Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1667606 original size:14 final size:14
Alignment explanation
Indices: 1667556--1667616 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
1667546 TTTAAATATT
* *
1667556 TAATGATTTAATAC
1 TAATGATTTATTAA
*
1667570 TAATGATTTACTAA
1 TAATGATTTATTAA
1667584 T--T-A-TTATTAA
1 TAATGATTTATTAA
*
1667594 TAATGATTTATTAT
1 TAATGATTTATTAA
1667608 TAAT-ATTTA
1 TAATGATTTA
1667617 ATTATTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
12 2 0.05
13 6 0.15
14 23 0.59
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (14 bp):
TAATGATTTATTAA
Found at i:1667618 original size:24 final size:24
Alignment explanation
Indices: 1667570--1667614 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1667560 GATTTAATAC
*
1667570 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
1667594 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
1667615 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:1667621 original size:17 final size:17
Alignment explanation
Indices: 1667581--1667622 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1667571 AATGATTTAC
1667581 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1667598 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1667615 TAATTATT
1 TAATTATT
1667623 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1668642 original size:23 final size:23
Alignment explanation
Indices: 1668616--1668660 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1668606 AAAATTACAA
*
1668616 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
1668639 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
1668661 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:1669894 original size:15 final size:16
Alignment explanation
Indices: 1669874--1669907 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1669864 ACAAAAAATT
1669874 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
1669889 TAATATAATAAACTTA
1 TAATATAATAAACTTA
1669905 TAA
1 TAA
1669908 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:1669985 original size:15 final size:16
Alignment explanation
Indices: 1669965--1670020 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 16
1669955 CCTTAAACAA
1669965 TTAATA-AACTATTCT
1 TTAATATAACTATTCT
*
1669980 TTAATATAAC--TTCAA
1 TTAATATAACTATTC-T
*
1669995 CTAATA-AACTATTCT
1 TTAATATAACTATTCT
1670010 TTAATATAACT
1 TTAATATAACT
1670021 TAAACTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 16 0.50
16 10 0.31
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATATAACTATTCT
Found at i:1670000 original size:30 final size:30
Alignment explanation
Indices: 1669966--1670067 Score: 134
Period size: 30 Copynumber: 3.3 Consensus size: 30
1669956 CTTAAACAAT
1669966 TAATAAACTATTCTTTAATATAACTTCAAC
1 TAATAAACTATTCTTTAATATAACTTCAAC
*
1669996 TAATAAACTATTCTTTAATATAACTTAAAC
1 TAATAAACTATTCTTTAATATAACTTCAAC
* *
1670026 TAATAAACGATTTTTTAATTATAA-TTCACTAC
1 TAATAAACTATTCTTTAA-TATAACTTCA--AC
*
1670058 TAAAAAACTA
1 TAATAAACTA
1670068 ATTAACTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
30 48 0.76
31 5 0.08
32 10 0.16
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (30 bp):
TAATAAACTATTCTTTAATATAACTTCAAC
Found at i:1670225 original size:17 final size:17
Alignment explanation
Indices: 1670203--1670238 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1670193 TAAATTTTTT
1670203 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
1670220 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
1670237 AC
1 AC
1670239 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:1670649 original size:29 final size:29
Alignment explanation
Indices: 1670599--1670685 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
1670589 CAGCGGGGAG
** *
1670599 CAAGGTCGCGGGGCGTGTATGGCGACCTA
1 CAAGGTCGCCCGGCGTGCATGGCGACCTA
* * * *
1670628 CCATGTCGCCTGGCGTGCATGGAGACCTA
1 CAAGGTCGCCCGGCGTGCATGGCGACCTA
*
1670657 CAAGGTCGCCCGGAG-GACATGGCGACCTA
1 CAAGGTCGCCCGGCGTG-CATGGCGACCTA
1670686 TGGGTTGGGT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.20, C:0.29, G:0.36, T:0.16
Consensus pattern (29 bp):
CAAGGTCGCCCGGCGTGCATGGCGACCTA
Found at i:1673705 original size:23 final size:23
Alignment explanation
Indices: 1673679--1673723 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1673669 CACCACAGCT
*
1673679 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1673702 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1673724 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1673891 original size:152 final size:149
Alignment explanation
Indices: 1673691--1674008 Score: 541
Period size: 152 Copynumber: 2.1 Consensus size: 149
1673681 TATAATTGCA
1673691 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
1673755 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGT
*
1673820 TCCACATA-ATATATATATATATC
129 TCCA-A-AGA-ATATACATATATC
1673843 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
1673908 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGTCCTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
*
1673973 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1673992 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1674009 CCCTCTACCC
Statistics
Matches: 160, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
149 29 0.18
150 2 0.01
151 20 0.12
152 109 0.68
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1674518 original size:19 final size:20
Alignment explanation
Indices: 1674481--1674518 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1674471 TTTTTTCTCA
*
1674481 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1674501 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1674519 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1675092 original size:19 final size:20
Alignment explanation
Indices: 1675046--1675082 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1675036 CCACGTTTGG
*
1675046 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
1675066 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
1675083 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:1680647 original size:23 final size:23
Alignment explanation
Indices: 1680621--1680665 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1680611 CACCACAGCT
*
1680621 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1680644 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1680666 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1680831 original size:150 final size:149
Alignment explanation
Indices: 1680633--1680948 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
1680623 TATAATTGCA
1680633 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
1680697 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGT
* *
1680762 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
*
1680783 CCGAAGGACCGCTTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
1680848 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGTCCTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
1680913 CAAAGAATATACATATATC
131 CAAAGAATATACATATATC
*
1680932 CCGAAGAACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1680949 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
149 50 0.32
150 108 0.68
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1681458 original size:19 final size:20
Alignment explanation
Indices: 1681421--1681458 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1681411 TTTTTTCTCA
*
1681421 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1681441 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1681459 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1682032 original size:19 final size:20
Alignment explanation
Indices: 1681986--1682022 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1681976 CCACGTTTGG
*
1681986 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
1682006 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
1682023 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:1690504 original size:22 final size:21
Alignment explanation
Indices: 1690473--1690544 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
1690463 CTATACCACT
*
1690473 AAGATCTAGGAGTCCATTATAG
