975 TATATGTAAT
* * *
143985 TAAGTATATATGATGCATA
1 TAAGTATATATTATACTTA
144004 TAAGTATATATTATACTTA
1 TAAGTATATATTATACTTA
144023 TAA-TATA-ATATATA-TTA
1 TAAGTATATAT-TATACTTA
* * * *
144040 TAATTACACATTATATATATA
1 TAAGTATATATTATA-CT-TA
144061 TAAGTATATA
1 TAAGTATATA
144071 CATAAGTGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
17 8 0.15
18 15 0.28
19 21 0.39
20 1 0.02
21 9 0.17
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (19 bp):
TAAGTATATATTATACTTA
Found at i:144070 original size:12 final size:12
Alignment explanation
Indices: 144001--144099 Score: 57
Period size: 12 Copynumber: 8.5 Consensus size: 12
143991 TATATGATGC
144001 ATATAAGTATAT
1 ATATAAGTATAT
**
144013 ATTATACTTATA-
1 A-TATAAGTATAT
144025 ATATAA-TATAT
1 ATATAAGTATAT
*
144036 ATTATAA-T-TAC
1 A-TATAAGTATAT
* *
144047 ACATTA-TATAT
1 ATATAAGTATAT
144058 ATATAAGTATAT
1 ATATAAGTATAT
* *
144070 ACATAAGTGTAT
1 ATATAAGTATAT
*
144082 ATATATGTA-AGT
1 ATATAAGTATA-T
144094 ATATAA
1 ATATAA
144100 TTAAACATGA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
10 8 0.12
11 15 0.23
12 35 0.53
13 8 0.12
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (12 bp):
ATATAAGTATAT
Found at i:144070 original size:14 final size:14
Alignment explanation
Indices: 144051--144098 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
144041 AATTACACAT
144051 TATATATATATAAG
1 TATATATATATAAG
* *
144065 TATATACATA-AGTG
1 TATATATATATA-AG
*
144079 TATATATATGTAAG
1 TATATATATATAAG
144093 TATATA
1 TATATA
144099 ATTAAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:151490 original size:9 final size:9
Alignment explanation
Indices: 151476--151515 Score: 53
Period size: 9 Copynumber: 4.1 Consensus size: 9
151466 AATAAAAATA
151476 AATAATATT
1 AATAATATT
151485 AATAATATT
1 AATAATATT
151494 AATAATAATAT
1 AATAAT-AT-T
151505 AATAATTATT
1 AATAA-TATT
151515 A
1 A
151516 TTATTATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 15 0.54
10 4 0.14
11 8 0.29
12 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATAATATT
Found at i:157427 original size:21 final size:21
Alignment explanation
Indices: 157385--157428 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
157375 ACTCCGGGAG
* *
157385 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
157406 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
157427 CT
1 CT
157429 CCTCCTCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:158620 original size:45 final size:46
Alignment explanation
Indices: 158571--158658 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
158561 GAACATCGAA
* * *
158571 TGCATTTTATGCATTGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
158616 TGCATTTGATGCATCGATGCACAAGACCATGCATTGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
158659 CAGGCTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:159434 original size:3 final size:3
Alignment explanation
Indices: 159414--159456 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
159404 TAACTCAACA
* *
159414 AAT ATT AAT AAT ATT AAT AAT AAT -AT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
159457 TATTATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:159443 original size:8 final size:8
Alignment explanation
Indices: 159430--159454 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
159420 AATAATATTA
159430 ATAATAAT
1 ATAATAAT
159438 ATAATAAT
1 ATAATAAT
159446 ATAATAAT
1 ATAATAAT
159454 A
1 A
