Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_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: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:890077 original size:4 final size:5
Alignment explanation
Indices: 890040--890149 Score: 59
Period size: 5 Copynumber: 21.2 Consensus size: 5
890030 TTTTCTTCCT
* *
890040 TCTTC TCTTC T-TTC TTTTCC TCTT- TCTTC TCTTC -CTTC TTCTCC TCTTTCC
1 TCTTC TCTTC TCTTC TCTT-C TCTTC TCTTC TCTTC TCTTC -TCTTC TC-TT-C
* * *
890091 TCTTC TCCTC -CTTC TTCTCC TCTT- TCTTT TCTTCC TTCTTC TCTTCC
1 TCTTC TCTTC TCTTC -TCTTC TCTTC TCTTC TCTT-C -TCTTC TCTT-C
890138 TTCTTC TCTTC T
1 -TCTTC TCTTC T
890150 TTAGCAGGTC
Statistics
Matches: 83, Mismatches: 8, Indels: 28
0.70 0.07 0.24
Matches are distributed among these distances:
4 19 0.23
5 37 0.45
6 16 0.19
7 11 0.13
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTC
Found at i:890106 original size:51 final size:52
Alignment explanation
Indices: 890035--890133 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
890025 ATTTCTTTTC
* * *
890035 TTCCTTCTTCTCTTCTTTCTTTTCCTCTTTCTTCTCTTCCTTCTTCTCCTCT
1 TTCCTTCTTCTCCTCCTTCTTCTCCTCTTTCTTCTCTTCCTTCTTCTCCTCT
*
890087 TTCC-TCTTCTCCTCCTTCTTCTCCTCTTTCTTTTCTTCCTTCTTCTC
1 TTCCTTCTTCTCCTCCTTCTTCTCCTCTTTCTTCTCTTCCTTCTTCTC
890134 TTCCTTCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 39 0.91
52 4 0.09
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (52 bp):
TTCCTTCTTCTCCTCCTTCTTCTCCTCTTTCTTCTCTTCCTTCTTCTCCTCT
Found at i:891255 original size:39 final size:39
Alignment explanation
Indices: 891211--891286 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
891201 TAATTGTTTG
*
891211 ATCGATTTTAAGAGTATGAATGACTAGATTAATTTCATA
1 ATCGATTTTAAGAGTATGAATGACTAGATTAAATTCATA
891250 ATCGATTTTAAGAGTATGAATGACTAGATTAAATTCA
1 ATCGATTTTAAGAGTATGAATGACTAGATTAAATTCA
891287 AAAACTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (39 bp):
ATCGATTTTAAGAGTATGAATGACTAGATTAAATTCATA
Found at i:892892 original size:20 final size:21
Alignment explanation
Indices: 892861--892906 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
892851 ACTAAAAATA
892861 TTATTATTTCTACC-GATTTTG
1 TTATTATTTCTACCTG-TTTTG
892882 TTATT-TTTCTACCTGTTTTG
1 TTATTATTTCTACCTGTTTTG
892902 TTATT
1 TTATT
892907 GTTGGACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63
Consensus pattern (21 bp):
TTATTATTTCTACCTGTTTTG
Found at i:892955 original size:20 final size:21
Alignment explanation
Indices: 892930--892976 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
892920 CCGAAAATAT
*
892930 TAAAAAAT-TGATATTTTAAA
1 TAAAAAATATAATATTTTAAA
892950 TAAAAAATAATAATATTTTAAA
1 TAAAAAAT-ATAATATTTTAAA
892972 TAAAA
1 TAAAA
892977 TTTTACCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
22 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAATATAATATTTTAAA
Found at i:895724 original size:2 final size:2
Alignment explanation
Indices: 895717--895784 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
895707 CGTGACTTCT
895717 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
895759 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
895785 ACACACACAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:898006 original size:60 final size:57
Alignment explanation
Indices: 897876--898011 Score: 130
Period size: 60 Copynumber: 2.3 Consensus size: 57
897866 TAATAAATAG
* * * * *
897876 TCAAGTGATCATTTTATAACTTTCAATAGTAGGACTCAACAAAGTAACACTCTATAG
1 TCAAGAGATCATTTTGTAACTTTCAATAGTAGAACTCAACAAAATAACACTCTATAA
* * * * *
897933 TCATA-AGAACATTTTGTAACTTTTAATAGTCGATGAACTTAATAAAATAATACTCTATAA
1 TCA-AGAGATCATTTTGTAACTTTCAATAGT--A-GAACTCAACAAAATAACACTCTATAA
897993 TCAAGAGATCATTTGTGTA
1 TCAAGAGATCATTT-TGTA
898012 TGTTACCCTA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
57 24 0.39
58 1 0.02
59 2 0.03
60 31 0.50
61 4 0.06
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (57 bp):
TCAAGAGATCATTTTGTAACTTTCAATAGTAGAACTCAACAAAATAACACTCTATAA
Found at i:901584 original size:17 final size:18
Alignment explanation
Indices: 901562--901595 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
901552 ATCTTTATTG
901562 AATAAAAATATT-TTTTT
1 AATAAAAATATTATTTTT
*
901579 AATAAATATATTATTTT
1 AATAAAAATATTATTTT
901596 GAGTTGGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAAAAATATTATTTTT
Found at i:910590 original size:24 final size:24
Alignment explanation
Indices: 910562--910640 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
910552 CGTTAATGTT
910562 TGTTCATTTATATCAGTTTGTTTA
1 TGTTCATTTATATCAGTTTGTTTA
* * *
910586 TGTTC-GTTATGTCTGTTTGTTTA
1 TGTTCATTTATATCAGTTTGTTTA
* * *
910609 TGTTAATTTACTTTCA-TTCGTTTA
1 TGTTCATTTA-TATCAGTTTGTTTA
910633 TGTTCATT
1 TGTTCATT
910641 CATTTCTGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 19 0.43
24 22 0.50
25 3 0.07
ACGTcount: A:0.16, C:0.10, G:0.14, T:0.59
Consensus pattern (24 bp):
TGTTCATTTATATCAGTTTGTTTA
Found at i:910705 original size:23 final size:23
Alignment explanation
Indices: 910678--910725 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
910668 ACTCATTTAA
*
910678 AATATTAATGCCCAATAA-ATTTT
1 AATA-TAATACCCAATAATATTTT
*
910701 AATATAATACCCATTAATATTTT
1 AATATAATACCCAATAATATTTT
910724 AA
1 AA
910726 AATTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATAATACCCAATAATATTTT
Found at i:910713 original size:22 final size:24
Alignment explanation
Indices: 910678--910734 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
910668 ACTCATTTAA
*
910678 AATATTAATGCCCAATAA-ATTTT
1 AATATTAATACCCAATAATATTTT
*
910701 AATA-TAATACCCATTAATATTTT
1 AATATTAATACCCAATAATATTTT
*
910724 AAAATTCAATA
1 AATATT-AATA
910735 AATTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 11 0.39
23 12 0.43
24 1 0.04
25 4 0.14
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATTAATACCCAATAATATTTT
Found at i:910734 original size:25 final size:23
Alignment explanation
Indices: 910672--910734 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
910662 CTCTAGACTC
* *
910672 ATTTAAAATATTAATGCCCAATAA
1 ATTTTAAA-ATTAATACCCAATAA
* *
910696 ATTTTAATA-TAATACCCATTAA
1 ATTTTAAAATTAATACCCAATAA
910718 TATTTTAAAATTCAATA
1 -ATTTTAAAATT-AATA
910735 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 11 0.35
23 9 0.29
24 7 0.23
25 4 0.13
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTTAAAATTAATACCCAATAA
Found at i:911023 original size:20 final size:21
Alignment explanation
Indices: 910998--911050 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 21
910988 GTTTGTTTTG
910998 TTCATTTAT-GTTCGTTTACA
1 TTCATTTATAGTTCGTTTACA
911018 TTCATTTATGTACGTTCGTTTACA
1 TTCATTTA--TA-GTTCGTTTACA
911042 TTCATTTAT
1 TTCATTTAT
911051 TGTGTTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.28
22 2 0.07
24 19 0.66
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (21 bp):
TTCATTTATAGTTCGTTTACA
Found at i:914569 original size:29 final size:29
Alignment explanation
Indices: 914536--914603 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
914526 TTTTAAAAAT
*
914536 TTACATTTTAGTCTCTGAAC-TTCTACAAC
1 TTACATTTTAGTCTCTAAACTTTC-ACAAC
* * * *
914565 TTACACTTTGGTCTCTAAACTTTCATAAT
1 TTACATTTTAGTCTCTAAACTTTCACAAC
914594 TTACATTTTA
1 TTACATTTTA
