Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 49 of 56
Found at i:11185729 original size:18 final size:20
Alignment explanation
Indices: 11185674--11185729 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 20
11185664 TAATGTTATG
11185674 GTATCGATACTACTATATAGTA
1 GTATCGATACTACT-T-TAGTA
* *
11185696 GTATCGACACTCCTTT-G-A
1 GTATCGATACTACTTTAGTA
11185714 GTATCGATACTACTTT
1 GTATCGATACTACTTT
11185730 TGCTTACTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 15 0.50
19 1 0.03
20 1 0.03
21 1 0.03
22 12 0.40
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATCGATACTACTTTAGTA
Found at i:11186027 original size:19 final size:19
Alignment explanation
Indices: 11186003--11186040 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11185993 ATTTGTTATC
11186003 AAAATAGGTTCTACAATCT
1 AAAATAGGTTCTACAATCT
11186022 AAAATAGGTTCTACAATCT
1 AAAATAGGTTCTACAATCT
11186041 CCTCCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAATAGGTTCTACAATCT
Found at i:11186674 original size:20 final size:20
Alignment explanation
Indices: 11186637--11186686 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11186627 CTTAAAATCA
***
11186637 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCGAATTTTG
11186657 TTTTTCAAAATCGAATTTTG
1 TTTTTCAAAATCGAATTTTG
*
11186677 -CTTTCAAAAT
1 TTTTTCAAAAT
11186687 AAAATCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTTCAAAATCGAATTTTG
Found at i:11187021 original size:34 final size:30
Alignment explanation
Indices: 11186983--11187051 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
11186973 TTGATATAAC
11186983 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
11187017 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
11187046 AATTTA
1 AATTTA
11187052 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:11187169 original size:20 final size:21
Alignment explanation
Indices: 11187141--11187222 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
11187131 TTCAAGATTG
*
11187141 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
11187162 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
11187180 CCC---GGGTACAGATACCCCCC
1 CCCAGGGGGTACAGATA--CCCC
* *
11187200 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATACCCC
11187221 CC
1 CC
11187223 TGTCTAAAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
15 11 0.22
18 4 0.08
20 4 0.08
21 22 0.44
23 9 0.18
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:11187188 original size:15 final size:15
Alignment explanation
Indices: 11187168--11187197 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11187158 CCCCCCCAGG
11187168 GGGTACAGATACCCC
1 GGGTACAGATACCCC
11187183 GGGTACAGATACCCC
1 GGGTACAGATACCCC
11187198 CCCCCAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:11187334 original size:21 final size:21
Alignment explanation
Indices: 11187308--11187350 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11187298 ATTTGAATAT
*
11187308 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11187329 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11187350 T
1 T
11187351 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:11187416 original size:20 final size:22
Alignment explanation
Indices: 11187378--11187417 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11187368 TTTGAGCATA
11187378 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
11187400 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
11187418 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:11187671 original size:34 final size:32
Alignment explanation
Indices: 11187632--11187701 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
11187622 TTTTGTAAAG
*
11187632 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
11187666 GGGAAAGGTTTTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
11187698 GGGA
1 GGGA
11187702 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:11190411 original size:34 final size:30
Alignment explanation
Indices: 11190373--11190441 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
11190363 TTGATATAAC
11190373 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
11190407 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
11190436 AATTTA
1 AATTTA
11190442 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:11190556 original size:21 final size:21
Alignment explanation
Indices: 11190531--11190595 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
11190521 TTCAAGATTG
11190531 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
11190552 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATTCCCC
*
11190573 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
11190594 CC
1 CC
11190596 TGTCTAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.18, C:0.42, G:0.28, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:11190661 original size:20 final size:21
Alignment explanation
Indices: 11190621--11190663 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11190611 AACAGAATGT
11190621 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
11190642 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
11190663 C
1 C
11190664 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:11190725 original size:21 final size:21
Alignment explanation
Indices: 11190699--11190741 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11190689 ATTTGAATAT
*
11190699 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11190720 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11190741 T
1 T
11190742 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:11190807 original size:20 final size:22
Alignment explanation
Indices: 11190769--11190808 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11190759 TTTGAGCATA
11190769 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
11190791 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
11190809 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:11191062 original size:34 final size:32
Alignment explanation
Indices: 11191023--11191092 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
11191013 TTTTGTAAAG
*
11191023 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
11191057 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
11191089 GGGA
1 GGGA
11191093 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:11192181 original size:18 final size:18
Alignment explanation
Indices: 11192158--11192196 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
11192148 CTAGTGATGG
11192158 AGTGTGAATCCTCGAGAT
1 AGTGTGAATCCTCGAGAT
11192176 AGTGTGAATCCTCGAGAT
1 AGTGTGAATCCTCGAGAT
11192194 AGT
1 AGT
11192197 ATGCCCCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (18 bp):
AGTGTGAATCCTCGAGAT
Found at i:11194505 original size:22 final size:21
Alignment explanation
Indices: 11194468--11194510 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
11194458 CGATGTTATG
11194468 GTATCGATACTACTTTATAGTA
1 GTATCGATACTACTTT-TAGTA
* *
11194490 GTATCGATATTCCTTTTAGTA
1 GTATCGATACTACTTTTAGTA
11194511 TATGTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
GTATCGATACTACTTTTAGTA
Found at i:11195674 original size:49 final size:49
Alignment explanation
Indices: 11195621--11195717 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
11195611 ACTTAAACCT
* *
11195621 AAACCCATTACAATGAAAGCCATGGACCCCTTACATAAAACTCAAGACC
1 AAACCCATTACAATGAAAACCATGGACCCCTTACATAAAACCCAAGACC
11195670 AAACCCATTACAATGAAAACCATGGACCCCTTACATAAAACCCAAGAC
1 AAACCCATTACAATGAAAACCATGGACCCCTTACATAAAACCCAAGAC
11195718 AACCCAGCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.44, C:0.31, G:0.09, T:0.15
Consensus pattern (49 bp):
AAACCCATTACAATGAAAACCATGGACCCCTTACATAAAACCCAAGACC
Found at i:11195697 original size:28 final size:28
Alignment explanation
Indices: 11195621--11195697 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
11195611 ACTTAAACCT
*
11195621 AAACCCATTACAATGAAAGCCATGGA-C
1 AAACCCATTACAATGAAAACCATGGACC
*
11195648 ---CCC-TTAC-AT-AAAACTCA-AGACC
1 AAACCCATTACAATGAAAAC-CATGGACC
11195670 AAACCCATTACAATGAAAACCATGGACC
1 AAACCCATTACAATGAAAACCATGGACC
11195698 CCTTACATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 17
0.66 0.05 0.29
Matches are distributed among these distances:
21 6 0.16
22 5 0.13
23 4 0.11
24 3 0.08
25 3 0.08
26 4 0.11
27 4 0.11
28 9 0.24
ACGTcount: A:0.44, C:0.30, G:0.10, T:0.16
Consensus pattern (28 bp):
AAACCCATTACAATGAAAACCATGGACC
Found at i:11195709 original size:21 final size:21
Alignment explanation
Indices: 11195640--11195711 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 21
11195630 ACAATGAAAG
11195640 CCATGGACCCCTTACATAAAA
1 CCATGGACCCCTTACATAAAA
*
11195661 CTCA-AGACCAAACCCATTACAATGAAAA
1 C-CATGGA-C---CCC-TTAC-AT-AAAA
11195689 CCATGGACCCCTTACATAAAA
1 CCATGGACCCCTTACATAAAA
11195710 CC
1 CC
11195712 CAAGACAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
21 9 0.22
22 5 0.12
23 4 0.10
24 3 0.08
25 3 0.08
26 4 0.10
27 5 0.12
28 7 0.17
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (21 bp):
CCATGGACCCCTTACATAAAA
Found at i:11206627 original size:16 final size:16
Alignment explanation
Indices: 11206606--11206638 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11206596 CCCATTTATC
11206606 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
11206622 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
11206638 A
1 A
11206639 AAACACTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:11208952 original size:20 final size:21
Alignment explanation
Indices: 11208898--11208960 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
11208888 GATTCCCCTG
11208898 TGGGGGGAATCGGTTCCTCTTCAA
1 TGGGGGG-ATCGGTTCC-C-TCAA
* *
11208922 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