1 AAGATATAGGAGTCCA-TATAG
* *
1690495 AAGATATAGGCA-TCCATAAACT
1 AAGATATAGG-AGTCCATATA-G
* *
1690517 AAGATATAGGAGTTCAATATGG
1 AAGATATAGGAG-TCCATATAG
1690539 AAGATA
1 AAGATA
1690545 CATGCATCCG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 4 0.10
22 29 0.74
23 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (21 bp):
AAGATATAGGAGTCCATATAG
Found at i:1690542 original size:44 final size:44
Alignment explanation
Indices: 1690470--1690553 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
1690460 ATCCTATACC
* * *
1690470 ACTAAGATCTAGGAGTCCATTATAGAAGATATAGGCATCCATAA
1 ACTAAGATATAGGAGTCCAATATAGAAGATACAGGCATCCATAA
* * *
1690514 ACTAAGATATAGGAGTTCAATATGGAAGATACATGCATCC
1 ACTAAGATATAGGAGTCCAATATAGAAGATACAGGCATCC
1690554 GACTTGCCGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (44 bp):
ACTAAGATATAGGAGTCCAATATAGAAGATACAGGCATCCATAA
Found at i:1690648 original size:59 final size:60
Alignment explanation
Indices: 1690567--1690721 Score: 185
Period size: 59 Copynumber: 2.6 Consensus size: 60
1690557 TTGCCGTATG
*
1690567 CCACTAAGATCTAGAAGTCCAATATGGGAGATACAGA-CATCCATAAGGACTTACTC-TAAA
1 CCACTAA-ATCTAGAAGTCCAATATGGAAGATACAGAGCATCCATAAGGACTTAC-CGTAAA
* * * **
1690627 CCACTAAATTTAGAAGTCCAATATGAAAGATACA-AGTATCCATAAGGACTTACCGTGGA
1 CCACTAAATCTAGAAGTCCAATATGGAAGATACAGAGCATCCATAAGGACTTACCGTAAA
1690686 CCACTAAAATCTAGGAA-TCCAATATGGAAGAT-CAGA
1 CCACT-AAATCTA-GAAGTCCAATATGGAAGATACAGA
1690722 AAAGGCAAGA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
58 2 0.02
59 49 0.60
60 28 0.34
61 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (60 bp):
CCACTAAATCTAGAAGTCCAATATGGAAGATACAGAGCATCCATAAGGACTTACCGTAAA
Found at i:1691731 original size:17 final size:17
Alignment explanation
Indices: 1691710--1691757 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1691700 TATGATAATT
*
1691710 TAAAATTTTAAAA-ATA
1 TAAAAATTTAAAATATA
*
1691726 TAAAAAAATTAAAATATA
1 T-AAAAATTTAAAATATA
*
1691744 TAATAATTTAAAAT
1 TAAAAATTTAAAAT
1691758 TTTTAAGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 1 0.04
17 21 0.81
18 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATTTAAAATATA
Found at i:1692977 original size:18 final size:18
Alignment explanation
Indices: 1692946--1693019 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
1692936 TTGAATATTT
* *
1692946 GTCCCCAAGAACCACTAA
1 GTCCCGAAGGACCACTAA
*
1692964 GTCCCGAAGGACCATTGGATA
1 GTCCCGAAGGACCACT--A-A
* *
1692985 TGTCCTGAAGGACCACTAC
1 -GTCCCGAAGGACCACTAA
1693004 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
1693020 GGATATATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 28 0.62
20 2 0.04
21 1 0.02
22 14 0.31
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAA
Found at i:1693000 original size:40 final size:40
Alignment explanation
Indices: 1692947--1693042 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
1692937 TGAATATTTG
* * * *
1692947 TCCCCAAGAACCACTAAGTCCCGAAGGACCATTGGATATG
1 TCCCAAAGGACCACTAAGTCCCGAAGGACCACTGGATATA
** *
1692987 TCCTGAAGGACCACTACGTCCCGAAGGACCACTGGATATA
1 TCCCAAAGGACCACTAAGTCCCGAAGGACCACTGGATATA
1693027 TCCCAAAGGACCACTA
1 TCCCAAAGGACCACTA
1693043 TAACCCTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.32, C:0.31, G:0.20, T:0.17
Consensus pattern (40 bp):
TCCCAAAGGACCACTAAGTCCCGAAGGACCACTGGATATA
Found at i:1693666 original size:64 final size:64
Alignment explanation
Indices: 1693591--1693751 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
1693581 TCCATAATGT
* * * *
1693591 GTGCATCGATGCACTACATGTGCATCGATACACAAATCACCTTTGATATTTTAATCTTAAGGGG
1 GTGCATCGATGCACTACATGTGCATCGATACACAAATCACATTCGATATTTTAATCTTAAAGGA
* * ** ** * * *
1693655 GTGCATCGATGCACTACTTGTGTATCGATACACTTATGGCATTCGATGTTTTTATTTTAAAGGA
1 GTGCATCGATGCACTACATGTGCATCGATACACAAATCACATTCGATATTTTAATCTTAAAGGA
* *
1693719 GTGCATCGATACACTTCATGTGCATCGATACAC
1 GTGCATCGATGCACTACATGTGCATCGATACAC
1693752 CTTGAACAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACATGTGCATCGATACACAAATCACATTCGATATTTTAATCTTAAAGGA
Found at i:1694944 original size:21 final size:21
Alignment explanation
Indices: 1694920--1694962 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1694910 AGAAACACTT
1694920 TGTCTCCCACTTGATATTCTA
1 TGTCTCCCACTTGATATTCTA
1694941 TGTCTCCCACTTGATATTCTA
1 TGTCTCCCACTTGATATTCTA
1694962 T
1 T
1694963 CTCATTTCTC
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:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (21 bp):
TGTCTCCCACTTGATATTCTA
Found at i:1696024 original size:16 final size:16
Alignment explanation
Indices: 1696003--1696033 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1695993 CTTAACGATA
1696003 ATCTTTCGACTCAAAT
1 ATCTTTCGACTCAAAT
1696019 ATCTTTCGACTCAAA
1 ATCTTTCGACTCAAA
1696034 GAATCCGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (16 bp):
ATCTTTCGACTCAAAT
Found at i:1700495 original size:64 final size:64
Alignment explanation
Indices: 1700399--1700559 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
1700389 TCCATAACGT
* * * * * * *
1700399 GTGCATCGATGCACTATCTGTGTATCGGTACACAAATCACCTTCGATATTTTAATCTTAAGGGG
1 GTGCATCGATGCACTATATGTGCATCGATACACAAATCACATTCAATATTTTAATCTTAAAGGA
* ** * * *
1700463 GTGTATCGATGCACTACT-TGTGCATCGATACACTTATGACATTCAATATTTTTATTTTAAAGGA
1 GTGCATCGATGCACTA-TATGTGCATCGATACACAAATCACATTCAATATTTTAATCTTAAAGGA
* *
1700527 GTGCATCGATACACTTTATGTGCATCGATACAC
1 GTGCATCGATGCACTATATGTGCATCGATACAC
1700560 CTTGAACAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.98
65 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (64 bp):
GTGCATCGATGCACTATATGTGCATCGATACACAAATCACATTCAATATTTTAATCTTAAAGGA
Found at i:1714970 original size:20 final size:20
Alignment explanation
Indices: 1714947--1714989 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1714937 TTCAGCTCGC
1714947 ATTGTGTGTTTTATGTTGAA
1 ATTGTGTGTTTTATGTTGAA
1714967 ATTGTGTGTTTTATGTTGAA
1 ATTGTGTGTTTTATGTTGAA
1714987 ATT
1 ATT
1714990 TTTATGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (20 bp):
ATTGTGTGTTTTATGTTGAA
Found at i:1716227 original size:35 final size:35
Alignment explanation
Indices: 1716181--1716255 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1716171 TTCATGTTCA
1716181 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
* * * *
1716216 AAATTTCAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
1716251 AAATT
1 AAATT
1716256 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAATACTTCAATTACATTCTAAACCCC
Found at i:1716326 original size:35 final size:35
Alignment explanation
Indices: 1716251--1716327 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
1716241 TCTAAACCCT
* * *
1716251 AAATTAAAGTATTTTAGAATTTTGGGTTTAAAATG
1 AAATTGAAGTATTTTAGAAATTTGGGTTTAAAATA
* * *
1716286 TAATTGAATTATTTT-GAAATTTGAGGTTTAGAATA
1 AAATTGAAGTATTTTAGAAATTTG-GGTTTAAAATA
1716321 AAATTGA
1 AAATTGA
1716328 GAATTGTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAAATTTGGGTTTAAAATA
Found at i:1721000 original size:20 final size:21
Alignment explanation
Indices: 1720975--1721067 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1720965 TTTTCCCAAT
*
1720975 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1720995 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1721016 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1721036 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1721057 TCGCAATGCGA
1 TCGCAATGCGA
1721068 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1721020 original size:41 final size:41
Alignment explanation
Indices: 1720975--1721067 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1720965 TTTTCCCAAT
1720975 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1721016 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1721057 TCGCAATGCGA
1 TCGCAATGCGA
1721068 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1721080 original size:41 final size:41
Alignment explanation
Indices: 1720994--1721128 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1720984 GAATAAGTAA
** *
1720994 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1721035 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1721076 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1721117 TTCGCAACGCGA
1 ATCGCAACGCGA