914604 ATCATTTGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.46
Consensus pattern (29 bp):
TTACATTTTAGTCTCTAAACTTTCACAAC
Found at i:915834 original size:31 final size:31
Alignment explanation
Indices: 915799--915877 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
915789 AGTTTTAAAA
* *
915799 GTAACAAATTGGTCACTAACGTTATTGATTT
1 GTAACAAAATGGTCACTAACGTTATCGATTT
*
915830 GTAACAAAATGGTCACTAATGTTATCGATTT
1 GTAACAAAATGGTCACTAACGTTATCGATTT
*
915861 GTAACAAAATGATCACT
1 GTAACAAAATGGTCACT
915878 CCACCTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (31 bp):
GTAACAAAATGGTCACTAACGTTATCGATTT
Found at i:918404 original size:21 final size:21
Alignment explanation
Indices: 918357--918406 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
918347 ATTACTACTG
* *
918357 AAAAATAAAAAATGTTGGATG
1 AAAAATAAAAAATATTGGATA
*
918378 ATAAATAAAAAATATT-GAGTA
1 AAAAATAAAAAATATTGGA-TA
918399 AAAAATAA
1 AAAAATAA
918407 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (21 bp):
AAAAATAAAAAATATTGGATA
Found at i:919888 original size:9 final size:10
Alignment explanation
Indices: 919860--919889 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
919850 AGCCTACTAT
919860 CTTACCTCCCC
1 CTTACC-CCCC
919871 CTTACCCCCC
1 CTTACCCCCC
919881 CTTACCCCC
1 CTTACCCCC
919890 ATCACATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.10, C:0.67, G:0.00, T:0.23
Consensus pattern (10 bp):
CTTACCCCCC
Found at i:920580 original size:29 final size:30
Alignment explanation
Indices: 920522--920586 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
920512 GGTACAGTTG
* *
920522 TATAATTGAAAGGAAAATCAAAATTTAGTAC
1 TATAATTGAAA-GAAAATCAAAATTCAGTAA
920553 TATAATTGAAA-AAAAT-AAAAGTTCAGTAA
1 TATAATTGAAAGAAAATCAAAA-TTCAGTAA
920582 TATAA
1 TATAA
920587 ATGATACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.13
29 16 0.52
31 11 0.35
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (30 bp):
TATAATTGAAAGAAAATCAAAATTCAGTAA
Found at i:946903 original size:21 final size:21
Alignment explanation
Indices: 946877--946921 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
946867 GATTTCTGGG
* *
946877 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
946898 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
946919 CAA
1 CAA
946922 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:947525 original size:18 final size:18
Alignment explanation
Indices: 947502--947536 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
947492 CTAGGAGATT
947502 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
947520 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
947537 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:947622 original size:21 final size:22
Alignment explanation
Indices: 947593--947636 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
947583 GTTGTATGAT
947593 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
947614 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
947636 A
1 A
947637 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:948592 original size:149 final size:149
Alignment explanation
Indices: 948411--948714 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
948401 GAGTCGAGGG
948411 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
948476 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
948541 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
948560 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
948625 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
948690 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
948709 TCTACG
1 TCTACG
948715 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:948737 original size:23 final size:23
Alignment explanation
Indices: 948693--948737 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
948683 ATCATTATAT
*
948693 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
948716 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
948738 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:952001 original size:21 final size:21
Alignment explanation
Indices: 951975--952019 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
951965 GATTTCTGGG
* *
951975 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
951996 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
952017 CAA
1 CAA
952020 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:952623 original size:18 final size:18
Alignment explanation
Indices: 952600--952634 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
952590 CTAGGAGATT
952600 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
952618 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
952635 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:952715 original size:21 final size:22
Alignment explanation
Indices: 952691--952734 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
952681 GTTTTATGAT
952691 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
952712 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
952734 A
1 A
952735 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:953696 original size:149 final size:148
Alignment explanation
Indices: 953516--953818 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 148
953506 GAGTCGAGGG
953516 TCTACGCGGTTCTTCGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
1 TCTACGCGGTTCTTCGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
*
953581 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTAT
953646 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
*
953664 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGATACAT
1 TCTACGCGGTTCTTC-GGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
953729 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
953794 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
953813 TCTACG
1 TCTACG
953819 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
148 15 0.10
149 137 0.90
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTTCTTCGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:953841 original size:23 final size:23
Alignment explanation
Indices: 953797--953841 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
953787 ATCATTATAT
*
953797 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
953820 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
953842 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:958231 original size:11 final size:11
Alignment explanation
Indices: 958211--958242 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
958201 CCTCCAAATG
958211 AATT-TACATT
1 AATTATACATT
958221 AATTATACATT
1 AATTATACATT
958232 AATTATACATT
1 AATTATACATT
958243 TATACTGCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTATACATT
Found at i:963571 original size:26 final size:23
Alignment explanation
Indices: 963517--963572 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
963507 AGTATTATTT
963517 TTTAAAAAAAATAAAAATTCAAA
1 TTTAAAAAAAATAAAAATTCAAA
*
963540 TATTAAAAAATATATAAAAATTGATAA
1 T-TTAAAAAA-A-ATAAAAATTCA-AA
963567 TTTAAA
1 TTTAAA
963573 TATTTAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 8 0.29
25 1 0.04
26 15 0.54
27 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TTTAAAAAAAATAAAAATTCAAA