11208942 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
11208961 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:11212786 original size:20 final size:20
Alignment explanation
Indices: 11212744--11212786 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11212734 TTGTTTTCAT
* *
11212744 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
11212764 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
11212784 TTT
1 TTT
11212787 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:11217866 original size:24 final size:23
Alignment explanation
Indices: 11217824--11217887 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
11217814 CATTTTGGCG
11217824 AATGAGGTATCGATACCCCCTTTA
1 AATG-GGTATCGATACCCCCTTTA
*
11217848 AATGGGTATCGATACCCCCTTTG
1 AATGGGTATCGATACCCCCTTTA
* *
11217871 AATGGGTACCCATACCC
1 AATGGGTATCGATACCC
11217888 TCCCCTAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 33 0.89
24 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (23 bp):
AATGGGTATCGATACCCCCTTTA
Found at i:11234657 original size:36 final size:36
Alignment explanation
Indices: 11234610--11234764 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
11234600 AGTCAATCCT
11234610 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
11234646 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
11234682 AAGCCTTCACCGGAGAATAGTAAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
11234718 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
11234754 AAGTCTTCACC
1 AAGCCTTCACC
11234765 AAAAAGTAGT
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
35 1 0.01
36 106 0.98
37 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:11234773 original size:36 final size:36
Alignment explanation
Indices: 11234609--11234798 Score: 168
Period size: 36 Copynumber: 5.2 Consensus size: 36
11234599 AAGTCAATCC
* *
11234609 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * * * *
11234645 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * * * *
11234681 GAAGCCTTCACCGGAGAATAGTAAAGCAAACCATCA
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * *
11234717 TAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGA-AAAATAGTGAAGCAAACCATCT
* * *
11234753 TAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGAAAAA-TAGTGAAGCA-AACCATCT
*
11234790 TAAGGCTTC
1 TAAGCCTTC
11234799 TCAGAAGAGT
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
35 2 0.02
36 117 0.88
37 14 0.11
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (36 bp):
TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
Found at i:11235245 original size:51 final size:51
Alignment explanation
Indices: 11235180--11235684 Score: 632
Period size: 51 Copynumber: 9.8 Consensus size: 51
11235170 AAGATTATTT
* * * *
11235180 GAGTTCCATACTCCCTAGAGAGAGAGGGACCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
11235231 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
11235282 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACTCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* *
11235333 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTCC
* * * * *
11235386 GAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * *
11235437 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * *
11235488 GAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTCC
* * * * *
11235541 GAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * *
11235592 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
11235643 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTT
1 GAGTTCCATACTCCCT-AAAGAAAGAAGGAGCGAACCCGTTT
11235685 CCAAAAGATT
Statistics
Matches: 399, Mismatches: 50, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
51 284 0.71
52 28 0.07
53 87 0.22
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
Found at i:11235460 original size:155 final size:155
Alignment explanation
Indices: 11235180--11235684 Score: 825
Period size: 155 Copynumber: 3.3 Consensus size: 155
11235170 AAGATTATTT
* * * * * *
11235180 GAGTTCCATACTCCCTAGAGAGAGAGGGACCGAACCCGTTTG-A-AGATGTCCGAGTTCCATACT
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
* *
11235243 CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAA
66 CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCTTAAAGAAAGAA
*
11235308 GGAGCGAACTCGTTTGAAGATGTTC
131 GGAGCGAACCCGTTTGAAGATGTTC
*
11235333 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATAAT
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
11235398 CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCTTAAAGAAAGAA
66 CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCTTAAAGAAAGAA
11235463 GGAGCGAACCCGTTTGAAGATGTTC
131 GGAGCGAACCCGTTTGAAGATGTTC
* *
11235488 GAGTTTCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTTCATACT
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
* *
11235553 CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCCTAAAGAAAGAG
66 CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCTTAAAGAAAGAA
11235618 GGAGCGAACCCGTTTGAAGATGTTC
131 GGAGCGAACCCGTTTGAAGATGTTC
* * * *
11235643 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTT
1 GAGTTCCATAC-TCCTTAAAGAAAGAAGGAGCGAACCCGTTT
11235685 CCAAAAGATT
Statistics
Matches: 329, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
153 37 0.11
154 1 0.00
155 264 0.80
156 27 0.08
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (155 bp):
GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
CCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTCCTTAAAGAAAGAA
GGAGCGAACCCGTTTGAAGATGTTC
Found at i:11235533 original size:206 final size:206
Alignment explanation
Indices: 11235179--11235833 Score: 779
Period size: 206 Copynumber: 3.2 Consensus size: 206
11235169 GAAGATTATT
* * * *
11235179 TGAGTTCCATACTCCCTAGAGAGAGAGGGACCGAACCCGTTTGAAGATGTCCGAGTTCCATACTC
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
* * * *
11235244 CCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAG
* * * *
11235309 GAGCGAACTCGTTTGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTT
131 GAGCGAACTCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAT
11235374 GAAGAGATGTC
196 GAAGAGATGTC
* *
11235385 TGAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCGAGTTCTATACTC
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
*
11235450 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTT-TCATACTCCTTAAAGAAAGAA
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATTCGAGTTCT-ATACTCCTTAAAGAAAGAA
* *
11235514 GGAGCGAACCCGTTTGAAGA-GATGTCTGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCC
130 GGAGCGAACTCGTTTGAAGATG-T-TC-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
* *
11235578 GTGTG-A-AGATATC
192 GTATGAAGAGATGTC
* * * * *
11235591 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTT
1 TGAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATAC-T
* * * *
11235656 CCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTCGAGTTCTATACTCCTTAAAGAA
65 CCTTAAAGAAAGAAGGAGCGAACCCGTTT---GAAGA-TATTCGAGTTCTATACTCCTTAAAGAA
* * * * *
11235721 A-AA-G-G-GAATTCGCTTACAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCG
126 AGAAGGAGCGAACTCG-TT--TGAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
* * *
11235782 AACCTGTAAGAAGAAGAGGT-
187 AACCCGTATGAAG-AGATGTC
*
11235802 TCGAGTTCCATAATCCCTAGAGAAATAGGGAG
1 T-GAGTTCCATAATCCCTAGAGAAAGAGGGAG
11235834 TAGACCCGAT
Statistics
Matches: 383, Mismatches: 47, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
205 2 0.01
206 198 0.52
207 35 0.09
208 40 0.10
209 37 0.10
210 14 0.04
211 26 0.07
212 31 0.08
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (206 bp):
TGAGTTCCATAATCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATACTC
CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAG
GAGCGAACTCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAT
GAAGAGATGTC
Found at i:11235884 original size:55 final size:55
Alignment explanation
Indices: 11235822--11236484 Score: 706
Period size: 55 Copynumber: 12.2 Consensus size: 55
11235812 TAATCCCTAG
* * * *
11235822 AGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
11235877 A-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGA
1 AGA-AATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * *
11235932 A-AGAATAGGGAGTAGACACGATCGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
1 AGA-AATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * * *
11235987 AGGAATAGGGAGCATACACG-TT-TTCAAAAGATT-TTCGAGT-TCTATACTCCCTGG
1 AGAAATAGGGGGCAGACACGATTGTT--GAAGATTGTTCGAGTCT-TATACTCTCTGA
* ** * *
11236041 AGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAG-ACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
** * * *
11236094 AGAAATAGGGGGCAGATGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * * *
11236149 AGAAATAGGGGGCAGACGCAATCGTTTAAGATTATTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * *
11236204 AGAAATAGGGGGCAGACGCAATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* *
11236257 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
** * *
11236312 AGAAATAGGGGGCAGATGCGATTGATGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * **
11236365 AGAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * * *
11236420 AGAAATAGGGGGCAGACAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGA
1 AGAAATAGGGGGCAGACACGATTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGA
11236475 AGAAATAGGG
1 AGAAATAGGG
11236485 AGCGAACCCA
Statistics
Matches: 522, Mismatches: 68, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
53 134 0.26
54 48 0.09
55 338 0.65
56 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
AGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:11236256 original size:163 final size:161
Alignment explanation
