Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2596102 original size:9 final size:9
Alignment explanation
Indices: 2596088--2596117 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2596078 TTACCACTAA
2596088 TAAGAAATT
1 TAAGAAATT
2596097 TAAGAAATT
1 TAAGAAATT
2596106 TAAGAAATT
1 TAAGAAATT
2596115 TAA
1 TAA
2596118 AACTCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (9 bp):
TAAGAAATT
Found at i:2597645 original size:20 final size:20
Alignment explanation
Indices: 2597622--2597671 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2597612 CTTTTCCCAA
2597622 TAAATCCATTCTCGATTTGG
1 TAAATCCATTCTCGATTTGG
2597642 TAAATCCATTCTCGATTTGG
1 TAAATCCATTCTCGATTTGG
*
2597662 TGAATCCATT
1 TAAATCCATT
2597672 TAGATCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (20 bp):
TAAATCCATTCTCGATTTGG
Found at i:2611358 original size:46 final size:46
Alignment explanation
Indices: 2611308--2611668 Score: 359
Period size: 46 Copynumber: 7.9 Consensus size: 46
2611298 CAATCGAAGC
** * *
2611308 ATTATTGCTACAATAAGTGACCTCTGAAAAGTAGCTGAAACGGT-A
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* * *
2611353 CATTATTGATGTAATAAATGGCCTCTGAAAAGTAGTTGAAATGGTGA
1 -ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* * * **
2611400 ATTATTGTTGTAATAAAGGGCCTCTGAAAAGTAGTTGAAACAATGA
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* * * *
2611446 ATTATTGTTGTAATAAATGACATCTGAAAAGTAGATGAAATGGTGA
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* ** * * *
2611492 ATTATTACTGTAATAAACAACCTCTTAAAAGTAGTTGAAATGGTGC
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* * * * *
2611538 ATTAATGCTGTAA-AAATGATCACTGAAAAATAGTTGAAACGCTGA
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
* * * *
2611583 ATTATTGTTATAATAAAT-AGCCTCTGAAAAGTAGTTGAAACGATGT
1 ATTATTGCTGTAATAAATGA-CCTCTGAAAAGTAGTTGAAACGGTGA
* * * * *
2611629 ATTATTGTTGTAATAAATTATCTCTAAAAAGTAGCTGAAA
1 ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAA
2611669 AATTGAAGAT
Statistics
Matches: 261, Mismatches: 50, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
45 34 0.13
46 225 0.86
47 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (46 bp):
ATTATTGCTGTAATAAATGACCTCTGAAAAGTAGTTGAAACGGTGA
Found at i:2611589 original size:183 final size:184
Alignment explanation
Indices: 2611327--2611668 Score: 481
Period size: 183 Copynumber: 1.9 Consensus size: 184
2611317 ACAATAAGTG
* * * *
2611327 ACCTCTGAAAAGTAGCTGAAACGGTACATTATTGATGTAATAAATGGCCTCTGAAAAGTAGTTGA
1 ACCTCTGAAAAGTAGCTGAAACGGTACATTAATGATGTAATAAATGACCACTGAAAAATAGTTGA
* * * *
2611392 AATGGTGAATTATTGTTGTAATAAAGGGCCTCTGAAAAGTAGTTGAAACAATGAATTATTGTTGT
66 AACGCTGAATTATTGTTATAATAAAGAGCCTCTGAAAAGTAGTTGAAACAATGAATTATTGTTGT
*
2611457 AATAAATGA-CATCTGAAAAGTAGATGAAATGGTGAATTATTACTGTAATAAACA
131 AATAAATGATC-TCTAAAAAGTAGATGAAATGGTGAATTATTACTGTAATAAACA
* * * * * *
2611511 ACCTCTTAAAAGTAGTTGAAATGGTGCATTAATGCTGTAA-AAATGATCACTGAAAAATAGTTGA
1 ACCTCTGAAAAGTAGCTGAAACGGTACATTAATGATGTAATAAATGACCACTGAAAAATAGTTGA
* * *
2611575 AACGCTGAATTATTGTTATAATAAATAGCCTCTGAAAAGTAGTTGAAACGATGTATTATTGTTGT
66 AACGCTGAATTATTGTTATAATAAAGAGCCTCTGAAAAGTAGTTGAAACAATGAATTATTGTTGT
* *
2611640 AATAAATTATCTCTAAAAAGTAGCTGAAA
131 AATAAATGATCTCTAAAAAGTAGATGAAA
2611669 AATTGAAGAT
Statistics
Matches: 137, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
183 102 0.74
184 35 0.26
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (184 bp):
ACCTCTGAAAAGTAGCTGAAACGGTACATTAATGATGTAATAAATGACCACTGAAAAATAGTTGA
AACGCTGAATTATTGTTATAATAAAGAGCCTCTGAAAAGTAGTTGAAACAATGAATTATTGTTGT
AATAAATGATCTCTAAAAAGTAGATGAAATGGTGAATTATTACTGTAATAAACA
Found at i:2612501 original size:6 final size:6
Alignment explanation
Indices: 2612490--2612571 Score: 53
Period size: 6 Copynumber: 14.2 Consensus size: 6
2612480 GCGGGTTTTT
* * ** *
2612490 TCCTTC TCCTTC TCCTTC TCATTC TCATTC T-CTT- T-CTTC TTATTA
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
* * * * *
2612535 TTCTTC TCTTTC TCCTTA TCCTTA TCCTTT TCCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
2612572 TCTTATTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
4 4 0.06
5 3 0.05
6 55 0.89
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.57
Consensus pattern (6 bp):
TCCTTC
Found at i:2612541 original size:21 final size:21
Alignment explanation
Indices: 2612517--2612581 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2612507 CTCATTCTCA
2612517 TTCTCTTTCTTCTTATTATTC
1 TTCTCTTTCTTCTTATTATTC
* *
2612538 TTCTCTTTCTCCTTATCCTTATCC
1 TTCTCTTTCTTCTTA---TTATTC
* *
2612562 TTTTCCTTCTTCTTATTATT
1 TTCTCTTTCTTCTTATTATT
2612582 ATTTTCCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 18 0.51
24 17 0.49
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCTCTTTCTTCTTATTATTC
Found at i:2612548 original size:45 final size:45
Alignment explanation
Indices: 2612492--2612593 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 45
2612482 GGGTTTTTTC
* * *
2612492 CTTCTCCTTCTCCTTCTCATTCTCATTCTCTTTCTTCTTATTATT
1 CTTCTCCTTCTCCTTATCATTATCATTCTCCTTCTTCTTATTATT
* * * *
2612537 CTTCTCTTTCTCCTTATCCTTATCCTTTTCCTTCTTCTTATTATT
1 CTTCTCCTTCTCCTTATCATTATCATTCTCCTTCTTCTTATTATT
* *
2612582 ATTTTCCTTCTC
1 CTTCTCCTTCTC
2612594 TTTCCTCTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (45 bp):
CTTCTCCTTCTCCTTATCATTATCATTCTCCTTCTTCTTATTATT
Found at i:2619911 original size:21 final size:21
Alignment explanation
Indices: 2619857--2619917 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
2619847 TTTTAGTGCA
2619857 GAGGGAATCGATACCCCCTTT
1 GAGGGAATCGATACCCCCTTT
* * *
2619878 AAGGGGAACCGATTCCCTCC-TT
1 GA-GGGAATCGATACCC-CCTTT
2619900 GAGGGAATCGATACCCCC
1 GAGGGAATCGATACCCCC
2619918 CACGGGTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.41
22 15 0.47
23 2 0.06
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (21 bp):
GAGGGAATCGATACCCCCTTT
Found at i:2621798 original size:22 final size:22
Alignment explanation
Indices: 2621790--2621837 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2621780 CCGTTGACCC
*
2621790 GACCCGACCCGACCTGACCGTT
1 GACCCGACCCGACCCGACCGTT
*
2621812 GACCTGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
2621834 GACC
1 GACC
2621838 AGTGCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:2621804 original size:27 final size:27
Alignment explanation
Indices: 2621773--2621830 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2621763 GATCGGTTCT
2621773 GACCTGACCGTTGACCCGACCCGACCC
1 GACCTGACCGTTGACCCGACCCGACCC
*
2621800 GACCTGACCGTTGACCTGACCCGACCC
1 GACCTGACCGTTGACCCGACCCGACCC
2621827 GACC
1 GACC
2621831 GTTGACCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (27 bp):
GACCTGACCGTTGACCCGACCCGACCC
Found at i:2621881 original size:29 final size:29
Alignment explanation
Indices: 2621839--2621911 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
2621829 CCGTTGACCA
2621839 GTGCTATTTTAGTAATTAAT-TCAAAATA-G
1 GTGCTATTTTAGTAATTAATAT-AAAA-AGG
2621868 GTGCTATTTTAGTAATTAATATAAAAAGG
1 GTGCTATTTTAGTAATTAATATAAAAAGG
*
2621897 GTGCTATTTTTGTAA
1 GTGCTATTTTAGTAA
2621912 AATGGTTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 39 0.95
30 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (29 bp):
GTGCTATTTTAGTAATTAATATAAAAAGG
Found at i:2622887 original size:42 final size:41
Alignment explanation
Indices: 2622827--2623031 Score: 234
Period size: 42 Copynumber: 4.8 Consensus size: 41
2622817 GGAAGTATTA
2622827 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTT
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTT
* *
2622869 TCAGGTCCCTTTGCTGTGTGCTAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTT
* * *
2622911 CCAGGTCCCTTTGATGTGTGCAAGGGTAAGCCTTAAAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTT
* * *
2622953 CCATGTCCCTTTGTTGTGTGCAAGGATAAACCTTACAGTTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTT
*
2622995 CCTAGG-CTCCTCTT-CTTTGTGCACAGGTTAAGCCTTA
1 CC-AGGTC-CCT-TTGCTGTGTGCA-AGG-TAAGCCTTA
2623032 ATGGTGTATA
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
41 4 0.03
42 111 0.79
43 12 0.09
44 13 0.09
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTT
Found at i:2624446 original size:31 final size:31
Alignment explanation
Indices: 2624403--2624479 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
2624393 GAAGGACCAG
**
2624403 TCCATA-GATCCCGAAGAACCTAGGTAAACAA
1 TCCATATG-TCCCGAAGAAAATAGGTAAACAA
*
2624434 TCCATATGTCCCGAAGAAAATAGGTAAACAG
1 TCCATATGTCCCGAAGAAAATAGGTAAACAA
2624465 TCCATATGTCCCGAA
1 TCCATATGTCCCGAA
2624480 TTACCACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAAAATAGGTAAACAA
Found at i:2625314 original size:64 final size:64
Alignment explanation
Indices: 2625213--2625429 Score: 237
Period size: 64 Copynumber: 3.4 Consensus size: 64
2625203 GAAGGTATGT
* * * *
2625213 ATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGGGATG
1 ATCGATGCACTACTTATGCATCGATGCACT-AATTGTATTCGATGTT-TCATTATTAATGGGATG
2625276 C
64 C
* *
2625277 ATCGATGCA-TGCCTTATGCATCGATGCACTAATTGTATTCGATGTTTCCTTATTAATGGGATGC
1 ATCGATGCACT-ACTTATGCATCGATGCACTAATTGTATTCGATGTTTCATTATTAATGGGATGC
* * * **
2625341 ATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAGAGTG
1 ATCGATGCACTACTTATGCATCGATGCACTAATTGTATTCGATGT-TTCATTATTAATGGGA-TG
2625404 C
64 C
**
2625405 ATCGATGCACTACCAATGCATCGAT
1 ATCGATGCACTACTTATGCATCGAT
2625430 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.03
64 122 0.92
65 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATCGATGCACTACTTATGCATCGATGCACTAATTGTATTCGATGTTTCATTATTAATGGGATGC
Found at i:2628811 original size:31 final size:31
Alignment explanation
Indices: 2628768--2628876 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
