Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015367.1 Kokia drynarioides strain JFW-HI SEQ_130414, 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: 471520
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 729 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:11327 original size:30 final size:29
Alignment explanation
Indices: 11283--11602 Score: 238
Period size: 29 Copynumber: 10.9 Consensus size: 29
11273 ACATCCGAGA
* *
11283 GTAAAATAGTAATTTTTGGATGTTTCGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
* *
11312 GTCAAAAATGG-AATTTTTAGAAG-TTCAAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTC-GGG
* *
11342 GTAAAATGGTAATTTTTAGAAGTTTTGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGG
* *
11371 GTCAAAAAT--AAGATTTTTGGGAGTTT-GGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTCGGG
* *
11400 GATAAAATGGTAATTTTTAGAAGCTT-GAGG
1 G-TAAAATGGTAATTTTTGGAAGTTTCG-GG
*
11430 GACAAAATTGG-AATTTTTGGAAG-TTCGAGG
1 G-TAAAA-TGGTAATTTTTGGAAGTTTCG-GG
11460 GTAAAATGGTAATTTTAT-GAAGTTTCGGG
1 GTAAAATGGTAATTTT-TGGAAGTTTCGGG
*
11489 GTCAAAATGG-GATTTTTGGAAG-TTCAGGG
1 GT-AAAATGGTAATTTTTGGAAGTTTC-GGG
*
11518 GTAAAATGGTAATTTTTGGACA-TTTCGTG
1 GTAAAATGGTAATTTTTGGA-AGTTTCGGG
11547 GTCAAAAT--TAGGATTTTTGGAAG-TTCGGGG
1 GT-AAAATGGTA--ATTTTTGGAAGTTTC-GGG
11577 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
11603 AGGGACCTCC
Statistics
Matches: 239, Mismatches: 20, Indels: 62
0.74 0.06 0.19
Matches are distributed among these distances:
28 28 0.12
29 103 0.43
30 90 0.38
31 18 0.08
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGG
Found at i:11346 original size:59 final size:59
Alignment explanation
Indices: 11283--11602 Score: 359
Period size: 59 Copynumber: 5.4 Consensus size: 59
11273 ACATCCGAGA
* * * *
11283 GTAAAATAGTAATTTTTGGATGTTTCGGGGTCAAAAATGGAATTTTTAGAAGTTCAAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGG
* * * * *
11342 GTAAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAAAT-AAGATTTTTGGGAGTT-TGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGA-ATTTTTGGAAGTTCAGGG
* * * *
11400 GATAAAATGGTAATTTTTAGAAGCTT-GAGGGACAAAATTGGAATTTTTGGAAGTTC-GAGG
1 G-TAAAATGGTAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTCAG-GG
*
11460 GTAAAATGGTAATTTTAT-GAAGTTTCGGGGTC-AAAATGGGATTTTTGGAAGTTCAGGG
1 GTAAAATGGTAATTTT-TGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGG
* * *
11518 GTAAAATGGTAATTTTTGGACA-TTTCGTGGTCAAAATTAGG-ATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGA-AGTTTCGGGGTCAAAAAT-GGAATTTTTGGAAGTTCAGGG
11577 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
11603 AGGGACCTCC
Statistics
Matches: 225, Mismatches: 22, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
57 1 0.00
58 54 0.24
59 159 0.71
60 11 0.05
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGG
Found at i:12779 original size:18 final size:17
Alignment explanation
Indices: 12756--12795 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
12746 TTCGGTTTTT
12756 TATTTTAATTAATAATAA
1 TATTTTAA-TAATAATAA
12774 TATTTTTAATAATAATAA
1 TA-TTTTAATAATAATAA
12792 -ATTT
1 TATTT
12796 CATTTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 1 0.05
18 11 0.52
19 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAATAATAATAA
Found at i:13470 original size:17 final size:17
Alignment explanation
Indices: 13450--13513 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
13440 AAATAAATTT
*
13450 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
13467 TAAATTTAAATTCAGAA
1 TAAATTTAAATTTAAAA
* *
13484 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
13501 TAAATTTAAATTT
1 TAAATTTAAATTT
13514 GTTGGGCCCG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:22320 original size:175 final size:176
Alignment explanation
Indices: 22023--22388 Score: 473
Period size: 175 Copynumber: 2.1 Consensus size: 176
22013 AAAACAAAAA
* * *
22023 AAAAAACCCTTACCATTTCAACTAACTCCCGTAATTAACTTATGACATATTTTAACCCAGTAACT
1 AAAAGACCCTTACCATTTCAACTAACTCCCGTAATTAACCTATGACATATTTTAACCCAATAACT
* * * * * * *
22088 AATCCTCCGTATTCTATCGGCCCATTAAGAGGGTAGATATTAGTCACGAGTTTTAAAGCTGTGCT
66 AATCCTCCGCAATCTATAGGCCCATTAAGAAGGTAGACATTAGTCACAAATTTTAAAGCTGTGCT
* * *
22153 CCATACCCAAGATCAGAATTGAACTCTCGACCACTGGTTAAGATAG
131 CCATACCCAAAATCAGAATTGAACCCTCGACAACTGGTTAAGATAG
* * * * * * * *
22199 GAAAGACCCTTATCATTTTACCTAACTCCCGTAGTTAACCTATGATATATTTTAA-CTAATTACT
1 AAAAGACCCTTACCATTTCAACTAACTCCCGTAATTAACCTATGACATATTTTAACCCAATAACT
* * * *
22263 AATCCTCCGCAATCTATAGGTCCATTAAGAAGGTAGACGTTGGTCACAAATTTTAAAGTTGTGCT
66 AATCCTCCGCAATCTATAGGCCCATTAAGAAGGTAGACATTAGTCACAAATTTTAAAGCTGTGCT
* *
22328 CCATACCCAAAATGAGAATTGAACCCTTGACAACTGGTTAAGATAG
131 CCATACCCAAAATCAGAATTGAACCCTCGACAACTGGTTAAGATAG
*
22374 AAAAGATCCTTACCA
1 AAAAGACCCTTACCA
22389 CTTAACTCCC
Statistics
Matches: 160, Mismatches: 30, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
175 113 0.71
176 47 0.29
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (176 bp):
AAAAGACCCTTACCATTTCAACTAACTCCCGTAATTAACCTATGACATATTTTAACCCAATAACT
AATCCTCCGCAATCTATAGGCCCATTAAGAAGGTAGACATTAGTCACAAATTTTAAAGCTGTGCT
CCATACCCAAAATCAGAATTGAACCCTCGACAACTGGTTAAGATAG
Found at i:24170 original size:31 final size:28
Alignment explanation
Indices: 24135--24239 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 28
24125 CTTAATATAA
24135 TATTTGGTACTTAAACTTAATATATTTTTCC
1 TATTTGGTACTTAAACTT-ATAT-TTTTT-C
* *
24166 TATTTTGATACTTAAA-TT-TTTTTTATTC
1 TA-TTTGGTACTTAAACTTATATTTT-TTC
*
24194 AATTTGGTACTTAAACTTGATACTTTTTTC
1 TATTTGGTACTTAAACTT-ATA-TTTTTTC
*
24224 TAATTTGGCACTTAAA
1 T-ATTTGGTACTTAAA
24240 ATTTTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
27 12 0.20
28 7 0.12
29 4 0.07
30 4 0.07
31 21 0.35
32 12 0.20
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (28 bp):
TATTTGGTACTTAAACTTATATTTTTTC
Found at i:24242 original size:59 final size:59
Alignment explanation
Indices: 24136--24282 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 59
24126 TTAATATAAT
* * * * **
24136 ATTTGGTACTTAAACTTAATATATTTTTCCTATTTTGATACTTAAATTTTTTTTATTCA
1 ATTTGGTACTTAAACTTGATATATTTTTCCTAATTTGACACTTAAATTTTTTTGACCCA
*
24195 ATTTGGTACTTAAACTTGATACT-TTTTT-CTAATTTGGCACTTAAAATTTTTTTGACCCA
1 ATTTGGTACTTAAACTTGATA-TATTTTTCCTAATTTGACACTT-AAATTTTTTTGACCCA
*
24254 ATTTAGTA-TCTAAACTTGATATATATTTT
1 ATTTGGTACT-TAAACTTGATATAT-TTTT
24283 TTAAATTTCG
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 13 0.17
59 57 0.76
60 5 0.07
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (59 bp):
ATTTGGTACTTAAACTTGATATATTTTTCCTAATTTGACACTTAAATTTTTTTGACCCA
Found at i:24298 original size:61 final size:59
Alignment explanation
Indices: 24136--24308 Score: 140
Period size: 59 Copynumber: 2.9 Consensus size: 59
24126 TTAATATAAT
* * * * **
24136 ATTTGGTACTTAAACTTAATA-TATTTTTCCT-ATTTTGATACTT-AAATTTTTTTTATTCA
1 ATTTAGTACTTAAACTTGATACT-TTTTT-CTAATTTCG-TACTTAAAATTTTTTTGACCCA
* * *
24195 ATTTGGTACTTAAACTTGATACTTTTTTCTAATTTGGCACTTAAAATTTTTTTGACCCA
1 ATTTAGTACTTAAACTTGATACTTTTTTCTAATTTCGTACTTAAAATTTTTTTGACCCA
* **
24254 ATTTAGTA-TCTAAACTTGATA-TATATTTTTTAAATTTCGTACTTAAGCTTTTTTT
1 ATTTAGTACT-TAAACTTGATACT-T-TTTTCT-AATTTCGTACTTAAAATTTTTTT
24309 TAAATTCAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 8 0.08
59 62 0.65
60 6 0.06
61 19 0.20
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.53
Consensus pattern (59 bp):
ATTTAGTACTTAAACTTGATACTTTTTTCTAATTTCGTACTTAAAATTTTTTTGACCCA
Found at i:24577 original size:29 final size:29
Alignment explanation
Indices: 24545--24660 Score: 107
Period size: 29 Copynumber: 4.0 Consensus size: 29
24535 AATTACCAAC
24545 TTAAAAAAATGTCAAATTTAAGTATCAAA
1 TTAAAAAAATGTCAAATTTAAGTATCAAA
* * *
24574 TTAAAAAAATATCAAATTTGAGTACCAAA
1 TTAAAAAAATGTCAAATTTAAGTATCAAA
*
24603 TTGAACAAAA----AAATTTAAGTA-CTAAA
1 TT-AAAAAAATGTCAAATTTAAGTATC-AAA
* *
24629 TTAAGAAAAAGTGTCAAATTCAGGTATCAAA
1 TTAA-AAAAA-TGTCAAATTTAAGTATCAAA
24660 T
1 T
24661 ATTATATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.04
26 19 0.27
29 28 0.40
30 6 0.09
31 13 0.19
32 1 0.01
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (29 bp):
TTAAAAAAATGTCAAATTTAAGTATCAAA
Found at i:25724 original size:11 final size:11
Alignment explanation
Indices: 25701--25824 Score: 87
Period size: 11 Copynumber: 11.5 Consensus size: 11
25691 ATAAAAAAAC
25701 TTATTATTTTTA
1 TTATTA-TTTTA
25713 TTATTATTTTA
1 TTATTATTTTA
* * *
25724 TCA-TGTTTTG
1 TTATTATTTTA
*
25734 TTGTT-TTTT-
1 TTATTATTTTA
25743 TT-TT-TTTTAA
1 TTATTATTTT-A
* * *
25753 TCATTGTTTTG
1 TTATTATTTTA
*
25764 CTATTATTTTA
1 TTATTATTTTA
* *
25775 TTATTATATTG
1 TTATTATTTTA
25786 TTATTATTTTA
1 TTATTATTTTA
* *
25797 TTATTATATTG
1 TTATTATTTTA
25808 TTATTATTTTA
1 TTATTATTTTA
25819 TTATTA
1 TTATTA
25825 ATGTTTAAAT
Statistics
Matches: 87, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
8 6 0.07
9 2 0.02
10 11 0.13
11 58 0.67
12 10 0.11
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:25778 original size:8 final size:8
Alignment explanation
Indices: 25765--25823 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
25755 ATTGTTTTGC
25765 TATTATTT
1 TATTATTT
25773 TATTA--T
1 TATTATTT
25779 TA-TATTGT
1 TATTATT-T
25787 TATTATTT
1 TATTATTT
25795 TATTA--T
1 TATTATTT
25801 TA-TATTGT
1 TATTATT-T
25809 TATTATTT
1 TATTATTT
25817 TATTATT
1 TATTATT
25824 AATGTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
5 4 0.09
6 6 0.14
8 25 0.58
9 8 0.19
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (8 bp):
TATTATTT
Found at i:25837 original size:22 final size:22
Alignment explanation
Indices: 25765--25824 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
25755 ATTGTTTTGC
25765 TATTATTTTATTATTATATTGT
1 TATTATTTTATTATTATATTGT
25787 TATTATTTTATTATTATATTGT
1 TATTATTTTATTATTATATTGT
25809 TATTATTTTATTATTA