159455 ATTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:159444 original size:11 final size:11
Alignment explanation
Indices: 159419--159456 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
159409 CAACAAATAT
159419 TAATAATATTAA
1 TAATAATA-TAA
159431 TAATAATATAA
1 TAATAATATAA
159442 TAAT-ATAATAA
1 TAATAAT-ATAA
159453 TAAT
1 TAAT
159457 TATTATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 15 0.60
12 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATAATATAA
Found at i:159692 original size:37 final size:36
Alignment explanation
Indices: 159642--159715 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
159632 ACTCGAGATC
*
159642 GATTTGCTTCACTACTCTTTGGTGAAGGCTTAGGATG
1 GATTTGCTTCACTACTCTTCGGTGAA-GCTTAGGATG
159679 GATTTGCTTCACTACTCTTCGGTGAAGCTTAGGATG
1 GATTTGCTTCACTACTCTTCGGTGAAGCTTAGGATG
159715 G
1 G
159716 CTTGGATGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (36 bp):
GATTTGCTTCACTACTCTTCGGTGAAGCTTAGGATG
Found at i:159892 original size:42 final size:41
Alignment explanation
Indices: 159760--159896 Score: 163
Period size: 42 Copynumber: 3.3 Consensus size: 41
159750 CTTCCTGAAG
* *
159760 GACTTA-TAGATGACCCGAAGGATTTATCATCTTGCTCGAAA
1 GACTTACT-GATGACCCAAAGGATTTATCATCATGCTCGAAA
**
159801 GA-TTCACAAATGACCCGAAA-GATTTAATCATCATGCTCGAAA
1 GACTT-ACTGATGACCC-AAAGGATTT-ATCATCATGCTCGAAA
*
159843 GACTTACTGATGACCCAAAGGATTTCATTATCATGCTCGAAA
1 GACTTACTGATGACCCAAAGGATTT-ATCATCATGCTCGAAA
159885 GACTTACTGATG
1 GACTTACTGATG
159897 GCACTTACTG
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
40 2 0.02
41 18 0.22
42 60 0.73
43 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (41 bp):
GACTTACTGATGACCCAAAGGATTTATCATCATGCTCGAAA
Found at i:159904 original size:13 final size:13
Alignment explanation
Indices: 159886--159910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
159876 TGCTCGAAAG
159886 ACTTACTGATGGC
1 ACTTACTGATGGC
159899 ACTTACTGATGG
1 ACTTACTGATGG
159911 ATTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:163228 original size:20 final size:19
Alignment explanation
Indices: 163178--163256 Score: 115
Period size: 19 Copynumber: 4.2 Consensus size: 19
163168 AAATCCAGAA
* *
163178 CCCC-AGGGGGTATCGATT
1 CCCCTAGGGGGAATCGGTT
*
163196 CCCCTATGGGGAATCGGTT
1 CCCCTAGGGGGAATCGGTT
163215 CCCCTAGGGGGGAATCGGTT
1 CCCCTA-GGGGGAATCGGTT
163235 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGGTT
163254 CCC
1 CCC
163257 TCATGGGGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
18 4 0.07
19 33 0.60
20 18 0.33
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGGTT
Found at i:163264 original size:19 final size:20
Alignment explanation
Indices: 163182--163279 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
163172 CCAGAACCCC
* *
163182 AGGGGGTATCGATTCCC-CT
1 AGGGGGAATCGGTTCCCTCT
*
163201 ATGGGGAATCGGTTCCC-CT
1 AGGGGGAATCGGTTCCCTCT
163220 AGGGGGGAATCGGTTCCC-CT
1 A-GGGGGAATCGGTTCCCTCT
163240 AGGGGGAATCGGTTCCCTC-
1 AGGGGGAATCGGTTCCCTCT
* *
163259 ATGGGGGTATCGATTCCCTCT
1 A-GGGGGAATCGGTTCCCTCT
163280 GCACCAAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
19 34 0.49
20 35 0.51
ACGTcount: A:0.15, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
AGGGGGAATCGGTTCCCTCT
Found at i:163265 original size:39 final size:39
Alignment explanation
Indices: 163183--163276 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
163173 CAGAACCCCA
*
163183 GGGGGTATCGATTCCCCTATGGGGAATCGGTTCCCCTAG
1 GGGGGTATCGATTCCCCTAGGGGGAATCGGTTCCCCTAG
* * *