2628758 GAAGGACCAA
*
2628768 TCCATA-GATCCCGAAGAACCTAGGTAAACAG
1 TCCATATG-TCCCGAAGAACATAGGTAAACAG
2628799 TCCATATGTCCCGAAGAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
2628830 TCCATATGTCCCGAAGAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
2628861 TCCATATGTCCCGAAG
1 TCCATATGTCCCGAAG
2628877 GACCACATAT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 75 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACAG
Found at i:2629807 original size:31 final size:31
Alignment explanation
Indices: 2629764--2629841 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
2629754 GAAGGACCAG
*
2629764 TCCATA-GATCCCGAAGAACCTAGGTAAACAA
1 TCCATATG-TCCCGAAGAACATAGGTAAACAA
* *
2629795 TCCATATGTCCCGAACAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAA
2629826 TCCATATGTCCCGAAG
1 TCCATATGTCCCGAAG
2629842 GACCACATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACAA
Found at i:2630217 original size:20 final size:22
Alignment explanation
Indices: 2630194--2630233 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2630184 ATTCATATAA
*
2630194 TTTAT-TC-TCATATCATATGG
1 TTTATATCATCATAACATATGG
2630214 TTTATATCATCATAACATAT
1 TTTATATCATCATAACATAT
2630234 CACATATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (22 bp):
TTTATATCATCATAACATATGG
Found at i:2630720 original size:64 final size:62
Alignment explanation
Indices: 2630569--2630788 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 62
2630559 TAATGAAGGT
* * * * *
2630569 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGTATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TATTATTAATGG
* *
2630632 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTT-ATTATTAAT-GG
* **
2630696 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATG--TTTATTATTAATGG
**
2630759 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
2630789 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
62 2 0.01
63 50 0.37
64 77 0.57
65 3 0.02
66 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTATTATTAATGG
Found at i:2636982 original size:17 final size:17
Alignment explanation
Indices: 2636960--2636997 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2636950 GACCGGTTCC
* *
2636960 GACCCGACCTGACCGTT
1 GACCCGACCCGACCATT
2636977 GACCCGACCCGACCATT
1 GACCCGACCCGACCATT
2636994 GACC
1 GACC
2636998 GTTGACCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCATT
Found at i:2637001 original size:24 final size:22
Alignment explanation
Indices: 2636958--2637004 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 22
2636948 TTGACCGGTT
2636958 CCGACCCGACCTGACCGTTGAC
1 CCGACCCGACCTGACCGTTGAC
2636980 CCGACCCGACCATTGACCGTTGAC
1 CCGACCCGACC--TGACCGTTGAC
2637004 C
1 C
2637005 AGTGCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.48
24 12 0.52
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.15
Consensus pattern (22 bp):
CCGACCCGACCTGACCGTTGAC
Found at i:2637078 original size:29 final size:29
Alignment explanation
Indices: 2637006--2637072 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
2636996 CCGTTGACCA
*
2637006 GTGCTATTTTAGTAATTAATTTGAAATAG
1 GTGCTATTTTAGTAATTAATTTGAAAAAG
*
2637035 GTTCTATTTTAGTAATTAATTT-AAAAAGG
1 GTGCTATTTTAGTAATTAATTTGAAAAA-G
2637064 GTGCTATTT
1 GTGCTATTT
2637073 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.46
Consensus pattern (29 bp):
GTGCTATTTTAGTAATTAATTTGAAAAAG
Found at i:2638032 original size:23 final size:23
Alignment explanation
Indices: 2638006--2638074 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 23
2637996 TTACCAGGTC
2638006 CCTTTGTTGTGTGCGAAGGTAAG
1 CCTTTGTTGTGTGCGAAGGTAAG
* * * ** *
2638029 CC-TTATAGT-TTCCCAGGT--C
1 CCTTTGTTGTGTGCGAAGGTAAG
2638048 CCTTTGTTGTGTGCGAAGGTAAG
1 CCTTTGTTGTGTGCGAAGGTAAG
2638071 CCTT
1 CCTT
2638075 ACAGTTTACC
Statistics
Matches: 30, Mismatches: 12, Indels: 8
0.60 0.24 0.16
Matches are distributed among these distances:
19 2 0.07
20 5 0.17
21 12 0.40
22 5 0.17
23 6 0.20
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (23 bp):
CCTTTGTTGTGTGCGAAGGTAAG
Found at i:2638144 original size:43 final size:42
Alignment explanation
Indices: 2637999--2638166 Score: 241
Period size: 42 Copynumber: 4.0 Consensus size: 42
2637989 GGAAGTATTA
* *
2637999 CCAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTATAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
* *
2638041 CCAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
*
2638083 CCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTATAGTTTCC
1 CCAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTT-C
*
2638126 CCAGGTCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTT
2638167 TCCTAGGCTC
Statistics
Matches: 116, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.02
42 78 0.67
43 36 0.31
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33
Consensus pattern (42 bp):
CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
Found at i:2642901 original size:20 final size:20
Alignment explanation
Indices: 2642861--2642915 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2642851 GTTGAAAATG
*
2642861 ATTTGATTTTG-AAAGCAAA
1 ATTTGATTTTGAAAAACAAA
2642880 ATTTGATTTTGAAAAACAAA
1 ATTTGATTTTGAAAAACAAA
***
2642900 ATAAAATTTTGAAAAA
1 ATTTGATTTTGAAAAA
2642916 TAATTTTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (20 bp):
ATTTGATTTTGAAAAACAAA
Found at i:2644245 original size:20 final size:20
Alignment explanation
Indices: 2644192--2644245 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2644182 TATTATTCTT
* *
2644192 ACAATATCAATACCACATGA
1 ACAATATCGATACTACATGA
*
2644212 ACATTATCGATACTACATGA
1 ACAATATCGATACTACATGA
2644232 ACAATATCGATACT
1 ACAATATCGATACT
2644246 GTTCTTGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (20 bp):
ACAATATCGATACTACATGA
Found at i:2646227 original size:42 final size:40
Alignment explanation
Indices: 2646175--2646463 Score: 185
Period size: 42 Copynumber: 7.0 Consensus size: 40
2646165 GATTTACATA
* *
2646175 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCCAAG
* * * *
2646217 TTCGCGTTGCGATTTATTTCAAATTTGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAG
* * *
2646259 TTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAG
* * * *
2646301 TT--CGTTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAA
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAG
* * * * *
2646343 TT--TGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAG
* *
2646385 TT--CGTTGCGATAGTCCAAGTTCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAG
* * *
2646423 TTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAA
2646464 AATCGCAACG
Statistics
Matches: 205, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
38 14 0.07
40 29 0.14
42 154 0.75
44 8 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCCAAG
Found at i:2646334 original size:61 final size:62
Alignment explanation
Indices: 2646243--2646374 Score: 203
Period size: 61 Copynumber: 2.1 Consensus size: 62
2646233 TTTCAAATTT
* *
2646243 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTT-C
1 GTTGCGATAGTCCAAGTTCGCGTTACGATTTATTACAAATTCGTTGCGATAATCCAAGTTCC
* * *
2646304 GTTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTTGTTGCGATAATCCAAGTTCGC
1 GTTGCGATAGTCCAAGTTCGCGTTACGATTTATTACAAATTCGTTGCGATAATCCAAGTTC-C
2646367 GTTGCGAT
1 GTTGCGAT
2646375 TTATTACAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 55 0.86
63 9 0.14
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (62 bp):
GTTGCGATAGTCCAAGTTCGCGTTACGATTTATTACAAATTCGTTGCGATAATCCAAGTTCC
Found at i:2646362 original size:103 final size:103
Alignment explanation
Indices: 2646181--2646463 Score: 494
Period size: 103 Copynumber: 2.7 Consensus size: 103
2646171 CATATTCGCA
*
2646181 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTTGTT
1 TTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTT
2646246 GCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
64 GCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
*
2646286 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTTGTTGC
1 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGC
*
2646351 GATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCG
66 GATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
* * *
2646389 TTGCGATAGTCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGC
1 TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGC
2646454 GATAGTCCAA
66 GATAGTCCAA
2646464 AATCGCAACG
Statistics
Matches: 170, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
103 153 0.90
105 17 0.10
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (103 bp):
TTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTGTTGC
GATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCG
Found at i:2646402 original size:61 final size:61
Alignment explanation
Indices: 2646337--2646464 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
2646327 TACGATTTAT
**
2646337 TCCAAATTTGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
1 TCCAAATTCATTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
* * * * *
2646398 TCCAAGTTCATTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAATTCATTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
2646459 TCCAAA
1 TCCAAA
2646465 ATCGCAACGA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (61 bp):
TCCAAATTCATTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
Found at i:2647346 original size:42 final size:42
Alignment explanation
Indices: 2647284--2647445 Score: 267
Period size: 42 Copynumber: 3.9 Consensus size: 42
2647274 TGCGATTTTG
*