Found at i:964635 original size:6 final size:6
Alignment explanation
Indices: 964624--964690 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
964614 AGACACGTAT
964624 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
964672 GACCAC GACCAC GACCAC G
1 GACCAC GACCAC GACCAC G
964691 GACGGCGGCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.33, C:0.49, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:965338 original size:20 final size:20
Alignment explanation
Indices: 965315--965400 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
965305 GAAAGACACT
*
965315 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
965335 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
965355 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
965376 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
965396 ATCGC
1 ATCGC
965401 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:965387 original size:41 final size:41
Alignment explanation
Indices: 965335--965425 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
965325 GAAATGGAAA
965335 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
***
965376 ATCGCAACGCGAAATGAAAAATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
965417 ATCGCAACG
1 ATCGCAACG
965426 ACAACTGTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
Found at i:966790 original size:27 final size:27
Alignment explanation
Indices: 966760--966825 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
966750 TTTTTTTTAA
*
966760 AAAAAAATTACGTAAAATATTTTATCT
1 AAAAAAATTACATAAAATATTTTATCT
* * *
966787 AAAAAAATATATATAAATTATTTTATGT
1 AAAAAAAT-TACATAAAATATTTTATCT
966815 AAAATAAATTA
1 AAAA-AAATTA
966826 TATTTTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 8 0.24
28 21 0.64
29 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
AAAAAAATTACATAAAATATTTTATCT
Found at i:966828 original size:28 final size:28
Alignment explanation
Indices: 966772--966828 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
966762 AAAAATTACG
966772 TAAAATATTTTATCTAAAAAAATATATA
1 TAAAATATTTTATCTAAAAAAATATATA
* *
966800 TAAATTATTTTATGTAAAATAAAT-TATA
1 TAAAATATTTTATCTAAAA-AAATATATA
966828 T
1 T
966829 TTTCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAAATATTTTATCTAAAAAAATATATA
Found at i:966836 original size:19 final size:19
Alignment explanation
Indices: 966799--966837 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
966789 AAAAATATAT
*
966799 ATAAATTATTTTATGTAAA
1 ATAAATTATTTTATCTAAA
966818 ATAAATTATATTT-TCTAAA
1 ATAAATTAT-TTTATCTAAA
966837 A
1 A
966838 AATAGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
ATAAATTATTTTATCTAAA
Found at i:967122 original size:14 final size:14
Alignment explanation
Indices: 967103--967129 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
967093 AGGAAAATGA
967103 GAAAAATATTTTTT
1 GAAAAATATTTTTT
967117 GAAAAATATTTTT
1 GAAAAATATTTTT
967130 CGGCTGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
GAAAAATATTTTTT
Found at i:984140 original size:2 final size:2
Alignment explanation
Indices: 984133--984162 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
984123 CATGTGAGTG
984133 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
984163 AAATTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:988713 original size:12 final size:12
Alignment explanation
Indices: 988696--988720 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
988686 TCCATGCTTC
988696 TTGTGGAGACAT
1 TTGTGGAGACAT
988708 TTGTGGAGACAT
1 TTGTGGAGACAT
988720 T
1 T
988721 CAGTGATGTA
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:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TTGTGGAGACAT
Found at i:991647 original size:18 final size:19
Alignment explanation
Indices: 991624--991659 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
991614 GCAAATAGAC
991624 TAAATAAAT-AAATAATAG
1 TAAATAAATAAAATAATAG
*
991642 TAAATATATAAAATAATA
1 TAAATAAATAAAATAATA
991660 TTAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAATAAATAAAATAATAG
Found at i:992111 original size:16 final size:16
Alignment explanation
Indices: 992087--992150 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
992077 ATCTATTTTA
*
992087 ATTACTATATTTATAT
1 ATTATTATATTTATAT
992103 ATTATTATATTTA-AT
1 ATTATTATATTTATAT
* *
992118 AATTAATATTATTAATAT
1 -ATTATTA-TATTTATAT
992136 ATTTATT-TA-TTATAT
1 A-TTATTATATTTATAT
992151 TCATTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.18
16 20 0.51
17 6 0.15
18 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:995068 original size:20 final size:20
Alignment explanation
Indices: 995045--995088 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
995035 ATCATTATTA
*
995045 ACCTTTTGGTATCGATACCC
1 ACCTGTTGGTATCGATACCC
995065 ACCTGTTGGTATCGATACCC
1 ACCTGTTGGTATCGATACCC
995085 -CCTG
1 ACCTG
995089 ACTAATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (20 bp):
ACCTGTTGGTATCGATACCC
Found at i:996043 original size:2 final size:2
Alignment explanation
Indices: 996036--996071 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
996026 AATATGTGTT
996036 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
996072 ATTTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:997130 original size:16 final size:18
Alignment explanation
Indices: 997109--997153 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
997099 AATATTCTCA
997109 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
997125 GTAATCTTGCATTCCCACTG
1 GTAATCTT--ATTCCCACTG
997145 GTAATCTTA
1 GTAATCTTA
997154 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:997147 original size:20 final size:20
Alignment explanation
Indices: 997122--997159 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
997112 ATCTTATTCC
*
997122 CTGGTAATCTTGCATTCCCA
1 CTGGTAATCTTACATTCCCA
997142 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
997160 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1001254 original size:19 final size:18
Alignment explanation
Indices: 1001230--1001297 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
1001220 ATTGACTAAT
1001230 TATATAATTAACAAATATA
1 TATATAATTAACAAAT-TA
1001249 TATATAATTAA-AAATTA
1 TATATAATTAACAAATTA
* * *
1001266 TA-AAAGATAAACCAATTA
1 TATATA-ATTAACAAATTA
1001284 TTATATAATTAACA
1 -TATATAATTAACA
1001298 CTGAAATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 9 0.23
19 18 0.46
20 2 0.05
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (18 bp):
TATATAATTAACAAATTA
Found at i:1001832 original size:18 final size:18
Alignment explanation
Indices: 1001811--1001846 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1001801 CGAGGGTACT
1001811 AAAATGAAAAAAAATTAA
1 AAAATGAAAAAAAATTAA
*
1001829 AAAATTAAAAAAAATTAA
1 AAAATGAAAAAAAATTAA
1001847 CGGTAGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAATGAAAAAAAATTAA
Found at i:1017153 original size:3 final size:3
Alignment explanation
Indices: 1017145--1017170 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1017135 CGGAAACCTC
1017145 GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GG
1017171 CGCCGCCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:1017472 original size:2 final size:2
Alignment explanation