Indices: 11235856--11236484 Score: 670
Period size: 163 Copynumber: 3.9 Consensus size: 161
11235846 TTGAAGTTTG
* * * *
11235856 TTCGAGTCTTATACTCTCTGAA-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGTCT
1 TTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACGCAATTGATGAAGATT-GTCGAGTCT
* * * * *
11235920 CATACTCTCTGAA-AGAATAGGGAGTAGACACGATCGTTGAAGATTGTTCGAGTCTCATACTCTC
64 TATACTCTCTGAAGA-AATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTC
* * *
11235984 TGAAGGAATAGGGAGCATA-CA-CGTTTTCAAAAGATT
128 TGAAGAAATAGGGGGCAGAGCATCG-TTT---AAGATT
* * * * * * * *
11236020 TTCGAGT-TCTATACTCCCTGGAGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTGT-GGGTCT
1 TTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCAG-ACGCAATTGATGAAGATTGTCGAGTCT
** * *
11236082 TATACTCTCTGAAGAAATAGGGGGCAGATGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCT
64 TATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCT
11236147 GAAGAAATAGGGGGCAGACGCAATCGTTTAAGATT
129 GAAGAAATAGGGGGCAGA-GC-ATCGTTTAAGATT
* *
11236182 ATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATTGATGAAGATTGT-GGGTCTT
1 -TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGATGAAGATTGTCGAGTCTT
11236246 ATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTG
65 ATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTG
* * *
11236311 AAGAAATAGGGGGCAGATGCGATTGATGAAGATT
130 AAGAAATAGGGGGCAGA-GC-ATCGTTTAAGATT
* * * * *
11236345 GT-GGGTCTTATACTCTCTGAAGAAAAAGGGGGCAGACGCAA-TCATTGAAGATTGTTCGAGTCT
1 TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGA-TGAAGATTG-TCGAGTCT
* * * *
11236408 TATACTCTCTGAAGAAATAGGGGGCAGACA-AGTTTGTTGAAGA-TGATTCAAGTCTTATACCCT
64 TATACTCTCTGAAGAAATAGGGGGCAGACACA-ATCGTTGAAGATTG-TTCGAGTCTTATACTCT
11236471 CTGAAGAAATAGGG
127 CTGAAGAAATAGGG
11236485 AGCGAACCCA
Statistics
Matches: 404, Mismatches: 45, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
160 2 0.00
161 46 0.11
162 85 0.21
163 218 0.54
164 46 0.11
165 5 0.01
166 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (161 bp):
TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCAATTGATGAAGATTGTCGAGTCTTA
TACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
AGAAATAGGGGGCAGAGCATCGTTTAAGATT
Found at i:11236279 original size:108 final size:109
Alignment explanation
Indices: 11235822--11236484 Score: 684
Period size: 108 Copynumber: 6.1 Consensus size: 109
11235812 TAATCCCTAG
* * * * * *
11235822 AGAAATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAA-AGAATAGG
1 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGG
* * * * * * *
11235886 GAGCAGACACGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGA
65 GGGCAGACGCAATTGATGAAGATT-GTCGGGTCTTATACTCTCTGA
* * * * *
11235932 A-AGAATAGGGAGTAGACACGATCGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGG
1 AGA-AATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * * ** * * * * * *
11235996 GAGCATACACGTTTTCA-AAAGATTTTCGAGT-TCTATACTCCCTGG
65 GGGCAGACGC-AATTGATGAAGATTGTCGGGTCT-TATACTCTCTGA
* ** * * * *
11236041 AGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGG
1 AGAAATAGGGGGCAG-ACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGG
* * *
11236103 GGGCAGATGCAATAGTTGAAGATTGTTCGGGTCTTATACTCTCTGA
65 GGGCAGACGCAATTGATGAAGATTG-TCGGGTCTTATACTCTCTGA
* * *
11236149 AGAAATAGGGGGCAGACGCAATCGTTTAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
11236214 GGCAGACGCAATTGATGAAGATTGT-GGGTCTTATACTCTCTGA
66 GGCAGACGCAATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
11236257 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
* *
11236322 GGCAGATGCGATTGATGAAGATTGT-GGGTCTTATACTCTCTGA
66 GGCAGACGCAATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
* * *
11236365 AGAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1 AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
* ** *
11236430 GGCAGA--CAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGA
66 GGCAGACGCAA--TTGATGAAGATTG--TCGGGTCTTATACTCTCTGA
11236475 AGAAATAGGG
1 AGAAATAGGG
11236485 AGCGAACCCA
Statistics
Matches: 474, Mismatches: 62, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
106 3 0.01
107 38 0.08
108 240 0.51
109 47 0.10
110 144 0.30
111 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (109 bp):
AGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
GGCAGACGCAATTGATGAAGATTGTCGGGTCTTATACTCTCTGA
Found at i:11240629 original size:12 final size:12
Alignment explanation
Indices: 11240612--11240714 Score: 64
Period size: 13 Copynumber: 7.9 Consensus size: 12
11240602 AGAGAAAATG
11240612 AGAAAAAAGAAA
1 AGAAAAAAGAAA
*
11240624 AGAAAATAAAAAA
1 AGAAAA-AAGAAA
*
11240637 AGGAAGAAAAAGAAG
1 A-G-A-AAAAAGAAA
11240652 AGAAAAAAGAGAAA
1 AG-AAAAA-AGAAA
*
11240666 ATGAAAAATGAAA
1 A-GAAAAAAGAAA
*
11240679 TGAAAAATAG-AA
1 AGAAAAA-AGAAA
* *
11240691 AGAAAAAATGGAG
1 AGAAAAAA-GAAA
11240704 AGAAAAAAGAA
1 AGAAAAAAGAA
11240715 TAAGGAAGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
11 1 0.01
12 23 0.32
13 24 0.33
14 14 0.19
15 7 0.10
16 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:11240637 original size:28 final size:28
Alignment explanation
Indices: 11240602--11240673 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
11240592 AAAGATGAAG
11240602 AGAGAAAATGAGAAAAAAGAAAAGAAAATA
1 AGAGAAAATGA-AAAAAAGAAAAGAAAA-A
* *
11240632 A-A-AAAAGGAAGAAAAAGAAGAGAAAAA
1 AGAGAAAATGAA-AAAAAGAAAAGAAAAA
11240659 AGAGAAAATGAAAAA
1 AGAGAAAATGAAAAA
11240674 TGAAATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 3 0.08
28 24 0.67
29 8 0.22
30 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (28 bp):
AGAGAAAATGAAAAAAAGAAAAGAAAAA
Found at i:11240643 original size:17 final size:20
Alignment explanation
Indices: 11240604--11240673 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
11240594 AGATGAAGAG
11240604 AGAAAATGAGAAAAAAGAAA
1 AGAAAATGAGAAAAAAGAAA
*
11240624 AGAAAAT-A-AAAAAAG-GA
1 AGAAAATGAGAAAAAAGAAA
* * *
11240641 AGAAAAAGAAGAGAAAA-AAG
1 AGAAAATG-AGAAAAAAGAAA
11240661 AGAAAATGA-AAAA
1 AGAAAATGAGAAAA
11240674 TGAAATGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 7 0.18
18 10 0.26
19 3 0.08
20 19 0.49
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAATGAGAAAAAAGAAA
Found at i:11240651 original size:9 final size:10
Alignment explanation
Indices: 11240602--11240666 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
11240592 AAAGATGAAG
11240602 AGAGAAAATG-
1 AGAGAAAA-GA
*
11240612 AGAAAAAAGA
1 AGAGAAAAGA
* *
11240622 AAAGAAAATA
1 AGAGAAAAGA
11240632 A-A-AAAAGGA
1 AGAGAAAA-GA
11240641 AGA-AAAAGA
1 AGAGAAAAGA
11240650 AGAGAAAA-A
1 AGAGAAAAGA
11240659 AGAGAAAA
1 AGAGAAAA
11240667 TGAAAAATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.09
9 18 0.39
10 24 0.52
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (10 bp):
AGAGAAAAGA
Found at i:11240685 original size:13 final size:12
Alignment explanation
Indices: 11240664--11240697 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
11240654 AAAAAAGAGA
11240664 AAATGAAAAATG
1 AAATGAAAAATG
11240676 AAATGAAAAATAG
1 AAATGAAAAAT-G
11240689 AAA-GAAAAA
1 AAATGAAAAA
11240698 ATGGAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (12 bp):
AAATGAAAAATG
Found at i:11240698 original size:40 final size:37
Alignment explanation
Indices: 11240573--11240698 Score: 114
Period size: 40 Copynumber: 3.3 Consensus size: 37
11240563 TAAATTTTTA
*
11240573 AAAGAAAAAAATGAAAATAAAAGATGAAGAGAGAAAATGAG
1 AAAGAAAAAAAAGAAAATAAAA-ATGAA-AGA-AAAAT-AG
* * *
11240614 AAA-AAAGAAAAGAAAATAAAAA--AAGGAAGAAAAAG
1 AAAGAAAAAAAAGAAAATAAAAATGAAAGAA-AAATAG
*
11240649 AAGAGAAAAAAGAGAAAATGAAAAATGAAATGAAAAATAG
1 AA-AGAAAAAAAAGAAAAT-AAAAATGAAA-GAAAAATAG
11240689 AAAGAAAAAA
1 AAAGAAAAAA
11240699 TGGAGAGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
35 5 0.07
36 6 0.09
37 14 0.20
38 5 0.07
39 9 0.13
40 25 0.36
41 6 0.09
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (37 bp):
AAAGAAAAAAAAGAAAATAAAAATGAAAGAAAAATAG
Found at i:11240699 original size:20 final size:20
Alignment explanation
Indices: 11240632--11240700 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
11240622 AAAGAAAATA
* *
11240632 AAAAAAGGAAGAAAAAGAAGAG
1 AAAAAATGAA-AAATAGAA-AG
11240654 AAAAAA-GAGAAAAT-GAAA-
1 AAAAAATGA-AAAATAGAAAG
*
11240672 AATGAAATGAAAAATAGAAAG
1 AA-AAAATGAAAAATAGAAAG
11240693 AAAAAATG
1 AAAAAATG
11240701 GAGAGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 9 0.23
20 14 0.36
21 7 0.18
22 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
AAAAAATGAAAAATAGAAAG
Found at i:11243263 original size:29 final size:29
Alignment explanation
Indices: 11243231--11243304 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
11243221 ATTCGAATCT
* * * *
11243231 TTTAATTTCT-TTCATTTACATTTTTGTCC
1 TTTAATTTATGTT-ATTAACATTTCTATCC
11243260 TTTAATTTATGTTATTAACATTTCTATCC
1 TTTAATTTATGTTATTAACATTTCTATCC
11243289 TTTAATTTATGTTATT
1 TTTAATTTATGTTATT
11243305 CTAATTTCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 38 0.95
30 2 0.05
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTAATTTATGTTATTAACATTTCTATCC
Found at i:11243325 original size:29 final size:29
Alignment explanation
Indices: 11243258--11243321 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
11243248 ACATTTTTGT
*
11243258 CCTTTAATTTATGTTATTAACATTTCTAT
1 CCTTTAATTTATGTTATTAACATTTCTAG
*
11243287 CCTTTAATTTATGTTATTCTA-ATTTC-AG
1 CCTTTAATTTATGTTATT-AACATTTCTAG
11243315 CCTTTAA
1 CCTTTAA
11243322 ATTTTAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 8 0.25
29 23 0.72
30 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.53
Consensus pattern (29 bp):
CCTTTAATTTATGTTATTAACATTTCTAG
Found at i:11247828 original size:46 final size:46
Alignment explanation
Indices: 11247778--11248232 Score: 555