2647284 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2647326 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2647368 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2647410 GACTACCGCAACGAACTT-GAACT--ATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAA-TAAATCGCAACGCGAA
2647446 TTTGGAATAA
Statistics
Matches: 115, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
40 13 0.11
41 3 0.03
42 99 0.86
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2647397 original size:63 final size:61
Alignment explanation
Indices: 2647330--2647493 Score: 172
Period size: 63 Copynumber: 2.6 Consensus size: 61
2647320 AACTTCGACT
*
2647330 ATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCG-ACTATCGCAA-CGAATTTGGAATA
1 ATCGCAACCGAACTTGGAAT--ACCGCAA--CGAACTT-GAACTATCGCAACCGAATTTGGAATA
2647392 A
61 A
* *
2647393 ATCGCAACGCGAACTTCGACTACCGCAACGAACTTGAACTATCGCAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAACTTGGAATACCGCAACGAACTTGAACTATCGCAAC-CGAATTTGGAATAA
* * * *
2647456 ATCGCAACGCGAACTTGGACTATCGTAACGAATTTGAA
1 ATCGCAAC-CGAACTTGGAATACCGCAACGAACTTGAA
2647494 AATTCGCATT
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
60 1 0.01
61 17 0.19
63 61 0.69
65 10 0.11
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (61 bp):
ATCGCAACCGAACTTGGAATACCGCAACGAACTTGAACTATCGCAACCGAATTTGGAATAA
Found at i:2647460 original size:84 final size:83
Alignment explanation
Indices: 2647287--2647464 Score: 270
Period size: 84 Copynumber: 2.1 Consensus size: 83
2647277 GATTTTGGAC
*
2647287 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGGAAT-AA
*
2647352 TCGCAACGCGAACTTCGAC
65 TCGCAACGCGAACTTCGAA
2647371 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTT-GAACT-A
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGGAA-TAA
* *
2647434 TCGCAACGCGAATTTGGAA
65 TCGCAACGCGAACTTCGAA
2647453 TAAATCGCAACG
1 T--ATCGCAACG
2647465 CGAACTTGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
82 18 0.21
83 3 0.03
84 66 0.76
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (83 bp):
TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGGAATAAT
CGCAACGCGAACTTCGAA
Found at i:2647501 original size:63 final size:63
Alignment explanation
Indices: 2647371--2647494 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
2647361 GAACTTCGAC
*
2647371 TATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGAAC
1 TATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGAAA
* * * *
2647432 TATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGTAACGAATTTGAAA
1 TATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGAAA
2647495 ATTCGCATTG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 8 0.14
63 48 0.86
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (63 bp):
TATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTACCGCAACGAACTTGAAA
Found at i:2647526 original size:21 final size:21
Alignment explanation
Indices: 2647496--2647570 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
2647486 AATTTGAAAA
* *
2647496 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGATG
*
2647517 TTCGCGTTGCGATTGTCGATG
1 TTCGCGTTGCGATAGTCGATG
2647538 TTCGCGTTGCGATAGTCGATG
1 TTCGCGTTGCGATAGTCGATG
2647559 TTCGCGTTGCGA
1 TTCGCGTTGCGA
2647571 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGATG
Found at i:2648267 original size:25 final size:24
Alignment explanation
Indices: 2648210--2648281 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 24
2648200 CTGACGAAGT
2648210 TTTCTTCATTTATGAGTCGAATG-TGGC
1 TTTCTT-ATTTAT--GTC-AATGATGGC
2648237 TTTCTTATTTATGTCAATGATGGTC
1 TTTCTTATTTATGTCAATGATGG-C
2648262 TTTCTTATTTATGTCAATGA
1 TTTCTTATTTATGTCAATGA
2648282 ACAGAAAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.09
24 6 0.14
25 21 0.49
26 6 0.14
27 6 0.14
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (24 bp):
TTTCTTATTTATGTCAATGATGGC
Found at i:2651641 original size:2 final size:2
Alignment explanation
Indices: 2651634--2651719 Score: 147
Period size: 2 Copynumber: 43.5 Consensus size: 2
2651624 GTGTCATGTT
2651634 TA TA 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 TA TA
* *
2651676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2651717 TA T
1 TA T
2651720 TATTTTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2653361 original size:25 final size:25
Alignment explanation
Indices: 2653328--2653401 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 25
2653318 TGCCACATAG
* *
2653328 ATTTTTCCCCAAGGACTGCGTAGAA
1 ATTTTTCCCAAAGGACCGCGTAGAA
* * *
2653353 ATTTGTCCCGAAGGACCACGTAG-A
1 ATTTTTCCCAAAGGACCGCGTAGAA
2653377 ATTTTTCCCAAAGGACCGCGTAGAA
1 ATTTTTCCCAAAGGACCGCGTAGAA
2653402 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTTTTCCCAAAGGACCGCGTAGAA
Found at i:2653385 original size:24 final size:24
Alignment explanation
Indices: 2653312--2653401 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
2653302 AGAATACTCA
*
2653312 CCGAAGTG-CCACATAG-ATTTTTC
1 CCGAAG-GACCACGTAGAATTTTTC
* ** *
2653335 CCCAAGGACTGCGTAGAAATTTGTC
1 CCGAAGGACCACGTAG-AATTTTTC
2653360 CCGAAGGACCACGTAGAATTTTTC
1 CCGAAGGACCACGTAGAATTTTTC
* *
2653384 CCAAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
2653402 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
22 1 0.02
23 10 0.19
24 23 0.43
25 19 0.36
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (24 bp):
CCGAAGGACCACGTAGAATTTTTC
Found at i:2653550 original size:30 final size:30
Alignment explanation
Indices: 2653505--2653583 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
2653495 GTGTGTTTTA
2653505 TTCACGTAG-GCAATTTCACATAAGGTATT
1 TTCACGTAGAGCAATTTCACATAAGGTATT
2653534 TTCACGTAGAGCAATTTCACATAAGGTATT
1 TTCACGTAGAGCAATTTCACATAAGGTATT
*
2653564 TTCACGTAGAGCATTTTCAC
1 TTCACGTAGAGCAATTTCAC
2653584 GTATTACATT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 9 0.19
30 39 0.81
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (30 bp):
TTCACGTAGAGCAATTTCACATAAGGTATT
Found at i:2653579 original size:15 final size:15
Alignment explanation
Indices: 2653505--2653586 Score: 71
Period size: 15 Copynumber: 5.5 Consensus size: 15
2653495 GTGTGTTTTA
*
2653505 TTCACGTAG-GCAAT
1 TTCACGTAGAGCATT
* *
2653519 TTCACATA-AGGTATT
1 TTCACGTAGA-GCATT
*
2653534 TTCACGTAGAGCAAT
1 TTCACGTAGAGCATT
* *
2653549 TTCACATA-AGGTATT
1 TTCACGTAGA-GCATT
2653564 TTCACGTAGAGCATT
1 TTCACGTAGAGCATT
2653579 TTCACGTA
1 TTCACGTA
2653587 TTACATTTTC
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
14 8 0.15
15 42 0.81
16 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (15 bp):
TTCACGTAGAGCATT
Found at i:2653593 original size:15 final size:15
Alignment explanation
Indices: 2653561--2653609 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2653551 CACATAAGGT
2653561 ATTTTCACGTA-GAGC
1 ATTTTCACGTATGA-C
*
2653576 ATTTTCACGTATTAC
1 ATTTTCACGTATGAC
*
2653591 ATTTTCACATATGAC
1 ATTTTCACGTATGAC
2653606 ATTT
1 ATTT
2653610 CCATATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 29 0.97
16 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (15 bp):
ATTTTCACGTATGAC
Found at i:2653595 original size:30 final size:30
Alignment explanation
Indices: 2653505--2653598 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
2653495 GTGTGTTTTA
**
2653505 TTCACGTAG-GCAATTTCACATAAGGTATT
1 TTCACGTAGAGCAATTTCACATAAGACATT
**
2653534 TTCACGTAGAGCAATTTCACATAAGGTATT
1 TTCACGTAGAGCAATTTCACATAAGACATT
* * **
2653564 TTCACGTAGAGCATTTTCACGTATTACATT
1 TTCACGTAGAGCAATTTCACATAAGACATT
2653594 TTCAC
1 TTCAC
2653599 ATATGACATT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 9 0.16
30 49 0.84
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (30 bp):
TTCACGTAGAGCAATTTCACATAAGACATT
Found at i:2658704 original size:17 final size:17
Alignment explanation
Indices: 2658669--2658706 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2658659 CCAGGTTAGT
2658669 AAAAATAAAAAAATCAGA
1 AAAAATAAAAAAA-CAGA
2658687 AAAAATTAAAAAAA-AGA
1 AAAAA-TAAAAAAACAGA
2658704 AAA
1 AAA
2658707 GAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAAAACAGA
Found at i:2660698 original size:17 final size:17
Alignment explanation
Indices: 2660678--2660736 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2660668 TTTAGGGAAG
2660678 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
2660695 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
2660711 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
2660728 TAGTTCATT
1 TAGTTCATT
2660737 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:2660770 original size:18 final size:18
Alignment explanation
Indices: 2660727--2660772 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2660717 ATTCATGCAT
*
2660727 TTAGTTCATTGAATAAAG
1 TTAGTTTATTGAATAAAG
*
2660745 TTAGTTTATTGAATAATG
1 TTAGTTTATTGAATAAAG
*
2660763 TTATTTTATT
1 TTAGTTTATT
2660773 AATCAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (18 bp):
TTAGTTTATTGAATAAAG
Found at i:2661860 original size:21 final size:21
Alignment explanation
Indices: 2661834--2661882 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2661824 ATGGGTCACG
2661834 TTCCATCCTCTTCCACCAAGA
1 TTCCATCCTCTTCCACCAAGA
**
2661855 TTCCATCCTCTTCCACCTTGA
1 TTCCATCCTCTTCCACCAAGA
2661876 TTCCATC
1 TTCCATC
2661883 ATATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.43, G:0.04, T:0.35
Consensus pattern (21 bp):
TTCCATCCTCTTCCACCAAGA
Found at i:2664473 original size:18 final size:18
Alignment explanation
Indices: 2664414--2664475 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 18
2664404 ATTCGTGCAT
2664414 TTAGTT-ATTGAATAAAG
1 TTAGTTCATTGAATAAAG
2664431 TTAGTT-ATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
2664448 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
