Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006894.1 Corchorus capsularis cultivar CVL-1 contig06915, 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: 137249
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:382 original size:22 final size:21
Alignment explanation
Indices: 357--482 Score: 94
Period size: 22 Copynumber: 5.8 Consensus size: 21
347 ATCAAAGAGA
*
357 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
379 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
401 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
423 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * * *
445 TTATCAAAATTTTATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
467 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
483 TGAATGTTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
21 5 0.06
22 72 0.87
23 6 0.07
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:423 original size:44 final size:44
Alignment explanation
Indices: 361--456 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
351 AAGAGATTAT
* * *
361 CAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGCGAGGTTACTAA-AATTTCATAGGGAGGTTAA
* * *
405 CAAAATTTCATTAG-GAGGTTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCA-TAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
449 CAAAATTT
1 CAAAATTT
457 TATAATGTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 38 0.86
45 6 0.14
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
Found at i:649 original size:22 final size:22
Alignment explanation
Indices: 604--652 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
594 ATAGGAAGAA
* * **
604 TATCAAAATTTCATAGTGCTGT
1 TATCAAAATTTCAAAGCGAGGT
626 TATCAAAATTTCAAAGCGAGGT
1 TATCAAAATTTCAAAGCGAGGT
648 TATCA
1 TATCA
653 CAATATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCAAAGCGAGGT
Found at i:739 original size:22 final size:22
Alignment explanation
Indices: 689--740 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
679 GGGGTCAACA
*
689 AAATTTT-ATAAAGAGATTCTC
1 AAATTTTCATAAAGAGATTATC
* *
710 AAAATTTCATAAAGAGGTTATC
1 AAATTTTCATAAAGAGATTATC
732 AAATTTTCA
1 AAATTTTCA
741 AAATGTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTCATAAAGAGATTATC
Found at i:981 original size:22 final size:22
Alignment explanation
Indices: 846--1294 Score: 191
Period size: 22 Copynumber: 20.6 Consensus size: 22
836 TTATGGAGTA
* *
846 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
*
866 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* * *
888 TTCAAATTTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GGTT
* * * *
910 ATCCAAATCTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* **
932 ATCAAAATTTCATAGGGAGAAT
1 ATCAAAATTTCATAGTGAGGTT
* *
954 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
** *
976 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
998 ATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1014 ATCAAGATTTCATAAG-AAAGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
1036 ATCAAAATTTAATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
*
1059 ATCAAAACTTT-ATAG-GAAGATTT
1 ATCAAAA-TTTCATAGTG-AG-GTT
*
1082 ATCAAATTTTCATAGTGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1104 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1126 ATCAAAATTTCAGAGTGCGATT
1 ATCAAAATTTCATAGTGAGGTT
1148 A-CTAACAA-TTCATA-TGGAGGTT
1 ATC-AA-AATTTCATAGT-GAGGTT
* * * ** *
1170 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* *
1192 ATCAATATATCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * * *
1214 ATGAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
1237 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGTGAGGT-T
* * *
1260 -TCAAAATTCCTTAG-GAAAGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
1281 AACAAAATTTCATA
1 ATCAAAATTTCATA
1295 AGAAGTTTAA
Statistics
Matches: 316, Mismatches: 79, Indels: 66
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
19 2 0.01
20 12 0.04
21 12 0.04
22 221 0.70
23 52 0.16
24 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:1004 original size:44 final size:44
Alignment explanation
Indices: 777--1294 Score: 229
Period size: 44 Copynumber: 12.0 Consensus size: 44
767 GGTATTTCTG
*
777 GGGAGGTTATCAAAATTTCATAGT-ATGGTTA-CCAAA--T--TA
1 GGGAGGTTATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATA
* * * * *
816 GGAAGGTTATTAAACTTTTATTA-TG-GAGTAATCAAAATTTC--A
1 GGGAGGTTATCAAAATTTCA-TAGTGAG-GTTATCAAAATTTCATA
* * * *