1 TATTATTTTATTATTA
25825 ATGTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TATTATTTTATTATTATATTGT
Found at i:27890 original size:22 final size:23
Alignment explanation
Indices: 27865--27909 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
27855 TGTTGAATCC
*
27865 TTTATATGTTG-TTGTTTGGTGT
1 TTTAAATGTTGTTTGTTTGGTGT
*
27887 TTTAAATGTTGTTTGTTTTGTGT
1 TTTAAATGTTGTTTGTTTGGTGT
27910 GTCCCTGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.11, C:0.00, G:0.24, T:0.64
Consensus pattern (23 bp):
TTTAAATGTTGTTTGTTTGGTGT
Found at i:31477 original size:22 final size:23
Alignment explanation
Indices: 31428--31478 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
31418 ATTCTCGATT
* *
31428 TAATAATAAAATAACAAAATCAA
1 TAATAAGAAAATAACAAAATAAA
* *
31451 CAATAAGAAAA-AACCAAATAAA
1 TAATAAGAAAATAACAAAATAAA
31473 TAATAA
1 TAATAA
31479 TAGAAACATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.18
Consensus pattern (23 bp):
TAATAAGAAAATAACAAAATAAA
Found at i:44793 original size:22 final size:22
Alignment explanation
Indices: 44768--44811 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44758 CTGTTAAGAA
44768 AAAACAATT-TGAAAAAAAAAAC
1 AAAAC-ATTATGAAAAAAAAAAC
* *
44790 AAAACTTTATGACAAAAAAAAC
1 AAAACATTATGAAAAAAAAAAC
44812 TCAAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAACATTATGAAAAAAAAAAC
Found at i:53553 original size:3 final size:3
Alignment explanation
Indices: 53545--53570 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53535 TCATGTTAAA
53545 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
53571 AATTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63823 original size:3 final size:3
Alignment explanation
Indices: 63817--63844 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
63807 ATTGTTGTTT
63817 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
63845 AGTTTAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:73465 original size:39 final size:40
Alignment explanation
Indices: 73419--73534 Score: 155
Period size: 39 Copynumber: 2.9 Consensus size: 40
73409 AAAGAAAACG
* *
73419 CCGCAAAAGATAAAGCAATAGCGGCGTTTATGAAAAAATA
1 CCGCAAAAGGTAAAACAATAGCGGCGTTTATGAAAAAATA
* ** *
73459 -CGCAAAAGGTAAAACAATAGC-GCGTTTTTTCATAAATA
1 CCGCAAAAGGTAAAACAATAGCGGCGTTTATGAAAAAATA
73497 CCGCAAAAGGTAAAACAATAGCGGCGTTTATAGAAAAA
1 CCGCAAAAGGTAAAACAATAGCGGCGTTTAT-GAAAAA
73535 GCGCCGCTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
38 13 0.21
39 40 0.63
40 7 0.11
41 3 0.05
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.20
Consensus pattern (40 bp):
CCGCAAAAGGTAAAACAATAGCGGCGTTTATGAAAAAATA
Found at i:73625 original size:41 final size:41
Alignment explanation
Indices: 73574--73748 Score: 169
Period size: 41 Copynumber: 4.3 Consensus size: 41
73564 GTTTATGTCG
*
73574 AAGCGTCGCTAAAGGTCAGAGCATTAGCGACGC-TTCCACAT
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTTCC-CAT
* * * * *
73615 AAGTGCCGCTAAAGGTCAGTGCATTAGTGGCACTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTTCCCAT
* * * * * *
73656 AAGCACCGCTAAAGGTCATAGCACTAGTGGC-CTTTCCCCT
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTTCCCAT
*
73696 AAGCGTCGCTAAAGGTCAGTA-CATTAGCGACGCTTTCTCC-T
1 AAGCGCCGCTAAAGGTCAG-AGCATTAGCGACGCTTTC-CCAT
*
73737 AAGGGCCGCTAA
1 AAGCGCCGCTAA
73749 TGCTCTGAGC
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
40 31 0.28
41 73 0.66
42 6 0.05
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTTCCCAT
Found at i:74620 original size:168 final size:168
Alignment explanation
Indices: 74341--74672 Score: 540
Period size: 168 Copynumber: 2.0 Consensus size: 168
74331 GCTGGAACAG
*
74341 TAACAATGAAAATGACACCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATATGGT
1 TAACAATGAAAATGACACCCTCTTTAGTGAAATTATATGAACAAATGCCCGAACCTAAATATGGT
*
74406 ATTGCTATGGGCGCGTGTACAATTACAGGAGGAATGTTCAGTACTGATTCTTATAGCACTGTTTG
66 ATTGCTATGGGCGCGTGTACAATTACAGGAGGAATGTTCAGTACTGATTCTTATAGCACTGTTCG
*
74471 GGGGGTCGATAAGTTAATTCCCGTGGATGTCTATACAA
131 GGGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAA
* * * *
74509 TAACAATGAAAATGGCGCCTTCTTTAGTGAAATTATATGAACAAATGCCCGAACCTAAATATGTT
1 TAACAATGAAAATGACACCCTCTTTAGTGAAATTATATGAACAAATGCCCGAACCTAAATATGGT
* ** *
74574 ATTGCTATGGGTGCGTGTACAATTACAGGATGG-ATGTTTGGTACTGATTCTTATAGTACTGTTC
66 ATTGCTATGGGCGCGTGTACAATTACAGGA-GGAATGTTCAGTACTGATTCTTATAGCACTGTTC
*
74638 GGGGGGTGGATAAGCTAATTCCCGTGGATGTCTAT
130 GGGGGGTCGATAAGCTAATTCCCGTGGATGTCTAT
74673 TTGCTGGGCT
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
168 149 0.99
169 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (168 bp):
TAACAATGAAAATGACACCCTCTTTAGTGAAATTATATGAACAAATGCCCGAACCTAAATATGGT
ATTGCTATGGGCGCGTGTACAATTACAGGAGGAATGTTCAGTACTGATTCTTATAGCACTGTTCG
GGGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAA
Found at i:74747 original size:17 final size:17
Alignment explanation
Indices: 74720--74790 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
74710 ATAAATTCTA
74720 AATAGACTAAATATAAAT
1 AATA-ACTAAATATAAAT
*
74738 AATAACTAAATAAAAAT
1 AATAACTAAATATAAAT
*
74755 AATAATTTAAATA-AAAT
1 AATAA-CTAAATATAAAT
*
74772 AATAA-TATATAT-AAT
1 AATAACTAAATATAAAT
74787 AATA
1 AATA
74791 GATAGAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 12 0.25
17 26 0.54
18 10 0.21
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
AATAACTAAATATAAAT
Found at i:74785 original size:12 final size:12
Alignment explanation
Indices: 74770--74816 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
74760 TTTAAATAAA
74770 ATAATAATATAT
1 ATAATAATATAT
*
74782 ATAATAATAGAT
1 ATAATAATATAT
* *
74794 AGAATAATA-AA
1 ATAATAATATAT
74805 ATAAATAATATA
1 AT-AATAATATA
74817 GAAATATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 2 0.07
12 26 0.90
13 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:74823 original size:44 final size:45
Alignment explanation
Indices: 74728--74824 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 45
74718 TAAATAGACT
**
74728 AAATATAAATAATAACTAAATAAAAATAATAATTTAAATAAAATA
1 AAATATAAATAATAACTAAATAAAAATAATAAAATAAATAAAATA
* * * *
74773 ATAATATATATAATAA-TAGAT-AGAATAATAAAATAAATAATATA
1 A-AATATAAATAATAACTAAATAAAAATAATAAAATAAATAAAATA
74817 GAAATATA
1 -AAATATA
74825 GATTTCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
44 25 0.57
45 6 0.14
46 13 0.30
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (45 bp):
AAATATAAATAATAACTAAATAAAAATAATAAAATAAATAAAATA
Found at i:74851 original size:6 final size:6
Alignment explanation
Indices: 74842--74896 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
74832 AAATCGAAAT
* * *
74842 ATATTA ATATAA ATA-TA ATATTA ATATAA ATATTA ATAATT- A-CTTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA AT-ATTA ATATTA
74888 ATATTA ATA
1 ATATTA ATA
74897 ACAAATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.05
5 5 0.13
6 29 0.74
7 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATTA
Found at i:74864 original size:17 final size:18
Alignment explanation
Indices: 74842--74896 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 18
74832 AAATCGAAAT
74842 ATATTAATATAAATA-TA
1 ATATTAATATAAATATTA
74859 ATATTAATATAAATATTA
1 ATATTAATATAAATATTA
*
74877 ATAATTACT-T-AATATTA
1 AT-ATTAATATAAATATTA
74894 ATA
1 ATA
74897 ACAAATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 1 0.03
17 24 0.69
18 5 0.14
19 5 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAATATAAATATTA
Found at i:74873 original size:12 final size:11
Alignment explanation
Indices: 74846--74879 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
74836 CGAAATATAT
*
74846 TAATATAAATA
1 TAATATTAATA
74857 TAATATTAATA
1 TAATATTAATA
74868 TAAATATTAATA
1 T-AATATTAATA
74880 ATTACTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATATTAATA
Found at i:74876 original size:29 final size:28
Alignment explanation
Indices: 74842--74921 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
74832 AAATCGAAAT
74842 ATATTAATATAAATATAATATTAATATA-A
1 ATATTAATATAAAT-TAATATTAATA-ACA
* *
74871 ATATTAATAATTACTTAATATTAATAACA
1 ATATTAAT-ATAAATTAATATTAATAACA
*
74900 A-A-TAATATAAATTAATAATAAT
1 ATATTAATATAAATTAATATTAAT
74922 TGATAATAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 13 0.30
27 4 0.09
28 2 0.05
29 21 0.48
30 4 0.09
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATTAATATAAATTAATATTAATAACA
Found at i:80524 original size:19 final size:19
Alignment explanation
Indices: 80468--80529 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
80458 GACCATCAAT
*
80468 AATTAAATAAATAATT-AAA
1 AATTTAATAAAT-ATTAAAA
*
80487 AATTTCATAGAA-ATCTAAAA
1 AATTTAATA-AATAT-TAAAA
*
80507 AATTTAATAAATATTAAAC
1 AATTTAATAAATATTAAAA
80526 AATT
1 AATT
80530 CAACCAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.06
19 18 0.51
20 15 0.43
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTTAATAAATATTAAAA
Found at i:83742 original size:42 final size:42
Alignment explanation
Indices: 83696--83793 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
83686 ACAAGGTGGT
*
83696 AGTGGTGGACATGGTGGAGGACGAGG-CGGTAGTGGTAGCGGA
1 AGTGGAGGACATGGTGGAGGAC-AGGACGGTAGTGGTAGCGGA
* * * *
83738 AGTGGAAGACATGGTGGAGGACAGGACGGTAGTGGTGGTGGT
1 AGTGGAGGACATGGTGGAGGACAGGACGGTAGTGGTAGCGGA
83780 AGTGGAGGACATGG
1 AGTGGAGGACATGG
83794 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 3 0.06
42 46 0.94
ACGTcount: A:0.23, C:0.08, G:0.51, T:0.17
Consensus pattern (42 bp):
AGTGGAGGACATGGTGGAGGACAGGACGGTAGTGGTAGCGGA
Found at i:111155 original size:16 final size:15
Alignment explanation
Indices: 111117--111165 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
111107 TAAAAGAAGC
*
111117 TAAATTT-TAAGAAA
1 TAAATTTATAAAAAA
*
111131 TAAAATTATAAAAAA
1 TAAATTTATAAAAAA
111146 TTAAATTTATAAAAAA
1 -TAAATTTATAAAAAA
111162 -AAAT
1 TAAAT