163222 GGGGGAATCGGTTCCCCTAGGGGGAATCGGTT-CCCTCAT
1 GGGGGTATCGATTCCCCTAGGGGGAATCGGTTCCCCT-AG
163261 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
163277 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 4 0.08
39 44 0.92
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.24
Consensus pattern (39 bp):
GGGGGTATCGATTCCCCTAGGGGGAATCGGTTCCCCTAG
Found at i:163278 original size:20 final size:20
Alignment explanation
Indices: 163183--163276 Score: 113
Period size: 19 Copynumber: 4.8 Consensus size: 20
163173 CAGAACCCCA
* *
163183 GGGGGTATCGATTCCCCTAT
1 GGGGGAATCGGTTCCCCTAT
*
163203 -GGGGAATCGGTTCCCCTAG
1 GGGGGAATCGGTTCCCCTAT
163222 GGGGGAATCGGTTCCCCTA-
1 GGGGGAATCGGTTCCCCTAT
163241 GGGGGAATCGGTT-CCCTCAT
1 GGGGGAATCGGTTCCCCT-AT
* *
163261 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
163277 TCTGCACCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.06
19 30 0.46
20 29 0.45
21 2 0.03
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCCTAT
Found at i:169568 original size:22 final size:22
Alignment explanation
Indices: 169508--169569 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
169498 AAAGGATTTA
169508 ATCATCATGCTCGAAAGAC--C
1 ATCATCATGCTCGAAAGACTTC
* * *
169528 -T-ATGATGGCCCGAAGGACTTC
1 ATCATCAT-GCTCGAAAGACTTC
169549 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
169570 ACTGATGGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
21 1 0.03
22 12 0.39
23 4 0.13
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (22 bp):
ATCATCATGCTCGAAAGACTTC
Found at i:169622 original size:128 final size:130
Alignment explanation
Indices: 169456--169707 Score: 409
Period size: 128 Copynumber: 2.0 Consensus size: 130
169446 AACTTACTGG
* *
169456 GGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCAAAGGATTTAATCATCATGCTCG
1 GGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATGCTCG
* *
169521 AAAGACCTA-TGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTAT
66 AAAGACCTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTGATGGCACTTAT
*
169585 GGTTTGCTTCA-TACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAATCATAATGCTCG
1 GGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATGCTCG
* * * *
169649 AAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGC
66 AAAGACCTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTGATGGC
169708 CCGAATGACT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 58 0.51
129 55 0.49
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (130 bp):
GGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCAAAGGATTTAATCATAATGCTCG
AAAGACCTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTGATGGCACTTAT
Found at i:169705 original size:42 final size:42
Alignment explanation
Indices: 169499--169712 Score: 184
Period size: 42 Copynumber: 5.0 Consensus size: 42
169489 AAATTACCCA
*
169499 AAGGATTTAATCATCATGCTCGAAAGACCTA-TGATGGCCCG
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCG
* * **
169540 AAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC-CCG
* ** * * ** **
169583 ATGG-TTTGCTTCAT-ACT-CTTCCATGAAGGCTTACAAATTACCCG
1 AAGGATTT-AATCATCA-TGC-TCGA--AAGACTTACTGATGGCCCG
* *
169627 AAGGATTTAATCATAATGCTCGAAAGACTTACTGATGGCCCT
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCG
* *
169669 AAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCG
1 AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCG
169711 AA
1 AA
169713 TGACTTACTA
Statistics