Period size: 46 Copynumber: 9.9 Consensus size: 46
11247768 TAGAGTCTCT
* * * * * *
11247778 TTTCAGGCATTAATACATCCGTTCATACATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* * * *
11247824 TTTCATGCCCTAATACATCCTTTCATGCATTTTAGTTATGGTATCAC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATC-C
* * *
11247871 -TTCATGCCTTAATACATCCTTTCATGCATTTTAATTATGGAATCA
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* *
11247916 TTTCATGCCTTAATGCATCCTTTCATGCATGTTAATTATGGCATTC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* * * *
11247962 TTTCATGCATTTTAATTATGTCATACTTTCATGC--CTT-A--AT-GCATTC
1 TTTCATGC--CTT-A--ATG-CATCCTTTCATGCATTTTAATTATGGCATCC
*
11248008 TTTCATGCCTTAATGCATTCTTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* *
11248054 TTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* *
11248100 TTTCATGCCTTAATGCATCCTTTCATGCATTTAAATTATGGCATCA
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* *
11248146 TTTCATGCCTTAATGCATCCTTTCATGAATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
*
11248192 TTTCATGCCTTAATACATCCTTTCATGCATTTTAATTATGG
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGG
11248233 ATTCGGAACA
Statistics
Matches: 357, Mismatches: 38, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
40 12 0.03
41 3 0.01
42 2 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 310 0.87
47 3 0.01
48 2 0.01
49 2 0.01
50 2 0.01
51 3 0.01
52 12 0.03
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
Found at i:11247896 original size:20 final size:20
Alignment explanation
Indices: 11247871--11247943 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
11247861 ATGGTATCAC
11247871 TTCATGCCTTAATACATCCT
1 TTCATGCCTTAATACATCCT
* * *
11247891 TTCATGCATTTTAATTATGGAATCAT
1 TTCATGC--CTTAA-TA---CATCCT
*
11247917 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATACATCCT
11247937 TTCATGC
1 TTCATGC
11247944 ATGTTAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 18 0.45
22 4 0.10
23 3 0.08
24 4 0.10
26 11 0.28
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (20 bp):
TTCATGCCTTAATACATCCT
Found at i:11248012 original size:20 final size:20
Alignment explanation
Indices: 11247987--11248219 Score: 160
Period size: 20 Copynumber: 10.4 Consensus size: 20
11247977 TTATGTCATA
*
11247987 CTTTCATGCCTTAATGCATT
1 CTTTCATGCCTTAATGCATC
*
11248007 CTTTCATGCCTTAATGCATT
1 CTTTCATGCCTTAATGCATC
*
11248027 CTTTCATGCATTTTAATTATGGCATC
1 CTTTCATGC--CTT-A--AT-GCATC
11248053 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
* *
11248073 ATTTCATGCATTTTAATTATGACATC
1 CTTTCATGC--CTT-A--ATG-CATC
11248099 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
*
11248119 CTTTCATGCATTTAAATTATGGCATC
1 CTTTCATGC-CTT--A--AT-GCATC
*
11248145 ATTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
**
11248165 CTTTCATGAATTTTAGTTATGGCATC
1 CTTTCATG--CCTTA---AT-GCATC
*
11248191 CTTTCATGCCTTAATACATC
1 CTTTCATGCCTTAATGCATC
11248211 CTTTCATGC
1 CTTTCATGC
11248220 ATTTTAATTA
Statistics
Matches: 173, Mismatches: 16, Indels: 48
0.73 0.07 0.20
Matches are distributed among these distances:
20 80 0.46
21 11 0.06
22 7 0.04
23 6 0.03
24 7 0.04
25 11 0.06
26 51 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (20 bp):
CTTTCATGCCTTAATGCATC
Found at i:11251704 original size:23 final size:23
Alignment explanation
Indices: 11251678--11251724 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11251668 AAAGAACCAC
*
11251678 AATAAACT-TAAATATACCATTAA
1 AATAAACTCTAAACAT-CCATTAA
*
11251701 AATAAAGTCTAAACATCCATTAA
1 AATAAACTCTAAACATCCATTAA
11251724 A
1 A
11251725 CCAACAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAAACTCTAAACATCCATTAA
Found at i:11261886 original size:23 final size:23
Alignment explanation
Indices: 11261860--11261906 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11261850 AAAGAACCAC
*
11261860 AATAAACT-TAAATATACCATTAA
1 AATAAACTCTAAACAT-CCATTAA
*
11261883 AATAAAGTCTAAACATCCATTAA
1 AATAAACTCTAAACATCCATTAA
11261906 A
1 A
11261907 CCAATCACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAAACTCTAAACATCCATTAA
Found at i:11266469 original size:46 final size:46
Alignment explanation
Indices: 11266409--11266600 Score: 215
Period size: 46 Copynumber: 4.2 Consensus size: 46
11266399 TAGGGTCTCT
** * ** *
11266409 TTTCATGCATTAATACATCCGTTCATAAATTTTAATCATGGAATCC
1 TTTCATGCCCTAATACATCCTTTCATGCATTTTAATTATGGAATCC
* * *
11266455 TTTTATGCCCTAATACATCCTTTCATGCATTTTAGTTATGGCATCC
1 TTTCATGCCCTAATACATCCTTTCATGCATTTTAATTATGGAATCC
* * * *
11266501 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCA
1 TTTCATGCCCTAATACATCCTTTCATGCATTTTAATTATGGAATCC
* * * *
11266547 TTACATGCCTTAATGCATCATTTCATGCATTTTAATTAT-GACATCC
1 TTTCATGCCCTAATACATCCTTTCATGCATTTTAATTATGGA-ATCC
11266593 TTTCATGC
1 TTTCATGC
11266601 ATTTTAATTA
Statistics
Matches: 126, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 1 0.01
46 125 0.99
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (46 bp):
TTTCATGCCCTAATACATCCTTTCATGCATTTTAATTATGGAATCC
Found at i:11266555 original size:92 final size:92
Alignment explanation
Indices: 11266409--11266603 Score: 255
Period size: 92 Copynumber: 2.1 Consensus size: 92
11266399 TAGGGTCTCT
* **
11266409 TTTCATGCATTAATACATCCGTTCATAAATTTTAATCATGGAATCCTTTTATGCCCTAATACATC
1 TTTCATGCATTAATACATCCGTTCATAAATTTTAATCATGGAATCATTACATGCCCTAATACATC
* * *
11266474 CTTTCATGCATTTTAGTTATGGCATCC
66 ATTTCATGCATTTTAATTATGACATCC
* * * ** * * * *
11266501 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCATTACATGCCTTAATGCATC
1 TTTCATGCATTAATACATCCGTTCATAAATTTTAATCATGGAATCATTACATGCCCTAATACATC
11266566 ATTTCATGCATTTTAATTATGACATCC
66 ATTTCATGCATTTTAATTATGACATCC
11266593 TTTCATGCATT
1 TTTCATGCATT
11266604 TTAATTATGA
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (92 bp):
TTTCATGCATTAATACATCCGTTCATAAATTTTAATCATGGAATCATTACATGCCCTAATACATC
ATTTCATGCATTTTAATTATGACATCC
Found at i:11266595 original size:72 final size:72
Alignment explanation
Indices: 11266516--11266672 Score: 251
Period size: 72 Copynumber: 2.2 Consensus size: 72
11266506 TGCCTTAATG
*
11266516 CATCCTTTCATGCATTTTAATTATGGCATCATTACATGCCTTAATGCATCATTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGACATCATTACATGCCTTAATGCATCATTTCATGCATTTTA
11266581 ATTATGA
66 ATTATGA
* * * *
11266588 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCGTCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGACATCATTACATGCCTTAATGCATCATTTCATGCATTTTA
* *
11266653 GTTATGG
66 ATTATGA
11266660 CATCCTTTCATGC
1 CATCCTTTCATGC
11266673 CGTAATGCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (72 bp):
CATCCTTTCATGCATTTTAATTATGACATCATTACATGCCTTAATGCATCATTTCATGCATTTTA
ATTATGA
Found at i:11266598 original size:118 final size:118
Alignment explanation
Indices: 11266469--11266704 Score: 391
Period size: 118 Copynumber: 2.0 Consensus size: 118
11266459 ATGCCCTAAT
* *
11266469 ACATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 ACATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* *
11266534 AATTATGGCATCATTACATGCCTTAATGCATCATTTCATGCATTTTAATTATG
66 AATTATGGCATCATTACATGCCGTAATGCATCATTTCATGAATTTTAATTATG
*
11266587 ACATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCGTCCTTTCATGCATTTT
1 ACATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* * * *
11266652 AGTTATGGCATCCTTTCATGCCGTAATGCATCCTTTCATGAATTTTAATTATG
66 AATTATGGCATCATTACATGCCGTAATGCATCATTTCATGAATTTTAATTATG
11266705 GATTCGGTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (118 bp):
ACATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
AATTATGGCATCATTACATGCCGTAATGCATCATTTCATGAATTTTAATTATG
Found at i:11266705 original size:46 final size:46
Alignment explanation
Indices: 11266588--11266705 Score: 191
Period size: 46 Copynumber: 2.6 Consensus size: 46
11266578 TTAATTATGA
* *
11266588 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCGTAATG
* *
11266634 CGTCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCGTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCGTAATG
*
11266680 CATCCTTTCATGAATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
11266706 ATTCGGTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCGTAATG
Found at i:11274945 original size:54 final size:53
Alignment explanation
Indices: 11274885--11275506 Score: 805
Period size: 54 Copynumber: 11.5 Consensus size: 53
11274875 TTCTTTGGGG
* ** * * * *
11274885 TGCACACGTAGTGCTGATACGATCATTCATAAGCTCATTATGAATTTCTTAGAT
1 TGCACACATAGTGCCAATACGA-AATTCATAAACTAATTATGAATTTCTTAGGT
* *
11274939 TTCACACATAGTGCCCATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * *
11274993 TGCACACACAGTGCAAATACGGAAATTCATGAACTAATTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * *
11275047 TGCACACATAGTGCAAATATGGAAATTTATAAACTAATTATGAATTTCTAAGGT
1 TGCACACATAGTGCCAATA-CGAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * *
11275101 TGAACACATAGTGCCAATACGCAAATTCTTAATCTAATTATGAATTTATTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
*
11275155 TGCACACATAGTACCAATACGAAATTTCATAAACTAATTATGAA-TTCTTAGGT
1 TGCACACATAGTGCCAATACGAAA-TTCATAAACTAATTATGAATTTCTTAGGT
*
11275208 TGCACACATAGTGCCAATATGAAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11275262 TGCAAACATAGTGTCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* ** * *
11275316 TGTACACGCAGTGCCAATATGAAAATTCATAAACTAATTATGAATTTCTTATGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11275370 TGCACACAAAGTGCCAAAACGAAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11275424 TGAACACATAGTGTCAATACGAAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11275478 TGCTCACACAGTGCCAATACGGAAATTCA
1 TGCACACATAGTGCCAATAC-GAAATTCA
11275507 ATACATACAT
Statistics
Matches: 499, Mismatches: 60, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
53 51 0.10
54 444 0.89