111166 ACATAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.33
15 6 0.20
16 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAATTTATAAAAAA
Found at i:118208 original size:45 final size:46
Alignment explanation
Indices: 118126--118219 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
118116 TCTTGTAAAG
*
118126 TTATAAATTTAGTAAATGTTGTCGGATAGTTTCAAGATTTTAAATT
1 TTATAAATTTAGTAAATATTGTCGGATAGTTTCAAGATTTTAAATT
*
118172 TTATAAATTTTA-TAAA-ATTGTCGGATTA-TTTTAAGATTTTAAATT
1 TTATAAA-TTTAGTAAATATTGTCGGA-TAGTTTCAAGATTTTAAATT
118217 TTA
1 TTA
118220 ATTTTGATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
45 27 0.61
46 13 0.30
47 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (46 bp):
TTATAAATTTAGTAAATATTGTCGGATAGTTTCAAGATTTTAAATT
Found at i:122687 original size:21 final size:20
Alignment explanation
Indices: 122656--122705 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
122646 TGAAAAATAA
*
122656 TAAAATAAATAATTCATGAAGT
1 TAAAA-AAATAACTC-TGAAGT
* *
122678 TAAAAAAATAACTCTTAATT
1 TAAAAAAATAACTCTGAAGT
122698 TAAAAAAA
1 TAAAAAAA
122706 AATAAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.48
21 8 0.32
22 5 0.20
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAACTCTGAAGT
Found at i:125232 original size:25 final size:25
Alignment explanation
Indices: 125195--125243 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
125185 GTCAATTTTT
125195 TAATAAAAATAATTAATATAAATTG
1 TAATAAAAATAATTAATATAAATTG
* *
125220 TAATGAAATTAATTAATATAAATT
1 TAATAAAAATAATTAATATAAATT
125244 ATAAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TAATAAAAATAATTAATATAAATTG
Found at i:126170 original size:26 final size:24
Alignment explanation
Indices: 126128--126179 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
126118 ACGACGACGA
126128 TGTCGTTGACCAGTTGTCGTTGACTG
1 TGTCGTTGACCAGTTGT-GTT-ACTG
*
126154 TGTCGTT-ACCTGTTTGTGTTACTG
1 TGTCGTTGACCAG-TTGTGTTACTG
126178 TG
1 TG
126180 GTGGTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 7 0.29
26 11 0.46
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (24 bp):
TGTCGTTGACCAGTTGTGTTACTG
Found at i:130354 original size:29 final size:29
Alignment explanation
Indices: 130308--130721 Score: 290
Period size: 29 Copynumber: 14.2 Consensus size: 29
130298 GCTCTAGAGG
* *
130308 TCCCTAAACTATCCAAAAATTCCA-TTTTA
1 TCCCCAAACT-TCCAAAAATCCCATTTTTA
*
130337 TCCCCAAACTTCAAAAAATCCCATTTTTGA
1 TCCCCAAACTTCCAAAAATCCCATTTTT-A
* * *
130367 -CTCTCGAACTTCCAAAAATCCCATTTTGA
1 TC-CCCAAACTTCCAAAAATCCCATTTTTA
*
130396 -CCTCGAAACTTCCAAAAAAT-CCATTTTTA
1 TCC-CCAAACTTCC-AAAAATCCCATTTTTA
***
130425 -CCCTCAAACTTTTGAAAATCCCATTTTTA
1 TCCC-CAAACTTCCAAAAATCCCATTTTTA
* **
130454 ACCCCAAAACTTCCAAAAATTTCATTTTTA
1 TCCCC-AAACTTCCAAAAATCCCATTTTTA
* *
130484 CCCCCGAACTTCCAAAAATCCCATTTTTA
1 TCCCCAAACTTCCAAAAATCCCATTTTTA
* *
130513 ACCCCAAAACTTCCAAAAATTCCATTTTTA
1 TCCCC-AAACTTCCAAAAATCCCATTTTTA
* * *
130543 CCCCCGAACTTTCAAAAATCCCATTTTTGA
1 TCCCCAAACTTCCAAAAATCCCATTTTT-A
* * ** *
130573 -CTCCGAAACTTTCAAAAATTTCGTTTTTA
1 TC-CCCAAACTTCCAAAAATCCCATTTTTA
** * *** *
130602 -CCCTTGAAGTTTTGAAAATCCCATTTTGA
1 TCCC-CAAACTTCCAAAAATCCCATTTTTA
* *
130631 -CCCCAAAACTTCCAAAAATTCAATTTTTA
1 TCCCC-AAACTTCCAAAAATCCCATTTTTA
* *
130660 CCCCCAAACTTTCAAAAATCCCATTTTTA
1 TCCCCAAACTTCCAAAAATCCCATTTTTA
* * *
130689 ACCTCAAAACTTCC-AAAATTCCATTTTTA
1 TCC-CCAAACTTCCAAAAATCCCATTTTTA
130718 -CCCC
1 TCCCC
130722 TCGAGTTTCC
Statistics
Matches: 307, Mismatches: 62, Indels: 34
0.76 0.15 0.08
Matches are distributed among these distances:
27 1 0.00
28 22 0.07
29 169 0.55
30 115 0.37
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
TCCCCAAACTTCCAAAAATCCCATTTTTA
Found at i:130420 original size:59 final size:59
Alignment explanation
Indices: 130342--130757 Score: 437
Period size: 59 Copynumber: 7.1 Consensus size: 59
130332 TTTTATCCCC
* * * *
130342 AAACTTCAAAAAATCCCATTTTTGACTCTCGAACTTCCAAAAATCCCA-TTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * *** * *
130401 AAACTTCCAAAAAATCCATTTTTACCCTCAAACTTTTGAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * *
130460 AAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * *
130519 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTCAAAAATCCCATTTTTGA-CTCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCT-CA
* * * * * *** *
130578 AAACTTTCAAAAATTTCGTTTTTACCCTTGAAGTTTTGAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * *
130636 AAACTTCCAAAAATTCAATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
** * * *
130695 AAACTTCC-AAAATTCCATTTTTACCCCTCGAGTTTCC-AAAATCCAATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
130753 AAACT
1 AAACT
130758 ATCAAAATTA
Statistics
Matches: 297, Mismatches: 55, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
58 100 0.34
59 197 0.66
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
Found at i:130465 original size:88 final size:87
Alignment explanation
Indices: 130313--130757 Score: 336
Period size: 88 Copynumber: 5.1 Consensus size: 87
130303 AGAGGTCCCT
* *
130313 AAACTATCCAAAAATTCCA-TTTTATCCC-CAAAC-TTCAAAAAATCCCATTTTTGACTCTC-GA
1 AAACT-TCCAAAAAATCCATTTTTA-CCCTCAAACTTTC-AAAAATCCCATTTTT-AC-CCCAGA
130374 ACTTCCAAAAATCCCATTTTGACCTCG
61 ACTTCCAAAAATCCCATTTTGACCTCG
** *
130401 AAACTTCCAAAAAATCCATTTTTACCCTCAAACTTTTGAAAATCCCATTTTTAACCCCAAAACTT
1 AAACTTCCAAAAAATCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTT-ACCCCAGAACTT
** * *
130466 CCAAAAATTTCATTTTTACCCCCG
65 CCAAAAATCCCATTTTGA-CCTCG
* * *
130490 -AACTTCC-AAAAATCCCATTTTTAACCC-CAAAACTTCCAAAAATTCCATTTTTACCCCCGAAC
1 AAACTTCCAAAAAAT-CCATTTTT-ACCCTC-AAACTTTCAAAAATCCCATTTTTACCCCAGAAC
*
130552 TTTCAAAAATCCCATTTTTGA-CTCCG
63 TTCCAAAAATCCCA-TTTTGACCT-CG
* * * * ** * ** * *
130578 AAACTTTCAAAAATTTCGTTTTTACCCTTGAAGTTTTGAAAATCCCATTTTGACCCCAAAACTTC
1 AAACTTCCAAAAAATCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTACCCCAGAACTTC
* * * * *
130643 CAAAAATTCAATTTTTACCCCC
66 CAAAAATCCCATTTTGACCTCG
* * * * * **
130665 AAACTTTC-AAAAATCCCATTTTTAACCTCAAAAC-TTCCAAAATTCCATTTTTACCCCTCGAGT
1 AAACTTCCAAAAAAT-CCATTTTTACCCTC-AAACTTTCAAAAATCCCATTTTTACCCC-AGAAC
*
130728 TTCC-AAAATCCAATTTTCGACCTCG
63 TTCCAAAAATCCCATTTT-GACCTCG
130753 AAACT
1 AAACT
130758 ATCAAAATTA
Statistics
Matches: 279, Mismatches: 60, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
86 5 0.02
87 79 0.28
88 144 0.52
89 46 0.16
90 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (87 bp):
AAACTTCCAAAAAATCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTACCCCAGAACTTC
CAAAAATCCCATTTTGACCTCG
Found at i:135867 original size:24 final size:23
Alignment explanation
Indices: 135816--135867 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
135806 CTTTGTGGAT
* *
135816 GTTTTTACTCTACTTTGTAACAC
1 GTTTTTACTCTACCTTATAACAC
* *
135839 GTTTTTCCTCTACCTTATGACAC
1 GTTTTTACTCTACCTTATAACAC
*
135862 GCTTTT
1 GTTTTT
135868 GTCTTATGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.10, T:0.48
Consensus pattern (23 bp):
GTTTTTACTCTACCTTATAACAC
Found at i:135875 original size:18 final size:18
Alignment explanation
Indices: 135852--135889 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
135842 TTTCCTCTAC
*
135852 CTTATGACACGCTTTTGT
1 CTTATGACACACTTTTGT
*
135870 CTTATGACACATTTTTGT
1 CTTATGACACACTTTTGT
135888 CT
1 CT
135890 ACTTTTGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (18 bp):
CTTATGACACACTTTTGT
Found at i:136559 original size:60 final size:61
Alignment explanation
Indices: 136446--136559 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 61
136436 CAAATCGAAT
* * * **
136446 AAAAAAAGATTAAGTATCAAATTAAGAAAATGAGTCAAGTTTAGGTATTAAATTGAACCCC
1 AAAAAAAGATTAAGTATCAAATTAAGAAAAAGAGTCAAATTTAAGTACCAAATTGAACCCC
* *
136507 AAAAAAA-ATTAAGTATCAACTTAAGAAAAAGTGTCAAATTTAAGTACCAAATT
1 AAAAAAAGATTAAGTATCAAATTAAGAAAAAGAGTCAAATTTAAGTACCAAATT
136560 AAAAAAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 39 0.85
61 7 0.15
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (61 bp):
AAAAAAAGATTAAGTATCAAATTAAGAAAAAGAGTCAAATTTAAGTACCAAATTGAACCCC
Found at i:136588 original size:29 final size:31
Alignment explanation
Indices: 136512--136586 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
136502 ACCCCAAAAA
* * *
136512 AAATT-AAGTATCAACTTAAGAAAAAGTGTC
1 AAATTCAAGTACCAAATTAAGAAAAAATGTC
*
136542 AAATTTAAGTACCAAATTAA-AAAAAATGTC
1 AAATTCAAGTACCAAATTAAGAAAAAATGTC
*
136572 AAATTCAATTACCAA
1 AAATTCAAGTACCAA
136587 TTTGTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 27 0.69
31 12 0.31
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (31 bp):
AAATTCAAGTACCAAATTAAGAAAAAATGTC
Found at i:137036 original size:23 final size:22
Alignment explanation
Indices: 137001--137043 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
136991 TTTCAATCCT
*
137001 TTAAAAATGATAAAATTATAAA
1 TTAAAAATAATAAAATTATAAA
137023 TTAATAAATAATAAAATTATA
1 TTAA-AAATAATAAAATTATA
137044 TTTTGACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAAATAATAAAATTATAAA
Found at i:137379 original size:17 final size:17
Alignment explanation
Indices: 137349--137382 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
137339 CATTTTAACT
137349 TTGTAAAAACTATTTAA
1 TTGTAAAAACTATTTAA
* *
137366 TTGTATAAATTATTTAA
1 TTGTAAAAACTATTTAA
137383 AATCTCATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
TTGTAAAAACTATTTAA
Found at i:150426 original size:27 final size:25
Alignment explanation
Indices: 150391--150456 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 25
150381 TTAATTGAAC
* *
150391 AAATTTTTTATTGACATATCAAGTTTG
1 AAATGTTTT-TTGACATAT-AAATTTG
* *
150418 AAATGTTTTTTTGATATGTAAATTTG
1 AAATG-TTTTTTGACATATAAATTTG
*
150444 AAACGTTTTTTGA
1 AAATGTTTTTTGA
150457 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 8 0.24
26 10 0.30
27 11 0.33