2664466 TTATTTCATT
1 TTAGTTCATT
2664476 AATCAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
17 23 0.55
18 19 0.45
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2667975 original size:17 final size:17
Alignment explanation
Indices: 2667950--2667991 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2667940 GTATGTTGTT
*
2667950 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
2667967 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
2667984 CATTTAAG
1 CATTTAAG
2667992 GAAGCAGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:2668068 original size:18 final size:18
Alignment explanation
Indices: 2668045--2668090 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2668035 ATTCTTGCAT
2668045 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
* *
2668063 TTAGTTCATAGAATAATG
1 TTAGTTCATTGAATAAAG
*
2668081 TTATTTCATT
1 TTAGTTCATT
2668091 AATCAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2671657 original size:17 final size:17
Alignment explanation
Indices: 2671637--2671695 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2671627 TTTAGAGAAG
2671637 TAGTTCATTTATGAATC
1 TAGTTCATTTATGAATC
*
2671654 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGAATC
* * * *
2671670 TACTTCATTCATGCATT
1 TAGTTCATTTATGAATC
2671687 TAGTTCATT
1 TAGTTCATT
2671696 GAATAAAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGAATC
Found at i:2671709 original size:18 final size:18
Alignment explanation
Indices: 2671686--2671731 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2671676 ATTCATGCAT
2671686 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
2671704 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
2671722 TTATTTCATT
1 TTAGTTCATT
2671732 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2678112 original size:21 final size:21
Alignment explanation
Indices: 2678065--2678125 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2678055 ATTCCCCTGT
2678065 GGGGGAATCGGTTCTCCTTCAAA
1 GGGGGAATCGGTTC-CC-TCAAA
2678088 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2678108 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2678126 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 2 0.06
23 14 0.39
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2688585 original size:18 final size:18
Alignment explanation
Indices: 2688562--2688605 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2688552 ATGCATTTAG
2688562 TTCATTAAATAAAGTTAA
1 TTCATTAAATAAAGTTAA
* * *
2688580 TTCATTGAATAATGTTAT
1 TTCATTAAATAAAGTTAA
2688598 TTCATTAA
1 TTCATTAA
2688606 TCAAACCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
TTCATTAAATAAAGTTAA
Found at i:2690122 original size:20 final size:20
Alignment explanation
Indices: 2690077--2690124 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2690067 ATTTCAATTA
*
2690077 CAGTATCGATACCTTCATCT
1 CAGTATCGATACCTCCATCT
**
2690097 TGGTATCGATACCTCCA-CAT
1 CAGTATCGATACCTCCATC-T
2690117 CAGTATCG
1 CAGTATCG
2690125 GTACTTCTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (20 bp):
CAGTATCGATACCTCCATCT
Found at i:2694988 original size:24 final size:24
Alignment explanation
Indices: 2694935--2694988 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2694925 TACATTTGCT
* *
2694935 CATATAATTTGCACCGAAGTGCAA
1 CATAGAATATGCACCGAAGTGCAA
** *
2694959 TGTAGAATATGCACCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCAA
2694983 CATAGA
1 CATAGA
2694989 TTTGTCCCGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
CATAGAATATGCACCGAAGTGCAA
Found at i:2695161 original size:15 final size:15
Alignment explanation
Indices: 2695116--2695178 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
2695106 GTGTGTTTTA
* *
2695116 TTCACATAGAGCAAT
1 TTCACGTAGAGCATT
* * *
2695131 TTCACATAGGGTATT
1 TTCACGTAGAGCATT
*
2695146 TTCACGTAGATCATT
1 TTCACGTAGAGCATT
*
2695161 TGCACGTAGAGCATT
1 TTCACGTAGAGCATT
2695176 TTC
1 TTC
2695179 TCATATGGCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (15 bp):
TTCACGTAGAGCATT
Found at i:2697736 original size:15 final size:17
Alignment explanation
Indices: 2697695--2697731 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
2697685 GATTGGTTGC
2697695 TATTAATTTAGTAAAAAAA
1 TATTAATTTAGT--AAAAA
2697714 TATTAATTTAGTAAAAA
1 TATTAATTTAGTAAAAA
2697731 T
1 T
2697732 TAATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TATTAATTTAGTAAAAA
Found at i:2698481 original size:20 final size:20
Alignment explanation
Indices: 2698439--2698486 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2698429 TCAAATTCTC
*
2698439 TTATATTTTATACTTGTTCT
1 TTATATTTTATACTTGTTAT
*
2698459 TTATATTTTTTA-TTGGTTAT
1 TTATATTTTATACTT-GTTAT
2698479 TTA-ATTTT
1 TTATATTTT
2698487 GTGCCTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (20 bp):
TTATATTTTATACTTGTTAT
Found at i:2701796 original size:17 final size:17
Alignment explanation
Indices: 2701761--2701794 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2701751 TCAAATACTA
2701761 TAATTTAGTTCAATTTT
1 TAATTTAGTTCAATTTT
*
2701778 TAATTT-GTTCGATTTT
1 TAATTTAGTTCAATTTT
2701794 T
1 T
2701795 TACCTAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (17 bp):
TAATTTAGTTCAATTTT
Found at i:2715485 original size:20 final size:19
Alignment explanation
Indices: 2715460--2715533 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
2715450 TGTAACGAAT
2715460 TTGACAAAACCGATTGGAAA
1 TTGACAAAACCGATT-GAAA
* *
2715480 TTGACAAAATCAATTGAAA
1 TTGACAAAACCGATTGAAA
** * *
2715499 TTTGACAAAATTGATTTTAAT
1 -TTGACAAAACCGA-TTGAAA
2715520 TTGACAAAACCGAT
1 TTGACAAAACCGAT
2715534 AAAGAGCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.11
20 35 0.80
21 4 0.09
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (19 bp):
TTGACAAAACCGATTGAAA
Found at i:2715500 original size:19 final size:21
Alignment explanation
Indices: 2715457--2715509 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
2715447 ACATGTAACG
* *
2715457 AATTTGACAAAACCGATTGGA
1 AATTTGACAAAATCAATTGGA
2715478 AA-TTGACAAAATCAATT-GA
1 AATTTGACAAAATCAATTGGA
2715497 AATTTGACAAAAT
1 AATTTGACAAAAT
2715510 TGATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 23 0.79
21 2 0.07
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.26
Consensus pattern (21 bp):
AATTTGACAAAATCAATTGGA
Found at i:2715524 original size:40 final size:38
Alignment explanation
Indices: 2715412--2715529 Score: 105
Period size: 40 Copynumber: 3.0 Consensus size: 38
2715402 ATATAACAGG
2715412 TTGAAATTTGAC-AAATCT-AGTTTTAATTTGACAAAACA
1 TTGAAATTTGACAAAAT-TGA-TTTTAATTTGACAAAACA
* ** ** *
2715450 TGTAACGAATTTGACAAAACCGATTGGAAATTGACAAAATCAA
1 T-TGA--AATTTGACAAAATTGATTTTAATTTGACAAAA-C-A
2715493 TTGAAATTTGACAAAATTGATTTTAATTTGACAAAAC
1 TTGAAATTTGACAAAATTGATTTTAATTTGACAAAAC
2715530 CGATAAAGAG
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
38 1 0.02
39 3 0.05
40 27 0.44
41 21 0.34
42 7 0.11
43 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (38 bp):
TTGAAATTTGACAAAATTGATTTTAATTTGACAAAACA
Found at i:2715847 original size:201 final size:200
Alignment explanation
Indices: 2715497--2716218 Score: 783
Period size: 201 Copynumber: 3.6 Consensus size: 200
2715487 AATCAATTGA
* * * * *
2715497 AATTTGACAAAAT-TGATTTTAATTTGACAAAACCGATAAAGAGCTACCAAAATTATTGAAATTT
1 AATTTGACAAAATCAG-TTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAATTGTTGAAATTT
* * * *
2715561 GTATTGATACGTTTATAAGTATATGTACCAAAGTATTAGTACTGTAAGAATTTAAAAGAATTACA
65 GTATCGATACGTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTACA
* * *
2715626 ATAATA-ATGACCACAAAGTATCGATACCTTACACACATGCATGTATCGATACATGACAATATAA
130 ATAATAGA-GA-TATAAAGTATCAATACCTTACACACATGCATGTATCGATACATGACAATATAA
2715690 CATGTTGT
193 CATGTTGT
* * * * * * *
2715698 AATTTGACAAAATCGGTTTCAATTTGACTAAACCGGTAAATAACTATCGGATTTGTTGAAATTTG
1 AATTTGACAAAATCAGTTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAATTGTTGAAATTTG
* * * *
2715763 TATCTATACGTTTATAAGTATATGTATCAAAATATCAGTACTTTAGGAATTTAAAAGAATTGCAA
66 TATCGATACGTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTACAA
* *
2715828 TAATAGAGGATATAAAGTATCAATACCTTATA-A-A--CATGTAATCGATACATGACAATATACC
131 TAATAGA-GATATAAAGTATCAATACCTTACACACATGCATGT-ATCGATACATGACAATATAAC
2715889 ATGTT-T
194 ATGTTGT
* * * * *
2715895 AAATTTGACAAAACCAGTTTCAATTTGACTAAACCGGTAAAGAGTTATCAGAATAGTTGAAATTT
1 -AATTTGACAAAATCAGTTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAATTGTTGAAATTT
* * * *
2715960 GTATCGATACTTTTATAAGTATATATACCAAAGTATCAATACTTTATGAA-TTAAAA-AATTACA
65 GTATCGATACGTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTACA
** * * *
2716023 ATAATAGCACCTATAAAGTATTAATA-CTTTCGACACATGTATAACATGTAT--ATACATGAAAA
130 ATAATAG-AGATATAAAGTATCAATACCTTAC-ACACATG-----CATGTATCGATACATGACAA
*
2716085 TATAACATGTTGA
188 TATAACATGTTGT
* * * *
2716098 AATTTGACAAAATCAGTTTCAATTTGACAAAATCGGTAAAGTGTTACCGGAATTGTTGAAA---G
1 AATTTGACAAAATCAGTTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAATTGTTGAAATTTG
* * *
2716160 TATCGATACATTTATAAGTATATGTACCATAGTATC-GATATTTTAGGAATTTAAAAGAA
66 TATCGATACGTTTATAAGTATATGTACCAAAGTATCAG-TACTTTAGGAATTTAAAAGAA
2716219 ATGAAAAAAG
Statistics
Matches: 440, Mismatches: 62, Indels: 38
0.81 0.11 0.07
Matches are distributed among these distances:
195 3 0.01
196 28 0.06
197 14 0.03
198 125 0.28
199 44 0.10
200 7 0.02
201 134 0.30
202 78 0.18
204 2 0.00
205 5 0.01
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (200 bp):
AATTTGACAAAATCAGTTTCAATTTGACAAAACCGGTAAAGAGCTACCAGAATTGTTGAAATTTG
TATCGATACGTTTATAAGTATATGTACCAAAGTATCAGTACTTTAGGAATTTAAAAGAATTACAA
TAATAGAGATATAAAGTATCAATACCTTACACACATGCATGTATCGATACATGACAATATAACAT
GTTGT
Found at i:2715919 original size:20 final size:21