55 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (53 bp):
TGCACACATAGTGCCAATACGAAATTCATAAACTAATTATGAATTTCTTAGGT
Found at i:11280913 original size:54 final size:53
Alignment explanation
Indices: 11280855--11281425 Score: 818
Period size: 54 Copynumber: 10.5 Consensus size: 53
11280845 TTCTTTGGGG
* * * * *
11280855 TGCACACGTAGTGCCGATACGATCATTCATAAGCTCATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGA-AATTCATAAACTAATTATGAATTTCTTAGGT
*
11280909 TGCACACATAGTGCCAATATGGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATA-CGAAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11280963 TGCACACATAGTACCAATACGGAAATTCATAAACTAATAATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11281017 TACACACATAGTGCCAATACTGAAATTCATAAACTAATTATGACTTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * *
11281071 TGCTCACATAGTGTCGATACAGAAATTCATATACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11281125 TGCACACATAGTGTCGATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATAC-GAAATTCATAAACTAATTATGAATTTCTTAGGT
*
11281179 TGCACACATAGTGCCAATATGGAAATTCATAAACTAATTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATA-CGAAATTCATAAACT-A--ATTATGAATTTCTTAGGT
* *
11281236 TGCACACATAGTGTCAATATGAAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
*
11281290 TGCACACACAGTGCCAATACGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAATTCATAAACTAATTATGAATTTCTTAGGT
*
11281343 TGCACACACAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
11281397 TGCACACACAGTGCCAATATAGAAATTCA
1 TGCACACATAGTGCCAATA-CGAAATTCA
11281426 ATACATACAT
Statistics
Matches: 476, Mismatches: 32, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
53 53 0.11
54 368 0.77
55 4 0.01
56 2 0.00
57 49 0.10
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (53 bp):
TGCACACATAGTGCCAATACGAAATTCATAAACTAATTATGAATTTCTTAGGT
Found at i:11283507 original size:23 final size:23
Alignment explanation
Indices: 11283480--11283548 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
11283470 ACCACAGCTC
*
11283480 GTATAAATGCACCGAAGTACCAT
1 GTATAAATGCACCGAAGTGCCAT
* * **
11283503 GTATAATTGCACCGTAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAT
*
11283526 GTAGAAATGCACCGAAGTGCCAT
1 GTATAAATGCACCGAAGTGCCAT
11283549 ATAAGGTTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAT
Found at i:11284027 original size:2 final size:2
Alignment explanation
Indices: 11284014--11284080 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
11284004 TTCATCTTCT
*
11284014 TA TA TT 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
11284056 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11284081 CATCTTTCCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11285318 original size:64 final size:64
Alignment explanation
Indices: 11285206--11285368 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 64
11285196 TCTTTAACAT
* *
11285206 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
* * * ** * *
11285270 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTTGATGTTTCCATTTTTTAA-T
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTCCA--TTTTAAGG
11285333 GG
63 GG
** * **
11285335 GTGCATTAATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTACCCATGCATCGATACACA
11285369 CTGAACGATT
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
63 2 0.02
64 43 0.53
65 28 0.35
66 8 0.10
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:11288167 original size:17 final size:19
Alignment explanation
Indices: 11288140--11288176 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
11288130 AATGAAATTT
11288140 AATTATAAATTTTAA-AAA
1 AATTATAAATTTTAACAAA
11288158 AATTAT-AATTTTAACAAA
1 AATTATAAATTTTAACAAA
11288176 A
1 A
11288177 CAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATAAATTTTAACAAA
Found at i:11290945 original size:2 final size:2
Alignment explanation
Indices: 11290938--11290976 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11290928 TAAATCTAAT
11290938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11290977 TCTTTAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11291044 original size:24 final size:24
Alignment explanation
Indices: 11291000--11291045 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
11290990 TCAATCTTAA
*
11291000 TTATTTTTTAATTATTTATTTTAT
1 TTATTTTTTAATTATTGATTTTAT
*
11291024 TTATTTTTATATTTA-TGATTTT
1 TTATTTTT-TAATTATTGATTTT
11291046 TGTTTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTTTTTAATTATTGATTTTAT
Found at i:11291738 original size:2 final size:2
Alignment explanation
Indices: 11291733--11291774 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
11291723 GAATTTTAAA
11291733 AT AT AT AT AT AT 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 AT AT AT AT AT AT
11291775 GAATTGGGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11294809 original size:24 final size:24
Alignment explanation
Indices: 11294780--11294832 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
11294770 CGTTAAAATG
*
11294780 ATAAACGAACACAAATGAATGAAC
1 ATAAACGAACACAAACGAATGAAC
*
11294804 GTAAACGAACACAAACGAATGAAC
1 ATAAACGAACACAAACGAATGAAC
11294828 ATAAA
1 ATAAA
11294833 AGAGCGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.17, G:0.13, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAACGAATGAAC
Found at i:11294841 original size:34 final size:34
Alignment explanation
Indices: 11294803--11294867 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
11294793 AATGAATGAA
* *
11294803 CGTAAACGAACACAAACGAATGAACATAAAAGAG
1 CGTAAACAAACACAAACGAATAAACATAAAAGAG
*
11294837 CGTAAACAAACATAAACGAATAAACATAAAA
1 CGTAAACAAACACAAACGAATAAACATAAAA
11294868 TTAATTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.60, C:0.17, G:0.12, T:0.11
Consensus pattern (34 bp):
CGTAAACAAACACAAACGAATAAACATAAAAGAG
Found at i:11297227 original size:37 final size:40
Alignment explanation
Indices: 11297125--11297230 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 40
11297115 TCTCCATTTT
* * *
11297125 TATACT-ATCAAATAATAACTAAAACAAATAATAAATTAAG
1 TATACTAATAAAATAATAATTAAAA-AAATAATAAATTAAA
*
11297165 TATACTAATAAAATAATTAAATTAAAAAAA-ATTAAA-TAAA
1 TATACTAATAAAATAA-T-AATTAAAAAAATAATAAATTAAA
11297205 TATAC-AA-AAAATAAGTAATTAAAAAA
1 TATACTAATAAAATAA-TAATTAAAAAA
11297231 TTTCATAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
37 10 0.17
38 8 0.14
39 2 0.03
40 14 0.24
41 13 0.22
42 4 0.07
43 7 0.12
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (40 bp):
TATACTAATAAAATAATAATTAAAAAAATAATAAATTAAA
Found at i:11299554 original size:54 final size:54
Alignment explanation
Indices: 11299443--11299547 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
11299433 ATTGCACCGA
* * * * *
11299443 AGTGCCGAAATGGAAATTCGTAAACTCATTATGAATTCCATGGATTGCACACAT
1 AGTGCCAAAATGGAAATTCATAAACACATTAGGAATACCATGGATTGCACACAT
** *
11299497 AGTGCCAAAATGGTCATTCATAAACACATTAGGAATACCATGGGTTGCACA
1 AGTGCCAAAATGGAAATTCATAAACACATTAGGAATACCATGGATTGCACA
11299548 TTTAGTGACA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (54 bp):
AGTGCCAAAATGGAAATTCATAAACACATTAGGAATACCATGGATTGCACACAT
Found at i:11299560 original size:54 final size:54
Alignment explanation
Indices: 11299458--11299560 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
11299448 CGAAATGGAA
* * * * *
11299458 ATTCGTAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCAAAATGGTC
1 ATTCATAAACACATTAGGAATACCATGGATTGCACACATAGTGACAAAATGGTC
* **
11299512 ATTCATAAACACATTAGGAATACCATGGGTTGCACATTTAGTGACAAAA
1 ATTCATAAACACATTAGGAATACCATGGATTGCACACATAGTGACAAAA
11299561 ATACACTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
ATTCATAAACACATTAGGAATACCATGGATTGCACACATAGTGACAAAATGGTC
Found at i:11319437 original size:118 final size:118
Alignment explanation
Indices: 11319273--11319519 Score: 305
Period size: 118 Copynumber: 2.1 Consensus size: 118
11319263 TTGTGCTATA
* * * *
11319273 ATCATAATCATAATATATAAGCACACACATTGCTATAATATTAGAATCGTAATACGCACACAAAG
1 ATCAGAATCATAACATATAAGCACACACAATGCTATAATATCAGAATCGTAATACGCACACAAAG
* *
11319338 TGCAATCATATCAGAACATATATACTAGTGTACCCACTAGTACACCACAATAT
66 TGCAATCACATCAGAACATATATAATAGTGTACCCACTAGTACACCACAATAT
* * * **
11319391 ATCAGAATCGTAACATATAAGCACACACAATGCTATCATATCAGAATCGTGATGTGCACACAAAG
1 ATCAGAATCATAACATATAAGCACACACAATGCTATAATATCAGAATCGTAATACGCACACAAAG
* * * * **** *
11319456 TGTAATCACATCATAATATATATAATAGTGTATCTTGAAGTAACAACACAATAT
66 TGCAATCACATCAGAACATATATAATAGTGTACCCACTAGT-ACACCACAATAT
11319510 ATCAGAATCA
1 ATCAGAATCA
11319520 CTCCACCTCT
Statistics
Matches: 107, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
118 87 0.81
119 20 0.19
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (118 bp):
ATCAGAATCATAACATATAAGCACACACAATGCTATAATATCAGAATCGTAATACGCACACAAAG
TGCAATCACATCAGAACATATATAATAGTGTACCCACTAGTACACCACAATAT
Found at i:11329806 original size:30 final size:30
Alignment explanation
Indices: 11329772--11329844 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
11329762 CTCGAAGGAC
*
11329772 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAAAGGTCATAAAGATCCTCAGTAA
*
11329802 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCCTCAGTAA
*
11329832 CTATCCATAGGTC
1 CTATCCAAAGGTC
11329845 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGATCCTCAGTAA
Found at i:11329861 original size:30 final size:30
Alignment explanation
Indices: 11329772--11329861 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
11329762 CTCGAAGGAC
* * *
11329772 CTATCCAGAGGTCATAAAGATCCTCA-GTAA
1 CTATCCAAAGGTCACAAAGAACCT-AGGTAA
* * *
11329802 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCACAAAGAACCTAGGTAA
* * *
11329832 CTATCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAAAGGTCACAAAGAACCTAGGTAA
11329862 ACCGTCCATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (30 bp):