1721129 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1721081 original size:20 final size:20
Alignment explanation
Indices: 1721056--1721149 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1721046 AATTGGGAAA
*
1721056 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
1721076 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
1721097 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1721117 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
* *
1721137 TTCACAACGCGAT
1 ATCGCAACGCGAT
1721150 TTACATAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1721727 original size:19 final size:19
Alignment explanation
Indices: 1721667--1721747 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1721657 TTCGAGAATG
1721667 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1721687 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1721703 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1721720 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1721739 AAAATCGCA
1 AAAATCGCA
1721748 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1721789 original size:20 final size:19
Alignment explanation
Indices: 1721743--1721894 Score: 143
Period size: 19 Copynumber: 8.1 Consensus size: 19
1721733 GAAACCAAAA
*
1721743 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1721762 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1721781 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1721801 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1721817 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
1721834 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1721853 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1721873 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1721893 TC
1 TC
1721895 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
19 49 0.44
20 49 0.44
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1721824 original size:39 final size:39
Alignment explanation
Indices: 1721748--1721824 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1721738 CAAAATCGCA
* **
1721748 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
1721787 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
1721825 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:1723956 original size:42 final size:42
Alignment explanation
Indices: 1723896--1723988 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1723886 GCCCGACTCG
* * *
1723896 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1723938 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
1723980 ACTGTCATC
1 CCTATCATC
1723989 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1725395 original size:14 final size:14
Alignment explanation
Indices: 1725376--1725411 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1725366 ATTGTTTAAT
1725376 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1725390 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1725404 TGATTTGT
1 TGATTTGT
1725412 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1725612 original size:19 final size:19
Alignment explanation
Indices: 1725590--1725740 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1725580 CGAAATTAAA
1725590 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1725609 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1725624 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1725642 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1725656 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1725675 TTCGCATTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
1725691 TT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1725708 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1725727 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1725741 GGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 26 0.27
16 9 0.09
17 9 0.09
19 43 0.44
20 10 0.10
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1725636 original size:33 final size:32
Alignment explanation
Indices: 1725594--1725720 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1725584 ATTAAATTCG
*
1725594 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CAT
*
1725627 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCAT
*
1725660 CGTTGCGATTTTCATTTCGCATTGCGATTCTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-AT
1725693 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1725721 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCAT
Found at i:1725683 original size:66 final size:66
Alignment explanation
Indices: 1725587--1725719 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1725577 ACGCGAAATT
*
1725587 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1725652 G
66 G
**
1725653 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1725718 G
66 G
1725719 A
1 A
1725720 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1728029 original size:12 final size:12
Alignment explanation
Indices: 1728012--1728036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1728002 TCTTCGGGGA
1728012 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1728024 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1728036 C
1 C
1728037 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1728245 original size:24 final size:24
Alignment explanation
Indices: 1728211--1728264 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1728201 CTGAAACATC
* *
1728211 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1728235 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1728259 ATCAAA
1 ATCAAA
1728265 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1729349 original size:20 final size:20
Alignment explanation
Indices: 1729324--1729380 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1729314 ATTCATTTGA
1729324 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1729344 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1729364 TTATCGCAACGAGAAAA
1 CTATCGCAACGCGAAAA
1729381 GCGCAATGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1729441 original size:19 final size:19
Alignment explanation
Indices: 1729400--1729453 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1729390 GAAATGAAAA
1729400 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1729416 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1729433 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1729452 TC
1 TC
1729454 AACACAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 11 0.33
16 3 0.09
17 3 0.09
19 16 0.48
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1731346 original size:19 final size:19
Alignment explanation
Indices: 1731321--1731406 Score: 102
Period size: 19 Copynumber: 4.5 Consensus size: 19
1731311 CGAAACTTAA
1731321 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
1731340 TATCGCAACGCAGAAATGGC
1 AATCGCAACGC-GAAATGAC
* ** *
1731360 TATCGCAATACGAAATGAA
1 AATCGCAACGCGAAATGAC
1731379 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
1731397 AATCGCAACG
1 AATCGCAACG
1731407 ACAAAATCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
18 10 0.18
19 31 0.54
20 16 0.28
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:1731365 original size:39 final size:38
Alignment explanation
Indices: 1731322--1731395 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
1731312 GAAACTTAAA
* **
1731322 ATCGCAACGCGAAATGACTATCGCAACGCAGAAATGGCT
1 ATCGCAACACGAAATGAAAATCGCAACGC-GAAATGGCT
*
1731361 ATCGCAATACGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACACGAAATGAAAATCGCAACGCGAAATG
1731396 AAATCGCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.15
Consensus pattern (38 bp):
ATCGCAACACGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:1731413 original size:19 final size:18
Alignment explanation
Indices: 1731320--1731425 Score: 94
Period size: 19 Copynumber: 5.9 Consensus size: 18
1731310 ACGAAACTTA
1731320 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
1731338 ACTATCGCAACGCAGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** **
1731359 CTATCGCAATACGAAATG
1 AAATCGCAACGCGAAATG
1731377 AAAATCGCAACGCGAAATG
1 -AAATCGCAACGCGAAATG
*
1731396 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