Alignment explanation
Indices: 2715877--2715929 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2715867 AATCGATACA
2715877 TGACAATATACCATGTTTAAATT
1 TGACAA-A-ACCATGTTTAAATT
*
2715900 TGACAAAACCA-GTTTCAATT
1 TGACAAAACCATGTTTAAATT
*
2715920 TGACTAAACC
1 TGACAAAACC
2715930 GGTAAAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.61
21 4 0.14
22 1 0.04
23 6 0.21
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
TGACAAAACCATGTTTAAATT
Found at i:2716258 original size:17 final size:17
Alignment explanation
Indices: 2716233--2716291 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
2716223 AAAAAGAAAA
*
2716233 ACGTCTCGATACATTTT
1 ACGTATCGATACATTTT
*
2716250 ACGTATCGATACTTTATAT
1 ACGTATCGATACATT-T-T
*
2716269 ATGTGTATCGATACATTTT
1 A--CGTATCGATACATTTT
2716288 ACGT
1 ACGT
2716292 GCAAATTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
19 4 0.12
20 1 0.03
21 12 0.36
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (17 bp):
ACGTATCGATACATTTT
Found at i:2716753 original size:130 final size:131
Alignment explanation
Indices: 2716514--2716991 Score: 551
Period size: 130 Copynumber: 3.7 Consensus size: 131
2716504 GCACTAAAAT
* *
2716514 GTATCGATACACATATATAAAATATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
** * * *
2716579 GATAAATTAACAATGA-ACACAATAAACATTTCTATCGGTTTAATGAAAATAGATGTAAATGTCC
66 GATAAATTAACAAT-ATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGATGTAAATGTCC
2716643 AA
130 AA
* * * * *
2716645 GTACCGATACTCATATACAAAGTATCGGTACTTATAATTT-TAAAACTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* *
2716709 TG-TATATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGA---CAATGTCC
66 -GATAAATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGATGTAAATGTCC
2716770 AA
130 AA
* * * * *
2716772 ATATCGATACTCATGTATAAAGTATCGATACTTATAATTTCGAAACCAATTAATTAAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* * * ** * * * *
2716837 GACAAATTAATAATGTATTCGGTAAACGTTTCTACCAG-AAATATGAAAATAGGTGTAAATGTAC
66 GATAAATTAACAATATACACGGTAAACGTTTCTACCGGTATA-ATGAAAATAGATGTAAATGTCC
2716901 AA
130 AA
* *
2716903 GTATCGATACT-GTCATAT-AAGTATCAATACTTATAATTTCGAAACCTATTACTTTAAAGTAAT
1 GTATCGATACTCAT-ATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAAT
* * * *
2716966 AGGTAAGTTAACAATGTATACGGTAA
65 AGATAAATTAACAATATACACGGTAA
2716992 TATGTTGATA
Statistics
Matches: 291, Mismatches: 47, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
127 47 0.16
128 58 0.20
129 1 0.00
130 128 0.44
131 57 0.20
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (131 bp):
GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
GATAAATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGATGTAAATGTCCA
A
Found at i:2716979 original size:258 final size:256
Alignment explanation
Indices: 2716515--2716991 Score: 618
Period size: 258 Copynumber: 1.8 Consensus size: 256
2716505 CACTAAAATG
* * *
2716515 TATCGATACACATATATAAAATATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAG
1 TATCGATACACATATATAAAATATCGATACTTATAATTTCGAAACCAATTAATTAAAAGTAATAG
* * *** *
2716580 ATAAATTAACAATGAACACAATAAACATTTCTATCGGTTTAATGAAAATAGATGTAAATGTCCAA
66 ACAAATTAACAATGAACACAATAAACATTTCTACCGAAATAATGAAAATAGATGTAAATGTACAA
** * *
2716645 GTACCGATACTCATATACAAAGTATCGGTACTTATAATTTTAAAACTATTACTTTAAAGTAATAT
131 GTACCGATACTCATAT--AAAGTATCAATACTTATAATTTGAAAACTATTACTTTAAAGTAATAG
2716710 GTATATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGACAATGTCCAAA
194 GTATATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGACAATGTCCAAA
* * *
2716773 TATCGATACTCATGTATAAAGTATCGATACTTATAATTTCGAAACCAATTAATTAAAAGTAATAG
1 TATCGATACACATATATAAAATATCGATACTTATAATTTCGAAACCAATTAATTAAAAGTAATAG
* * ** ** * *
2716838 ACAAATTAATAATGTATTCGGTAAACGTTTCTACCAGAAAT-ATGAAAATAGGTGTAAATGTACA
66 ACAAATTAACAATGAACACAATAAACATTTCTACC-GAAATAATGAAAATAGATGTAAATGTACA
* *
2716902 AGTATCGATACTGTCATAT-AAGTATCAATACTTATAATTTCGAAACCTATTACTTTAAAGTAAT
130 AGTACCGATAC--TCATATAAAGTATCAATACTTATAATTT-GAAAACTATTACTTTAAAGTAAT
* *
2716966 AGGTA-AGTTAACAATGTATACGGTAA
192 AGGTATA-TTAACAATATACACGGTAA
2716992 TATGTTGATA
Statistics
Matches: 186, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
257 20 0.11
258 158 0.85
259 2 0.01
260 6 0.03
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (256 bp):
TATCGATACACATATATAAAATATCGATACTTATAATTTCGAAACCAATTAATTAAAAGTAATAG
ACAAATTAACAATGAACACAATAAACATTTCTACCGAAATAATGAAAATAGATGTAAATGTACAA
GTACCGATACTCATATAAAGTATCAATACTTATAATTTGAAAACTATTACTTTAAAGTAATAGGT
ATATTAACAATATACACGGTAAACGTTTCTACCGGTATAATGAAAATAGACAATGTCCAAA
Found at i:2718510 original size:14 final size:14
Alignment explanation
Indices: 2718491--2718533 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2718481 GTTAGATTAC
2718491 ACCCTAAACCTTAA
1 ACCCTAAACCTTAA
* *
2718505 ACCCTAAGCCCTAA
1 ACCCTAAACCTTAA
*
2718519 ATCCTAAATCCTTAA
1 ACCCTAAA-CCTTAA
2718534 CCTGATTATG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.40, C:0.35, G:0.02, T:0.23
Consensus pattern (14 bp):
ACCCTAAACCTTAA
Found at i:2718654 original size:7 final size:7
Alignment explanation
Indices: 2718639--2718683 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
2718629 CCTAAATCTC
*
2718639 AAACTCT
1 AAACCCT
2718646 AAACCCT
1 AAACCCT
*
2718653 AAACCTT
1 AAACCCT
*
2718660 AAAACCT
1 AAACCCT
*
2718667 AAACACT
1 AAACCCT
2718674 AAACCCT
1 AAACCCT
2718681 AAA
1 AAA
2718684 TCTTTAATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:2718668 original size:21 final size:22
Alignment explanation
Indices: 2718639--2718683 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2718629 CCTAAATCTC
* *
2718639 AAACTCTAAACCCTAAACCTTA
1 AAACTCTAAACACTAAACCCTA
2718661 AAAC-CTAAACACTAAACCCTA
1 AAACTCTAAACACTAAACCCTA
2718682 AA
1 AA
2718684 TCTTTAATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (22 bp):
AAACTCTAAACACTAAACCCTA
Found at i:2722060 original size:29 final size:29
Alignment explanation
Indices: 2722023--2722092 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
2722013 GTATTATTAT
*
2722023 CGATCTAACACCGGTCAGACTATATTTCC
1 CGATTTAACACCGGTCAGACTATATTTCC
* *
2722052 CGATTTAACATCGGTCAGACTATATTTTC
1 CGATTTAACACCGGTCAGACTATATTTCC
2722081 CGATCTT-ACACC
1 CGAT-TTAACACC
2722093 CTTAGCAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (29 bp):
CGATTTAACACCGGTCAGACTATATTTCC
Found at i:2722164 original size:50 final size:50
Alignment explanation
Indices: 2722106--2722229 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 50
2722096 AGCAGGAAAA
* * *
2722106 CGCGCCCCCTGCACCGCGCTATATGCTGATTTGGCGCCACGTGGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
* * *
2722156 CGCGCCCCCTGCCCCGCGATATACGGTGATCTGACGCCACGTGGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
* *
2722206 TGTGCCCCCTG-ATCCGCGCTATAC
1 CGCGCCCCCTGCA-CCGCGCTATAC
2722230 CTGGATATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.21
Consensus pattern (50 bp):
CGCGCCCCCTGCACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
Found at i:2722392 original size:12 final size:10
Alignment explanation
Indices: 2722351--2722391 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
2722341 TTTATCACAC
2722351 CAAATTCTCT
1 CAAATTCTCT
2722361 CAAATTCTCT
1 CAAATTCTCT
2722371 -AAATTTCTCT
1 CAAA-TTCTCT
*
2722381 CAAATACTCT
1 CAAATTCTCT
2722391 C
1 C
2722392 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2722652 original size:111 final size:111
Alignment explanation
Indices: 2722521--2722734 Score: 383
Period size: 111 Copynumber: 1.9 Consensus size: 111
2722511 TCATATATCT
* * *
2722521 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
* *
2722586 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTCATTTAATGCATGATTATTAGATTAAAAATTAAATATCTCG
2722632 ACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
2722697 TGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
66 TGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
2722735 TTTCTGTAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (111 bp):
ACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTCATTTAATGCATGATTATTAGATTAAAAATTAAATATCTCG
Found at i:2724638 original size:15 final size:15
Alignment explanation
Indices: 2724620--2724660 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
2724610 ACCTGCTCAG
2724620 GATGACGACGATGAT
1 GATGACGACGATGAT
2724635 GATGACGAC-A--AT
1 GATGACGACGATGAT
*
2724647 GACGACGACGATGA
1 GATGACGACGATGA
2724661 CTATGATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 1 0.05
15 10 0.45
ACGTcount: A:0.37, C:0.17, G:0.32, T:0.15
Consensus pattern (15 bp):
GATGACGACGATGAT
Found at i:2724925 original size:35 final size:33
Alignment explanation
Indices: 2724886--2724970 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
2724876 ATATTTTAGT
2724886 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
2724921 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
2724956 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
2724971 TAAATATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:2728633 original size:50 final size:50
Alignment explanation
Indices: 2728572--2728698 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
2728562 CCCTACGTGG
* * *
2728572 CGTATAGCGCGGAACAGGGGGCGTGCTATACCCACGTGGCACCATATCAC
1 CGTATAGCGCGGAACAAGGGGCGCGCTATACCCACGTGGCACCAAATCAC
* ** * *
2728622 CGTATATCGCGGGGCAAGGGGCGCGCTATACCCACGTGGCGCCAAATCAG
1 CGTATAGCGCGGAACAAGGGGCGCGCTATACCCACGTGGCACCAAATCAC
* * ** *
2728672 CATATAGTGCGGTGCAGGGGGCGCGCT
1 CGTATAGCGCGGAACAAGGGGCGCGCT
2728699 TTCCTGCTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.21, C:0.28, G:0.35, T:0.16
Consensus pattern (50 bp):
CGTATAGCGCGGAACAAGGGGCGCGCTATACCCACGTGGCACCAAATCAC