CTATCCAAAGGTCACAAAGAACCTAGGTAA
Found at i:11330694 original size:19 final size:19
Alignment explanation
Indices: 11330670--11330721 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
11330660 TTTAAGTAGG
11330670 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
11330689 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
11330708 TGCATCGATGCACT
1 TGCATCGATGCACT
11330722 AATTGCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:11331928 original size:23 final size:23
Alignment explanation
Indices: 11331898--11331946 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
11331888 TGGTGGTTGG
*
11331898 TTTAATGG-ATGTTTAAGCTTTAT
1 TTTAATGGTATATTTAAG-TTTAT
11331921 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAAGTTTAT
11331944 TTT
1 TTT
11331947 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAAGTTTAT
Found at i:11338881 original size:46 final size:46
Alignment explanation
Indices: 11338789--11338884 Score: 111
Period size: 46 Copynumber: 2.1 Consensus size: 46
11338779 GCACTGTTAC
* * * * * *
11338789 TTATGTATTTGGATATTATTATTTTTTTAATATGGTATAGTCTTAA
1 TTATGCATTTGAATAATATTATTTGTTTAACATGGTATAGTATTAA
* * *
11338835 TTATGCATTTGAATAATATTATTTGTTTAACATTGTGTATTATTAA
1 TTATGCATTTGAATAATATTATTTGTTTAACATGGTATAGTATTAA
11338881 TTAT
1 TTAT
11338885 ATAGTAGACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.55
Consensus pattern (46 bp):
TTATGCATTTGAATAATATTATTTGTTTAACATGGTATAGTATTAA
Found at i:11339022 original size:190 final size:188
Alignment explanation
Indices: 11338701--11339077 Score: 709
Period size: 190 Copynumber: 2.0 Consensus size: 188
11338691 TGCAATAAGT
*
11338701 TAGACTATTAATTCTAAAAGACATCCTCTTTCTACTTTATTTTGTTCATTTTTTTATCAAAAAGA
1 TAGACTATTAATTCTAAAAGACATCCTCTTTCTACTTTATTTTGTTCATTTTTTTATCAAAAACA
*
11338766 TGAATTAATTGGTGCACTGTTACTTATGTATTTGGATATTATTATTTTTTTAATATGGTATAGTC
66 TGAATTAATTGGTGCACTGTTACTTATGTATTTGGATATTATTATTGTTTTAATATGGTATAGTC
11338831 TTAATTATGCATTTGAATAATATTATTTGTTTAACATTGTGTATTATTAATTATATAG
131 TTAATTATGCATTTGAATAATATTATTTGTTTAACATTGTGTATTATTAATTATATAG
11338889 TAGACTATTAATTCTAAAAGACATCCTCTTTCTACTTTATTTTGTTCATTTTTTTATATCAAAAA
1 TAGACTATTAATTCTAAAAGACATCCTCTTTCTACTTTATTTTGTTCA-TTTTTT-TATCAAAAA
11338954 CATGAATTAATTGGTGCACTGTTACTTATGTATTTGGATATTATTATTGTTTTAATATGGTATAG
64 CATGAATTAATTGGTGCACTGTTACTTATGTATTTGGATATTATTATTGTTTTAATATGGTATAG
*
11339019 TCTTAATTATGCATTTGAATAATATTATTTGTTTAACTTTGTGTATTATTAATTATATA
129 TCTTAATTATGCATTTGAATAATATTATTTGTTTAACATTGTGTATTATTAATTATATA
11339078 CAACAACAAC
Statistics
Matches: 184, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
188 48 0.26
189 6 0.03
190 130 0.71
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (188 bp):
TAGACTATTAATTCTAAAAGACATCCTCTTTCTACTTTATTTTGTTCATTTTTTTATCAAAAACA
TGAATTAATTGGTGCACTGTTACTTATGTATTTGGATATTATTATTGTTTTAATATGGTATAGTC
TTAATTATGCATTTGAATAATATTATTTGTTTAACATTGTGTATTATTAATTATATAG
Found at i:11344431 original size:51 final size:51
Alignment explanation
Indices: 11344367--11344481 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
11344357 ATGATTAGAT
* * * *
11344367 TTATTATTTTATTAGAAATTAAGATAGAGTTAAAATATTATCTTTAATTTA
1 TTATTATTTTATTAGAAATTAAGATAAAATCAAAACATTATCTTTAATTTA
** * *
11344418 TTATTATTTTATTAGGTATTAGGATAAAATCAAAACATTATCTTTAGTTTA
1 TTATTATTTTATTAGAAATTAAGATAAAATCAAAACATTATCTTTAATTTA
11344469 TTATTATTTTATT
1 TTATTATTTTATT
11344482 TAGTCGTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (51 bp):
TTATTATTTTATTAGAAATTAAGATAAAATCAAAACATTATCTTTAATTTA
Found at i:11357432 original size:6 final size:6
Alignment explanation
Indices: 11357421--11357499 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
11357411 ACGCGTAGAC
* *
11357421 TATATA TATATA TATATA TATATA TATATA TATATA TATGTA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
11357469 TGTATA TGTATA TGTATA TGTATA TGTATA T
1 TATATA TATATA TATATA TATATA TATATA T
11357500 GGTACTTTCC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:11360332 original size:70 final size:71
Alignment explanation
Indices: 11360217--11360450 Score: 224
Period size: 71 Copynumber: 3.3 Consensus size: 71
11360207 AAATGAGTGA
* * * *
11360217 ATGATTGAGGCTCTGAGTTTTGTGTTTAACTTCC-CCTATGATTGAGGGTTCGTTTACTAACAAG
1 ATGATTGAGGCTC-GAG-GTTGAGTTTGACTTCCTCC-ATGATTGAGGGTTCGCTTACTAACAAG
11360281 G-GTCCTCC
63 GTGTCCTCC
* * * *
11360289 ATGATTGAGGCTCG-GGATTGCGTTTGACTTCCTCCATGATTGAGGGTTTC-CCTACTAGCATGG
1 ATGATTGAGGCTCGAGG-TTGAGTTTGACTTCCTCCATGATTGAGGG-TTCGCTTACTAACAAGG
* *
11360352 TGTCTTCT
64 TGTCCTCC
* * * * * ***
11360360 ATGATTGAGGCTCGAGGTTGAATTTGACTTCTTCCATGGTTGAGTGTTTGCTTACTAATGGGGTG
1 ATGATTGAGGCTCGAGGTTGAGTTTGACTTCCTCCATGATTGAGGGTTCGCTTACTAACAAGGTG
11360425 TCCTCC
66 TCCTCC
*
11360431 ATGATTGAGACTCGAGGTTG
1 ATGATTGAGGCTCGAGGTTG
11360451 TATTTAGTTT
Statistics
Matches: 133, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
70 36 0.27
71 82 0.62
72 15 0.11
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (71 bp):
ATGATTGAGGCTCGAGGTTGAGTTTGACTTCCTCCATGATTGAGGGTTCGCTTACTAACAAGGTG
TCCTCC
Found at i:11360500 original size:71 final size:71
Alignment explanation
Indices: 11360282--11360510 Score: 203
Period size: 71 Copynumber: 3.2 Consensus size: 71
11360272 ACTAACAAGG
* * ** * * * *
11360282 GTCCTCCATGATTGAGGCTCG-GGATTGCGTTTGACTTCCTCCATGATTGAGGGTTTCCCTACTA
1 GTCCTCTATGATTGAGACTCGAGG-TTGAATTTGACTTCTTACATGGTTGAGGGTTTGCCTACTA
11360346 GC-ATGGT
65 GCGA-GGT
* * * * * *
11360353 GTCTTCTATGATTGAGGCTCGAGGTTGAATTTGACTTCTTCCATGGTTGAGTGTTTGCTTACTAA
1 GTCCTCTATGATTGAGACTCGAGGTTGAATTTGACTTCTTACATGGTTGAGGGTTTGCCTACTAG
* *
11360418 TGGGGT
66 CGAGGT
* * * * * *
11360424 GTCCTCCATGATTGAGACTCGAGGTTGTATTT-AGTTTTTTATATGGTTGAGGGTTTGCCTAATA
1 GTCCTCTATGATTGAGACTCGAGGTTGAATTTGA-CTTCTTACATGGTTGAGGGTTTGCCTACTA
11360488 GCGAGGT
65 GCGAGGT
*
11360495 ATCCTCTATGATTGAG
1 GTCCTCTATGATTGAG
11360511 GCTTAGGGAG
Statistics
Matches: 127, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
70 1 0.01
71 124 0.98
72 2 0.02
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (71 bp):
GTCCTCTATGATTGAGACTCGAGGTTGAATTTGACTTCTTACATGGTTGAGGGTTTGCCTACTAG
CGAGGT
Found at i:11365799 original size:21 final size:20
Alignment explanation
Indices: 11365771--11365820 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
11365761 TTTACGACAA
11365771 TCAAATATGTTCAAT-AAAAC
1 TCAAATAT-TTCAATGAAAAC
11365791 TCAAGATA-TTCAATGGAAAAC
1 TCAA-ATATTTCAAT-GAAAAC
11365812 TCAACATAT
1 TCAA-ATAT
11365821 CTGAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 15 0.60
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (20 bp):
TCAAATATTTCAATGAAAAC
Found at i:11365804 original size:19 final size:20
Alignment explanation
Indices: 11365780--11365820 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
11365770 ATCAAATATG
*
11365780 TTCAAT-AAAACTCAAGATA
1 TTCAATGAAAACTCAACATA
11365799 TTCAATGGAAAACTCAACATA
1 TTCAAT-GAAAACTCAACATA
11365820 T
1 T
11365821 CTGAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (20 bp):
TTCAATGAAAACTCAACATA
Found at i:11367036 original size:11 final size:11
Alignment explanation
Indices: 11367015--11367052 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
11367005 TGGTGTATCT
11367015 AAAAT-ATGAA
1 AAAATAATGAA
11367025 AAAATAATG-A
1 AAAATAATGAA
*
11367035 AAAATAATAAA
1 AAAATAATGAA
11367046 AAAATAA
1 AAAATAA
11367053 ATTAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAATAATGAA
Found at i:11373597 original size:32 final size:31
Alignment explanation
Indices: 11373561--11373636 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
11373551 GGGGCCGTGA
*
11373561 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
11373593 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
11373624 AGCCTACCTAAGA
1 GGCCTACCTAAGA
11373637 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:11373619 original size:63 final size:63
Alignment explanation
Indices: 11373513--11373636 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
11373503 CCCTAAGGGA
* * *
11373513 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
11373576 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
11373637 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:11374539 original size:17 final size:17
Alignment explanation
Indices: 11374517--11374571 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
11374507 AACGGTCAAC
*
11374517 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
11374534 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
11374551 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
11374568 GGTC
1 GGTC
11374572 GGGTCAGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:11374607 original size:10 final size:10
Alignment explanation
Indices: 11374589--11374657 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
11374579 TCAGGTCGGG
*
11374589 TCAACCCGGT
1 TCAAACCGGT
*
11374599 TCAGACCGG-
1 TCAAACCGGT
11374608 TCAAACCGGT
1 TCAAACCGGT
*
11374618 TCAGACCGG-
1 TCAAACCGGT
11374627 TCAAACCGGT
1 TCAAACCGGT
*
11374637 TCAAAACTGG-
1 TC-AAACCGGT
11374647 TCAAACCGGT
1 TCAAACCGGT
11374657 T
1 T
11374658 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:11374609 original size:19 final size:19
Alignment explanation
Indices: 11374587--11374657 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
11374577 AGTCAGGTCG
*
11374587 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
11374606 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
11374625 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
11374645 GGTCAAACCGGTT
1 GGTCAAACCGGTT
11374658 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:11380966 original size:63 final size:63
Alignment explanation
Indices: 11380860--11380983 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