Matches: 133, Mismatches: 30, Indels: 19
0.73 0.16 0.10
Matches are distributed among these distances:
41 28 0.21
42 64 0.48
43 13 0.10
44 12 0.09
45 16 0.12
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (42 bp):
AAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCG
Found at i:169885 original size:41 final size:41
Alignment explanation
Indices: 169835--169937 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 41
169825 AGGTCTTATG
* * *
169835 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * *
169876 GATGACCCGAAGGATTTTTAATCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGA--CTT-ATCATCATGCTCGAAAGACTTACA
169920 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
169938 AATTGTTTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
41 14 0.27
42 2 0.04
43 2 0.04
44 33 0.65
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:176811 original size:47 final size:46
Alignment explanation
Indices: 176657--176826 Score: 205
Period size: 46 Copynumber: 3.6 Consensus size: 46
176647 TCACAAAAAT
* *
176657 CCTAACCACATGATATCTAATTCGCATACTTGTTCAAGAAAAAATAAA
1 CCTAACCACATGATTTCTAGTTCGCATACTTGTTC-AG-AAAAATAAA
* * * *
176705 CCTAACAACATGATTTTTAGTTCGCATACATGTTCAAAAAAATAAA
1 CCTAACCACATGATTTCTAGTTCGCATACTTGTTCAGAAAAATAAA
* ** * *
176751 CTTAACCGTATGATTTCTAGTTTGCATGCTTGTTCGAGAAAAATAAA
1 CCTAACCACATGATTTCTAGTTCGCATACTTGTTC-AGAAAAATAAA
*
176798 CCTAACCGCATGATTTCTAGTTCGCATAC
1 CCTAACCACATGATTTCTAGTTCGCATAC
176827 ATTTATTCAA
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
46 36 0.35
47 36 0.35
48 30 0.29
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (46 bp):
CCTAACCACATGATTTCTAGTTCGCATACTTGTTCAGAAAAATAAA
Found at i:178323 original size:2 final size:2
Alignment explanation
Indices: 178282--178308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
178272 GTGACATACA
178282 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
178309 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:179893 original size:3 final size:3
Alignment explanation
Indices: 179881--179912 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
179871 TAAACAGTAT
179881 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
179913 ATATATCCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:181806 original size:27 final size:28
Alignment explanation
Indices: 181776--181833 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
181766 AAAAATTGGG
*
181776 TTCGGGTCGGG-TTTTTTAAGTTTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
181803 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
181831 TTC
1 TTC
181834 AGGTTTAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.14, C:0.09, G:0.29, T:0.48
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:182427 original size:18 final size:16
Alignment explanation
Indices: 182379--182428 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
182369 ATGTTTCAGA
* *
182379 TTCAGATTCTAATTCC
1 TTCAAATTCCAATTCC
182395 TTCAAATTCCAATTCC
1 TTCAAATTCCAATTCC
*
182411 TTCACAGATTTCAATTCC
1 TTCA-A-ATTCCAATTCC
182429 CTCGTAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.62
17 1 0.03
18 10 0.34
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (16 bp):
TTCAAATTCCAATTCC
Found at i:186288 original size:21 final size:20
Alignment explanation
Indices: 186241--186289 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
186231 TATAATTTAA
*
186241 TTTTTTTAATTTACTTCAAT
1 TTTTTTTAATTAACTTCAAT
* *