Indices: 1017465--1017495 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1017455 GAGATTCGGA
1017465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1017496 AATATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1018443 original size:25 final size:26
Alignment explanation
Indices: 1018400--1018463 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
1018390 TATTAAATGA
1018400 AAATAT-TTTTA-TATCAACTT-TTT
1 AAATATATTTTATTATCAACTTATTT
*
1018423 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATTATCAACTT-ATTT
* *
1018450 AAAAACATTTTATT
1 AAATATATTTTATT
1018464 TTTATTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 8 0.24
27 15 0.44
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATATATTTTATTATCAACTTATTT
Found at i:1019843 original size:18 final size:17
Alignment explanation
Indices: 1019822--1019859 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1019812 TTATACATTA
*
1019822 TATTATAAATATAATATT
1 TATTATAAAGATAAT-TT
1019840 TATTATAAAGATAATTT
1 TATTATAAAGATAATTT
1019857 TAT
1 TAT
1019860 CTAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTATAAAGATAATTT
Found at i:1020420 original size:13 final size:13
Alignment explanation
Indices: 1020394--1020435 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
1020384 TTGTTAAAAC
1020394 TTTAATTT-TTAT
1 TTTAATTTATTAT
1020406 TTTAATTTATTAT
1 TTTAATTTATTAT
*
1020419 TTTTATTTA-TAT
1 TTTAATTTATTAT
1020431 TTTAA
1 TTTAA
1020436 CGTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTAATTTATTAT
Found at i:1021857 original size:13 final size:12
Alignment explanation
Indices: 1021815--1021857 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
1021805 TTTAATAGTT
1021815 TATTATTTTATTA
1 TATTATTTT-TTA
*
1021828 TACTATTTTTT-
1 TATTATTTTTTA
1021839 TATTATTTTTTA
1 TATTATTTTTTA
1021851 TAGTTAT
1 TA-TTAT
1021858 AAAATGAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 10 0.38
12 4 0.15
13 12 0.46
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:1024570 original size:23 final size:23
Alignment explanation
Indices: 1024508--1024585 Score: 63
Period size: 27 Copynumber: 3.3 Consensus size: 23
1024498 CACAACCATA
*
1024508 AAAAATAATATAAAATAATT-AGT
1 AAAAA-AATATAAAATAATTAAAT
1024531 ACAATAAAATTTGATAAAATAATTAAAT
1 A-AA-AAAA--T-ATAAAATAATTAAAT
*
1024559 AAAAAAATATAATATAA-TAAA-
1 AAAAAAATATAAAATAATTAAAT
1024580 AAAAAA
1 AAAAAA
1024586 TTATCTTCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
21 6 0.13
22 4 0.09
23 9 0.19
24 5 0.11
25 2 0.04
26 5 0.11
27 13 0.28
28 3 0.06
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (23 bp):
AAAAAAATATAAAATAATTAAAT
Found at i:1026139 original size:21 final size:21
Alignment explanation
Indices: 1026113--1026165 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1026103 GTTTCCAGAT
1026113 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1026134 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1026155 TCGCAATGCGA
1 TCGCAACGCGA
1026166 TTTATTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1026185 original size:21 final size:21
Alignment explanation
Indices: 1026161--1026229 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
1026151 ACTATCGCAA
1026161 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
* * *
1026182 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
1026203 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
1026224 TGCGAT
1 TGCGAT
1026230 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.21
21 22 0.58
23 8 0.21
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
TGCGATTTATTCCAAATTCGT
Found at i:1026237 original size:19 final size:19
Alignment explanation
Indices: 1026171--1026237 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1026161 TGCGATTTAT
1026171 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
1026190 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
1026213 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
1026232 TCCAAA
1 TCCAAA
1026238 ATCGCAACGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 14 0.37
21 16 0.42
23 8 0.21
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:1026835 original size:6 final size:6
Alignment explanation
Indices: 1026824--1026850 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1026814 TCTCGTCTCG
1026824 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1026851 AATACATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1027079 original size:42 final size:42
Alignment explanation
Indices: 1027010--1027238 Score: 336
Period size: 42 Copynumber: 5.4 Consensus size: 42
1027000 CTTGGAATAA
1027010 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* *
1027054 ATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1027096 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1027138 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
1027180 ATCGCAACGAATTTGG-A-AAATCGCAATGCGAACTTCGGCT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1027220 ATCGTAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1027239 CTATCGTAAT
Statistics
Matches: 171, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
40 26 0.15
41 1 0.01
42 138 0.81
44 6 0.04
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1027129 original size:107 final size:107
Alignment explanation
Indices: 1026943--1027135 Score: 359
Period size: 107 Copynumber: 1.8 Consensus size: 107
1026933 TGCGATTTTG
* * *
1026943 GACTATCGCAAGGAATTTGGAATAAATCTCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1027008 AAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
66 AAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
1027050 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1027115 AAATCGCAACGCGAACTTGGA
66 AAATCGCAACGCGAACTTGGA
1027136 CTATCGCAAC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 83 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (107 bp):
GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
AAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1027177 original size:107 final size:106
Alignment explanation
Indices: 1026946--1027177 Score: 337
Period size: 107 Copynumber: 2.2 Consensus size: 106
1026936 GATTTTGGAC
*
1026946 TATCGCAAG-GAATTTGGAATAAATCTCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 TATCGCAAGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
*
1027010 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGAC
66 ATCGCAACGCGAACTTGGAAT-AATCGCAAC-CGAACTTCGAA
*
1027053 TATCACAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 TATCGCAAGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* *
1027117 ATCGCAACGCGAACTTGGACT-ATCGCAA-CGAACTTGGAA
66 ATCGCAACGCGAACTTGGAATAATCGCAACCGAACTTCGAA
*
1027156 TAAATCGCAACGCGAACTTGGA
1 T--ATCGCAA-GCGAATTTGGA
1027178 CTATCGCAAC
Statistics
Matches: 113, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
103 10 0.09
105 13 0.12
107 90 0.80
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (106 bp):
TATCGCAAGCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
ATCGCAACGCGAACTTGGAATAATCGCAACCGAACTTCGAA
Found at i:1027223 original size:21 final size:21
Alignment explanation
Indices: 1026940--1027253 Score: 240
Period size: 21 Copynumber: 15.0 Consensus size: 21