1731410 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
1731426 CACAAACCGC
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.12
16 8 0.11
18 11 0.15
19 29 0.40
20 14 0.19
21 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:1731485 original size:32 final size:33
Alignment explanation
Indices: 1731435--1731527 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
1731425 ACACAAACCG
*
1731435 CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
1731468 CATTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
* *
1731500 CGTTGCAATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
1731528 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.52
33 27 0.48
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:1731564 original size:20 final size:20
Alignment explanation
Indices: 1731512--1731565 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1731502 TTGCAATTTT
*
1731512 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1731531 CATTTCCGCG-TGCGATAGT
1 CATTTCCGCGTTGCGATAGC
* *
1731550 CATTTTCGTGTTGCGA
1 CATTTCCGCGTTGCGA
1731566 AAGTAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1732064 original size:18 final size:18
Alignment explanation
Indices: 1732038--1732082 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1732028 GTCGATCAGA
*
1732038 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1732056 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1732074 TGATGGCTC
1 TGATGGCTC
1732083 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1733426 original size:20 final size:20
Alignment explanation
Indices: 1733401--1733438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1733391 AATAGTTTCT
1733401 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1733421 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1733439 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1733726 original size:22 final size:22
Alignment explanation
Indices: 1733700--1733743 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1733690 AGATTAGATA
1733700 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1733722 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1733744 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1733956 original size:20 final size:20
Alignment explanation
Indices: 1733931--1734024 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1733921 GATTATGTAT
1733931 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1733951 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1733971 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1733992 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1734012 TATCGCATTGCGA
1 TATCGCGTTGCGA
1734025 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1733996 original size:41 final size:41
Alignment explanation
Indices: 1733951--1734028 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1733941 CGAAAGTCAG
* * *
1733951 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1733992 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1734029 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1734025 original size:20 final size:20
Alignment explanation
Indices: 1733911--1734025 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1733901 CGCTTTGAAA
*
1733911 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1733932 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1733952 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1733972 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1733993 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1734013 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1734026 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1734044 original size:41 final size:41
Alignment explanation
Indices: 1733951--1734046 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1733941 CGAAAGTCAG
* * * ** *
1733951 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
1733992 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
1734034 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1734047 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:1736085 original size:31 final size:32
Alignment explanation
Indices: 1736040--1736103 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
1736030 CCATCACCGT
*
1736040 AAAAATGGGATACTAAAATGAAATAAAAAGTA
1 AAAAATGGGATACTAAAATGAAACAAAAAGTA
1736072 AAAAATGGG-TACTAAAATGAAACAAAAAGTA
1 AAAAATGGGATACTAAAATGAAACAAAAAGTA
1736103 A
1 A
1736104 CATTAGGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.62, C:0.05, G:0.16, T:0.17
Consensus pattern (32 bp):
AAAAATGGGATACTAAAATGAAACAAAAAGTA
Found at i:1737235 original size:47 final size:47
Alignment explanation
Indices: 1737183--1737273 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
1737173 TAAATTGTCT
* * * * *
1737183 CTATTATTAGAAATTTA-AATTTTCAAAAATATATTTAATTTATAATC
1 CTATTATTACAAAATTATAATTATAAAAAAAATA-TTAATTTATAATC
*
1737230 CTATTATTTCAAAATTATAATTATAAAAAAAATATTAATTTATA
1 CTATTATTACAAAATTATAATTATAAAAAAAATATTAATTTATA
1737274 TATTTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 24 0.65
48 13 0.35
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (47 bp):
CTATTATTACAAAATTATAATTATAAAAAAAATATTAATTTATAATC
Found at i:1737282 original size:27 final size:27
Alignment explanation
Indices: 1737245--1737299 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1737235 ATTTCAAAAT
1737245 TATAATTATAAAAAAAATATTAATTTA
1 TATAATTATAAAAAAAATATTAATTTA
* * *
1737272 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAAAAAAATATTAATTTA
1737299 T
1 T
1737300 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATAATTATAAAAAAAATATTAATTTA
Found at i:1737394 original size:20 final size:19
Alignment explanation
Indices: 1737355--1737406 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1737345 TTTCTTCGAT
1737355 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1737374 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1737394 ATTTAAAAAATAA
1 A-TTAAAAAATAA
1737407 GATATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1737507 original size:120 final size:120
Alignment explanation
Indices: 1737263--1737500 Score: 304
Period size: 120 Copynumber: 2.0 Consensus size: 120
1737253 TAAAAAAAAT
* * * * *
1737263 ATTAATTTATATATTT-ATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAAGACTTCTAG
1 ATTAATATATA-ATTTAAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAG
* *
1737327 GTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACA
65 GTGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
* *
1737383 ATTAATATATAATTTAAAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAG
1 ATTAATATATAATTTAAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCAG
* ** * *
1737448 TTGTTTTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
65 GTGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
1737501 TGATTAAAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 9 0.09
119 23 0.23
120 52 0.51
121 18 0.18
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
ATTAATATATAATTTAAAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGG
TGCCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:1738894 original size:3 final size:3
Alignment explanation
Indices: 1738886--1738948 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
1738876 TAAAATTATT
* * * *
1738886 TAA TAA TAA TAA TAA T-A TAA TAA TTA TTA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1738933 TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
1738949 TTCAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 6 0.12
3 44 0.85
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1738932 original size:32 final size:31
Alignment explanation
Indices: 1738880--1738939 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
1738870 AATAAATAAA
*
1738880 ATTATTTAATAATAATAATAATATAATAATT
1 ATTATTTAATAATAATAATAATAAAATAATT
*
1738911 ATTATTATAATTATAATAATAATAAAATA
1 ATTATT-TAATAATAATAATAATAAAATA
1738940 TAAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
ATTATTTAATAATAATAATAATAAAATAATT
Found at i:1739455 original size:113 final size:113
Alignment explanation
Indices: 1739207--1739996 Score: 1172
Period size: 113 Copynumber: 7.0 Consensus size: 113