186261 TTGTTTTTAATTAATTTAGAAT
1 TT-TTTTTAATTAACTT-CAAT
186283 TTTTTTT
1 TTTTTTT
186290 CTATTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTTTAATTAACTTCAAT
Found at i:194023 original size:30 final size:30
Alignment explanation
Indices: 193988--194091 Score: 136
Period size: 30 Copynumber: 3.5 Consensus size: 30
193978 ACCCAAGGAC
* *
193988 CCCGAGAAGAAACCGGAAAAGCCTAAAGAG
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
*
194018 GCCGAGAAGAAACCGGAAAAACCTAAAGAA
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
* * *
194048 CCCGAGAAGAAACCCGAGAAACCGAAAGAA
1 CCCGAGAAGAAACCGGAAAAACCTAAAGAA
* *
194078 CCTGAAAAGAAACC
1 CCCGAGAAGAAACC
194092 CGAGAAGCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.50, C:0.24, G:0.23, T:0.03
Consensus pattern (30 bp):
CCCGAGAAGAAACCGGAAAAACCTAAAGAA
Found at i:194092 original size:30 final size:30
Alignment explanation
Indices: 193994--194116 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
193984 GGACCCCGAG
* * *
193994 AAGAAACCGGA-AAAGCCTAAAGAGGCC-GAG
1 AAGAAACCCGAGAAA-CCTAAAGA-ACCTGAA
* * * *
194024 AAGAAACCGGAAAAACCTAAAGAACCCGAG
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
*
194054 AAGAAACCCGAGAAACCGAAAGAACCTGAA
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
* * *
194084 AAGAAACCCGAGAAGCCTAAGGAGCCTGAA
1 AAGAAACCCGAGAAACCTAAAGAACCTGAA
194114 AAG
1 AAG
194117 CCCAAAGAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 2 0.02
30 76 0.94
31 3 0.04
ACGTcount: A:0.50, C:0.22, G:0.24, T:0.04
Consensus pattern (30 bp):
AAGAAACCCGAGAAACCTAAAGAACCTGAA
Found at i:194103 original size:60 final size:60
Alignment explanation
Indices: 193988--194103 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
193978 ACCCAAGGAC
* * * * *
193988 CCCGAGAAGAAACCGGAAAAGCCTAAAGAGGCCGAGAAGAAACCGGAAAAACCTAAAGAA
1 CCCGAGAAGAAACCCGAAAAGCCGAAAGAGACCGAAAAGAAACCCGAAAAACCTAAAGAA
* *
194048 CCCGAGAAGAAACCCGAGAAA-CCGAAAGA-ACCTGAAAAGAAACCCGAGAAGCCTAA
1 CCCGAGAAGAAACCCGA-AAAGCCGAAAGAGACC-GAAAAGAAACCCGAAAAACCTAA
194104 GGAGCCTGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 42 0.89
61 3 0.06
ACGTcount: A:0.49, C:0.24, G:0.23, T:0.03
Consensus pattern (60 bp):
CCCGAGAAGAAACCCGAAAAGCCGAAAGAGACCGAAAAGAAACCCGAAAAACCTAAAGAA
Found at i:202793 original size:27 final size:27
Alignment explanation
Indices: 202754--202818 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
202744 ATAGAACGGG
*
202754 CAACTAAAAAACCCTTTGTACCTGTTT
1 CAACCAAAAAACCCTTTGTACCTGTTT
*
202781 CAACCAAACAACCCTTTGTACCTGTTT
1 CAACCAAAAAACCCTTTGTACCTGTTT
202808 CAACCAAAAAA
1 CAACCAAAAAA
202819 AAGTCAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.26
Consensus pattern (27 bp):
CAACCAAAAAACCCTTTGTACCTGTTT
Found at i:203116 original size:14 final size:14
Alignment explanation
Indices: 203081--203123 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
203071 GGAAATATAA
203081 AAAAATTATATAAAT
1 AAAAATTA-ATAAAT
* *
203096 AATAATTAATAAGT
1 AAAAATTAATAAAT
203110 AAAAATTAA-AAAT
1 AAAAATTAATAAAT
203123 A
1 A
203124 TTCATTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAAATTAATAAAT
Found at i:203122 original size:27 final size:29
Alignment explanation
Indices: 203081--203134 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
203071 GGAAATATAA
203081 AAAAATTATATAAATAATAATTAATAAGT
1 AAAAATTATATAAATAATAATTAATAAGT
* *
203110 AAAAATTA-A-AAATATTCATTAATAA
1 AAAAATTATATAAATAATAATTAATAA
203135 AAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 1 0.04