Found at i:2730795 original size:29 final size:30
Alignment explanation
Indices: 2730504--2730798 Score: 164
Period size: 30 Copynumber: 9.9 Consensus size: 30
2730494 TAAATTCCGG
* * * *
2730504 TTTTTATTATTTTAGCCCTTTTAGTTTATA
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * * * * *
2730534 TTTTTGCAATTTTATTCCTTTAATTTTTTG
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
** * * * *
2730564 TTAGTGCCATTTTAGTCCTTTAAGTTTATG
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * * * *
2730594 TGTTTAGTGTTTTGGCCCTTTAAGTTTCT-
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * * * * *
2730623 GTTTAACCAGTTTAATCCTTTAAATTT-TA
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * * *
2730652 GTTTTTATTTTTTTAGCCCTTTAAGTTTTTA
1 -TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * * * * *
2730683 TTTTTGCAATTTTATTCCTTTAAATTTATG
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
* * *
2730713 TTTGTGCTATTTTATTCCTTTAAGTTTCTA
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
** *
2730743 TTTTTGGTGTTTTAGTCCTTTAAGTTTCTA
1 TTTTTACTATTTTAGTCCTTTAAGTTTCTA
*
2730773 TTTTTACTATTTTGGTCC-TTAAGTTT
1 TTTTTACTATTTTAGTCCTTTAAGTTT
2730799 TAGTAATTAT
Statistics
Matches: 195, Mismatches: 67, Indels: 7
0.72 0.25 0.03
Matches are distributed among these distances:
28 1 0.01
29 24 0.12
30 168 0.86
31 2 0.01
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTTTACTATTTTAGTCCTTTAAGTTTCTA
Found at i:2730802 original size:149 final size:149
Alignment explanation
Indices: 2730484--2730771 Score: 423
Period size: 149 Copynumber: 1.9 Consensus size: 149
2730474 AATTTCTATT
*** * * *
2730484 TTTAATCCTTTAAATTCCGGTTTTTATTATTTTAGCCCTTTTAGTTTATATTTTTGCAATTTTAT
1 TTTAATCCTTTAAATTTTAGTTTTTATTTTTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTAT
* * * *
2730549 TCCTTTAATTTTTTGTTAGTGCCATTTTAGTCCTTTAAGTTTATGTGTTTAGTGTTTTGGCCCTT
66 TCCTTTAAATTTATGTTAGTGCCATTTTAGTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTT
2730614 TAAGTTTCTGTTTAACCAG
131 TAAGTTTCTGTTTAACCAG
2730633 TTTAATCCTTTAAATTTTAGTTTTTATTTTTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTAT
1 TTTAATCCTTTAAATTTTAGTTTTTATTTTTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTAT
* * * * * * *
2730698 TCCTTTAAATTTATGTTTGTGCTATTTTATTCCTTTAAGTTTCTATTTTTGGTGTTTTAGTCCTT
66 TCCTTTAAATTTATGTTAGTGCCATTTTAGTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTT
2730763 TAAGTTTCT
131 TAAGTTTCT
2730772 ATTTTTACTA
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
149 122 1.00
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (149 bp):
TTTAATCCTTTAAATTTTAGTTTTTATTTTTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTAT
TCCTTTAAATTTATGTTAGTGCCATTTTAGTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTT
TAAGTTTCTGTTTAACCAG
Found at i:2730814 original size:149 final size:149
Alignment explanation
Indices: 2730513--2730833 Score: 385
Period size: 149 Copynumber: 2.2 Consensus size: 149
2730503 GTTTTTATTA
* * * *
2730513 TTTTAGCCCTTTTAGTTTATATTTTTGCAATTTTATTCCTTTAATTTTTTGTTAGTGCCATTTTA
1 TTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTATTCCTTTAAATTTATGTTAGTGCCATTTTA
* *
2730578 GTCCTTTAAGTTTATGTGTTTAGTGTTTTGGCCCTTTAAGTTTCTGTTTAACCAGTTTAATCCTT
66 GTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTTTAAGTTTCTGTTTAACCAGTTTAATCCTT
** *
2730643 TAAATTTTAGTTTTTATTT
131 TAAATTTTAGTAATTATAT
* *
2730662 TTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTATTCCTTTAAATTTATGTTTGTGCTATTTTA
1 TTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTATTCCTTTAAATTTATGTTAGTGCCATTTTA
* * * * * * * * * **
2730727 TTCCTTTAAGTTTCTATTTTTGGTGTTTTAGTCCTTTAAGTTTCTATTTTTACTATTTTGGTCC-
66 GTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTTTAAGTTTCT-GTTTAACCAGTTTAATCCT
*
2730791 TTAAGTTTTAGTAATTATAT
130 TTAAATTTTAGTAATTATAT
* *
2730811 TTTTA-TCCTTTAAATATTTTATT
1 TTTTAGCCCTTTAAGT-TTTTATT
2730834 GTTTTTTTAA
Statistics
Matches: 145, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
148 8 0.06
149 125 0.86
150 12 0.08
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.59
Consensus pattern (149 bp):
TTTTAGCCCTTTAAGTTTTTATTTTTGCAATTTTATTCCTTTAAATTTATGTTAGTGCCATTTTA
GTCCTTTAAGTTTATATGTTTAGTGTTTTAGCCCTTTAAGTTTCTGTTTAACCAGTTTAATCCTT
TAAATTTTAGTAATTATAT
Found at i:2730823 original size:29 final size:30
Alignment explanation
Indices: 2730752--2730823 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
2730742 ATTTTTGGTG
**
2730752 TTTTAGTCCTTTAAGTTTCTATTTTTACTAT
1 TTTTA-TCCTTTAAGTTTCTATAATTACTAT
**
2730783 TTTGGTCC-TTAAGTTT-TAGTAATTA-TAT
1 TTTTATCCTTTAAGTTTCTA-TAATTACTAT
2730811 TTTTATCCTTTAA
1 TTTTATCCTTTAA
2730824 ATATTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
28 11 0.33
29 16 0.48
30 3 0.09
31 3 0.09
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTATCCTTTAAGTTTCTATAATTACTAT
Found at i:2733799 original size:22 final size:20
Alignment explanation
Indices: 2733769--2733812 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2733759 TTAACATTCC
*
2733769 TTCTCTTTGAGACCTTGAAACA
1 TTCTCTTT--GACCATGAAACA
*
2733791 TTCTTTTTGACCATGAAACA
1 TTCTCTTTGACCATGAAACA
2733811 TT
1 TT
2733813 GCCCTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
22 7 0.35
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
TTCTCTTTGACCATGAAACA
Found at i:2734423 original size:18 final size:18
Alignment explanation
Indices: 2734400--2734461 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
2734390 AGATCCAATC
*
2734400 AAAACAAAGAGTAAAGAA
1 AAAACAAAGAGCAAAGAA
2734418 AAAACAAAGAGCAAAGAA
1 AAAACAAAGAGCAAAGAA
*
2734436 AAAAGAAA-A-CAAAGGAAA
1 AAAACAAAGAGCAAA-G-AA
2734454 AAAACAAA
1 AAAACAAA
2734462 AAGAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
16 4 0.10
17 2 0.05
18 33 0.85
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAACAAAGAGCAAAGAA
Found at i:2734462 original size:23 final size:22
Alignment explanation
Indices: 2734418--2734486 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
2734408 GAGTAAAGAA
* *
2734418 AAAACAAAGAGCAAAGAAAAAAG
1 AAAACAAAG-GAAAAAAAAAAAG
2734441 AAAACAAAGGAAAAAAACAAAAAG
1 AAAACAAAGG-AAAAAA-AAAAAG
*
2734465 AAAA-AAA-GAAAGAAAGAAAAG
1 AAAACAAAGGAAA-AAAAAAAAG
2734486 A
1 A
2734487 TAAGAAGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 9 0.22
22 5 0.12
23 16 0.40
24 10 0.25
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAACAAAGGAAAAAAAAAAAG
Found at i:2734470 original size:8 final size:8
Alignment explanation
Indices: 2734430--2734484 Score: 60
Period size: 8 Copynumber: 7.0 Consensus size: 8
2734420 AACAAAGAGC
2734430 AAAG-AAA
1 AAAGAAAA
2734437 AAAGAAAA
1 AAAGAAAA
*
2734445 CAAAGGAAA
1 -AAAGAAAA
*
2734454 AAA-ACAA
1 AAAGAAAA
2734461 AAAGAAAA
1 AAAGAAAA
*
2734469 AAAGAAAG
1 AAAGAAAA
2734477 AAAGAAAA
1 AAAGAAAA
2734485 GATAAGAAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 9 0.23
8 23 0.59
9 7 0.18
ACGTcount: A:0.82, C:0.04, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2734484 original size:13 final size:13
Alignment explanation
Indices: 2734430--2734492 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
2734420 AACAAAGAGC
2734430 AAAGAAA-AAAGA
1 AAAGAAAGAAAGA
* *
2734442 AAACAAAGGAAAAA
1 AAAGAAA-GAAAGA
*
2734456 AACAAAAAGAAA-A
1 AA-AGAAAGAAAGA
2734469 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
2734482 AAAGATAAGAA
1 AAAGA-AAGAA
2734493 GCACATACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
12 14 0.33
13 9 0.21
14 15 0.36
15 4 0.10
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:2735019 original size:15 final size:15
Alignment explanation
Indices: 2734999--2735033 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2734989 TGCAACTATT
2734999 GCATAGAAGGTGATC
1 GCATAGAAGGTGATC
2735014 GCATAGAAGGTGATC
1 GCATAGAAGGTGATC
*
2735029 ACATA
1 GCATA
2735034 AATATCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (15 bp):
GCATAGAAGGTGATC
Found at i:2735969 original size:66 final size:62
Alignment explanation
Indices: 2735863--2736081 Score: 219
Period size: 66 Copynumber: 3.3 Consensus size: 62
2735853 TTTCTCTTGC
* *
2735863 AAAATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGATTCTTTTGAA
1 AAAATCTTTGAGTCTGTTT-CTATGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAA
* *
2735927 GGAAAATCTTTGAGTCTATTTCTATGAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTATT-A
1 --AAAATCTTTGAGTCTGTTTCTATG-AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTTTTGA
2735991 A
62 A
* * *
2735992 AACCAA-CATTTGAGATC-GTTTCTATTGAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTTTGG
1 AA--AATC-TTTGAG-TCTGTTTCTA-TGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTG
2736055 AAACA
61 --A-A
2736060 CAAAATCTTTGAGTCTGTTTCT
1 -AAAATCTTTGAGTCTGTTTCT
2736082 CTTAAAACAA
Statistics
Matches: 130, Mismatches: 9, Indels: 27
0.78 0.05 0.16
Matches are distributed among these distances:
63 2 0.02
64 25 0.19
65 30 0.23
66 54 0.42
67 15 0.12
68 2 0.02
69 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (62 bp):
AAAATCTTTGAGTCTGTTTCTATGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAA
Found at i:2736080 original size:31 final size:31
Alignment explanation
Indices: 2736055--2736122 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
2736045 GTTTCTTTGG
2736055 AAACACAAA-ATCTTTGAGTCTGTTTCTCTTA
1 AAACA-AAACATCTTTGAGTCTGTTTCTCTTA
* *
2736086 AAACAAAACCATCTTTGAGTC-ATTTC-CTTG
1 AAACAAAA-CATCTTTGAGTCTGTTTCTCTTA
2736116 AAACAAA
1 AAACAAA
2736123 TTTTGTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 13 0.39
31 9 0.27
32 11 0.33
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (31 bp):
AAACAAAACATCTTTGAGTCTGTTTCTCTTA