1739197 ATAGAGTTAT
* * *
1739207 GCAAAAGGTTGAACAAGTTCTT-TTCATTATGAAATTCCTCTTCCTTTTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTT-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * * * **
1739271 CATTATGAACACT-TCTGGCAATGCTGATCCATCAAATGATGAATTCAA
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * *
1739319 ACAAAAGATTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1739384 ATTATGAACTTTCTCTGGAAATA-CTAATCCATCAGGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAA-AGCTGATCCATCAAGTGATGGATTTGA
* * *
1739432 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1739497 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
1739545 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** *
1739610 ATTATGAACTTCCTCTGGAAAAGCTGATCCATTTAGTAATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
1739658 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1739723 ATTATGAACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGGATTTAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
1739771 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1739836 ATTATGAACTTTCTCTGGAAAAGCTGATCCATTAAGTGATGAATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
1739884 GCAAAAGGATGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1739949 ATTAAGAACTTTCTCTAGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
1739997 ATCTTTGCTA
Statistics
Matches: 616, Mismatches: 58, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
112 66 0.11
113 550 0.89
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:1741158 original size:19 final size:17
Alignment explanation
Indices: 1741130--1741178 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1741120 AAAATAAAAG
*
1741130 AATAAGTTGAATTTTCAAA
1 AATAAATTGAATTTTC--A
*
1741149 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1741165 AATAAATTGAATTT
1 AATAAATTGAATTT
1741179 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1741544 original size:9 final size:9
Alignment explanation
Indices: 1741530--1741645 Score: 99
Period size: 9 Copynumber: 12.2 Consensus size: 9
1741520 TCTTGACCCT
1741530 TTTTTTTTC
1 TTTTTTTTC
*
1741539 TTTTTTATC
1 TTTTTTTTC
1741548 TTTTTTTTCTC
1 -TTTTTTT-TC
1741559 TTTTTTTTC
1 TTTTTTTTC
*
1741568 TTTTTCTTC
1 TTTTTTTTC
* *
1741577 TTCTTCTTC
1 TTTTTTTTC
1741586 TTTTTCTTT-
1 TTTTT-TTTC
1741595 TTATTTTTTC
1 TT-TTTTTTC
1741605 TTTTTCTTTTC
1 -TTTT-TTTTC
* *
1741616 TTCTTCTTC
1 TTTTTTTTC
1741625 TTTTTTTTTC
1 -TTTTTTTTC
*
1741635 ATTTTTTTC
1 TTTTTTTTC
1741644 TT
1 TT
1741646 CAAGCATAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
9 48 0.55
10 30 0.34
11 9 0.10
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1741553 original size:11 final size:10
Alignment explanation
Indices: 1741528--1741642 Score: 92
Period size: 11 Copynumber: 10.8 Consensus size: 10
1741518 CATCTTGACC
1741528 CTTTTTTTTT
1 CTTTTTTTTT
*
1741538 C-TTTTTTAT
1 CTTTTTTTTT
1741547 C-TTTTTTTT
1 CTTTTTTTTT
1741556 CTCTTTTTTTT
1 CT-TTTTTTTT
1741567 CTTTTTCTTCTT
1 CTTTTT-TT-TT
1741579 CTTCTTCTTTTT
1 CTT-TT-TTTTT
1741591 CTTTTTATTTTTT
1 C--TTT-TTTTTT
1741604 CTTTTTCTTTT
1 CTTTTT-TTTT
* *
1741615 C-TTCTTCTT
1 CTTTTTTTTT
1741624 CTTTTTTTTT
1 CTTTTTTTTT
1741634 CATTTTTTT
1 C-TTTTTTT
1741643 CTTCAAGCAT
Statistics
Matches: 87, Mismatches: 6, Indels: 23
0.75 0.05 0.20
Matches are distributed among these distances:
9 20 0.23
10 17 0.20
11 27 0.31
12 8 0.09
13 11 0.13
14 4 0.05
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1741571 original size:39 final size:38
Alignment explanation
Indices: 1741528--1741645 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 38
1741518 CATCTTGACC
*
1741528 CTTTTTTTTTCTT-TTTTATCTTTTTTTTCTCTTTTTTTT
1 CTTTTTTTTTCTTCTTCT-TCTTTTTTTT-TCTTTTTTTT
* *
1741567 C-TTTTTCTTCTTCTTCTTCTTTTTCTTTT-TATTTTTT
1 CTTTTTTTTTCTTCTTCTTCTTTTT-TTTTCTTTTTTTT
*
1741604 CTTTTTCTTTTCTTCTTCTTCTTTTTTTTTCATTTTTTT
1 CTTTTT-TTTTCTTCTTCTTCTTTTTTTTTCTTTTTTTT
1741643 CTT
1 CTT
1741646 CAAGCATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
37 8 0.12
38 26 0.38
39 34 0.50
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (38 bp):
CTTTTTTTTTCTTCTTCTTCTTTTTTTTTCTTTTTTTT
Found at i:1741573 original size:6 final size:6
Alignment explanation
Indices: 1741529--1741640 Score: 90
Period size: 6 Copynumber: 18.7 Consensus size: 6
1741519 ATCTTGACCC
*
1741529 TTTT-T TTTTCT TTTT-T ATCTTT-T TTTTCT CTTT-T TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT -T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * *
1741575 TCTTCT TCTTCT TTTTCT TTTTATT TTTTCT TTTTC- TTTTCT TCTTCT
1 TTTTCT TTTTCT TTTTCT TTTT-CT TTTTCT TTTTCT TTTTCT TTTTCT
*
1741623 TCTTTTT TTTTCAT TTTT
1 T-TTTCT TTTTC-T TTTT
1741641 TTCTTCAAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
5 17 0.19
6 53 0.60
7 18 0.20
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:1748996 original size:15 final size:15
Alignment explanation
Indices: 1748956--1749004 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1748946 ATACATAAAG
1748956 AAAAT-AATGTAATG-
1 AAAATGAATGT-ATGC
1748970 AATAATGAATGTATGC
1 AA-AATGAATGTATGC
*
1748986 AAAATGCATGTATGC
1 AAAATGAATGTATGC
1749001 AAAA
1 AAAA
1749005 GGTATTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 22 0.71
16 7 0.23
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (15 bp):
AAAATGAATGTATGC
Found at i:1752296 original size:23 final size:23
Alignment explanation
Indices: 1752257--1752312 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1752247 ACAGAAAAAT
* *
1752257 AAATAATGAAATAAAATGCT-TGC
1 AAATAAT-AAATAAAATACTATGA
*
1752280 AAATAATATATATAAATACTATGA
1 AAATAATAAATA-AAATACTATGA
1752304 AAATAATAA
1 AAATAATAA
1752313 GTATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 13 0.48
24 10 0.37
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (23 bp):
AAATAATAAATAAAATACTATGA
Found at i:1752317 original size:24 final size:22
Alignment explanation
Indices: 1752280--1752329 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
1752270 AAATGCTTGC
1752280 AAATAATATATATAAATACTATGA
1 AAATAATATATATAAATA-TAT-A
*
1752304 AAATAATA-AGTATATATATATA
1 AAATAATATA-TATAAATATATA
1752326 AAAT
1 AAAT
1752330 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (22 bp):
AAATAATATATATAAATATATA
Found at i:1752814 original size:47 final size:46
Alignment explanation
Indices: 1752761--1752850 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 46
1752751 TAAATTGTCT
* * * *
1752761 CTATTATTAGAAATTTA-AATTTTCAAAAATATATTTAATTTATAATC
1 CTATTATTACAAAATTATAATTAT-AAAAAAATA-TTAATTTATAATC
*
1752808 CTATTATTTCAAAATTATAATTATAAAAAAATATTAATTTATA
1 CTATTATTACAAAATTATAATTATAAAAAAATATTAATTTATA
1752851 TATTTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 10 0.27
47 22 0.59
48 5 0.14
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.46
Consensus pattern (46 bp):
CTATTATTACAAAATTATAATTATAAAAAAATATTAATTTATAATC
Found at i:1752857 original size:26 final size:27
Alignment explanation
Indices: 1752823--1752876 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1752813 ATTTCAAAAT
1752823 TATAATTATAAA-AAAATATTAATTTA
1 TATAATTATAAATAAAATATTAATTTA
* *
1752849 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
1752876 T
1 T
1752877 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:1754499 original size:3 final size:3
Alignment explanation
Indices: 1754491--1754556 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
1754481 TAAAATTATT
* * * *
1754491 TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1754538 TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
1754557 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.12
3 43 0.84
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1760020 original size:3 final size:3
Alignment explanation
Indices: 1760014--1760062 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
1760004 ATTATTTTTT
1760014 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1760060 TAA
1 TAA
1760063 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1760341 original size:17 final size:17
Alignment explanation
Indices: 1760319--1760377 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1760309 TTGAACAAGC