29 8 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTATATAAATAATAATTAATAAGT
Found at i:203122 original size:149 final size:147
Alignment explanation
Indices: 202882--203155 Score: 335
Period size: 151 Copynumber: 1.9 Consensus size: 147
202872 TAAATAAGAG
* * * *
202882 ATAAAAACTAAGAATTATTTCTTCAATTAACAATAATTAAAAATATATAAAAATGTTTTAAATAA
1 ATAAAAACTAAGAATCATTTCTTCAATTAACAAAAATTAAAAATATAAAAAAATGTTATAAATAA
* * *
202947 AAGTTAATAAGTAAAATTTTAAAAAATTTATTTCATTAAGAATAAT-TAAAAATATATAAATTTT
66 AAGTTAATAAGTAAAATATTAAAAAA--TA-TTCATTAAGAAAAATATAAAAATATAAAAATTTT
203011 TTATAAAATATAGTTAATAA
128 TTATAAAATATAGTTAATAA
* **
203031 ATAAAAA-TAAAGAATCATTTCTTCCATTAACAAAAATATTGGAAATATAAAAAAAT-TATATAA
1 ATAAAAACT-AAGAATCATTTCTTCAATTAAC-AAAA-ATTAAAAATATAAAAAAATGT-TATAA
*
203094 ATAATAA-TTAATAAGTAAAA-ATT-AAAAATATTCATTAATAAAAATATAAAAATATAAAAATT
62 ATAA-AAGTTAATAAGTAAAATATTAAAAAATATTCATTAAGAAAAATATAAAAATATAAAAATT
203156 ATATTTAAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
146 13 0.12
147 17 0.16
148 1 0.01
149 32 0.30
150 6 0.06
151 37 0.34
152 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (147 bp):
ATAAAAACTAAGAATCATTTCTTCAATTAACAAAAATTAAAAATATAAAAAAATGTTATAAATAA
AAGTTAATAAGTAAAATATTAAAAAATATTCATTAAGAAAAATATAAAAATATAAAAATTTTTTA
TAAAATATAGTTAATAA
Found at i:203165 original size:70 final size:71
Alignment explanation
Indices: 202907--203166 Score: 196
Period size: 74 Copynumber: 3.5 Consensus size: 71
202897 TATTTCTTCA
* * * *
202907 ATTAACAATAAT-TAAAAATATATAAAAATGTTTTAAATAA-AAGTTAATAAGTAAAATTTTAAA
1 ATTAACAAAAATATAAAAATATA-AAAATTATTTTAAATAATAAGTTAATAAGTAAAA-ATT-AA
202970 AAATTTATTTC
63 AAA--TATTTC
* * * *
202981 ATTAAGAATAAT-TAAAAATATATAAATT-TTTTATAA-AATATAGTTAATAAATAAAAA-TAAA
1 ATTAACAAAAATATAAAAATATAAAAATTATTTTA-AATAATA-AGTTAATAAGTAAAAATTAAA
203042 GAATCATTTCTTCC
64 -AAT-A--T-TT-C
* * *
203056 ATTAACAAAAATATTGGAAATATAAAAAAATTA-TATAAATAATAA-TTAATAAGTAAAAATTAA
1 ATTAACAAAAATA-T--AAAAATATAAAAATTATTTTAAATAATAAGTTAATAAGTAAAAATTAA
203119 AAATA-TTC
63 AAATATTTC
*
203127 ATTAATAAAAATATAAAAATATAAAAATTATATTTAAATA
1 ATTAACAAAAATATAAAAATATAAAAATTAT-TTTAAATA
203167 TGTCATTGGG
Statistics
Matches: 152, Mismatches: 16, Indels: 40
0.73 0.08 0.19
Matches are distributed among these distances:
68 14 0.09
70 9 0.06
71 17 0.11
72 12 0.08
73 8 0.05
74 37 0.24
75 11 0.07
76 1 0.01
77 17 0.11
78 7 0.05
79 19 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (71 bp):
ATTAACAAAAATATAAAAATATAAAAATTATTTTAAATAATAAGTTAATAAGTAAAAATTAAAAA
TATTTC
Found at i:213359 original size:16 final size:16
Alignment explanation
Indices: 213329--213359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
213319 AAAACTCGAA
*
213329 TCGAACTCGAAAAAAC
1 TCGAACTCAAAAAAAC
213345 TCGAACTCAAAAAAA
1 TCGAACTCAAAAAAA
213360 ATTCAGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.10, T:0.13
Consensus pattern (16 bp):
TCGAACTCAAAAAAAC
Found at i:213381 original size:11 final size:11
Alignment explanation
Indices: 213365--213408 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
213355 AAAAAATTCA
213365 GAAGCTCAATT
1 GAAGCTCAATT
213376 GAAGCTCAATACT
1 GAAGCTCAAT--T
* *
213389 CAAGCTCGATT
1 GAAGCTCAATT
213400 GAAGCTCAA
1 GAAGCTCAA
213409 GACTCGAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (11 bp):
GAAGCTCAATT
Found at i:213400 original size:24 final size:24
Alignment explanation
Indices: 213366--213432 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