1026930 CGTTGCGATT
*
1026940 TTGGACTATCGCAA-G-GAAT
1 TTGGACTATCGCAACGCGAAC
* *
1026959 TTGGAATAAATCTCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1026982 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1027001 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1027024 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
1027047 TTCGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1027066 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1027089 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1027108 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
1027131 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1027150 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1027173 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
** *
1027192 TTGGAAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1027213 TTCGG-CTATCGTAACGCGAAC
1 TT-GGACTATCGCAACGCGAAC
* *
1027234 TTGGACTATCGTAATGCGAA
1 TTGGACTATCGCAACGCGAA
1027254 TATGTAAATC
Statistics
Matches: 239, Mismatches: 32, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
19 62 0.26
20 2 0.01
21 100 0.42
22 3 0.01
23 72 0.30
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1036628 original size:11 final size:11
Alignment explanation
Indices: 1036612--1036636 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1036602 ATTTGATGAG
1036612 GTTTTATAATA
1 GTTTTATAATA
1036623 GTTTTATAATA
1 GTTTTATAATA
1036634 GTT
1 GTT
1036637 GTTACGATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
GTTTTATAATA
Found at i:1039665 original size:12 final size:12
Alignment explanation
Indices: 1039648--1039673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1039638 TTATGCACAC
1039648 ACAAAAAAAAAA
1 ACAAAAAAAAAA
1039660 ACAAAAAAAAAA
1 ACAAAAAAAAAA
1039672 AC
1 AC
1039674 GCCGGTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAAAAAAAAAA
Found at i:1050333 original size:34 final size:34
Alignment explanation
Indices: 1050295--1050370 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
1050285 CCAAATAATC
1050295 ATAAGAACACAATAAATTATAAAAAATGAAAAGG
1 ATAAGAACACAATAAATTATAAAAAATGAAAAGG
1050329 ATAAGAACACAATAAATTATAAAAAATGAAAAGG
1 ATAAGAACACAATAAATTATAAAAAATGAAAAGG
*
1050363 ATTAGAAC
1 ATAAGAAC
1050371 TATCAGAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.18
Consensus pattern (34 bp):
ATAAGAACACAATAAATTATAAAAAATGAAAAGG
Found at i:1051341 original size:57 final size:57
Alignment explanation
Indices: 1051253--1051372 Score: 231
Period size: 57 Copynumber: 2.1 Consensus size: 57
1051243 CAACATAAAA
1051253 TACTTTAACAAGATCAAAACATGGCGAAGTACACGAATACTACACAGATACATGAAT
1 TACTTTAACAAGATCAAAACATGGCGAAGTACACGAATACTACACAGATACATGAAT
*
1051310 TACTTTAACAAGATCACAACATGGCGAAGTACACGAATACTACACAGATACATGAAT
1 TACTTTAACAAGATCAAAACATGGCGAAGTACACGAATACTACACAGATACATGAAT
1051367 TACTTT
1 TACTTT
1051373 TATGTCATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (57 bp):
TACTTTAACAAGATCAAAACATGGCGAAGTACACGAATACTACACAGATACATGAAT
Found at i:1052736 original size:21 final size:22
Alignment explanation
Indices: 1052710--1052752 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1052700 AAATAATAAT
*
1052710 AAAATATT-ATTTTATTCAATA
1 AAAATATTGATTTAATTCAATA
*
1052731 AAAATATTGATTTAATTGAATA
1 AAAATATTGATTTAATTCAATA
1052753 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
AAAATATTGATTTAATTCAATA
Found at i:1052757 original size:2 final size:2
Alignment explanation
Indices: 1052750--1052792 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1052740 ATTTAATTGA
1052750 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
1052792 A
1 A
1052793 ATAGTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1057673 original size:22 final size:22
Alignment explanation
Indices: 1057646--1057692 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1057636 TACAAGGGAA
*
1057646 AAATAAAATAA-ATAAAATAAGT
1 AAATAAAATAAGAAAAAAT-AGT
*
1057668 AAATAAGATAAGAAAAAATAGT
1 AAATAAAATAAGAAAAAATAGT
1057690 AAA
1 AAA
1057693 GTAATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (22 bp):
AAATAAAATAAGAAAAAATAGT
Found at i:1057735 original size:2 final size:2
Alignment explanation
Indices: 1057730--1057831 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
1057720 AAAAAGGAAA
1057730 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
1057772 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
1057814 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1057832 CAAAGTATTA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1058273 original size:28 final size:28
Alignment explanation
Indices: 1058261--1058391 Score: 78
Period size: 28 Copynumber: 4.6 Consensus size: 28
1058251 AATATTAAAG
1058261 AAATATATATATAATAATAATAATAATA
1 AAATATATATATAATAATAATAATAATA
*
1058289 AAATATAGTA-AAAATCAAATGAA-AATAATTTA
1 AAATATA-TATATAAT--AAT-AATAATAA--TA
*
1058321 ATATATATATATACAT-ATAATAATAATA
1 AAATATATATATA-ATAATAATAATAATA
* *
1058349 ACATGA-ATA-ATAAAAAT-A-AATGAATA
1 AAAT-ATATATATAATAATAATAAT-AATA
**
1058375 AAATATCCATATAATAA
1 AAATATATATATAATAA
1058392 ATAAAGGGAC
Statistics
Matches: 80, Mismatches: 9, Indels: 29
0.68 0.08 0.25
Matches are distributed among these distances:
25 4 0.05
26 10 0.12
27 11 0.14
28 19 0.24
29 5 0.06
30 15 0.19
31 4 0.05
32 10 0.12
33 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATATATATATAATAATAATAATAATA
Found at i:1058360 original size:18 final size:17
Alignment explanation
Indices: 1058337--1058379 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1058327 ATATATACAT
1058337 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1058355 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1058372 ATAA-AATA
1 ATAATAATA
1058380 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1063863 original size:24 final size:22
Alignment explanation
Indices: 1063830--1063901 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
1063820 CTCCTCTAAA
1063830 TCCT-AAAAATCCTAAAAGATAAT
1 TCCTAAAAAAT-C-AAAAGATAAT
* * *
1063853 TCCTGATAAATGAAAAGATAAT
1 TCCTAAAAAATCAAAAGATAAT
*
1063875 TGCCTAAAAAATACAATAGATAAT
1 T-CCTAAAAAAT-CAAAAGATAAT
1063899 TCC
1 TCC
1063902 CTTAATTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
22 11 0.28
23 14 0.35
24 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.26
Consensus pattern (22 bp):
TCCTAAAAAATCAAAAGATAAT
Found at i:1063868 original size:22 final size:21
Alignment explanation
Indices: 1063842--1063901 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1063832 CTAAAAATCC
* *
1063842 TAAAAGATAATTCCTGATAAA
1 TAAAAGATAATTCCTAAAAAA
1063863 TGAAAAGATAATTGCCTAAAAAA
1 T-AAAAGATAATT-CCTAAAAAA
1063886 TACAATAGATAATTCC
1 TA-AA-AGATAATTCC
1063902 CTTAATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 12 0.36
23 12 0.36
24 8 0.24
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (21 bp):
TAAAAGATAATTCCTAAAAAA
Found at i:1064568 original size:2 final size:2
Alignment explanation
Indices: 1064561--1064623 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1064551 AGTTGACCAC
1064561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1064603 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1064624 CATAAGTACT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1065766 original size:18 final size:19