Found at i:2736122 original size:30 final size:32
Alignment explanation
Indices: 2736064--2736122 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2736054 GAAACACAAA
*
2736064 ATCTTTGAGTCTGTTTCTCTTAAAACAAAACC
1 ATCTTTGAGTCTATTTCTCTTAAAACAAAACC
*
2736096 ATCTTTGAGTC-ATTTC-CTTGAAACAAA
1 ATCTTTGAGTCTATTTCTCTTAAAACAAA
2736123 TTTTGTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 4 0.16
32 11 0.44
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (32 bp):
ATCTTTGAGTCTATTTCTCTTAAAACAAAACC
Found at i:2736165 original size:95 final size:97
Alignment explanation
Indices: 2736016--2736194 Score: 231
Period size: 97 Copynumber: 1.8 Consensus size: 97
2736006 ATCGTTTCTA
* * * *
2736016 TTGAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTTTGGAAACACAAAATCTTTGAGTCTGTTTC
1 TTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTTTGGAAACAC--AATCTTTGAGTCGGTTTA
2736081 TCTT-AAAACAAAA-CCATCTTTGAGTCATTTCC
64 TCTTGAAAACAAAATCCATCTTTGAGTCATTTCC
* *
2736113 TTGAAACAAATTTTGTCTCTCTTGAGACAGCTTCTCTT-GAAGCATC-ATCTTTGAGTCGGTTTA
1 TTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCT-TTGGAAACA-CAATCTTTGAGTCGGTTTA
*
2736176 TCTTGAAACCAAAATCCAT
64 TCTTGAAAACAAAATCCAT
2736195 AAAGATGGCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
95 19 0.27
96 8 0.11
97 41 0.58
98 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (97 bp):
TTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTTTGGAAACACAATCTTTGAGTCGGTTTATC
TTGAAAACAAAATCCATCTTTGAGTCATTTCC
Found at i:2738528 original size:89 final size:91
Alignment explanation
Indices: 2738361--2738529 Score: 207
Period size: 90 Copynumber: 1.9 Consensus size: 91
2738351 TATTTTAGCC
* * * * * * * *
2738361 CTTTAAGTTTTTTGTTTTTGCCATTTTATTCCTTTAAATTTCTATTAGTGTCATTTTAGTCCTTT
1 CTTTAAGTTTTATGTTTGTGCCAGTTTAATCCTTTAAATTTCAATTAGTATCATTTTAGCCCTTA
2738426 AAGTTTATGGTTTTACTGTTCTGGCG
66 AAGTTTATGGTTTTACTGTTCTGGCG
** *
2738452 CTTTAAG-TTTATGTTTGT-CCAGTTTAATCCTTTAAATTTCAATTTTTATTATTTTTAGCCCTT
1 CTTTAAGTTTTATGTTTGTGCCAGTTTAATCCTTTAAATTTCAATTAGTATCA-TTTTAGCCCTT
*
2738515 AAAGTTTATGTTTTT
65 AAAGTTTATGGTTTT
2738530 TTCCATTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
89 26 0.40
90 32 0.49
91 7 0.11
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (91 bp):
CTTTAAGTTTTATGTTTGTGCCAGTTTAATCCTTTAAATTTCAATTAGTATCATTTTAGCCCTTA
AAGTTTATGGTTTTACTGTTCTGGCG
Found at i:2738568 original size:151 final size:150
Alignment explanation
Indices: 2738241--2738582 Score: 394
Period size: 151 Copynumber: 2.3 Consensus size: 150
2738231 TTATTTTAGC
* * * * *
2738241 CCTTTAAATATCTGTATTTACTA-TTTAGACCCTTAAGTTTATACTTTTAACTATTTTGGTCCTT
1 CCTTTAAATTTCTGT-TTGACTATTTTAGTCCTTTAAGTTTATACTTTTAACTATTCTGGTCCTT
* ** *
2738305 TAAGTTTCTATATTTCCAGTTTAATCCTTTAAAATTTTGTTTTTATTATTTTAGCCCTTTAAGTT
65 TAAGTTTATATATTTCCAGTTTAATCCTTTAAAATTTAATTTTTATTATTTTAGCCCTTAAAGTT
2738370 TTTTGTTTTTGCCATTTTATT
130 TTTTGTTTTTGCCATTTTATT
* * ** *
2738391 CCTTTAAATTTCTATTAGTGTC-ATTTTAGTCCTTTAAGTTTATGGTTTT-ACTGTTCTGG-CGC
1 CCTTTAAATTTCTGTT--TGACTATTTTAGTCCTTTAAGTTTATACTTTTAACTATTCTGGTC-C
*
2738453 TTTAAGTTTATGT-TTGTCCAGTTTAATCCTTT-AAATTTCAATTTTTATTATTTTTAGCCCTTA
63 TTTAAGTTTATATATT-TCCAGTTTAATCCTTTAAAATTT-AATTTTTATTA-TTTTAGCCCTTA
2738516 AAGTTTATGTT-TTTTT-CCATTTTATT
125 AAGTTT-T-TTGTTTTTGCCATTTTATT
*
2738542 CCTTTAAATTTCTGTTTGAACTATTTTAGTCCTTTATGTTT
1 CCTTTAAATTTCTGTTTG-ACTATTTTAGTCCTTTAAGTTT
2738583 CTATTTTTTA
Statistics
Matches: 163, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
149 12 0.07
150 60 0.37
151 83 0.51
152 6 0.04
153 2 0.01
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (150 bp):
CCTTTAAATTTCTGTTTGACTATTTTAGTCCTTTAAGTTTATACTTTTAACTATTCTGGTCCTTT
AAGTTTATATATTTCCAGTTTAATCCTTTAAAATTTAATTTTTATTATTTTAGCCCTTAAAGTTT
TTTGTTTTTGCCATTTTATT
Found at i:2738599 original size:30 final size:30
Alignment explanation
Indices: 2738565--2738621 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2738555 GTTTGAACTA
*
2738565 TTTTAGTCC-TTTATGTTTCTATTTTTTATG
1 TTTTAGACCTTTTA-GTTTCTATTTTTTATG
2738595 TTTTAGACCTTTTAGTTTCTATTTTTT
1 TTTTAGACCTTTTAGTTTCTATTTTTT
2738622 TCTATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.14, C:0.11, G:0.09, T:0.67
Consensus pattern (30 bp):
TTTTAGACCTTTTAGTTTCTATTTTTTATG
Found at i:2738637 original size:31 final size:31
Alignment explanation
Indices: 2738562--2738637 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
2738552 TCTGTTTGAA
2738562 CTATTTTAGTCC-TTTATGTTTCTATTTTTT
1 CTATTTTAGTCCTTTTATGTTTCTATTTTTT
* * *
2738592 ATGTTTTAGACCTTTTA-GTTTCTATTTTTTT
1 CTATTTTAGTCCTTTTATGTTTCTA-TTTTTT
*
2738623 CTATTTTGGTCCTTT
1 CTATTTTAGTCCTTT
2738638 AAAATTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.64
Consensus pattern (31 bp):
CTATTTTAGTCCTTTTATGTTTCTATTTTTT
Found at i:2740033 original size:33 final size:33
Alignment explanation
Indices: 2739986--2740051 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2739976 GGATCACATG
*
2739986 TGCTAGTCTTTCAACACACAACACAAACAAATA
1 TGCTAGTCTATCAACACACAACACAAACAAATA
*
2740019 TGCTAGTCTATCAACAGACAACACAAACAAATA
1 TGCTAGTCTATCAACACACAACACAAACAAATA
2740052 AGGAGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.20
Consensus pattern (33 bp):
TGCTAGTCTATCAACACACAACACAAACAAATA
Found at i:2740617 original size:20 final size:20
Alignment explanation
Indices: 2740571--2740620 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2740561 TTTGAGTTAA
*
2740571 TTAAAATACGTTTAAAGTGT
1 TTAAAATATGTTTAAAGTGT
2740591 TTAAAATATGTTTAAAGCT-T
1 TTAAAATATGTTTAAAG-TGT
*
2740611 TTTAAATATG
1 TTAAAATATG
2740621 AAAAACACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (20 bp):
TTAAAATATGTTTAAAGTGT
Found at i:2741417 original size:83 final size:83
Alignment explanation
Indices: 2741251--2741473 Score: 212
Period size: 83 Copynumber: 2.7 Consensus size: 83
2741241 CAAAATGGTA
* * * ** * * *
2741251 AATTTACCGACGTTTTTATACAAATGCAACAATATGATTCATATATAGTGGCATTTTTTCAACAA
1 AATTTAGCGACGTTGTTATACAAATACCGCAATAGGGTTCATATATAGTGGTATTTTTTCAACAA
* * *
2741316 ACACCGTAACATAGTAGT
66 ACACAGCAACATAATAGT
* * * *
2741334 ACTTTAGCGATGTTGTTATACAAATGCCGTAATAGGGTTCATATATAGTGGTATTTTTTCAACAA
1 AATTTAGCGACGTTGTTATACAAATACCGCAATAGGGTTCATATATAGTGGTATTTTTTCAACAA
** *
2741399 ATGCAGCAATATAATAGT
66 ACACAGCAACATAATAGT
* * * * * * * *
2741417 AATTTAGTGGCGTTTTTATTCAAATATCGCAATAGGGTACATCTATAGTGGTGTTTT
1 AATTTAGCGACGTTGTTATACAAATACCGCAATAGGGTTCATATATAGTGGTATTTT
2741474 CCCAAAAATT
Statistics
Matches: 112, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
83 112 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (83 bp):
AATTTAGCGACGTTGTTATACAAATACCGCAATAGGGTTCATATATAGTGGTATTTTTTCAACAA
ACACAGCAACATAATAGT
Found at i:2741745 original size:41 final size:41
Alignment explanation
Indices: 2741648--2741876 Score: 178
Period size: 41 Copynumber: 5.6 Consensus size: 41
2741638 ATGCCGTAAA
* * *
2741648 AGACTCTTACTTTAGTGGCGA-TTGTATACAAACAACG-TGAT
1 AGACTCGTACTTTAGTGGC-ATTTTTATACAAACACCGCT-AT
* *
2741689 AAACTCGTTCTTTAGTGGCATTTTTATACAAACACCGCTAT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAT
* * * * * **
2741730 AGACTTGTACCTTAGTGACGTTTTTATAAAAATGCCGCTAT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAT
** * * ** *
2741771 AGACTCGTACTTTAGAAGCGTTTTCATACAAATGCCGATAT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAT
* * * * *
2741812 AGACTCGTACTTTAGTGGCTTTTTTGTTCAAACATCGCAAT
1 AGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAT
*
2741853 AGAACT-TTACTTTAGTGG-ATTTTT
1 AG-ACTCGTACTTTAGTGGCATTTTT
2741877 TTGTAATAAA
Statistics
Matches: 150, Mismatches: 35, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
40 6 0.04
41 140 0.93
42 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (41 bp):
AGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAT
Found at i:2747586 original size:25 final size:25
Alignment explanation
Indices: 2747537--2747587 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2747527 TTTTTCATTC
2747537 TTTAACGACATAATATACTTTATAG
1 TTTAACGACATAATATACTTTATAG
2747562 TTTAACGACATAATATACTTTATAG
1 TTTAACGACATAATATACTTTATAG
2747587 T
1 T
2747588 GAGTTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTAACGACATAATATACTTTATAG
Found at i:2749307 original size:30 final size:30
Alignment explanation
Indices: 2749266--2749334 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2749256 TGTAATTATG
* *
2749266 AATTAATTAAAAAATAATTTAATTATTCCA
1 AATTAAATAAAAAATAATTTAATAATTCCA
** * *
2749296 AATTAAATAAAATCTTATTTAATAATTCCG
1 AATTAAATAAAAAATAATTTAATAATTCCA
2749326 AATTAAATA
1 AATTAAATA
2749335 TTCATTAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (30 bp):
AATTAAATAAAAAATAATTTAATAATTCCA
Found at i:2753017 original size:37 final size:34
Alignment explanation
Indices: 2752974--2753073 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 34
2752964 GTTTGAAATA
* *
2752974 AAATAAATAATTATAATTTAAAAAGAAAAAAATAAT
1 AAATAAATAATAATAA-ATAAAAAG-AAAAAATAAT
**
2753010 ATAATAAATAATAATAAATAAAAAGGGAAAATAAT
1 A-AATAAATAATAATAAATAAAAAGAAAAAATAAT
* * *
2753045 AAATAAATAATAGT-AATAAAGATAAAAAA
1 AAATAAATAATAATAAATAAAAAGAAAAAA
2753074 GGGGTTTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
33 11 0.20
34 12 0.22
35 9 0.17
36 8 0.15
37 14 0.26
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (34 bp):
AAATAAATAATAATAAATAAAAAGAAAAAATAAT
Found at i:2753033 original size:30 final size:31
Alignment explanation
Indices: 2752999--2753056 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
2752989 ATTTAAAAAG
* *
2752999 AAAAAAATAATATAATAAAT-AATAATAAAT
1 AAAAAAAGAAAATAATAAATAAATAATAAAT
**
2753029 AAAAAGGGAAAATAATAAATAAATAATA
1 AAAAAAAGAAAATAATAAATAAATAATA