11380850 CCCTAAGGGA
* * *
11380860 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
11380923 ACATCTTAGGG-CTGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
11380984 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 4 0.08
63 47 0.89
64 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:11381863 original size:7 final size:7
Alignment explanation
Indices: 11381851--11381881 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
11381841 GTCAAAGGAA
11381851 GTCAACG
1 GTCAACG
11381858 GTCAACG
1 GTCAACG
11381865 GTCAACG
1 GTCAACG
11381872 GTCAACG
1 GTCAACG
11381879 GTC
1 GTC
11381882 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:11381893 original size:17 final size:17
Alignment explanation
Indices: 11381871--11381947 Score: 102
Period size: 17 Copynumber: 4.4 Consensus size: 17
11381861 AACGGTCAAC
*
11381871 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
11381888 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
11381905 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
11381922 GGT-AGGGTCAGTCGGGTCG
1 GGTCA---ACAGTCGGGTCG
11381941 GGTCAAC
1 GGTCAAC
11381948 CCGGTTCAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.02
17 37 0.70
19 14 0.26
20 1 0.02
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:11381965 original size:19 final size:19
Alignment explanation
Indices: 11381941--11382011 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
11381931 AGTCGGGTCG
*
11381941 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
11381960 GGTCAAACTGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
11381979 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
11381999 GGTCAAACCGGTT
1 GGTCAAACCGGTT
11382012 TTCGAGCAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 30 0.65
20 16 0.35
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:11381990 original size:9 final size:9
Alignment explanation
Indices: 11381941--11382010 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
11381931 AGTCGGGTCG
*
11381941 GGTCAACCC
1 GGTCAAACC
*
11381950 GGTTCAGACC
1 GG-TCAAACC
*
11381960 GGTCAAACT
1 GGTCAAACC
*
11381969 GGTTCAGACC
1 GG-TCAAACC
11381979 GGTCAAACC
1 GGTCAAACC
*
11381988 GGTTCAAAACT
1 GG-TC-AAACC
11381999 GGTCAAACC
1 GGTCAAACC
11382008 GGT
1 GGT
11382011 TTTCGAGCAG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 24 0.50
10 18 0.38
11 6 0.12
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:11383113 original size:9 final size:9
Alignment explanation
Indices: 11383099--11383141 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
11383089 TTCAGATTTA
11383099 ATTTTTATT
1 ATTTTTATT
11383108 ATTTTTA-T
1 ATTTTTATT
11383116 ATTCTTTATT
1 ATT-TTTATT
11383126 ATTTTTATT
1 ATTTTTATT
11383135 -TTTTTAT
1 ATTTTTAT
11383142 GAACTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 11 0.34
9 17 0.53
10 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTTATT
Found at i:11391224 original size:19 final size:20
Alignment explanation
Indices: 11391200--11391252 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
11391190 ACTATTCTTT
* *
11391200 AAAAAA-AGGAAATAAAAAG
1 AAAAAATAGAAAAGAAAAAG
11391219 AAAAAATAGAAAAGAAAAAG
1 AAAAAATAGAAAAGAAAAAG
*
11391239 AAAAGAAAAGAAAA
1 AAAA-AATAGAAAA
11391253 ATAGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 6 0.21
20 15 0.52
21 8 0.28
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAATAGAAAAGAAAAAG
Found at i:11391247 original size:16 final size:15
Alignment explanation
Indices: 11391214--11391269 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
11391204 AAAGGAAATA
*
11391214 AAAAG-AAAAAATAG
1 AAAAGAAAAAAAAAG
11391228 AAAAGAAAAAGAAAAG
1 AAAAGAAAAA-AAAAG
*
11391244 AAAAGAAAAATAGAA-
1 AAAAGAAAAA-AAAAG
11391259 AAAAGAAAAAA
1 AAAAGAAAAAA
11391270 GAGTTTAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 6 0.16
15 14 0.38
16 17 0.46
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:11391264 original size:20 final size:19
Alignment explanation
Indices: 11391213--11391267 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
11391203 AAAAGGAAAT
11391213 AAAAAGAAAAAATAGAAAAG-
1 AAAAAG-AAAAA-AGAAAAGA
11391233 AAAAAG--AAAAGAAAAGA
1 AAAAAGAAAAAAGAAAAGA
11391250 AAAATAGAAAAAAGAAAA
1 AAAA-AGAAAAAAGAAAA
11391268 AAGAGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 2 0.06
20 15 0.48
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAGA
Found at i:11391267 original size:5 final size:5
Alignment explanation
Indices: 11391214--11391252 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
11391204 AAAGGAAATA
*
11391214 AAAAG AAAA- AATAG AAAAG AAAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAA
11391253 ATAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:11391268 original size:7 final size:7
Alignment explanation
Indices: 11391213--11391271 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
11391203 AAAAGGAAAT
11391213 AAAAAGA
1 AAAAAGA
*
11391220 AAAAATA
1 AAAAAGA
*
11391227 GAAAAGA
1 AAAAAGA
*
11391234 AAAAGAAA
1 AAAA-AGA
11391242 AGAAAAGA
1 A-AAAAGA
11391250 AAAATAGA
1 AAAA-AGA
11391258 AAAAAGA
1 AAAAAGA
11391265 AAAAAGA
1 AAAAAGA
11391272 GTTTAAGATG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 27 0.63
8 13 0.30
9 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:11391548 original size:16 final size:16
Alignment explanation
Indices: 11391524--11391554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11391514 GTTTGGAGGC
*
11391524 ATTTGTATTTTTTTTT
1 ATTTCTATTTTTTTTT
11391540 ATTTCTATTTTTTTT
1 ATTTCTATTTTTTTT
11391555 CTATAGTTGC
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:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTCTATTTTTTTTT
Found at i:11395013 original size:30 final size:31
Alignment explanation
Indices: 11394977--11395064 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 31
11394967 CAAAATATAT
*
11394977 AACTTTTAAAACTTAAATATTTGGTCCA-TG
1 AACTTTTAAAACTTAAATATTTGGACCACTG
* **
11395007 AACTTTTATAA-TTTTATACTTT-GACCACTG
1 AACTTTTAAAACTTAAATA-TTTGGACCACTG
*
11395037 AACTTTTAAAACTTACAT-TTTGG-CCACT
1 AACTTTTAAAACTTAAATATTTGGACCACT
11395065 ACCCAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 17 0.36
30 26 0.55
31 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (31 bp):
AACTTTTAAAACTTAAATATTTGGACCACTG
Found at i:11395146 original size:10 final size:10
Alignment explanation
Indices: 11395131--11395163 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
11395121 CTAAGTCTCT
11395131 CTCTCCCTCC
1 CTCTCCCTCC
11395141 CTCTCCCT-C
1 CTCTCCCTCC
11395150 C-CTCCCTCC
1 CTCTCCCTCC
11395159 CTCTC
1 CTCTC
11395164 TCTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.29
9 4 0.19
10 11 0.52
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (10 bp):
CTCTCCCTCC
Found at i:11395150 original size:14 final size:14
Alignment explanation
Indices: 11395127--11395157 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11395117 AAAGCTAAGT
*
11395127 CTCTCTCTCCCTCC
1 CTCTCCCTCCCTCC
11395141 CTCTCCCTCCCTCC
1 CTCTCCCTCCCTCC
11395155 CTC
1 CTC
11395158 CCTCTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (14 bp):
CTCTCCCTCCCTCC
Found at i:11396006 original size:2 final size:2
Alignment explanation
Indices: 11395910--11396096 Score: 91
Period size: 2 Copynumber: 97.0 Consensus size: 2
11395900 TGGAAAATAA
* * * *
11395910 AT AT A- AT A- AT A- AT AT AT AA AT AT AA AT AT AC A- AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11395948 -T AT AT -T AT AT -T AT ACT AT ACT AT ACT AT ACT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT A-T AT A-T AT A-T AT A-T AT AT AT AT AT
*
11395987 AT A- AC AT -T A- AT A- 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 AT AT AT AT AT AT
* *
11396025 AT AT AT A- AT AT ACT AT ACT AT ACT A- AGT AT AA AT AT AT AT AC
1 AT AT AT AT AT AT A-T AT A-T AT A-T AT A-T AT AT AT AT AT AT AT
* * *
11396067 ACT AT AT AA AT AC AT AT AT AA AT AT A- AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11396097 TACATAATAA
Statistics
Matches: 143, Mismatches: 17, Indels: 50
0.68 0.08 0.24
Matches are distributed among these distances:
1 16 0.11
2 111 0.78
3 16 0.11
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:11396047 original size:5 final size:5
Alignment explanation
Indices: 11395948--11396049 Score: 67
Period size: 5 Copynumber: 21.4 Consensus size: 5
11395938 TACAACATAT
* * * * *
11395948 TATAT TATAT TATAC TATAC TATAC TATAC TATAA TATAA TA-AC ATTAATAA
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC --T-ATAC
*
11396000 TATA- TATA- TATA- TATA- TATA- TATA- TATA- TATAA TATAC TATAC
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC
11396043 TATAC TA
1 TATAC TA
11396050 AGTATAAATA
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
4 29 0.33
5 54 0.62
6 2 0.02
7 1 0.01
8 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAC
Found at i:11396432 original size:32 final size:32
Alignment explanation
Indices: 11396353--11396564 Score: 174
Period size: 32 Copynumber: 6.6 Consensus size: 32
11396343 ATTACTATCG
* * *
11396353 TGTCACATGTGATATCATCATATTGGGTGATA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
* * * *
11396385 AGCCACGTGACATATCATCATCTTGGGTGACA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
* * * * * *
11396417 TGTCATATGTTATATCATTATCTTAGATGATA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
* * *
11396449 GGTCACATGTCATATCATCATCTTGTGTGGCA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
* * * * * * *
11396481 TGTCATATGTTACATCATTATCTTAGATGATA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
* *
11396513 GGTCACATGTCATATCATCATCTTGAGTGACA
1 TGTCACATGTCATATCATCATCTTGGGTGACA
*
11396545 TGAT-ACATGTCATATTATCA