1760319 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
1760336 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
1760355 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
1760372 TCTTCT
1 TCTTCT
1760378 GGAAATGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:1760760 original size:113 final size:112
Alignment explanation
Indices: 1760421--1760975 Score: 689
Period size: 113 Copynumber: 5.0 Consensus size: 112
1760411 ATAAAATTAT
* * *
1760421 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTTCTTCTTCAAATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
**** * * * * *
1760483 TTATGAACTTTCTCTGGAAAAGCTGATCCA-TCAAGTGATGGATTTGA
66 TTATGAACTCGAACTGGAAATGTTGATCCATTGAA-TGATGAATTTAA
*
1760530 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTC
* * * **
1760592 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAA
63 TCATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
* * *
1760642 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTC
* * *
1760707 ATTATGAACTCGAACTGGTAATGTTGATCCATTGAATCATGAATTCAA
65 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
* * *
1760755 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTTTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
* * *
1760820 ATTATGAACTCGAACTGGAAATGCTGATCCATCGAGTGATGAATTTAA
65 ATTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
*
1760868 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC--CTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
*
1760931 TTATGAACTC-AGACTGGAAATGTTGATCCATTGAATGATGGATTT
66 TTATGAACTCGA-ACTGGAAATGTTGATCCATTGAATGATGAATTT
1760976 TAATCTTTGC
Statistics
Matches: 394, Mismatches: 41, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
109 46 0.12
110 61 0.15
112 78 0.20
113 191 0.48
114 2 0.01
115 6 0.02
116 10 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAATGTTGATCCATTGAATGATGAATTTAA
Found at i:1761862 original size:114 final size:114
Alignment explanation
Indices: 1761662--1761998 Score: 611
Period size: 114 Copynumber: 3.0 Consensus size: 114
1761652 GATCATGCAG
* * *
1761662 TTCATCTTTCAATTCCAATGATTGCTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1761727 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
1761776 TTCATCTTTCAAATCTAATGATTGGTTCCGTGGTTCCTACCGAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1761841 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
1761890 TTCATCTTTCAAATCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
* *
1761955 ACACTTCCAGAAGATGCTATTAGGTATCCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
1761999 TAACGTGGTA
Statistics
Matches: 214, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 214 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1762711 original size:16 final size:18
Alignment explanation
Indices: 1762692--1762735 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
1762682 TCTTGACCCC
1762692 TTTTTTTC-TCTCTTC-T
1 TTTTTTTCATCTCTTCAT
*
1762708 TTTTTTTCATCTTTTCAT
1 TTTTTTTCATCTCTTCAT
1762726 TTTTTCTTCA
1 TTTTT-TTCA
1762736 AGCATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 6 0.25
19 4 0.17
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTTCATCTCTTCAT
Found at i:1762728 original size:17 final size:16
Alignment explanation
Indices: 1762692--1762730 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1762682 TCTTGACCCC
*
1762692 TTTTTTTCTCTCTTCT
1 TTTTTTTCTCTCTTCA
*
1762708 TTTTTTTCATCTTTTCA
1 TTTTTTTC-TCTCTTCA
1762725 TTTTTT
1 TTTTTT
1762731 CTTCAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTCTCTTCA
Found at i:1775149 original size:25 final size:24
Alignment explanation
Indices: 1775107--1775157 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1775097 TGTGGTTTGC
* *
1775107 TTTTTGTCTTTTTTTTTTGTTCTCTG
1 TTTTTGTCTTCTTCTTTT-TT-TCTG
1775133 TTTTTG-CTTCTTCTTTTTTTCTG
1 TTTTTGTCTTCTTCTTTTTTTCTG
1775156 TT
1 TT
1775158 GGTTGTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 2 0.09
25 9 0.39
26 6 0.26
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (24 bp):
TTTTTGTCTTCTTCTTTTTTTCTG
Found at i:1789349 original size:30 final size:30
Alignment explanation
Indices: 1789294--1789367 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1789284 TGTTCTAAGG
* *
1789294 AACATATGGACAGTTTACCGAGGATCTTTAC
1 AACATCTGGATAG-TTACCGAGGATCTTTAC
* * *
1789325 GACATCTGGATAGTTACTGAGGATCTTTAT
1 AACATCTGGATAGTTACCGAGGATCTTTAC
*
1789355 AACCTCTGGATAG
1 AACATCTGGATAG
1789368 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (30 bp):
AACATCTGGATAGTTACCGAGGATCTTTAC
Found at i:1791274 original size:15 final size:15
Alignment explanation
Indices: 1791254--1791284 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1791244 CAGAAGTCAA
1791254 CCTGAATCCTCTACT
1 CCTGAATCCTCTACT
1791269 CCTGAATCCTCTACT
1 CCTGAATCCTCTACT
1791284 C
1 C
1791285 AACAGGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.06, T:0.32
Consensus pattern (15 bp):
CCTGAATCCTCTACT
Found at i:1793230 original size:21 final size:21
Alignment explanation
Indices: 1793168--1793223 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1793158 TTCTGGGTTG
1793168 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
1793189 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
1793210 TGTGCATCGATGCA
1 TGTGCATCGATGCA
1793224 CTCTCAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:1794124 original size:30 final size:30
Alignment explanation
Indices: 1794088--1794147 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1794078 TATGGACAGT
1794088 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1794118 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1794148 GTCCTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:1796926 original size:16 final size:18
Alignment explanation
Indices: 1796884--1796928 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1796874 TCACGGAATG
1796884 TAAGATTACCAGTGAGAA
1 TAAGATTACCAGTGAGAA
1796902 TAAAAGATTACCAG-G-GAA
1 T--AAGATTACCAGTGAGAA
1796920 TAAGATTAC
1 TAAGATTAC
1796929 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 5 0.20
19 1 0.04
20 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGTGAGAA
Found at i:1797143 original size:37 final size:37
Alignment explanation
Indices: 1797070--1797144 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1797060 GTTGGAAAAT
*
1797070 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* * *
1797107 ATTTATATAATTTTTTTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATTAAAATCATAAA
1797144 A
1 A
1797145 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:1799718 original size:28 final size:27
Alignment explanation
Indices: 1799650--1799733 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 27
1799640 GCAACCGCTT
*
1799650 AGGGCCCATATATTTTTGTATTTATAATC
1 AGGGCCC-TA-ATTTTTATATTTATAATC
* *
1799679 AGGGCCCTAATTTTTATGTTTATAATT
1 AGGGCCCTAATTTTTATATTTATAATC
*
1799706 AGGGTCCTTAATTTTTATAATTTCATAA
1 AGGG-CCCTAATTTTTAT-ATTT-ATAA
1799734 ATTTTTTAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 19 0.40
28 14 0.30
29 10 0.21
30 4 0.09
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (27 bp):
AGGGCCCTAATTTTTATATTTATAATC
Found at i:1799914 original size:113 final size:111
Alignment explanation
Indices: 1799685--1799906 Score: 277
Period size: 113 Copynumber: 2.0 Consensus size: 111
1799675 AATCAGGGCC
* * * * *
1799685 CTAA-TTTTTATGTTTATAATTAGGGTCCTTAATTTTTATAATTTCATAAATTTTTTAGTTTTTA
1 CTAATTTTTTATATTTATAATTAGGGTCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTGA
* *
1799749 CCTTTTTATTTCTCTTATTAATTCATTTTAATTTCGAATTATATTTAA
66 CCTTTTCATTTCTCTTATTAATTCATTTCAATTTCGAATTATA--TAA
1799797 CTAATTTTTTATATTTATAATTAGGGTCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTGA
1 CTAATTTTTTATATTTATAATTAGGGTCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTGA
* * *
1799862 CATTTCTTTTCCATTTTTCTTATTTATTCA-TTCAATTTTGAATTA
66 C----CTTTT-CATTTCTCTTATTAATTCATTTCAATTTCGAATTA
1799907 AATCTAATCA
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
112 4 0.04
113 56 0.60
117 18 0.19
118 16 0.17
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (111 bp):
CTAATTTTTTATATTTATAATTAGGGTCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTGA
CCTTTTCATTTCTCTTATTAATTCATTTCAATTTCGAATTATATAA
Found at i:1800641 original size:15 final size:16
Alignment explanation
Indices: 1800610--1800643 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1800600 ATTAATTTGC
1800610 AATTAATCAATAATAT
1 AATTAATCAATAATAT
*
1800626 AATTGATCAA-AATAT
1 AATTAATCAATAATAT
1800641 AAT
1 AAT
1800644 AATTGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTAATCAATAATAT
Found at i:1800866 original size:39 final size:38
Alignment explanation
Indices: 1800775--1800899 Score: 241
Period size: 38 Copynumber: 3.3 Consensus size: 38
1800765 GCATGTGGGG
1800775 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTAT
1 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTAT
1800813 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTATT
1 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTA-T
1800852 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTAT
1 TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTAT
1800890 TGATTTGGGT
1 TGATTTGGGT
1800900 ATGATTAGAT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
38 48 0.56
39 38 0.44
ACGTcount: A:0.13, C:0.12, G:0.25, T:0.50
Consensus pattern (38 bp):
TGATTTGGGTTTGTTTTACAGGTCCAGTCGTCTTTTAT
Found at i:1813278 original size:44 final size:44
Alignment explanation
Indices: 1813230--1813313 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
1813220 CTCTGCATTC
1813230 TGGATGCAATTCTTTGCTATTACTAACGGGATATATTTTGCATG
1 TGGATGCAATTCTTTGCTATTACTAACGGGATATATTTTGCATG
* *
1813274 TGGATGCGATTCTTTGCTATTACTAACTGGATATATTTTG
1 TGGATGCAATTCTTTGCTATTACTAACGGGATATATTTTG
1813314 TTCTTAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (44 bp):
TGGATGCAATTCTTTGCTATTACTAACGGGATATATTTTGCATG
Found at i:1817796 original size:203 final size:202
Alignment explanation
Indices: 1817293--1817804 Score: 602
Period size: 204 Copynumber: 2.5 Consensus size: 202
1817283 AAAATTATCA
* * * * * * *
1817293 TAATTTATAAGATTAGATGTGTAATATTGTAACTTATCTTTCATTTGAGGGTAATACCATCACAT
1 TAATTTTTAAGCTTAGAGGTGTAGTATTGCAACTTATCTTTCATTTGAGGGTAATATCAGCACAT
* * * *
1817358 ACGAGACATTGTAAGCGGGGTAAAAATCATGTTGAAAATGATTCCAAAGCTTGGTTTTGTGCATG
66 ACAAGACATTGTAAGCGGGGTAAAAATCACGTTGAAAATGACTCCAAAGCTTGGTTTTATGCATG
* * * * * *
1817423 AAAAATAAACTAAAATGGCTTCATAGACATGTTCGAGGGGTATTTCTAGGATATGAAGTTAATTG
131 AAAAACAAACTAAAATAGCTTCATAGACACGTTCGAAGAGTATTTCTACG--A-GAAGTTAATTG
1817488 ATTTTTTTTT
193 ATTTTTTTTT
* * *
1817498 TAA-TTTTAAGCTTAGAGGCGTAGTGTTACAACTTATCTTTCATTTGAGGGTAATATCAGCACAT
1 TAATTTTTAAGCTTAGAGGTGTAGTATTGCAACTTATCTTTCATTTGAGGGTAATATCAGCACAT
* * * * * *
1817562 GCAAGACATTGTAAGCGAGATAAAAATCACGTTGAAAGTGGCTCCAAAGTTTGGTTTTATGCATG
66 ACAAGACATTGTAAGCGGGGTAAAAATCACGTTGAAAATGACTCCAAAGCTTGGTTTTATGCATG
* * * * *
1817627 AAGAACAAGCTAAAATAGCTTGATAGACACGTTCGAAGAGTATTT-TCCG-GAAGTTAGTTGATT
131 AAAAACAAACTAAAATAGCTTCATAGACACGTTCGAAGAGTATTTCTACGAGAAGTTAATTGATT
1817690 TCTTTGTTGT
196 T-TTT-TT-T
*
1817700 TAATTTTTAAGCTTAGAGGTGTAGTATTGCAA-TATATCTTTCATTTTAGGGTAATATCTA-CAC
1 TAATTTTTAAGCTTAGAGGTGTAGTATTGCAACT-TATCTTTCATTTGAGGGTAATATC-AGCAC
* * *
1817763 ATACAAGATATTATAAGCGGGGTAAATATCACGTTGAAAATG
64 ATACAAGACATTGTAAGCGGGGTAAAAATCACGTTGAAAATG
1817805 GTTCGAAACC
Statistics
Matches: 259, Mismatches: 42, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
199 14 0.05
200 3 0.01
201 2 0.01
202 5 0.02
203 88 0.34
204 144 0.56
205 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (202 bp):
TAATTTTTAAGCTTAGAGGTGTAGTATTGCAACTTATCTTTCATTTGAGGGTAATATCAGCACAT
ACAAGACATTGTAAGCGGGGTAAAAATCACGTTGAAAATGACTCCAAAGCTTGGTTTTATGCATG
AAAAACAAACTAAAATAGCTTCATAGACACGTTCGAAGAGTATTTCTACGAGAAGTTAATTGATT
TTTTTTT
Found at i:1821344 original size:19 final size:19
Alignment explanation
Indices: 1821317--1821367 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1821307 TACTGTTCAC
*
1821317 AGTACTGTTCATACAGTAT
1 AGTATTGTTCATACAGTAT
*
1821336 AGTATTGTTCATACCGTAT
1 AGTATTGTTCATACAGTAT
*
1821355 ATTATTGTTCATA
1 AGTATTGTTCATA
1821368 AAAACGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (19 bp):
AGTATTGTTCATACAGTAT
Found at i:1822326 original size:16 final size:18
Alignment explanation
Indices: 1822301--1822338 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1822291 AATTCATCAC
1822301 AAGATGGAAG-CTCAACA
1 AAGATGGAAGACTCAACA
1822318 AAGAT-GAAGACTCAACA
1 AAGATGGAAGACTCAACA
1822335 AAGA
1 AAGA
1822339 AGAAAAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.53, C:0.16, G:0.21, T:0.11
Consensus pattern (18 bp):
AAGATGGAAGACTCAACA
Found at i:1824619 original size:31 final size:30
Alignment explanation
Indices: 1824533--1824620 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 30
1824523 GAGTCGAGGG
* *
1824533 TATACCTATGTTCTACGGAACATATGGACA
1 TATACCTATGTTCTAAGGAACATATAGACA
***
1824563 TAATTACCTATG-TCTTTCGAGACATATAGACAA
1 T-A-TACCTATGTTCTAAGGA-ACATATAGAC-A
1824596 TATACCTATGTTCTAAGGAACATAT
1 TATACCTATGTTCTAAGGAACATAT
1824621 GGATAGTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
30 1 0.02
31 20 0.43
32 23 0.50
33 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (30 bp):
TATACCTATGTTCTAAGGAACATATAGACA
Found at i:1824633 original size:31 final size:31
Alignment explanation
Indices: 1824535--1824659 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 31
1824525 GTCGAGGGTA
1824535 TACCTATGTTCTACGGAACATATGGACA-TAAT
1 TACCTATGTTCTACGGAACATATGGACAGT--T
* * * *
1824567 TACCTATG-TCTTTC-GAGACATATAGACAATA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
* *
1824598 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1824629 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1824660 GCCAAGGATC
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
31 49 0.66
32 24 0.32
33 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1824697 original size:30 final size:30
Alignment explanation
Indices: 1824646--1824717 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1824636 GTTCTTCGGA
* * *
1824646 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
1824676 ACCTCTGGATAGTTACCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
1824706 ACCTCTGGATAG
1 ACCTCTGGATAG
1824718 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:1827904 original size:81 final size:81
Alignment explanation
Indices: 1827762--1827919 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 81
1827752 AAGGCAGTGC
* * * * * * * * *
1827762 CTTTTGTATGGGGAATCTATAGAAAAGTCTCGCAACTATAATGGAAGTGTGTTTTCGAGGATTTT
1 CTTTTATATAGGGAATCTATAGAAAAGTCTCGCAACTACAAGGGAAGCGGGTTTCCAAGGATTGT
1827827 TCATA-AAAAGGCATT
66 TCATATAAAAGGCATT
*
1827842 CTTTTATATAGGGAATCTATGGAAAAAGTCTC-CAAACTACAAGGGAAGCGGGTTTCCAAGGATT
1 CTTTTATATAGGGAATCTATAG-AAAAGTCTCGC-AACTACAAGGGAAGCGGGTTTCCAAGGATT
*
1827906 GTTCGTATAAAAGG
64 GTTCATATAAAAGG
1827920 AAGTCCTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
80 20 0.31
81 38 0.59
82 6 0.09
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (81 bp):
CTTTTATATAGGGAATCTATAGAAAAGTCTCGCAACTACAAGGGAAGCGGGTTTCCAAGGATTGT
TCATATAAAAGGCATT
Found at i:1836409 original size:2 final size:2
Alignment explanation
Indices: 1836397--1836452 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1836387 GCCAATCTTC
*
1836397 TA TA AA 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
1836439 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1836453 ATACACTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1849735 original size:23 final size:24
Alignment explanation
Indices: 1849687--1849743 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
1849677 AATTCCTATG
** *
1849687 AGATAATTCCTAATAAATTTCCAA
1 AGATAATTCCTAATAAATCACAAA
1849711 AGATAATTCCTAA-AAATCACAAA
1 AGATAATTCCTAATAAATCACAAA
1849734 AGATAATTCC
1 AGATAATTCC
1849744 CATCATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (24 bp):
AGATAATTCCTAATAAATCACAAA
Found at i:1855807 original size:3 final size:3
Alignment explanation
Indices: 1855799--1855849 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
1855789 TCTAATTGTA
1855799 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1855845 ATT AT
1 ATT AT
1855850 CTTATTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1855879 original size:23 final size:23
Alignment explanation