28 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (25 bp):
AAATGTTTTTTGACATATAAATTTG
Found at i:151854 original size:17 final size:17
Alignment explanation
Indices: 151834--151868 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
151824 TCATTTAATT
151834 TTGTAAAAACTATTTAA
1 TTGTAAAAACTATTTAA
* *
151851 TTGTATAAATTATTTAA
1 TTGTAAAAACTATTTAA
151868 T
1 T
151869 ATCTCGGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (17 bp):
TTGTAAAAACTATTTAA
Found at i:154202 original size:59 final size:59
Alignment explanation
Indices: 154091--154238 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 59
154081 TATTTGACAT
* * * * * *
154091 TTGAACTTGATATTTTTT--TAAATTTGGTATCTAAATTTTTTTTTACCTAATTTGGAAA
1 TTGAACTTGACATTTTTTCCT-AATTTGGTACCTAAAGTTTTGTTGACCCAATTTGGAAA
* *
154149 TTGAACTTGACATTTTTTCCTAATTTGGTACCTAAAGTTTTGTTGACCCAATTTGGTAC
1 TTGAACTTGACATTTTTTCCTAATTTGGTACCTAAAGTTTTGTTGACCCAATTTGGAAA
154208 TTGAACTTGACATTTTTTCCTAATTTGGTAC
1 TTGAACTTGACATTTTTTCCTAATTTGGTAC
154239 ATAAGCTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
58 17 0.21
59 62 0.77
60 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (59 bp):
TTGAACTTGACATTTTTTCCTAATTTGGTACCTAAAGTTTTGTTGACCCAATTTGGAAA
Found at i:154236 original size:31 final size:31
Alignment explanation
Indices: 154129--154238 Score: 102
Period size: 31 Copynumber: 3.6 Consensus size: 31
154119 ATCTAAATTT
* *
154129 TTTTTTACCTAATTTGGAAATTGAACTTGACA
1 TTTTTT-CCTAATTTGGTACTTGAACTTGACA
* * *
154161 TTTTTTCCTAATTTGGTACCTAAAGTT----
1 TTTTTTCCTAATTTGGTACTTGAACTTGACA
** *
154188 TTGTTGACCCAATTTGGTACTTGAACTTGACA
1 TT-TTTTCCTAATTTGGTACTTGAACTTGACA
154220 TTTTTTCCTAATTTGGTAC
1 TTTTTTCCTAATTTGGTAC
154239 ATAAGCTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
27 2 0.03
28 19 0.32
31 30 0.51
32 8 0.14
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTTTTCCTAATTTGGTACTTGAACTTGACA
Found at i:154534 original size:89 final size:89
Alignment explanation
Indices: 154425--154615 Score: 235
Period size: 89 Copynumber: 2.1 Consensus size: 89
154415 TTAAAAAAGA
* * ***
154425 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAG-GTACCAAA-TAGGACCCCAAAAAATTTAA
1 TTAGGTATCAAATTAAGAAAAAGAGTCAAGTT-AGAGT-CCAAATTA-GACAAAAAAAAATTTAA
*
154488 GTACCAACTTAA-AAAAAATGTCAAGT
63 GTACCAAATTAAGAAAAAATGTCAAGT
* * *
154514 TTAGGTATCAAATTAAGAAAAAGTGTCAAGTTAGAGTTCAAATTAGACAAAAAAAAATTTAATTA
1 TTAGGTATCAAATTAAGAAAAAGAGTCAAGTTAGAGTCCAAATTAGACAAAAAAAAATTTAAGTA
**
154579 CCAAATTAAGAAAACGTGTCAAGT
66 CCAAATTAAGAAAAAATGTCAAGT
154603 TTAGGTATCAAAT
1 TTAGGTATCAAAT
154616 ATTATCTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
88 30 0.34
89 58 0.66
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (89 bp):
TTAGGTATCAAATTAAGAAAAAGAGTCAAGTTAGAGTCCAAATTAGACAAAAAAAAATTTAAGTA
CCAAATTAAGAAAAAATGTCAAGT
Found at i:154541 original size:31 final size:31
Alignment explanation
Indices: 154496--154615 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
154486 AAGTACCAAC
*
154496 TTAA-AAAAAATGTCAAGTTTAGGTATCAAA
1 TTAAGAAAAAGTGTCAAGTTTAGGTATCAAA
154526 TTAAGAAAAAGTGTCAAG-TTAGAGT-TCAAA
1 TTAAGAAAAAGTGTCAAGTTTAG-GTATCAAA
** * ** *
154556 TT-AGACAAAA---AAAAATTTAATTACCAAA
1 TTAAGA-AAAAGTGTCAAGTTTAGGTATCAAA
*
154584 TTAAGAAAACGTGTCAAGTTTAGGTATCAAA
1 TTAAGAAAAAGTGTCAAGTTTAGGTATCAAA
154615 T
1 T
154616 ATTATCTTAA
Statistics
Matches: 67, Mismatches: 14, Indels: 17
0.68 0.14 0.17
Matches are distributed among these distances:
27 3 0.04
28 12 0.18
29 6 0.09
30 19 0.28
31 27 0.40
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.28
Consensus pattern (31 bp):
TTAAGAAAAAGTGTCAAGTTTAGGTATCAAA
Found at i:164239 original size:16 final size:17
Alignment explanation
Indices: 164207--164253 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
164197 GGTCTATTGG
164207 AAATTAAATTTATTTTT
1 AAATTAAATTTATTTTT
*
164224 AAATTAAGTTTA-TTTT
1 AAATTAAATTTATTTTT
164240 AAATTTAAATTTAT
1 AAA-TTAAATTTAT
164254 CTGAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATTAAATTTATTTTT
Found at i:166195 original size:12 final size:12
Alignment explanation
Indices: 166178--166202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
166168 AAAAAATTCC
166178 AAACTTCCAAAA
1 AAACTTCCAAAA
166190 AAACTTCCAAAA
1 AAACTTCCAAAA
166202 A
1 A
166203 TCCCATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
AAACTTCCAAAA
Found at i:166275 original size:30 final size:29
Alignment explanation
Indices: 166190--166381 Score: 186
Period size: 29 Copynumber: 6.5 Consensus size: 29
166180 ACTTCCAAAA
****
166190 AAACTTCCAAAAATCCCATTTTTTTACGTTG
1 AAACTTCCAAAAATCCCA--TTTTTACCCCC
****
166221 AAACTTCCAAAAATTTTGTTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
* *
166250 AAACTTCAAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCC
*
166280 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
** *
166309 AAACTTCCAAAAATCCCATTTTTGACATCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCC
* ***
166339 AAACTTACAAAAATTTTATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCC
166368 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
166382 TACCACTTTA
Statistics
Matches: 130, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
29 68 0.52
30 48 0.37
31 14 0.11
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCC
Found at i:166289 original size:59 final size:59
Alignment explanation
Indices: 166190--166381 Score: 285
Period size: 59 Copynumber: 3.2 Consensus size: 59
166180 ACTTCCAAAA
* * *
166190 AAACTTCCAAAAATCCCATTTTTTTACGTTGAAACTTCCAAAAATTTTGTTTTTACCCCC
1 AAACTTCCAAAAATCCCA-TTTTTTACATCGAAACTTCCAAAAATTTTATTTTTACCCCC
* ** **
166250 AAACTTCAAAAAATCCCATTTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTTACATCGAAACTTCCAAAAATTTTATTTTTACCCCC
* *
166309 AAACTTCCAAAAATCCCATTTTTGACATCGAAACTTACAAAAATTTTATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTTACATCGAAACTTCCAAAAATTTTATTTTTACCCCC
166368 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
166382 TACCACTTTA
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
59 101 0.86
60 17 0.14
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTTACATCGAAACTTCCAAAAATTTTATTTTTACCCCC
Found at i:166394 original size:29 final size:29
Alignment explanation
Indices: 166221--166382 Score: 189
Period size: 29 Copynumber: 5.5 Consensus size: 29
166211 TTTTACGTTG
***
166221 AAACTTCCAAAAATTTTGTTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
166250 AAACTTCAAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
166280 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* ** *
166309 AAACTTCCAAAAATCCCATTTTTGACATCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* **
166339 AAACTTACAAAAATTTTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
166368 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
166383 ACCACTTTAC
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
29 62 0.56
30 48 0.44
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:169799 original size:36 final size:36
Alignment explanation
Indices: 169752--169823 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
169742 TCTTTGCAAG
*
169752 ATAATGAAATACGAACTAAGATTTTGGAAAGGACGT
1 ATAATCAAATACGAACTAAGATTTTGGAAAGGACGT
*
169788 ATAATCAAATACGAACTGAGATTTTGGAAAGGACGT
1 ATAATCAAATACGAACTAAGATTTTGGAAAGGACGT
169824 TGAAGACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
ATAATCAAATACGAACTAAGATTTTGGAAAGGACGT
Found at i:174040 original size:48 final size:48
Alignment explanation
Indices: 173985--174081 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
173975 CTTCAGGACC
*
173985 TTGAAGATAATCAAGATTGTGATCCACCTTCGGATATGTTAAGAATGA
1 TTGAAGATAATCAAGATTGTGATCCACCTCCGGATATGTTAAGAATGA
*
174033 TTGAAGATAATCAAGATTGTGATCCACCTCCGGATCTGTTAAGAATGA
1 TTGAAGATAATCAAGATTGTGATCCACCTCCGGATATGTTAAGAATGA
174081 T
1 T
174082 AGAAAAGGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (48 bp):
TTGAAGATAATCAAGATTGTGATCCACCTCCGGATATGTTAAGAATGA
Found at i:178387 original size:207 final size:207
Alignment explanation
Indices: 178032--178505 Score: 804
Period size: 207 Copynumber: 2.3 Consensus size: 207
178022 TGTGATACCC
* * *
178032 ACAAACGACGCAGTTAGCTTGCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCAA
1 ACAAACGACGCGGTCAGCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCAA
* *
178097 AGCGAGCAAAATTTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAAGTCGAAGTAATAAA
66 AGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
*
178162 ACGGATAGCTTCCTGATGAGACACTGAGGAGTGAACCAAATTCATCTTCCTGATGAGATACAGAG
131 ACGGATAGCTTCCTGATGAGACACTGAGGAGTGAACCAAATTCATCTTCCTGATGAGATACAGAA
178227 AAGCGGACTGAA
196 AAGCGGACTGAA
*
178239 ACAAACGACGCGGTCAGCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCTACGTTCAA
1 ACAAACGACGCGGTCAGCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCAA
* *
178304 AGTGAGCAAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
66 AGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
* *
178369 ACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAA
131 ACGGATAGCTTCCTGATGAGACACTGAGGAGTGAACCAAATTCATCTTCCTGATGAGATACAGAA
178434 AAGCGGACTGAA
196 AAGCGGACTGAA
* * * * *
178446 ACAAACGACGCGATCATCTTCCTGATGAAATACTAAGAAGATGACCAAATCAAACCCACG
1 ACAAACGACGCGGTCAGCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
178506 CGCGATAAAT
Statistics
Matches: 250, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
207 250 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (207 bp):
ACAAACGACGCGGTCAGCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCAA
AGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
ACGGATAGCTTCCTGATGAGACACTGAGGAGTGAACCAAATTCATCTTCCTGATGAGATACAGAA
AAGCGGACTGAA
Found at i:178901 original size:17 final size:17
Alignment explanation
Indices: 178882--178957 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