1 TG-TCACATGTCATATCATCA
11396565 ATTTATATTA
Statistics
Matches: 132, Mismatches: 47, Indels: 2
0.73 0.26 0.01
Matches are distributed among these distances:
32 131 0.99
33 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTCACATGTCATATCATCATCTTGGGTGACA
Found at i:11396433 original size:64 final size:64
Alignment explanation
Indices: 11396395--11396546 Score: 268
Period size: 64 Copynumber: 2.4 Consensus size: 64
11396385 AGCCACGTGA
*
11396395 CATATCATCATCTTGGGTGACATGTCATATGTTATATCATTATCTTAGATGATAGGTCACATGT
1 CATATCATCATCTTGAGTGACATGTCATATGTTATATCATTATCTTAGATGATAGGTCACATGT
* * *
11396459 CATATCATCATCTTGTGTGGCATGTCATATGTTACATCATTATCTTAGATGATAGGTCACATGT
1 CATATCATCATCTTGAGTGACATGTCATATGTTATATCATTATCTTAGATGATAGGTCACATGT
11396523 CATATCATCATCTTGAGTGACATG
1 CATATCATCATCTTGAGTGACATG
11396547 ATACATGTCA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (64 bp):
CATATCATCATCTTGAGTGACATGTCATATGTTATATCATTATCTTAGATGATAGGTCACATGT
Found at i:11397897 original size:15 final size:16
Alignment explanation
Indices: 11397867--11397900 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11397857 CTGTTCATTT
*
11397867 TTATTTTTAATTTATC
1 TTATTTTTAATATATC
11397883 TTATTTTT-ATATATC
1 TTATTTTTAATATATC
11397898 TTA
1 TTA
11397901 ACAATATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTTAATATATC
Found at i:11398038 original size:31 final size:30
Alignment explanation
Indices: 11397966--11398039 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
11397956 ATTCCTGAAT
* *
11397966 TTTAGATAGAATATTAATGTAATCGTAAAC
1 TTTAGATAAAATACTAATGTAATCGTAAAC
* *
11397996 TTTAGACAAAATACTAATGTAATCCCTTAAA-
1 TTTAGATAAAATACTAATGTAAT--CGTAAAC
11398027 TTTAGATAAAATA
1 TTTAGATAAAATA
11398040 TCAATTTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.54
31 12 0.32
32 5 0.14
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (30 bp):
TTTAGATAAAATACTAATGTAATCGTAAAC
Found at i:11406191 original size:85 final size:83
Alignment explanation
Indices: 11405970--11406245 Score: 444
Period size: 83 Copynumber: 3.3 Consensus size: 83
11405960 TGTATATCTG
*
11405970 TTTAATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAAGATGTTTAGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAATATGTTTAGT
* *
11406035 TGGACTAAAACTCTCATT
66 TGGAGTAAAACTCTCAAT
* * * *
11406053 TTTAATATTTTAAATTTAAAATATATTATTATATGTTTAAAGTTAGATATTAAAATATATTTAAT
1 TTTAATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAATATGTTTAGT
11406118 TGGAGTAAAACTCTCAAT
66 TGGAGTAAAACTCTCAAT
* * *
11406136 TTTAATATTTTTAAATTTAAAAAGATATTATTATCTTTTTAAATTTAGATATTAAAATATGTTTC
1 TTTAATA-TTTTAAATTT-AAAAGATATTATTATATGTTTAAATTTAGATATTAAAATATGTTTA
11406201 GTTGGAGTAAAACTCTCAAT
64 GTTGGAGTAAAACTCTCAAT
11406221 TTTAATATTTTAAATTTAAAAGATA
1 TTTAATATTTTAAATTTAAAAGATA
11406246 CTTAAATGTA
Statistics
Matches: 177, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
83 91 0.51
84 20 0.11
85 66 0.37
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAATATGTTTAGT
TGGAGTAAAACTCTCAAT
Found at i:11406398 original size:23 final size:22
Alignment explanation
Indices: 11406355--11406403 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
11406345 ATTCAAGAAG
*
11406355 TTTTCTTCTCTTGAAAATATT-
1 TTTTCTCCTCTTGAAAATATTC
*
11406376 TTTTCTCCTTCTTAGAAATTATTC
1 TTTTCTCC-TCTT-GAAAATATTC
11406400 TTTT
1 TTTT
11406404 TCCCTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 4 0.17
23 8 0.35
24 4 0.17
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTCTCCTCTTGAAAATATTC
Found at i:11413005 original size:16 final size:16
Alignment explanation
Indices: 11412981--11413011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11412971 ATATTTATTT
11412981 ATTTAATCCAATTTAC
1 ATTTAATCCAATTTAC
*
11412997 ATTTTATCCAATTTA
1 ATTTAATCCAATTTA
11413012 AGTGAAAAAA
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:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAATCCAATTTAC
Found at i:11416210 original size:24 final size:24
Alignment explanation
Indices: 11416183--11416235 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
11416173 TCAAAATATC
11416183 AAGAGACATGTCTTGTGAATCACA
1 AAGAGACATGTCTTGTGAATCACA
*
11416207 AAGAGACATGTCTTGTGGATCACA
1 AAGAGACATGTCTTGTGAATCACA
11416231 AAGAG
1 AAGAG
11416236 TCACGCCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (24 bp):
AAGAGACATGTCTTGTGAATCACA
Found at i:11422853 original size:18 final size:17
Alignment explanation
Indices: 11422830--11422864 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11422820 ATGCCATTTT
*
11422830 AGTATCGGTACTCTAGGG
1 AGTATCGATACTC-AGGG
11422848 AGTATCGATACTCAGGG
1 AGTATCGATACTCAGGG
11422865 TCCAAGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (17 bp):
AGTATCGATACTCAGGG
Found at i:11423670 original size:17 final size:15
Alignment explanation
Indices: 11423634--11423663 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11423624 AAGTAACCCG
*
11423634 AACCGAAACTAAATT
1 AACCCAAACTAAATT
11423649 AACCCAAACTAAATT
1 AACCCAAACTAAATT
11423664 TTAACCCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.20
Consensus pattern (15 bp):
AACCCAAACTAAATT
Found at i:11423729 original size:33 final size:32
Alignment explanation
Indices: 11423655--11423729 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
11423645 AATTAACCCA
11423655 AACTAAATTTTAACCCGATCCAAAAACAACCTG
1 AACTAAA-TTTAACCCGATCCAAAAACAACCTG
* *
11423688 AACCAAATTTAACCCGA-CCTAAAAGCAA-CTCG
1 AACTAAATTTAACCCGATCC-AAAAACAACCT-G
11423720 AACATAAATT
1 AAC-TAAATT
11423730 AATCTAAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 4 0.11
32 21 0.58
33 11 0.31
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (32 bp):
AACTAAATTTAACCCGATCCAAAAACAACCTG
Found at i:11423765 original size:22 final size:22
Alignment explanation
Indices: 11423723--11423765 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11423713 CAACTCGAAC
*
11423723 ATAAATTAATCTAAACCAAATA
1 ATAAATTAATCTAAACAAAATA
* *
11423745 ATAAATTAATTTAAATAAAAT
1 ATAAATTAATCTAAACAAAAT
11423766 TTATAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATTAATCTAAACAAAATA
Found at i:11423774 original size:18 final size:20
Alignment explanation
Indices: 11423751--11423801 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
11423741 AATAATAAAT
11423751 TAATTTA-AATAAAAT-TTA
1 TAATTTATAATAAAATATTA
11423769 TAATTTATTAA-AAAATATTA
1 TAATTTA-TAATAAAATATTA
11423789 T-ATTTATAATAAA
1 TAATTTATAATAAA
11423802 TATAATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.34
19 13 0.45
20 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATTTATAATAAAATATTA
Found at i:11423793 original size:19 final size:19
Alignment explanation
Indices: 11423751--11423804 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
11423741 AATAATAAAT
11423751 TAATTTA-AATAAAAT-TTA
1 TAATTTATAA-AAAATATTA
11423769 TAATTTATTAAAAAATATTA
1 TAATTTA-TAAAAAATATTA
*
11423789 T-ATTTATAATAAATAT
1 TAATTTATAAAAAATAT
11423805 AATAGAAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 16 0.50
19 10 0.31
20 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTTATAAAAAATATTA
Found at i:11424499 original size:32 final size:32
Alignment explanation
Indices: 11424432--11424502 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
11424422 CTAAGATCCA
* * *
11424432 ATATTGACCTGACCCAAAATCTAACCGATTCG
1 ATATTGACCCGACCAAAAATCTAACCAATTCG
11424464 ATATTGACCCGACCTAAAAATC-AACCAA-TCTG
1 ATATTGACCCGACC-AAAAATCTAACCAATTC-G
11424496 ATATTGA
1 ATATTGA
11424503 TTCGAACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.06
32 26 0.76
33 6 0.18
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (32 bp):
ATATTGACCCGACCAAAAATCTAACCAATTCG
Found at i:11425863 original size:59 final size:59
Alignment explanation
Indices: 11425797--11425920 Score: 185
Period size: 59 Copynumber: 2.1 Consensus size: 59
11425787 GTATACAAAG
**
11425797 TAGTGCTAACCCAAATATGACACATGTGGTCGTGCCCACCATCAGCACTAGTTATACTT
1 TAGTGCTAACCCAAATATGACACATAAGGTCGTGCCCACCATCAGCACTAGTTATACTT
* * **
11425856 TAGTGCTAACCCGAATATGACACATAAGGTCGTTCCCACCATTTGCACTAGTTATACTT
1 TAGTGCTAACCCAAATATGACACATAAGGTCGTGCCCACCATCAGCACTAGTTATACTT
*
11425915 AAGTGC
1 TAGTGC
11425921 AGTCCCGAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
TAGTGCTAACCCAAATATGACACATAAGGTCGTGCCCACCATCAGCACTAGTTATACTT
Found at i:11431878 original size:18 final size:18
Alignment explanation
Indices: 11431855--11431904 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
11431845 GTTTCTATGG
11431855 GAATTGGAATCTGTGAAA
1 GAATTGGAATCTGTGAAA
11431873 GAATTGGAATCTGTGAAA
1 GAATTGGAATCTGTGAAA
11431891 GAATTGGAATCTGT
1 GAATTGGAATCTGT
11431905 CAGGAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (18 bp):
GAATTGGAATCTGTGAAA
Found at i:11431970 original size:44 final size:44
Alignment explanation
Indices: 11431907--11431990 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
11431897 GAATCTGTCA
* *
11431907 GGAATTAGAATCCAATTCCATATTTTGTTTGGTTGGCAGAAAAT
1 GGAATTAGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAAAT
*
11431951 GGAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAGA
1 GGAATTAGAATCCAATTCCATATTCTGTTTGGTTCGCAGA
11431991 CATGTCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (44 bp):
GGAATTAGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAAAT
Found at i:11432530 original size:27 final size:27
Alignment explanation
Indices: 11432499--11432553 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
11432489 CTAAACCTGA
11432499 ACCCGAATATCACACTTAAAAAACCCG
1 ACCCGAATATCACACTTAAAAAACCCG
*
11432526 ACCCGAATATCACACTTAGAAAACCCG
1 ACCCGAATATCACACTTAAAAAACCCG
11432553 A
1 A
11432554 ATCGACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.15
Consensus pattern (27 bp):
ACCCGAATATCACACTTAAAAAACCCG
Done.