Alignment explanation
Indices: 1065731--1065766 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1065721 AGCCCAAACC
1065731 ATTTAAAACCCAAATAATA
1 ATTTAAAACCCAAATAATA
*
1065750 ATTTAAAATCC-AATAAT
1 ATTTAAAACCCAAATAAT
1065767 TTTTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTAAAACCCAAATAATA
Found at i:1067871 original size:3 final size:3
Alignment explanation
Indices: 1067865--1067890 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1067855 TTATTATTGT
1067865 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1067891 TTTTTGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1074514 original size:2 final size:2
Alignment explanation
Indices: 1074507--1074565 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1074497 ATACATGCAA
1074507 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
1074549 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1074566 AACCTTTTGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1074926 original size:6 final size:6
Alignment explanation
Indices: 1074915--1074940 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1074905 AGAATTTTTC
1074915 TAGATA TAGATA TAGATA TAGATA TA
1 TAGATA TAGATA TAGATA TAGATA TA
1074941 TTAATCTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
TAGATA
Found at i:1077928 original size:3 final size:3
Alignment explanation
Indices: 1077920--1077957 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1077910 ATGTATCCTG
1077920 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1077958 TGCTTCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1082493 original size:2 final size:2
Alignment explanation
Indices: 1082486--1082525 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1082476 CGGCGACGAC
1082486 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
1082526 GTTCTAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1083632 original size:23 final size:23
Alignment explanation
Indices: 1083562--1083619 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1083552 ATGACATAAC
1083562 GACAAAGATAAACGTGTCACAAA
1 GACAAAGATAAACGTGTCACAAA
1083585 GACAAAGATAAACGTGTCACAAA
1 GACAAAGATAAACGTGTCACAAA
*
1083608 GACATAGATAAA
1 GACAAAGATAAA
1083620 TGTTTCATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.17, T:0.14
Consensus pattern (23 bp):
GACAAAGATAAACGTGTCACAAA
Found at i:1084716 original size:31 final size:31
Alignment explanation
Indices: 1084636--1084716 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
1084626 CTTTTTTATT
*
1084636 TAAGTACTCAAAGTA-T-TTTTTGATCAAAA
1 TAAGTACTTAAAGTATTCTTTTTGATCAAAA
* * *
1084665 TAAATACCTAAAGT-TATCTTTTTGGTCAAAA
1 TAAGTACTTAAAGTAT-TCTTTTTGATCAAAA
1084696 TAAGTACTTAAAGTATTCTTT
1 TAAGTACTTAAAGTATTCTTT
1084717 CATTAATGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 11 0.26
30 1 0.02
31 29 0.69
32 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (31 bp):
TAAGTACTTAAAGTATTCTTTTTGATCAAAA
Found at i:1085706 original size:21 final size:21
Alignment explanation
Indices: 1085680--1085719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1085670 ATAATTTTAA
1085680 AAAATTAAAAGTTTAAATATT
1 AAAATTAAAAGTTTAAATATT
* *
1085701 AAAATTGATAGTTTAAATA
1 AAAATTAAAAGTTTAAATA
1085720 CTAACTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAATATT
Found at i:1088669 original size:2 final size:2
Alignment explanation
Indices: 1088662--1088689 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1088652 AAATAACTTA
1088662 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
1088690 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1088842 original size:51 final size:51
Alignment explanation
Indices: 1088782--1089028 Score: 309
Period size: 51 Copynumber: 4.8 Consensus size: 51
1088772 CAGATGTACA
* *
1088782 TACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTGTT
1 TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATT
* * *
1088833 TACTTACATCGTTGTAAGTATGTGTCAAGTGCTACATTTATTTTATTTTATT
1 TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTT-TTTTATTTTATT
* * * * *
1088885 CACTTACATTGGTGT-AGTATGTGTCAAGTGTTACACTTTTTTGTTTTATT
1 TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATT
* * * *
1088935 CACTTACATTGGTGTAAGTATGTGTTAAGTGCTACACTTATTT-TTTTCTT
1 TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATT
* * *
1088985 TCACTTACACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTT
1 T-ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
1089029 GTAATATGAA
Statistics
Matches: 172, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 32 0.19
51 117 0.68
52 23 0.13
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (51 bp):
TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATT
Found at i:1089027 original size:102 final size:103
Alignment explanation
Indices: 1088783--1089030 Score: 349
Period size: 102 Copynumber: 2.4 Consensus size: 103
1088773 AGATGTACAT
* * * *
1088783 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTGTTTACTTACATCGTTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTCACTTACATCGGTGT
*
1088848 AAGTATGTGTCAAGTGCTACATTTATTTTATTTTATTC
66 AAGTATGTGTCAAGTGCTACACTTATTTTATTTTATTC
* * *
1088886 ACTTACATTGGTGT-AGTATGTGTCAAGTGTTACACTTTTTTGTTTTATTCACTTACATTGGTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTCACTTACATCGGTGT
*
1088950 AAGTATGTGTTAAGTGCTACACTTATTTT-TTTCT-TTC
66 AAGTATGTGTCAAGTGCTACACTTATTTTATTT-TATTC
* * * *
1088987 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTGT
1089031 AATATGAATT
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
101 18 0.14
102 97 0.76
103 13 0.10
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (103 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTCACTTACATCGGTGT
AAGTATGTGTCAAGTGCTACACTTATTTTATTTTATTC
Found at i:1100577 original size:7 final size:7
Alignment explanation
Indices: 1100565--1100610 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
1100555 GTCTTTGTAA
1100565 TAAACCC
1 TAAACCC
1100572 TAAACCC
1 TAAACCC
**
1100579 TAAACTA
1 TAAACCC
*
1100586 TAAACAC
1 TAAACCC
1100593 TAAACCC
1 TAAACCC
*
1100600 TAAAACC
1 TAAACCC
1100607 TAAA
1 TAAA
1100611 TATGATTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:1100610 original size:21 final size:21
Alignment explanation
Indices: 1100564--1100603 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1100554 TGTCTTTGTA
*
1100564 ATAAACCCTAAACCCTAAACT
1 ATAAACACTAAACCCTAAACT
1100585 ATAAACACTAAACCCTAAA
1 ATAAACACTAAACCCTAAA
1100604 ACCTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAAACACTAAACCCTAAACT
Found at i:1109620 original size:20 final size:20
Alignment explanation
Indices: 1109595--1109642 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1109585 TGTCTTGTTG
*
1109595 AATATTTATACATTTTTTGT
1 AATATTTATACATTTTTTAT
*
1109615 AATATTTATATATTTTTTAT
1 AATATTTATACATTTTTTAT
1109635 AATATTTA
1 AATATTTA
1109643 ATATTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
AATATTTATACATTTTTTAT
Found at i:1110993 original size:3 final size:3
Alignment explanation
Indices: 1110985--1111046 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
1110975 AACAAAACCC
1110985 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