178872 CTATTGGAAA
178882 TTAAATTTATTTTTAAA-
1 TTAAATTTA-TTTTAAAT
* *
178899 TTAAGTATATTTTAAAT
1 TTAAATTTATTTTAAAT
*
178916 TTAAATTTATTTGAAAT
1 TTAAATTTATTTTAAAT
*
178933 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
178950 TTAAATTT
1 TTAAATTT
178958 CAAATGTCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
16 7 0.14
17 44 0.86
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:178934 original size:7 final size:6
Alignment explanation
Indices: 178909--178962 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
178899 TTAAGTATAT
178909 TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
178955 TTTCAAA T
1 TTT-AAA T
178963 GTCCAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 7 0.17
5 1 0.02
6 22 0.54
7 11 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:179030 original size:10 final size:10
Alignment explanation
Indices: 179010--179042 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
179000 GGCCTAATTA
179010 CAAAT-GGCC
1 CAAATAGGCC
179019 CAAATAGGCC
1 CAAATAGGCC
179029 CAAATAGGCC
1 CAAATAGGCC
179039 CAAA
1 CAAA
179043 CTCATTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.42, C:0.30, G:0.18, T:0.09
Consensus pattern (10 bp):
CAAATAGGCC
Found at i:180819 original size:162 final size:160
Alignment explanation
Indices: 180591--180926 Score: 573
Period size: 162 Copynumber: 2.1 Consensus size: 160
180581 AGCACTAGGA
*
180591 GCTGCCACGTGTCATATTTTTGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAA
1 GCTGCCACGTGTCATATTTTGGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAA
* *
180656 TTTAATCCTTAAATCAGGTTCGCTTCAATTACAAAATTGCCCCAAAAATTTTCCATCGTTTTCAA
66 TTTAATCCTTAAATCAGGTTCGCTTCAATTACAAAATTACCACAAAAATTTTCCATCGTTTTCAA
180721 AATAGTCCTCTAACTTCAGGATCCCTAAGGG
131 AATAGTCCTCTAACTTCAGGATCCCTAA-GG
*
180752 GCTGCCATGTGTCATGATTTTGGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTA
1 GCTGCCACGTGTCAT-ATTTTGGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTA
* *
180817 ATTTAATCCTTAAATCATGTTCGCTTCAATTACAAAATTACCACAGAAATTTTCCATCGTTTTCA
65 ATTTAATCCTTAAATCAGGTTCGCTTCAATTACAAAATTACCACAAAAATTTTCCATCGTTTTCA
* * *
180882 AAATAGTCCTCTGACTTCAGGATGCCTGAGG
130 AAATAGTCCTCTAACTTCAGGATCCCTAAGG
180913 GCTGCCACGTGTCA
1 GCTGCCACGTGTCA
180927 CCTGTATTAG
Statistics
Matches: 164, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
161 29 0.18
162 135 0.82
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (160 bp):
GCTGCCACGTGTCATATTTTGGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAA
TTTAATCCTTAAATCAGGTTCGCTTCAATTACAAAATTACCACAAAAATTTTCCATCGTTTTCAA
AATAGTCCTCTAACTTCAGGATCCCTAAGG
Found at i:180999 original size:29 final size:29
Alignment explanation
Indices: 180966--181297 Score: 352
Period size: 29 Copynumber: 11.3 Consensus size: 29
180956 CCCTAAATTG
*
180966 TCCAAAAATTCTATTTTTACCCTC-AAACT
1 TCCAAAAATTCCATTTTTACCC-CGAAACT
* *
180995 TCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCGAAACT
**
181025 TCCAAAAATTCCATTTTTACCCTTAAACT
1 TCCAAAAATTCCATTTTTACCCCGAAACT
* * *
181054 TCCAAAAATCCCATTTTCAACCCCAAAACT
1 TCCAAAAATTCCATTTT-TACCCCGAAACT
* *
181084 TCCAAAAATTCCGTTTTTACCGCC-AAATT
1 TCCAAAAATTCCATTTTTACC-CCGAAACT
*
181113 TCCAAAAA-TCTCATTTTTGACCTCGAAACT
1 TCCAAAAATTC-CATTTTT-ACCCCGAAACT
*
181143 TCCAAAAATTTCATTTTTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCC-CGAAACT
*
181172 TCCAAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCGAAACT
*
181202 TACAAAAATTCCATTTTTACCCCTG-AACT
1 TCCAAAAATTCCATTTTTACCCC-GAAACT
* * *
181231 TCCAAAAATCCCATTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCCGAAACT
* **
181260 TCCCAAAATTTTATTTTTACCCCG-AACT
1 TCCAAAAATTCCATTTTTACCCCGAAACT
*
181288 TCCACAAATT
1 TCCAAAAATT
181298 ACCACTTTAC
Statistics
Matches: 256, Mismatches: 34, Indels: 27
0.81 0.11 0.09
Matches are distributed among these distances:
28 15 0.06
29 139 0.54
30 101 0.39
31 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCGAAACT
Found at i:181058 original size:59 final size:59
Alignment explanation
Indices: 180966--181296 Score: 427
Period size: 59 Copynumber: 5.6 Consensus size: 59
180956 CCCTAAATTG
* * *
180966 TCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* ** *
181025 TCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTCAACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * * *
181084 TCCAAAAATTCCGTTTTTACCGC-CAAATTTCCAAAAATCTCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTACC-CTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* *
181143 TCCAAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
181202 TACAAAAATTCCATTTTTACCC-CTGAACTTCCAAAAATCCCA-TTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* ** * *
181260 TCCCAAAATTTTATTTTTACCC-CGAACTTCCACAAAT
1 TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAAT
181297 TACCACTTTA
Statistics
Matches: 244, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
57 13 0.05
58 36 0.15
59 194 0.80
60 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
Found at i:187234 original size:239 final size:239
Alignment explanation
Indices: 186815--187292 Score: 938
Period size: 239 Copynumber: 2.0 Consensus size: 239
186805 AAAATCCTCC
186815 TAAAATATCTCAACTAAATTGAGAGTAACTCATGTACTCCTTTATTTACACAAATTAAGGAATAT
1 TAAAATATCTCAACTAAATTGAGAGTAACTCATGTACTCCTTTATTTACACAAATTAAGGAATAT
186880 ACTAACTGTTGATTGACTCCTAAAATAAAAGACTTGACCAAATTCAAATAACAAAAAGTTACACT
66 ACTAACTGTTGATTGACTCCTAAAATAAAAGACTTGACCAAATTCAAATAACAAAAAGTTACACT
*
186945 AACCTTTGACAAAGTTTTTCTGGCTGTGATGAATCAAAATCTTCATCTATTTATTTTATGATCGT
131 AACCTTTGACAAAGTTTTTCTGGCTGTGATGAATCAAAATCTTCATCTATTTATTTTATGATCAT
187010 CTTCTAATATTGAAGAAAGCATTACCTCTTTTTCTTCTTTGTTT
196 CTTCTAATATTGAAGAAAGCATTACCTCTTTTTCTTCTTTGTTT
187054 TAAAATATCTCAACTAAATTGAGAGTAACTCATGTACTCCTTTATTTACACAAATTAAGGAATAT
1 TAAAATATCTCAACTAAATTGAGAGTAACTCATGTACTCCTTTATTTACACAAATTAAGGAATAT
187119 ACTAACTGTTGATTGACTCCTAAAATAAAAGACTTGACCAAATTCAAATAACAAAAAGTTACACT
66 ACTAACTGTTGATTGACTCCTAAAATAAAAGACTTGACCAAATTCAAATAACAAAAAGTTACACT
187184 AACCTTTGACAAAGTTTTTCTGGCTGTGATGAATCAAAATCTTCATCTATTTATTTTATGATCAT
131 AACCTTTGACAAAGTTTTTCTGGCTGTGATGAATCAAAATCTTCATCTATTTATTTTATGATCAT
*
187249 CTTCTGATATTGAAGAAAGCATTACCTCTTTTTCTTCTTTGTTT
196 CTTCTAATATTGAAGAAAGCATTACCTCTTTTTCTTCTTTGTTT
187293 GAATTTTGTT
Statistics
Matches: 237, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 237 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (239 bp):
TAAAATATCTCAACTAAATTGAGAGTAACTCATGTACTCCTTTATTTACACAAATTAAGGAATAT
ACTAACTGTTGATTGACTCCTAAAATAAAAGACTTGACCAAATTCAAATAACAAAAAGTTACACT
AACCTTTGACAAAGTTTTTCTGGCTGTGATGAATCAAAATCTTCATCTATTTATTTTATGATCAT
CTTCTAATATTGAAGAAAGCATTACCTCTTTTTCTTCTTTGTTT
Found at i:196297 original size:30 final size:30
Alignment explanation
Indices: 196261--196322 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
196251 CAATGAGTCT
196261 ATTTTTATGGACCATTTTATAACTAATTTA
1 ATTTTTATGGACCATTTTATAACTAATTTA
196291 ATTTTTATGGACCATTTTATAACTAATTTA
1 ATTTTTATGGACCATTTTATAACTAATTTA
196321 AT
1 AT
196323 ACAATAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (30 bp):
ATTTTTATGGACCATTTTATAACTAATTTA
Found at i:197416 original size:74 final size:73
Alignment explanation
Indices: 197270--197419 Score: 232
Period size: 74 Copynumber: 2.0 Consensus size: 73
197260 GAAGGAAAAG
* *
197270 AAAGTTTTGAAAGGAAACTAGTTTTTTTATTTTTCCTTTTTTTGGTAGAAGGAAAATAGGAGGGA
1 AAAGGTTTGAAAGGAAACTAGTTTTATTATTTTTCCTTTTTTTGGTAGAAGGAAAATAGGAGGGA
*
197335 AGGAAGGA
66 AGAAAGGA
197343 AAAGGTTTGAAAGGAAACTAG-TTTATT-TTTTTCCATTTTTTTTTGGTAGAAGGAAAATAGGAG
1 AAAGGTTTGAAAGGAAACTAGTTTTATTATTTTTCC---TTTTTTTGGTAGAAGGAAAATAGGAG
197406 GGAAGAAAGGA
63 GGAAGAAAGGA
197417 AAA
1 AAA
197420 TGGGTTTAGA
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
71 7 0.10
72 5 0.07
73 20 0.28
74 39 0.55
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (73 bp):
AAAGGTTTGAAAGGAAACTAGTTTTATTATTTTTCCTTTTTTTGGTAGAAGGAAAATAGGAGGGA
AGAAAGGA
Found at i:197449 original size:98 final size:101
Alignment explanation
Indices: 197332--197513 Score: 264
Period size: 103 Copynumber: 1.8 Consensus size: 101
197322 AAAATAGGAG
197332 GGAAGGAAGGAAAAGGTTTGAAAGGAAACTAGTTT-A-TTT-TTTTCCATTTTTTTTTGGTAGAA
1 GGAAGGAAGGAAAAGGTTTGAAAGGAAACTAGTTTCATTTTCTTTTCCATTTTTTTTTGGTAGAA
*
197394 GGAAAATAGGAGGGAAGAAAGGAAAATGGGTTTAGA
66 GGAAAATAGAAGGGAAGAAAGGAAAATGGGTTTAGA
* ***
197430 GGAAGGAA-GAGAAAGGTTTGAAAGGAAATTAGTTTCATTTTTGCTTTTTTTTTTTTTTTTGGTA
1 GGAAGGAAGGA-AAAGGTTTGAAAGGAAACTAGTTTCA-TTTT-CTTTTCCATTTTTTTTTGGTA
197494 GAAGGAAAATAGAAGGGAAG
63 GAAGGAAAATAGAAGGGAAG
197514 GAAAAAAAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
97 2 0.03
98 31 0.42
99 1 0.01
101 3 0.04
103 36 0.49
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (101 bp):
GGAAGGAAGGAAAAGGTTTGAAAGGAAACTAGTTTCATTTTCTTTTCCATTTTTTTTTGGTAGAA
GGAAAATAGAAGGGAAGAAAGGAAAATGGGTTTAGA
Found at i:198460 original size:12 final size:12
Alignment explanation
Indices: 198443--198499 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
198433 AAATGAAAAG
198443 GAAAAGGAACGT
1 GAAAAGGAACGT
* *
198455 GAAAAGGAAAGG
1 GAAAAGGAACGT
* *
198467 GAGAAGGAACGC
1 GAAAAGGAACGT
*
198479 GAGAAGGAACGT
1 GAAAAGGAACGT
198491 GAAAAGGAA
1 GAAAAGGAA
198500 AGGGAGAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.39, T:0.04
Consensus pattern (12 bp):
GAAAAGGAACGT
Found at i:198497 original size:24 final size:24
Alignment explanation
Indices: 198437--198509 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
198427 AGAAAGAAAT
* * *
198437 GAAAAGGAAAAGGAACGTGAAAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
*
198461 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
* * * *
198485 GAACGTGAAAAGGAAAGGGAGAAG
1 GAAAGGGAAAAGGAACGCGAGAAG
198509 G
1 G