2753057 GTAATAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (31 bp):
AAAAAAAGAAAATAATAAATAAATAATAAAT
Found at i:2753112 original size:7 final size:7
Alignment explanation
Indices: 2753095--2753128 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2753085 AGTTATTTTT
2753095 AAAAT-A
1 AAAATAA
2753101 AAAATAA
1 AAAATAA
2753108 AAAATAA
1 AAAATAA
2753115 AAAATAA
1 AAAATAA
*
2753122 GAAATAA
1 AAAATAA
2753129 TTAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:2753141 original size:14 final size:14
Alignment explanation
Indices: 2753124--2753151 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2753114 AAAAATAAGA
2753124 AATAATTAAATAAT
1 AATAATTAAATAAT
2753138 AATAATTAAATAAT
1 AATAATTAAATAAT
2753152 CTAAAGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATTAAATAAT
Found at i:2755919 original size:128 final size:126
Alignment explanation
Indices: 2755660--2755921 Score: 287
Period size: 128 Copynumber: 2.0 Consensus size: 126
2755650 AAAATTTTAT
*
2755660 TGCACTGTTTGAATCTGCTGTGTATTTTTCTGCTCTATTCGAACCGTTTTTTTCTGCATTGTTCT
1 TGCACTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAACCGTTTTTTTCTGCATTGTTCT
* * * ** *
2755725 GTTCAAACTTTTCTGCACAGTTCGATCCAAATCTTTTTTCTGCATTGGTTTTTTTTTCTGCAC
66 GTTCAAACTTTTCTGCACAATTCGAACCAAATATTTTTTCTG-A-TACTATTTTTTTCTGCAC
* *
2755788 TGCATTGTTTGAATCTGCTGTGTATTTTTCTGCACTGTTCGAATCAAATCAG-TTTTTTCTGCAT
1 TGCACTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAA-C----C-GTTTTTTTCTGCAT
** *
2755852 TGTTCTGTTCCAATTTTTTTTGCACAATTCGAACCAAATATGTTTTT-TG-TACTATTTTTTTTC
60 TGTTCTGTT-CAAACTTTTCTGCACAATTCGAACCAAATAT-TTTTTCTGATACTA-TTTTTTT-
2755915 CTGCAC
121 CTGCAC
2755921 T
1 T
2755922 TCATTGTTCT
Statistics
Matches: 112, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
128 40 0.36
129 1 0.01
131 2 0.02
132 7 0.06
133 29 0.26
134 28 0.25
135 5 0.04
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.49
Consensus pattern (126 bp):
TGCACTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAACCGTTTTTTTCTGCATTGTTCT
GTTCAAACTTTTCTGCACAATTCGAACCAAATATTTTTTCTGATACTATTTTTTTCTGCAC
Found at i:2755929 original size:133 final size:128
Alignment explanation
Indices: 2755660--2755929 Score: 321
Period size: 133 Copynumber: 2.1 Consensus size: 128
2755650 AAAATTTTAT
* *
2755660 TGCACTGTTTGAATCTGCTGTGTATTTTTCTGCTCTATTCGAACCGTTTTTTTCTGCATTGTTCT
1 TGCATTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAACCGTTTTTTTCTGCATTGTTCT
* * * * * *
2755725 GTTCAAACTTTTCTGCACAGTTCGATCCAAATCTTTTTTCTGCATTGGTTTTTTTTTCTGCAC
66 GTTCAAACTTTTCTGCACAATTCGAACCAAATATTTTTTCTGCACTGATTTTTTTTCCTGCAC
*
2755788 TGCATTGTTTGAATCTGCTGTGTATTTTTCTGCACTGTTCGAATCAAATCAG-TTTTTTCTGCAT
1 TGCATTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAA-C----C-GTTTTTTTCTGCAT
** * *
2755852 TGTTCTGTTCCAATTTTTTTTGCACAATTCGAACCAAATATGTTTTT-TGTACT-ATTTTTTTTC
60 TGTTCTGTT-CAAACTTTTCTGCACAATTCGAACCAAATAT-TTTTTCTGCACTGATTTTTTTTC
2755915 CTGCAC
123 CTGCAC
*
2755921 TTCATTGTT
1 TGCATTGTT
2755930 CTAATATGAT
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
128 40 0.33
129 1 0.01
133 44 0.37
134 30 0.25
135 5 0.04
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (128 bp):
TGCATTGTTTGAATCTGCTGTGTATTTTTCTGCACTATTCGAACCGTTTTTTTCTGCATTGTTCT
GTTCAAACTTTTCTGCACAATTCGAACCAAATATTTTTTCTGCACTGATTTTTTTTCCTGCAC
Found at i:2763269 original size:13 final size:13
Alignment explanation
Indices: 2763251--2763297 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
2763241 TGCGTCATAA
2763251 ATTTATGACGCGC
1 ATTTATGACGCGC
*
2763264 ATTTATGACACGC
1 ATTTATGACGCGC
* *
2763277 ATTTATAACGTGC
1 ATTTATGACGCGC
2763290 ATTTATGA
1 ATTTATGA
2763298 TATTCATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2796597 original size:18 final size:17
Alignment explanation
Indices: 2796556--2796597 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2796546 TGATATCATG
2796556 TTGTC-TCTCATTCCCC
1 TTGTCTTCTCATTCCCC
*
2796572 TT-TTTTCTCATTCTCCC
1 TTGTCTTCTCATTC-CCC
2796589 TTGTCTTCT
1 TTGTCTTCT
2796598 TCCTTCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.05
16 10 0.48
17 5 0.24
18 5 0.24
ACGTcount: A:0.05, C:0.36, G:0.05, T:0.55
Consensus pattern (17 bp):
TTGTCTTCTCATTCCCC
Found at i:2804981 original size:20 final size:20
Alignment explanation
Indices: 2804953--2805004 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2804943 AATAAGTCAA
* *
2804953 TAGTTTTGATACCCAGAGGT
1 TAGTATTGATACCCAGAGGC
2804973 TAGTATTGATACCCAGAGGC
1 TAGTATTGATACCCAGAGGC
*
2804993 TAGTATCGATAC
1 TAGTATTGATAC
2805005 TAAGGAGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGTATTGATACCCAGAGGC
Found at i:2813091 original size:19 final size:18
Alignment explanation
Indices: 2813051--2813092 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2813041 TTAAAGTTTA
*
2813051 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
2813068 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
2813087 TAAATT
1 TAAATT
2813093 AACTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:2824666 original size:21 final size:20
Alignment explanation
Indices: 2824634--2824672 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2824624 CTACACAGTT
2824634 AAATAACCATCGCAAAAATA
1 AAATAACCATCGCAAAAATA
* *
2824654 AAATTACCTATCGTAAAAA
1 AAATAACC-ATCGCAAAAA
2824673 AGTTACATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.18, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAACCATCGCAAAAATA
Found at i:2825343 original size:41 final size:43
Alignment explanation
Indices: 2825248--2825364 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 43
2825238 TGCGATCTAT
* * *
2825248 AATTCGTAACGCGATCTC-CG-GTATCGCAAAT-C-AGTTTCCA
1 AATTCGTAACGCGATTTCTCGACTATCGC-AATGCGATTTTCCA
* *
2825288 GATTCGTAACGCGA-TTCT-GACTATCGCATTGCGATTTTCCA
1 AATTCGTAACGCGATTTCTCGACTATCGCAATGCGATTTTCCA
** *
2825329 AATTCGTATTGCGATTTTTCGACTATCGCAATGCGA
1 AATTCGTAACGCGATTTCTCGACTATCGCAATGCGA
2825365 ATATGTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
39 5 0.08
40 20 0.33
41 18 0.30
42 3 0.05
43 15 0.25
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (43 bp):
AATTCGTAACGCGATTTCTCGACTATCGCAATGCGATTTTCCA
Found at i:2825396 original size:20 final size:20
Alignment explanation
Indices: 2825373--2825546 Score: 267
Period size: 20 Copynumber: 8.7 Consensus size: 20
2825363 GAATATGTAA
* * *
2825373 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
2825393 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2825413 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2825433 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2825453 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2825473 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2825493 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
2825513 GTCGCAACGCGATACTGACT
1 ATCGCAACGCGATTCTGACT
*
2825533 ATCGCAATGCGATT
1 ATCGCAACGCGATT
2825547 TTCAAAGCGT
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 144 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2826236 original size:20 final size:20
Alignment explanation
Indices: 2826199--2826265 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2826189 GATTCTTGCA
** *
2826199 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGTG
2826219 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
* ** *
2826239 TTGCAATTTTCTTTTTCGTG
1 TTGCGATAGTCATTTTCGTG
2826259 TTGCGAT
1 TTGCGAT
2826266 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:2826275 original size:20 final size:20
Alignment explanation
Indices: 2826232--2826275 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2826222 CGATAGTCAT
***
2826232 TTTCGTGTTGCAATTTTCTT
1 TTTCGTGTTGCAATTTTAAG
*
2826252 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
2826272 TTTC
1 TTTC
2826276 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:2828208 original size:20 final size:20
Alignment explanation
Indices: 2828183--2828250 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
2828173 TAGTTTACTT
2828183 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
2828203 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
2828223 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
2828243 TCGCAACG
1 TCGCAACG
2828251 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2828320 original size:20 final size:20
Alignment explanation
Indices: 2828295--2828348 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2828285 GATTCTCTCA
2828295 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
2828315 TTGCGATAGTCATTTTCGGG
1 TTGCGATAGTCATTTTCGCG
2828335 TTGCGATAGTCATT
1 TTGCGATAGTCATT
2828349 CGTGTTGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:2828355 original size:18 final size:19
Alignment explanation
Indices: 2828295--2828359 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 19
2828285 GATTCTCTCA
2828295 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCA-TTTCGCG
*
2828315 TTGCGATAGTCATTTTCGGG
1 TTGCGATAGTCA-TTTCGCG
*
2828335 TTGCGATAGTCA-TTCGTG
1 TTGCGATAGTCATTTCGCG
2828353 TTGCGAT
1 TTGCGAT
2828360 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.28
20 31 0.72
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.40
Consensus pattern (19 bp):
TTGCGATAGTCATTTCGCG
Found at i:2828877 original size:21 final size:21
Alignment explanation
Indices: 2828851--2828907 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2828841 CTCACCTGTC
2828851 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
2828872 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCCTCCCCT
2828893 ATCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
2828908 CCTATCATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCCT
Done.