*
1111033 CAT CAT CAC CAT CA
1 CAT CAT CAT CAT CA
1111047 CCACCACCAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:1114811 original size:21 final size:21
Alignment explanation
Indices: 1114787--1114862 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
1114777 GCGAATAAGT
*
1114787 AAATCGCAACGTGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1114808 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
1114828 AAATCGCAACGCGAATTGGAA
1 AAATCGCAACGCGAATTGGGA
*
1114849 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1114863 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1114819 original size:41 final size:41
Alignment explanation
Indices: 1114774--1114862 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
1114764 CCCAATTCGT
* *
1114774 AATGCGAATAAGTAAATCGCAACGTGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAATCGC
1114815 AATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAATCGC
1114856 AATGCGA
1 AATGCGA
1114863 TACTGACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (41 bp):
AATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAATCGC
Found at i:1114833 original size:20 final size:20
Alignment explanation
Indices: 1114774--1114862 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
1114764 CCCAATTCGT
*
1114774 AATGCGAATAAGTAAATCGC
1 AATGCGAATAAGAAAATCGC
* * **
1114794 AACGTGAATTGGGAAAATCGC
1 AATGCGAA-TAAGAAAATCGC
*
1114815 AATGCGAATAAGTAAATCGC
1 AATGCGAATAAGAAAATCGC
* **
1114835 AACGCGAATTGGAAAAATCGC
1 AATGCGAATAAG-AAAATCGC
1114856 AATGCGA
1 AATGCGA
1114863 TACTGACTAT
Statistics
Matches: 52, Mismatches: 15, Indels: 3
0.74 0.21 0.04
Matches are distributed among these distances:
20 24 0.46
21 28 0.54
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
AATGCGAATAAGAAAATCGC
Found at i:1114875 original size:41 final size:41
Alignment explanation
Indices: 1114789--1114923 Score: 116
Period size: 41 Copynumber: 3.3 Consensus size: 41
1114779 GAATAAGTAA
* * * *
1114789 ATCGCAACGTGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCG-ATACTG-ACT
1114830 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
* * * * *
1114871 ATCGCAATGCGATAAT--ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGA-AAAATCGCAATGCGATACTGACT
*
1114912 TTCGCAACGCGA
1 ATCGCAACGCGA
1114924 TACTGACTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 5 0.06
41 72 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
Found at i:1114876 original size:20 final size:20
Alignment explanation
Indices: 1114851--1114965 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
1114841 AATTGGAAAA
*
1114851 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1114871 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1114892 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1114912 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1114932 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1114952 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1114966 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1114924 original size:41 final size:41
Alignment explanation
Indices: 1114848--1114985 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
1114838 GCGAATTGGA
* * *
1114848 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
1114889 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
1114931 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1114970 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1114986 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1115181 original size:22 final size:22
Alignment explanation
Indices: 1115153--1115196 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1115143 CACTCTCTCA
1115153 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1115175 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1115197 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1115485 original size:20 final size:20
Alignment explanation
Indices: 1115460--1115497 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1115450 CGATTATCTC
1115460 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1115480 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1115498 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1116813 original size:18 final size:18
Alignment explanation
Indices: 1116792--1116836 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1116782 TCCACTTCGG
*
1116792 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1116810 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1116828 GAGCCATCA
1 GAGCCATCA
1116837 TCTGATCGAC
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:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1117366 original size:19 final size:20
Alignment explanation
Indices: 1117312--1117367 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1117302 TAGTTTGCTT
* *
1117312 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1117332 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1117352 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1117368 AAACCGCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1117375 original size:19 final size:19
Alignment explanation
Indices: 1117351--1117432 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
1117341 GGAAATGGCT
1117351 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1117370 ACCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1117384 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1117402 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1117421 ATCGCAATGCGA
1 ATCGCAATGCGA
1117433 TTTGTGTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.35
19 19 0.37
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1117463 original size:14 final size:14
Alignment explanation
Indices: 1117444--1117501 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1117434 TTGTGTTTCG
1117444 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1117458 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1117474 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1117490 CGTTGCGATTTT
1 CGTTGCGATTTT
1117502 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1117478 original size:32 final size:33
Alignment explanation
Indices: 1117439--1117517 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1117429 GCGATTTGTG
1117439 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1117471 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1117504 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1117518 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1117516 original size:19 final size:19
Alignment explanation
Indices: 1117458--1117575 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1117448 GCGATTTTGT
1117458 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1117476 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1117490 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1117509 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1117529 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1117548 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1117568 TGTTGCGA
1 CGTTGCGA
1117576 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1120167 original size:24 final size:24