198510 CTGGAAGCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.51, C:0.05, G:0.41, T:0.03
Consensus pattern (24 bp):
GAAAGGGAAAAGGAACGCGAGAAG
Found at i:198509 original size:12 final size:12
Alignment explanation
Indices: 198458--198509 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
198448 GGAACGTGAA
198458 AAGGAAAGGGAG
1 AAGGAAAGGGAG
* *
198470 AAGGAACGCGAG
1 AAGGAAAGGGAG
* * *
198482 AAGGAACGTGAA
1 AAGGAAAGGGAG
198494 AAGGAAAGGGAG
1 AAGGAAAGGGAG
198506 AAGG
1 AAGG
198510 CTGGAAGCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.02
Consensus pattern (12 bp):
AAGGAAAGGGAG
Found at i:207059 original size:27 final size:26
Alignment explanation
Indices: 206985--207059 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
206975 TTATTTTCAC
*
206985 TATATTAAATATAAAAT-ACTTATTTT
1 TATATTAAATA-AAAATAAATTATTTT
*
207011 TATA-T-CATAAAAATTAAAAATTATTTT
1 TATATTAAATAAAAA-T--AAATTATTTT
207038 TATATTAAATAAAAATAGAATT
1 TATATTAAATAAAAATA-AATT
207060 CGATTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
23 4 0.10
24 4 0.10
25 1 0.03
26 5 0.13
27 16 0.41
28 2 0.05
29 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
TATATTAAATAAAAATAAATTATTTT
Found at i:208282 original size:16 final size:16
Alignment explanation
Indices: 208257--208287 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
208247 CATGCATGCT
208257 TGTATATATGTATGTG
1 TGTATATATGTATGTG
*
208273 TGTATGTATGTATGT
1 TGTATATATGTATGT
208288 TTTGCAGGAT
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:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (16 bp):
TGTATATATGTATGTG
Found at i:209079 original size:17 final size:18
Alignment explanation
Indices: 209049--209088 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
209039 ATTTAACTCT
*
209049 TTTTTTTCACATAATACA
1 TTTTTTTCACATAACACA
*
209067 TTTTTTTC-TATAACACA
1 TTTTTTTCACATAACACA
209084 TTTTT
1 TTTTT
209089 ACATTTGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTTCACATAACACA
Found at i:209118 original size:2 final size:2
Alignment explanation
Indices: 209111--209136 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
209101 TTTTAATAAT
209111 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
209137 AAGTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209918 original size:22 final size:22
Alignment explanation
Indices: 209867--209924 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
209857 TAACAAAATG
* * *
209867 ACAGCAAAATAATGAAAAAGCA
1 ACAGCAAAACAATAAAAAAACA
*
209889 ACAACAAAACAATAAAAAAACA
1 ACAGCAAAACAATAAAAAAACA
*
209911 ATAGCAAAACAATA
1 ACAGCAAAACAATA
209925 TTTTTTTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.09
Consensus pattern (22 bp):
ACAGCAAAACAATAAAAAAACA
Found at i:236555 original size:31 final size:29
Alignment explanation
Indices: 236511--236570 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
236501 CAATTTTTTG
*
236511 CAAAAAGTTGAATTTAATCATCAACATTT
1 CAAAAAGTTGAATTTAACCATCAACATTT
*
236540 CAAAAAGATTCGAATTTAACCATCAATATTT
1 CAAAAAG-TT-GAATTTAACCATCAACATTT
236571 TAAATAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 18 0.67
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (29 bp):
CAAAAAGTTGAATTTAACCATCAACATTT
Found at i:241373 original size:6 final size:6
Alignment explanation
Indices: 241362--241389 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
241352 ATTAGCACCA
241362 CCTCAT CCTCAT CCTCAT CCTCAT CCTC
1 CCTCAT CCTCAT CCTCAT CCTCAT CCTC
241390 CCTCATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.54, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCAT
Found at i:244101 original size:26 final size:27
Alignment explanation
Indices: 244049--244103 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
244039 ATTTGGAAAT
*
244049 TAAATTGAACTAGAGAAATATATTAAA
1 TAAATTGAACTAAAGAAATATATTAAA
*
244076 TAAATTGAATTAAAG-AATATATTAAA
1 TAAATTGAACTAAAGAAATATATTAAA
244102 TA
1 TA
244104 CGTAGGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (27 bp):
TAAATTGAACTAAAGAAATATATTAAA
Found at i:246610 original size:165 final size:165
Alignment explanation
Indices: 246371--246763 Score: 583
Period size: 165 Copynumber: 2.4 Consensus size: 165
246361 GTATTGATGT
* * * ** * * **
246371 TTGAATTACTAAGACTGGTTATATGATTCTAAATGGTTACCAACTTGCTTGATGTCAAGGAACTT
1 TTGAATTACTAAAACTGGTT-TATGAATCAAAATGGTTATTAGCTTGATCAATGTCAAGGAACTT
* * *
246436 CACCTCAGATTCTAGGAAAGTATCT-ACTCCGTTGTTCGAAAATCCGGGCTAGCAATGATCT-AT
65 CACCTCAGATTCTAGGAAAGTAT-TGACTCCATTGTTCAAAAATCCGGGCTAGCAATGATCTAAA
* *
246499 CTTATCTTTCCCCAGAATTGTCATGTTGGTAGTTCTGC
129 C-TATCTTTCCCCAGAATAGTCATGGTGGTAGTTCTGC
*
246537 TTGAATTACTAAAACTGGTTTATGAATCAAAATGGTAATTAGCTTGATCAATGTCAAGGAACTTC
1 TTGAATTACTAAAACTGGTTTATGAATCAAAATGGTTATTAGCTTGATCAATGTCAAGGAACTTC
* *
246602 ATCTCAGATTCTAGGAAAGTATTGACTCCATTGTTCAAAAATCCGGGTTAGCAATGATCTAAACT
66 ACCTCAGATTCTAGGAAAGTATTGACTCCATTGTTCAAAAATCCGGGCTAGCAATGATCTAAACT
246667 ATCTTTCCCCAGAATAGTCATGGTGGTAGTTCTGC
131 ATCTTTCCCCAGAATAGTCATGGTGGTAGTTCTGC
*
246702 TTGAATTACTAAAACTGGTTTATAAATCAAAATGGTTATTAGCTTGATCAATGTCAAGGAAC
1 TTGAATTACTAAAACTGGTTTATGAATCAAAATGGTTATTAGCTTGATCAATGTCAAGGAAC
246764 GTTGTTTCGA
Statistics
Matches: 206, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
164 1 0.00
165 184 0.89
166 21 0.10
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (165 bp):
TTGAATTACTAAAACTGGTTTATGAATCAAAATGGTTATTAGCTTGATCAATGTCAAGGAACTTC
ACCTCAGATTCTAGGAAAGTATTGACTCCATTGTTCAAAAATCCGGGCTAGCAATGATCTAAACT
ATCTTTCCCCAGAATAGTCATGGTGGTAGTTCTGC
Found at i:248591 original size:2 final size:2
Alignment explanation
Indices: 248584--248621 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
248574 TAAAACGTGT
248584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
248622 GAATAACTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:249156 original size:14 final size:14
Alignment explanation
Indices: 249137--249163 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
249127 AATAAAAAGA
249137 CTATGGTCTATAGT
1 CTATGGTCTATAGT
249151 CTATGGTCTATAG
1 CTATGGTCTATAG
249164 GCATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
CTATGGTCTATAGT
Found at i:280075 original size:15 final size:16
Alignment explanation
Indices: 280056--280107 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
280046 ATTTAATTAA
280056 ATTATATTTTAATCAT
1 ATTATATTTTAATCAT
*
280072 -TTATA-TTTAA-AAT
1 ATTATATTTTAATCAT
280085 ATTATATTTTAATC-T
1 ATTATATTTTAATCAT
*
280100 CTTATATT
1 ATTATATT
280108 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 18 0.60
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATATTTTAATCAT
Found at i:280131 original size:22 final size:22
Alignment explanation
Indices: 280105--280163 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
280095 AATCTCTTAT
*
280105 ATTATTTTTTTATTATAAAGTG
1 ATTATTTTCTTATTATAAAGTG
280127 ATTATTTTCTTATTATAAAGTG
1 ATTATTTTCTTATTATAAAGTG
280149 ATTATTTTC-TATTAT
1 ATTATTTTCTTATTAT
280164 CTCTTTAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTATTTTCTTATTATAAAGTG
Found at i:285568 original size:20 final size:20
Alignment explanation
Indices: 285543--285587 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
285533 ATCGATCCAA
*
285543 TAATTTCCCATTTTTTTGAT
1 TAATTTACCATTTTTTTGAT
** *
285563 TAATTTAGTATTTTTTTTAT
1 TAATTTACCATTTTTTTGAT
285583 TAATT
1 TAATT
285588 CTATTTGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (20 bp):
TAATTTACCATTTTTTTGAT
Found at i:287554 original size:2 final size:2
Alignment explanation
Indices: 287547--287582 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
287537 TGGAGGTCGA
287547 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
287583 CTGTCTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:287720 original size:12 final size:13
Alignment explanation
Indices: 287688--287737 Score: 68
Period size: 12 Copynumber: 3.9 Consensus size: 13
287678 TGCGTGCTGT
*
287688 AGAGACAGAGACAA
1 AGAGAGAGAGA-AA
287702 AGAGAGAGAGAAA
1 AGAGAGAGAGAAA
287715 AG-GAGAG-GAAA
1 AGAGAGAGAGAAA
287726 AGAGAGAGAGAA
1 AGAGAGAGAGAA
287738 TTAGAAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 6 0.18
12 10 0.30
13 7 0.21
14 10 0.30
ACGTcount: A:0.58, C:0.04, G:0.38, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGAAA
Found at i:294059 original size:248 final size:245
Alignment explanation
Indices: 293510--294079 Score: 628
Period size: 246 Copynumber: 2.3 Consensus size: 245
293500 TACATTTCGC
* * ** *
293510 TATTTATTGTATGTTATTTTTAAACACATATTTATGTTCAAAATTTGTGATTT-TCACACGCATA
1 TATTTATTGTATGTTATTTTTAAATACACATTTATGTTTTATATTTGTGATTTCT-ACACGCATA
* * * * *
293574 CGTATGTGATAAGATTTCTAGTATTAATAATGTATTTGATTGAATTGGTGTCACAAGTTAACTCG
65 CGTGTGTGATAAGATTTATAATATTAATAATATATTTGATTGAATTGGTGTCACAAGTTAACTCA
* * * * *
293639 ACACAAATTCAAAATTGATAACACAATGATAAACAATTAAATCTATTTTTTAATTTTAATATGTA
130 ACACAAACTCAAAATTAATAACACAATGATAAACAATTAAATATATTTTTTAATTATAATATATA
* * * *** *
293704 AATATTTTATGTGTAATTATTTTATTAATCAGTTTCAAGTTATATTTTTCAT
195 AATACTTCATGTGTAATTA-TTTATTAATCAGTATCAAACCATAATTTTCAT
** **
293756 TATTTATTGTATGTTATTTTTAAATGTACATTTGGGTTTTATATTTGTGATTTCTACACGCATAC
1 TATTTATTGTATGTTATTTTTAAATACACATTTATGTTTTATATTTGTGATTTCTACACGCATAC
* * *
293821 GTGTGTGATAGGATTTATAATATTAATAATATATTTGATT-AAGTTGGTGTTATAAGTTAACTCA
66 GTGTGTGATAAGATTTATAATATTAATAATATATTTGATTGAA-TTGGTGTCACAAGTTAACTCA
** * * *
293885 ACACCGACTCAAATTTAATAACAACATAATGATACATAATTAAATA-ATTTTTTTAATTATAATA
130 ACACAAACTCAAAATTAATAAC-AC--AATGATAAACAATTAAATATA-TTTTTTAATTATAATA
* *
293949 CTATACATACTTCATGTGTAATTA-TTATTAATTAGTATCAAACCATACATTTT-AT
191 -TATAAATACTTCATGTGTAATTATTTATTAATCAGTATCAAACCATA-ATTTTCAT
* * * * * *
294004 TATTTATTATATATTATTTTTAAATACACATTTATATTTTATATTTGTAATTTCTATATGCATAC
1 TATTTATTGTATGTTATTTTTAAATACACATTTATGTTTTATATTTGTGATTTCTACACGCATAC
* *
294069 ATGTATGATAA