213356 AAAAATTCAG
* *
213366 AAGCTCAATTGAAGCTCAATACTC
1 AAGCTCGATTGAAGCTCAAGACTC
213390 AAGCTCGATTGAAGCTCAAGACTC
1 AAGCTCGATTGAAGCTCAAGACTC
*
213414 GAGCTCGATTGAAGCTCAA
1 AAGCTCGATTGAAGCTCAA
213433 ATTTGAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (24 bp):
AAGCTCGATTGAAGCTCAAGACTC
Found at i:216348 original size:11 final size:11
Alignment explanation
Indices: 216332--216392 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
216322 ATTATAGAAC
216332 TTTTAATATAT
1 TTTTAATATAT
216343 TTTTAA-A-AT
1 TTTTAATATAT
216352 TTTATAAT-TAT
1 TTT-TAATATAT
*** *
216363 CAATAATGTAT
1 TTTTAATATAT
216374 TTTTAATATAT
1 TTTTAATATAT
216385 TTTTAATA
1 TTTTAATA
216393 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:217348 original size:1 final size:1
Alignment explanation
Indices: 217315--217339 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
217305 CCAAAACAGC
217315 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
217340 GGGCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:221013 original size:26 final size:26
Alignment explanation
Indices: 220972--221030 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
220962 ATAAGAGGAA
220972 AAAAAGAAAAATGAAGGAAAA-TGAAG
1 AAAAAGAAAAATGAA-GAAAAGTGAAG
*
220998 AGAAAGAAAGAA-GAAGAAAAGTGAAG
1 AAAAAGAAA-AATGAAGAAAAGTGAAG
221024 AAAAAGA
1 AAAAAGA
221031 TAGGGAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 22 0.76
27 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAATGAAGAAAAGTGAAG
Found at i:224297 original size:22 final size:22
Alignment explanation
Indices: 224270--224311 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
224260 GAACTATACA
* *
224270 AATATCCATCAAATTATGCATC
1 AATATCCAACAAAATATGCATC
224292 AATATCCAACAAAATATGCA
1 AATATCCAACAAAATATGCA
224312 AATAGTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
AATATCCAACAAAATATGCATC
Found at i:226033 original size:62 final size:62
Alignment explanation
Indices: 225904--226034 Score: 144
Period size: 62 Copynumber: 2.1 Consensus size: 62
225894 AAATTTAAAT
* * *
225904 AGGGTTTCGAAACCTTTAGCCCATGAAAACATTTTGCCTGAGGGATTTTGAAGCCACAAGGAG
1 AGGGTTTCGAAACCTTTAGCCCA-GAAAACATTCTGCCTGAGGGATTTCGAAACCACAAGGAG
* * *
225967 -GGGTTTCGAAACCTTTAGCCCA-AAAAGCATTCTGCCAT-ACTGG-TTTCGAAACCTCATGGAG
1 AGGGTTTCGAAACCTTTAGCCCAGAAAA-CATTCTGCC-TGA-GGGATTTCGAAACCACAAGGAG
226028 AGGGTTT
1 AGGGTTT
226035 TAAAACCTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
60 4 0.07
61 23 0.40
62 31 0.53
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (62 bp):
AGGGTTTCGAAACCTTTAGCCCAGAAAACATTCTGCCTGAGGGATTTCGAAACCACAAGGAG
Found at i:227957 original size:26 final size:26
Alignment explanation
Indices: 227928--227982 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
227918 TTCTTAGGTT
*
227928 TTATGCATGAGATAAATGCATCATAA
1 TTATGCATGAGATAAATGCAACATAA
227954 TTATGCATGAGATAAATGCAACATAA
1 TTATGCATGAGATAAATGCAACATAA
227980 TTA
1 TTA
227983 CAAATATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (26 bp):
TTATGCATGAGATAAATGCAACATAA
Found at i:233362 original size:21 final size:21
Alignment explanation
Indices: 233338--233385 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
233328 CACCATAGCT
233338 CACATAATTG-CACCGAAGTG-C
1 CACATAATTGTC-CCGAA-TGAC
*
233359 CACATATTTGTCCCGAATGAC
1 CACATAATTGTCCCGAATGAC
233380 CACATA
1 CACATA
233386 TTTTTTTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (21 bp):
CACATAATTGTCCCGAATGAC
Done.