Alignment explanation
Indices: 1120116--1120169 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1120106 GTATTCAAAA
* * *
1120116 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
1120140 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
1120164 TTTGAT
1 TTTGAT
1120170 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:1120361 original size:12 final size:12
Alignment explanation
Indices: 1120344--1120368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1120334 AAATAATCCT
1120344 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1120356 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1120368 G
1 G
1120369 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1122682 original size:19 final size:19
Alignment explanation
Indices: 1122660--1122776 Score: 92
Period size: 19 Copynumber: 6.7 Consensus size: 19
1122650 GGAAATTACT
1122660 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1122679 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1122698 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
1122712 TTCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1122731 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1122745 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1122764 ATTGCAACGCGAA
1 ATCGCAATGCGAA
1122777 TTTAATTTCG
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
14 16 0.22
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.62
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1122725 original size:33 final size:33
Alignment explanation
Indices: 1122683--1122779 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 33
1122673 ATGAAAATCG
*
1122683 CAATGCGAAATGAAAATCGCAACGCTAATTTCA
1 CAATGCGAAATGAAAATCGCAACGCGAATTTCA
* *
1122716 CAATGCGAAATGAAAATCGCAACGAGGGAA--TCG
1 CAATGCGAAATGAAAATCGCAAC--GCGAATTTCA
*
1122749 CAATGCGAAATGAAAATTGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGCGAATTT
1122780 AATTTCGCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 4 0.07
33 48 0.87
35 3 0.05
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGCGAATTTCA
Found at i:1122794 original size:19 final size:19
Alignment explanation
Indices: 1122772--1122834 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
1122762 AAATTGCAAC
*
1122772 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
1122791 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
1122811 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
1122830 GCGAT
1 GCGAT
1122835 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:1122807 original size:20 final size:19
Alignment explanation
Indices: 1122781--1122834 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
1122771 CGCGAATTTA
1122781 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1122800 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
1122820 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1122835 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1122960 original size:14 final size:15
Alignment explanation
Indices: 1122941--1122977 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1122931 CATCAATTAA
1122941 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
1122955 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
1122969 ACAAATCAA
1 ACAAATCAA
1122978 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:1124399 original size:21 final size:21
Alignment explanation
Indices: 1124333--1124399 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1124323 ATGAATCGGG
*
1124333 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1124353 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1124375 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1124396 CTCT
1 CTCT
1124400 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1124418 original size:42 final size:41
Alignment explanation
Indices: 1124333--1124455 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1124323 ATGAATCGGG
* * * *
1124333 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1124375 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1124417 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1124456 CGATTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1126502 original size:20 final size:19
Alignment explanation
Indices: 1126457--1126515 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
1126447 TCTTTTGGTT
*
1126457 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGA
* *
1126476 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1126497 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1126516 TAGAATCGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1126525 original size:14 final size:14
Alignment explanation
Indices: 1126506--1126542 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1126496 GGAAATGACT
*
1126506 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
1126520 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1126534 ATCGCAACG
1 ATCGCAACG
1126543 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1126570 original size:47 final size:48
Alignment explanation
Indices: 1126482--1126575 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
1126472 ATGAGATAAT
* * *
1126482 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
*
1126530 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACG
1126576 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:1126588 original size:19 final size:19
Alignment explanation
Indices: 1126566--1126655 Score: 162
Period size: 19 Copynumber: 4.7 Consensus size: 19
1126556 GCGACCAGAC
1126566 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1126585 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
1126605 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1126624 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1126643 AATCGCAATGCGA
1 AATCGCAACGCGA
1126656 TTTTTGTTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 50 0.72
20 19 0.28
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1126590 original size:33 final size:33
Alignment explanation
Indices: 1126519--1126632 Score: 120
Period size: 33 Copynumber: 3.3 Consensus size: 33
1126509 GCAACGATAG
* * *
1126519 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGAAAATCGCAACGCGAAATGAA
* * *
1126552 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGAAAATCGCAACGCGAAATGAA
1126585 AATCGCAACCGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GAAAATCGCAACGCGAAATGAA
1126624 AATCGCAAC
1 AATCGCAAC
1126633 GCGAAATGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
33 34 0.51
34 1 0.01
35 1 0.01
38 2 0.03
39 29 0.43
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGAAAATCGCAACGCGAAATGAA
Found at i:1126609 original size:39 final size:38
Alignment explanation
Indices: 1126566--1126655 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
1126556 GCGACCAGAC
1126566 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATGAA
1126605 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
*
1126643 AATCGCAATGCGA
1 AATCGCAACGCGA
1126656 TTTTTGTTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 23 0.46
39 27 0.54
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
Done.