66 GTGTGTGATAA
294080 AAATTTTAAT
Statistics
Matches: 267, Mismatches: 49, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
245 2 0.01
246 124 0.46
247 3 0.01
248 84 0.31
249 35 0.13
250 19 0.07
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (245 bp):
TATTTATTGTATGTTATTTTTAAATACACATTTATGTTTTATATTTGTGATTTCTACACGCATAC
GTGTGTGATAAGATTTATAATATTAATAATATATTTGATTGAATTGGTGTCACAAGTTAACTCAA
CACAAACTCAAAATTAATAACACAATGATAAACAATTAAATATATTTTTTAATTATAATATATAA
ATACTTCATGTGTAATTATTTATTAATCAGTATCAAACCATAATTTTCAT
Found at i:297699 original size:181 final size:183
Alignment explanation
Indices: 297385--297748 Score: 610
Period size: 181 Copynumber: 2.0 Consensus size: 183
297375 ATGAAAATGT
*
297385 TTCTTAGAATCAGATTCCTAACCTTTTAGTAGTTTTCCTTGTAATTGCTTTTTAGCTGTGATGTC
1 TTCTTAGAATCAGATTCCTAACCTTTTAGTAG-TTTCCTTGTAATTGCTTTTCAGCTGTGATGTC
**
297450 ATTTTGATTATTTTATGTTGTTGCTTTTATTGAATTTTTTTAATCTGCTTACAGAGATGCATTTA
65 ATTTTGATTATTTTATGTTGTTGCTTTTATTGAATTTTCCTAATCTGCTTACAGAGATGCATTTA
*
297515 TTGATTATTGGATCAACGGCAGCATGTTGACAATGGATGTAGCAACCCAAATAG
130 TTGATTATTGGATCAACGGCAGCATGTTGACAATGGATGTAGCAACACAAATAG
*
297569 TTCTTATAATCAGATTCCTAA-CTTTTCAGTAG-TT-CTTGTAATTGCTTTTCAGCTGTGATGTC
1 TTCTTAGAATCAGATTCCTAACCTTTT-AGTAGTTTCCTTGTAATTGCTTTTCAGCTGTGATGTC
* *
297631 ATTTTG-TTAATTTTATGTTGTTGCTTTTATTGAATTTTCCTCATTTGCTTACAGAGATGCATTT
65 ATTTTGATT-ATTTTATGTTGTTGCTTTTATTGAATTTTCCTAATCTGCTTACAGAGATGCATTT
297695 ATTGATTATTGGATCAACGGCAGCATGTTGACAATGGATGTAGCAACACAAATA
129 ATTGATTATTGGATCAACGGCAGCATGTTGACAATGGATGTAGCAACACAAATA
297749 TTTACAATAT
Statistics
Matches: 171, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
180 2 0.01
181 137 0.80
182 2 0.01
183 5 0.03
184 25 0.15
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (183 bp):
TTCTTAGAATCAGATTCCTAACCTTTTAGTAGTTTCCTTGTAATTGCTTTTCAGCTGTGATGTCA
TTTTGATTATTTTATGTTGTTGCTTTTATTGAATTTTCCTAATCTGCTTACAGAGATGCATTTAT
TGATTATTGGATCAACGGCAGCATGTTGACAATGGATGTAGCAACACAAATAG
Found at i:312593 original size:20 final size:19
Alignment explanation
Indices: 312557--312597 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
312547 CACGAAAATT
312557 GAAGGAAAAGAGAAAGAAA
1 GAAGGAAAAGAGAAAGAAA
*
312576 GAAGGAAGAAGGGAAAGAAA
1 GAAGGAA-AAGAGAAAGAAA
312596 GA
1 GA
312598 GAAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
GAAGGAAAAGAGAAAGAAA
Found at i:312795 original size:12 final size:12
Alignment explanation
Indices: 312778--312802 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
312768 TTTAGTATGG
312778 TTAATTTTAAAA
1 TTAATTTTAAAA
312790 TTAATTTTAAAA
1 TTAATTTTAAAA
312802 T
1 T
312803 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:312978 original size:20 final size:21
Alignment explanation
Indices: 312937--312979 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
312927 TAATTTACTT
312937 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
312958 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
312978 TA
1 TA
312980 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:313283 original size:16 final size:16
Alignment explanation
Indices: 313238--313287 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
313228 TAAACCTAGT
*
313238 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
313254 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
313268 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
313284 TAAT
1 TAAT
313288 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:314674 original size:43 final size:43
Alignment explanation
Indices: 314592--314676 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
314582 ATTAACATGT
* * *
314592 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGAATCGTATTAATATGATTGCATGTTAC
* *
314635 TAAATTATATTACTTTAATCTTATTAATAT-ATTGACATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATGATTG-CATGTTA
314677 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGAATCGTATTAATATGATTGCATGTTAC
Found at i:315316 original size:45 final size:45
Alignment explanation
Indices: 315243--315379 Score: 159
Period size: 45 Copynumber: 3.0 Consensus size: 45
315233 GCATAGCTCA
* * *
315243 TCAACCCAAGGATATCAGCCTCAGTTTGACAAGCCACTGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACAAGCCACCGCAATAC
* *
315288 TCAAGCCAAGGATTTCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACAAGCCACCGCAATAC
** * * * *
315333 TCAAGGGAAGGATATCAAG-CTGAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATC-AGCCTCAATTTGACAAGCCACCGCAATAC
315378 TC
1 TC
315380 TATTCCTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 78 0.98
46 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACAAGCCACCGCAATAC
Found at i:315688 original size:28 final size:28
Alignment explanation
Indices: 315666--315720 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
315656 TATAAACTTT
315666 AGACTTAAAACCCTAAACCATAAACACC
1 AGACTTAAAACCCTAAACCATAAACACC
* * *
315694 AGACTTAAAACTCTAAATCGTAAACAC
1 AGACTTAAAACCCTAAACCATAAACAC
315721 TAAATTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.18
Consensus pattern (28 bp):
AGACTTAAAACCCTAAACCATAAACACC
Found at i:317597 original size:81 final size:81
Alignment explanation
Indices: 317462--317626 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 81
317452 TCTCACTGCG
317462 GCTATCCATCATTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTTCATTGCCAT
1 GCTATCCATCATTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTTCATTGCCAT
317527 CTGTTTCGTAATCCAT
66 CTGTTTCGTAATCCAT
*
317543 GCTATCCATCATTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTTCATTGTCAT
1 GCTATCCATCATTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTTCATTGCCAT
317608 CTGTTTCGTAATCCAT
66 CTGTTTCGTAATCCAT
317624 GCT
1 GCT
317627 TTTTAATATG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (81 bp):
GCTATCCATCATTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTTCATTGCCAT
CTGTTTCGTAATCCAT
Found at i:318880 original size:16 final size:19
Alignment explanation
Indices: 318857--318909 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 19
318847 TACAAATTAC
318857 CTTTCTTTCCTCCCCTTCTT
1 CTTTCTTTCCTCCCC-TCTT
318877 CTTTCTTTCCTCCCCTTCTT
1 CTTTCTTTCCTCCCC-TCTT
318897 CTTTTCTTTCCTC
1 C-TTTCTTTCCTC
318910 TCATTCTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTTCTTTCCTCCCCTCTT
Found at i:318904 original size:21 final size:20
Alignment explanation
Indices: 318857--318926 Score: 104
Period size: 21 Copynumber: 3.4 Consensus size: 20
318847 TACAAATTAC
318857 CTTTCTTTCCTCCCCTTCTT
1 CTTTCTTTCCTCCCCTTCTT
318877 CTTTCTTTCCTCCCCTTCTT
1 CTTTCTTTCCTCCCCTTCTT
* *
318897 CTTTTCTTTCCTCTCATTCTT
1 C-TTTCTTTCCTCCCCTTCTT
318918 CCTTTCTTT
1 -CTTTCTTT
318927 TGTTTCTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 21 0.46
21 24 0.52
22 1 0.02
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (20 bp):
CTTTCTTTCCTCCCCTTCTT
Found at i:319679 original size:140 final size:141
Alignment explanation
Indices: 319421--319702 Score: 548
Period size: 140 Copynumber: 2.0 Consensus size: 141
319411 GAGTAAAAAA
*
319421 TCCGAATCTTAACATATTGTTGTTTTCATAGTATTTAAAACTAAGGTATTAGCTTTAGCTTCTAT
1 TCCGAATCTTAACATATTGTTGTTTTCATAGTATTTAAAACTAAGGGATTAGCTTTAGCTTCTAT
319486 GAAACATAGATTCCTCGGTTTTTTTATGTTGAAATATTTGTTTTTTGTTATAATATATTCGAAAA
66 GAAACATAGATTCCTCGGTTTTTTTATGTTGAAATATTTGTTTTTTGTTATAATATATTCGAAAA
319551 AATAATCAACG
131 AATAATCAACG
319562 TCCGAATCTTAACATATTGTTGTTTTCATAGTATTTAAAACTAAGGGATTAGC-TTAGCTTCTAT
1 TCCGAATCTTAACATATTGTTGTTTTCATAGTATTTAAAACTAAGGGATTAGCTTTAGCTTCTAT
319626 GAAACATAGATTCCTCGGTTTTTTTATGTTGAAATATTTGTTTTTTGTTATAATATATTCGAAAA
66 GAAACATAGATTCCTCGGTTTTTTTATGTTGAAATATTTGTTTTTTGTTATAATATATTCGAAAA
319691 AATAATCAACG
131 AATAATCAACG
319702 T
1 T
319703 ATATATTTGT
Statistics
Matches: 140, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
140 88 0.63
141 52 0.37
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (141 bp):
TCCGAATCTTAACATATTGTTGTTTTCATAGTATTTAAAACTAAGGGATTAGCTTTAGCTTCTAT
GAAACATAGATTCCTCGGTTTTTTTATGTTGAAATATTTGTTTTTTGTTATAATATATTCGAAAA
AATAATCAACG
Found at i:322625 original size:30 final size:28
Alignment explanation
Indices: 322586--322642 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
322576 CTATTCAAAC
*
322586 TTTAATAAATTAATAAAAAATATTTTTTAA
1 TTTAATAAATT--TAAAAAATAATTTTTAA
* *
322616 TTTATTAAATTTAAATAATAATTTTTA
1 TTTAATAAATTTAAAAAATAATTTTTA
322643 TTATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
30 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAATAAATTTAAAAAATAATTTTTAA
Found at i:323602 original size:3 final size:3
Alignment explanation
Indices: 323594--323633 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
323584 CCCTAAAGGG
323594 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
323634 GCAAATCCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:324602 original size:8 final size:8
Alignment explanation
Indices: 324586--324615 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
324576 ATCGAGCTCG
324586 AAAAAAAT
1 AAAAAAAT
*
324594 AAAAGAAT
1 AAAAAAAT
324602 AAAAAAAT
1 AAAAAAAT
324610 AAAAAA
1 AAAAAA
324616 TTCAAGTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:329567 original size:24 final size:25
Alignment explanation
Indices: 329535--329581 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
329525 AATTAAAAAC
329535 TAAATTTAATTAAAAAA-ATAAATTA
1 TAAATTTAA-TAAAAAATATAAATTA
329560 TAAA-TTAATAAAAAATATAAAT
1 TAAATTTAATAAAAAATATAAAT
329582 ATTAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAATTTAATAAAAAATATAAATTA
Found at i:332012 original size:30 final size:30
Alignment explanation
Indices: 331976--332062 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 30
331966 TCTAATTATC
*
331976 TTTTAAAATTAAAAAAATTATATTTTTAAA
1 TTTTTAAATTAAAAAAATTATATTTTTAAA
* *