Indices: 1855836--1855880 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1855826 ATTATTATTA
**
1855836 TTATTATATATTATCTTATTTTG
1 TTATTATATATTATCAAATTTTG
1855859 TTATTAATATATTA-CAAATTTT
1 TTATT-ATATATTATCAAATTTT
1855881 TGCAGGCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTATATATTATCAAATTTTG
Found at i:1858916 original size:10 final size:10
Alignment explanation
Indices: 1858901--1858931 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1858891 CTAACATTTG
1858901 ATTTTTTTTT
1 ATTTTTTTTT
1858911 ATTTTTTTTTT
1 A-TTTTTTTTT
1858922 ATTTTTTTTT
1 ATTTTTTTTT
1858932 TCAGATCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:1858919 original size:12 final size:11
Alignment explanation
Indices: 1858902--1858932 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1858892 TAACATTTGA
1858902 TTTTTTTTTAT
1 TTTTTTTTTAT
1858913 TTTTTTTTTAT
1 TTTTTTTTTAT
1858924 TTTTTTTTT
1 TTTTTTTTT
1858933 CAGATCGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:1863523 original size:4 final size:4
Alignment explanation
Indices: 1863514--1863629 Score: 188
Period size: 4 Copynumber: 30.2 Consensus size: 4
1863504 GATCGAGAAA
1863514 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1863562 ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1863608 AC-- ACAT ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
1863630 AAATTTGCAT
Statistics
Matches: 105, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
2 4 0.04
3 3 0.03
4 98 0.93
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:1864056 original size:36 final size:36
Alignment explanation
Indices: 1864024--1864105 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1864014 ATTTTGTTTT
* *
1864024 GCTTGAGACAATTTCT-TTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTCTT-AAAACAAACTTTGTATC
* * * *
1864060 ACTTAAGACAAATTCTCTTAAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCTCTTAAAACAAACTTTGTATC
1864096 GCTTGAGACA
1 GCTTGAGACA
1864106 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTCTTAAAACAAACTTTGTATC
Found at i:1864422 original size:29 final size:27
Alignment explanation
Indices: 1864332--1864422 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 27
1864322 TCTTGAGACA
*
1864332 GTTTCTTTTGAAACAAATCTTTGAGTT
1 GTTTCTTTTGAAAAAAATCTTTGAGTT
1864359 -TGTTCATTTTGAATAAAAATCTTTGAGTT
1 GT-TTC-TTTTGAA-AAAAATCTTTGAGTT
*
1864388 ATTTCTTTTGAGAAAAAATCTTTGAGTAT
1 GTTTCTTTTGA-AAAAAATCTTTGAGT-T
1864417 GTTTCT
1 GTTTCT
1864423 CTTAAAACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.02
27 3 0.05
28 27 0.48
29 24 0.43
30 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (27 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTT
Found at i:1864551 original size:120 final size:121
Alignment explanation
Indices: 1864303--1864578 Score: 346
Period size: 120 Copynumber: 2.3 Consensus size: 121
1864293 TTTGAATATT
* * * *
1864303 TTAAAACGAT-TTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAATCTTTGAGTTTGTTCATT
1 TTAAAAC-ATATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTGGAGTCTATTCATT
** * * *
1864367 TTGAATAAAAATCTTTGAGTTATTTCTTTTGAGAAAAAATCTTTGAGTATGTTTCTC
65 TTGAATAAAAATCTTTGAGTTATTTCTACTAACAAAAAATCTTTGAGTATATTTCTC
*
1864424 TTAAAACATATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-AAATCTTGGAGTCTATTCCTTT
1 TTAAAACATATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTGGAGTCTATTCATTT
* * * *
1864488 TG-A-AAAAATCTTTGAGTTTGTTTCTACTAACAAAATCATCTTTTAGTTTATTTCT-
66 TGAATAAAAATCTTTGAG-TTATTTCTACTAACAAAA-AATCTTTGAGTATATTTCTC
*
1864543 TTAAAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
1 TT-AAAACATATTTTGTCTCTCTTGAGACAGTTTCT
1864579 AACGAAAAAC
Statistics
Matches: 136, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
118 13 0.10
119 16 0.12
120 69 0.51
121 38 0.28
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (121 bp):
TTAAAACATATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTGGAGTCTATTCATTT
TGAATAAAAATCTTTGAGTTATTTCTACTAACAAAAAATCTTTGAGTATATTTCTC
Found at i:1864857 original size:31 final size:31
Alignment explanation
Indices: 1864821--1864881 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
1864811 CCCTGAGGCA
1864821 GTTTCTC-TAGAAATACAAA-ATCTTTGAGTTT
1 GTTTCTCTTA-AAATA-AAACATCTTTGAGTTT
1864852 GTTTCTCTTAAAATAAAACCATCTTTGAGT
1 GTTTCTCTTAAAATAAAA-CATCTTTGAGT
1864882 CGTTTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 12 0.44
32 12 0.44
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (31 bp):
GTTTCTCTTAAAATAAAACATCTTTGAGTTT
Found at i:1865465 original size:28 final size:28
Alignment explanation
Indices: 1865419--1865515 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
1865409 GAGACAGTTG
1865419 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
1865450 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
*
1865478 CTTTTGAAACAAATCTTTGAATC-GATTT
1 CTTTTGAAACAAATCTTTGAGTCTG-TTT
*
1865506 CTCTTGAAAC
1 CTTTTGAAAC
1865516 CATGATTCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.02
28 45 0.75
29 3 0.05
30 3 0.05
31 8 0.13
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:1865738 original size:40 final size:40
Alignment explanation
Indices: 1865694--1865826 Score: 135
Period size: 40 Copynumber: 3.2 Consensus size: 40
1865684 CGTAGGAACC
*
1865694 GTGTCATCCCTCGACAAGAACTCTTCATCACGTATGAGCA
1 GTGTCATCCCTCGACCAGAACTCTTCATCACGTATGAGCA
* ** * *
1865734 GTGTCAACCCTCGACCAGATTTCCTCATCACGTATGAACCA
1 GTGTCATCCCTCGACCAGAACTCTTCATCACGTATG-AGCA
*
1865775 -TGTCA-CCCTTAGACGACCCGAACTCTTCATCACGTATGAGCA
1 GTGTCATCCC-T---CGACCAGAACTCTTCATCACGTATGAGCA
*
1865817 GTGTCGTCCC
1 GTGTCATCCC
1865827 CAACAACCAA
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
39 3 0.04
40 37 0.50
41 3 0.04
42 3 0.04
43 25 0.34
44 3 0.04
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (40 bp):
GTGTCATCCCTCGACCAGAACTCTTCATCACGTATGAGCA
Found at i:1865995 original size:3 final size:3
Alignment explanation
Indices: 1865987--1866036 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1865977 TCTAATTGTA
1865987 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1866035 AT
1 AT
1866037 ATATGCTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1871146 original size:19 final size:19
Alignment explanation
Indices: 1871122--1871224 Score: 93
Period size: 19 Copynumber: 5.4 Consensus size: 19
1871112 TATGCATTGG
1871122 GTTATGAATTTGAAAATAA
1 GTTATGAATTTGAAAATAA
*
1871141 GTTATGAATCT-AACAATAA
1 GTTATGAATTTGAA-AATAA
* * **
1871160 GCTATGAGTCAGAAAATAA
1 GTTATGAATTTGAAAATAA
*
1871179 GTTATGAATTTGGAAATAA
1 GTTATGAATTTGAAAATAA
* *
1871198 GTTCTG-ATTCAGAAAATAA
1 GTTATGAATT-TGAAAATAA
*
1871217 ATTATGAA
1 GTTATGAA
1871225 ATGTGATAGT
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
18 5 0.08
19 58 0.88
20 3 0.05
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.32
Consensus pattern (19 bp):
GTTATGAATTTGAAAATAA
Found at i:1871175 original size:38 final size:38
Alignment explanation
Indices: 1871133--1871224 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
1871123 TTATGAATTT
1871133 GAAAATAAGTTATGAATCT-AACAATAAGCTATGAGTCA
1 GAAAATAAGTTATGAATCTGAA-AATAAGCTATGAGTCA
* * * * *
1871171 GAAAATAAGTTATGAATTTGGAAATAAGTTCTGATTCA
1 GAAAATAAGTTATGAATCTGAAAATAAGCTATGAGTCA
*
1871209 GAAAATAAATTATGAA
1 GAAAATAAGTTATGAA
1871225 ATGTGATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 46 0.98
39 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (38 bp):
GAAAATAAGTTATGAATCTGAAAATAAGCTATGAGTCA
Found at i:1871268 original size:12 final size:12
Alignment explanation
Indices: 1871241--1871284 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1871231 TAGTATTTAT
*
1871241 TATGAACATGGAA
1 TATGAAAAT-GAA
1871254 TATGAAAATGAA
1 TATGAAAATGAA
**
1871266 TATGTGAATGAA
1 TATGAAAATGAA
1871278 TATGAAA
1 TATGAAA
1871285 GTGGAGAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:1871461 original size:19 final size:20
Alignment explanation
Indices: 1871429--1871466 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1871419 GAGGAAAAAC
1871429 GATTTTATTTTGAATTTAAT
1 GATTTTATTTTGAATTTAAT
1871449 GATTTTA-TTTGAATTTAA
1 GATTTTATTTTGAATTTAA
1871467 GTTTAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
GATTTTATTTTGAATTTAAT
Done.