332006 -TTTTAAA--AATAAAATGTATAATTTTAAA
1 TTTTTAAATTAAAAAAAT-TATATTTTTAAA
*
332034 TTTTTTAAATTAAATTAAAATTAGATTTT
1 -TTTTTAAATTAAA--AAAATTATATTTT
332063 AAAAAAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.16
28 11 0.25
29 6 0.14
30 7 0.16
32 2 0.05
33 6 0.14
34 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTTTAAATTAAAAAAATTATATTTTTAAA
Found at i:332038 original size:29 final size:27
Alignment explanation
Indices: 331989--332076 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
331979 TAAAATTAAA
*
331989 AAAATTATATTTTTAAATTTTAAAAAT
1 AAAATTATAATTTTAAATTTTAAAAAT
**
332016 AAAATGTATAATTTTAAATTTTTTAAAT
1 AAAAT-TATAATTTTAAATTTTAAAAAT
* * *
332044 TAAATTA-AA-ATTAGATTTTAAAAA-
1 AAAATTATAATTTTAAATTTTAAAAAT
332068 AAAACTTAT
1 AAAA-TTAT
332077 TAAAAAGTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
24 3 0.06
25 14 0.29
26 2 0.04
27 7 0.14
28 23 0.47
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAATTATAATTTTAAATTTTAAAAAT
Found at i:340006 original size:29 final size:30
Alignment explanation
Indices: 339913--340320 Score: 319
Period size: 30 Copynumber: 13.7 Consensus size: 30
339903 TTTTCAGGGT
* * *
339913 AAAATGGTAATTTTGGGAAAG-TTCAGGGTTAA
1 AAAATGG-AATTTTTGG-AAGTTTC-GGGGTCA
*
339945 AAAATGGAATTTTTAGACA--TTCGGGGGT-A
1 AAAATGGAATTTTTGGA-AGTTTC-GGGGTCA
* * *
339974 AAAATAGAATTTTTGG-AGTTTTGAGGTCGA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTC-A
* *
340004 AAACA-GG-GTTTTTGGACA--TTCGGGGGC-
1 AAA-ATGGAATTTTTGGA-AGTTTCGGGGTCA
* * * *
340031 -AAATGGTAATTTTTGAAAGTTTCGAGTTCG
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCA
*
340061 AAAATGGAATTTTTGGAAGTTTCGGGGTCG
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
*
340091 AAAATGGAATTTTTGGAAG-TTCAAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTCA
*
340120 AAAATGGAATTTTTGGAAGTTTCGGGATCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
*
340150 AAAATGGAATTTTTTGAAG-TTCGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTCA
* * **
340179 AAAATGGAATTTTTGGAAGTTTTGAGGTTG
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
*
340209 AAAATGGATTTTTTGGAAG-TTCGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTCA
** * *
340238 AAAATATAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
* * *
340268 AAAATAGATTTTTTGGGAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
340298 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
340321 AGGGACCGTC
Statistics
Matches: 304, Mismatches: 47, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
25 1 0.00
26 4 0.01
27 2 0.01
28 11 0.04
29 110 0.36
30 148 0.49
31 21 0.07
32 7 0.02
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCA
Found at i:340052 original size:58 final size:57
Alignment explanation
Indices: 339954--340064 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 57
339944 AAAAATGGAA
* *
339954 TTTTTAGACATTCGGGGGTAAAAATAGAATTTTTGGAGTTTTGAGGTCGAAAACAGGG
1 TTTTTAGACATTCGGGGG-AAAAATAGAATTTTTGAAGTTTCGAGGTCGAAAACAGGG
* * * *
340012 TTTTTGGACATTCGGGGG-CAAATGGTAATTTTTGAAAGTTTCGAGTTCGAAAA
1 TTTTTAGACATTCGGGGGAAAAATAG-AATTTTTG-AAGTTTCGAGGTCGAAAA
340065 TGGAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 5 0.11
57 8 0.18
58 32 0.71
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (57 bp):
TTTTTAGACATTCGGGGGAAAAATAGAATTTTTGAAGTTTCGAGGTCGAAAACAGGG
Found at i:340124 original size:59 final size:59
Alignment explanation
Indices: 340061--340320 Score: 333
Period size: 59 Copynumber: 4.4 Consensus size: 59
340051 TTCGAGTTCG
* **
340061 AAAATGGAATTTTTGGAAGTTTCGGGGTCGAAAATGGAATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* *
340120 AAAATGGAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTTGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
* * ** *
340179 AAAATGGAATTTTTGGAAGTTTTGAGGTTGAAAATGGATTTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
** * * * * *
340238 AAAATATAATTTTTGGAAGTTTTGGGGTTAAAAATAGATTTTTTGGGAGTTTC-GGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGGT-A
340298 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
340321 AGGGACCGTC
Statistics
Matches: 178, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
59 154 0.87
60 19 0.11
61 5 0.03
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTA
Found at i:341384 original size:21 final size:21
Alignment explanation
Indices: 341360--341428 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
341350 TACTAAAATA
* *
341360 ATTAATAATATTATTATTATT
1 ATTAATAACATCATTATTATT
* *
341381 ATTAGTAAGA-CGATTATTATT
1 ATTAATAACATC-ATTATTATT
*
341402 ATTAAAAACATCATTATTATT
1 ATTAATAACATCATTATTATT
341423 ATTAAT
1 ATTAAT
341429 GTCATTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
ATTAATAACATCATTATTATT
Found at i:342186 original size:17 final size:17
Alignment explanation
Indices: 342161--342223 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
342151 TAACTAGATT
342161 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
342179 TAAATTTAAATTT-TAA
1 TAAATTTAAATTTATAA
* *
342195 GTAAATTTAAACTTAAAA
1 -TAAATTTAAATTTATAA
342213 TAAATTTAAAT
1 TAAATTTAAAT
342224 CCTGTTGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 3 0.08
17 31 0.77
18 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:342188 original size:6 final size:6
Alignment explanation
Indices: 342158--342223 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
342148 ATTTAACTAG
* *
342158 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
342205 ACTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
342224 CCTGTTGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.04
5 9 0.19
6 28 0.60
7 8 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:342729 original size:22 final size:22
Alignment explanation
Indices: 342703--342747 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
342693 TACTTGTAAA
342703 TTTG-ACAATTTGTGTATTTTTT
1 TTTGAACAATTTGTGT-TTTTTT
*
342725 TTTGAATAATTTGTGTTTTTTT
1 TTTGAACAATTTGTGTTTTTTT
342747 T
1 T
342748 GTCATAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (22 bp):
TTTGAACAATTTGTGTTTTTTT
Found at i:358799 original size:76 final size:76
Alignment explanation
Indices: 358673--358826 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
358663 TTCCTCTTAA
358673 AACATCAACTTTAGCTTGAAAACCAGAAAATCAACAAATAAACACACACATCTCTCACTCTATGT
1 AACATCAACTTTAGCTTGAAAACCAGAAAATCAACAAATAAACACACACATCTCTCACTCTATGT
358738 ATATATGCACC
66 ATATATGCACC
358749 AACATCAACTTTAGCTTGAAAACCAGAAAATCAACAAATAAACACACACATCTCTCACTCTATGT
1 AACATCAACTTTAGCTTGAAAACCAGAAAATCAACAAATAAACACACACATCTCTCACTCTATGT
358814 ATATATGCACC
66 ATATATGCACC
358825 AA
1 AA
358827 TGAGATATTC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.23
Consensus pattern (76 bp):
AACATCAACTTTAGCTTGAAAACCAGAAAATCAACAAATAAACACACACATCTCTCACTCTATGT
ATATATGCACC
Found at i:365230 original size:18 final size:18
Alignment explanation
Indices: 365207--365243 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
365197 TTTGCACCGA
365207 TCAAAATCTTCCATTTTC
1 TCAAAATCTTCCATTTTC
365225 TCAAAATCTTCCATTTTC
1 TCAAAATCTTCCATTTTC
365243 T
1 T
365244 TTCTCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (18 bp):
TCAAAATCTTCCATTTTC
Found at i:368088 original size:36 final size:36
Alignment explanation
Indices: 368038--368145 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
368028 TGGAGGGTCC
368038 TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
1 TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
*
368074 TTAGTGGGTAATATCCCCATAATGATGTTTGAATAT
1 TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
368110 TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
1 TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
368146 ATGTCAAACA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (36 bp):
TTAGTGGGTCATATCCCCATAATGATGTTTGAATAT
Found at i:370542 original size:18 final size:18
Alignment explanation
Indices: 370519--370555 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
370509 AATATTGTTA
370519 TTTGACATAACTATTTCT
1 TTTGACATAACTATTTCT
*
370537 TTTGACATTACTATTTCT
1 TTTGACATAACTATTTCT
370555 T
1 T
370556 CGCATTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTGACATAACTATTTCT
Found at i:373884 original size:5 final size:5
Alignment explanation
Indices: 373874--373900 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
373864 AGACCAAAAA
373874 TTGTT TTGTT TTGTT TTGTT TTGTT TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TT
373901 TTGGGCTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTGTT
Found at i:374331 original size:28 final size:28
Alignment explanation
Indices: 374279--374345 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
374269 TTAATTTTTT
* **
374279 ATTTTTTATTTTAATTTTAAAAGGTCCTA
1 ATTTTTT-TTTAAATTTTAAAAGGTCAAA
* * *
374308 ATTTTTTTTTAAATTTTTATAGGTTAAA
1 ATTTTTTTTTAAATTTTAAAAGGTCAAA
374336 ATTTTTTTTT
1 ATTTTTTTTT
374346 TATCAACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (28 bp):
ATTTTTTTTTAAATTTTAAAAGGTCAAA
Found at i:374368 original size:30 final size:29
Alignment explanation
Indices: 374309--374368 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
374299 AAGGTCCTAA
* *
374309 TTTTTTTTTAAATTTTTATAGGTTAAAAT
1 TTTTTTTTTAAACTTTTATAGGCTAAAAT
*
374338 TTTTTTTTTATCAACTTTTA-AGGCTCAAAT
1 TTTTTTTTTA--AACTTTTATAGGCTAAAAT
374368 T
1 T
374369 CCAACTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.38
30 9 0.35
31 7 0.27
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTTTTTTTAAACTTTTATAGGCTAAAAT
Found at i:374446 original size:2 final size:2
Alignment explanation
Indices: 374439--374468 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
374429 AAAATATTTC
374439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
374469 GTAAGCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.