858 GGGAGGATATCAAAATTTCATAGTTTA-GTTTTCAAATTTTCATA
1 GGGAGGTTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATA
* * * * *
902 -AGAGGGTTATCCAAATCTCATAGT-ATGTAGATCAAAATTTCATA
1 GGGA-GGTTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATA
** * * **
946 GGGAGAATAACAAAATTTCATAATGAGGTTATCAAAAAATCATA
1 GGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
*
990 GGGAGGTTATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATA
1 GGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
* * * * *
1028 AGAAAGTTATCAAAATTTAATAGGGAGGTTTATCAAAACTTT-ATA
1 GGGAGGTTATCAAAATTTCATAGTGAGG-TTATCAAAA-TTTCATA
* * * *
1073 GGAAGATTTATCAAATTTTCATAGTGAGGTTATCACAATTTCATA
1 GGGAG-GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
* * * * * *
1118 GTGTGATTATCAAAATTTCAGAGTGCGATTA-CTAACAA-TTCATA
1 GGGAGGTTATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCATA
* * * * ** * * *
1162 TGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATCATA
1 GGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
* * * * *
1206 TGGAGGTTATGAACATCTCATAGTGTTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATA
** * * * *
1251 TTGAGGTCT-TCAAAATTCCTTAG-GAAAGTTAACAAAATTTCATA
1 GGGAGGT-TATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATA
1295 AGAAGTTTAA
Statistics
Matches: 352, Mismatches: 94, Indels: 61
0.69 0.19 0.12
Matches are distributed among these distances:
38 27 0.08
39 23 0.07
40 7 0.02
41 4 0.01
42 30 0.09
43 11 0.03
44 160 0.45
45 67 0.19
46 23 0.07
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
GGGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
Found at i:5125 original size:13 final size:13
Alignment explanation
Indices: 5107--5133 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5097 TACTAATAAG
5107 ACGTGAGATGAAC
1 ACGTGAGATGAAC
5120 ACGTGAGATGAAC
1 ACGTGAGATGAAC
5133 A
1 A
5134 AAGTAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGTGAGATGAAC
Found at i:9638 original size:15 final size:15
Alignment explanation
Indices: 9618--9653 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
9608 CGGGAATCAC
9618 GATTATCATACCTCT
1 GATTATCATACCTCT
9633 GATTATCATACCTCT
1 GATTATCATACCTCT
*
9648 GGTTAT
1 GATTAT
9654 TTTGTCCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (15 bp):
GATTATCATACCTCT
Found at i:11644 original size:22 final size:22
Alignment explanation
Indices: 11602--11647 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11592 CTTAATTAAT
* *
11602 GAACATAAACGAGCTATTAAAC
1 GAACATAAACGAACTACTAAAC
11624 GAACAATAAACGAAC-ACTAAAC
1 GAAC-ATAAACGAACTACTAAAC
11646 GA
1 GA
11648 GCATTAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (22 bp):
GAACATAAACGAACTACTAAAC
Found at i:12628 original size:22 final size:22
Alignment explanation
Indices: 12598--12846 Score: 151
Period size: 22 Copynumber: 11.5 Consensus size: 22
12588 TCCAACATAG
*
12598 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* * *
12621 AAATTTGATAATCTCATTATG-
1 AAATTTGATAACCACACTATGA
12642 AAATTTCGAT-A--AC-CTATGA
1 AAATTT-GATAACCACACTATGA
* *
12661 AAATTTGATAATCACACTGTGA
1 AAATTTGATAACCACACTATGA
*
12683 AATTTTGATAACCACACTATGA
1 AAATTTGATAACCACACTATGA
* ** * *
12705 AATTTTGATAACCTTAGTGTGA
1 AAATTTGATAACCACACTATGA
* * *
12727 AATTTTGATAATCTC-CTTATGA
1 AAATTTGATAACCACAC-TATGA
* *
12749 AATTTTGATAATCACACTAT-A
1 AAATTTGATAACCACACTATGA
* *
12770 AAA-TTGGTAACCGCACTATGA
1 AAATTTGATAACCACACTATGA
* * *
12791 AAATTTTGATAATCTC-TTCAT-A
1 AAA-TTTGATAACCACACT-ATGA
12813 AAATTTTGATAACCACACTAT-A
1 AAA-TTTGATAACCACACTATGA
*
12835 AAGTTTCGATAA
1 AAATTT-GATAA
12847 GTACCTCCCT
Statistics
Matches: 181, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
18 7 0.04
19 8 0.04
20 13 0.07
21 19 0.10
22 118 0.65
23 16 0.09
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:12714 original size:44 final size:44
Alignment explanation
Indices: 12597--12846 Score: 212
Period size: 44 Copynumber: 5.8 Consensus size: 44
12587 CTCCAACATA
* * * *
12597 GAAATATTGATAACCACACTGTGAAAATTTGATAATCTCATTAT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAATCTCACTAT
* * * *
12641 GAAATTTCGAT-A--AC-CTATGAAAATTTGATAATCACACTGT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAATCTCACTAT
* * * *
12681 GAAATTTTGATAACCACACTATGAAATTTTGATAACCTTAGTGT
1 GAAATTTTGATAACCACACTATGAAATTTTGATAATCTCACTAT
* * *
12725 GAAATTTTGATAATCTC-CTTATGAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACAC-TATGAAATTTTGATAATCTCACTAT
* * * *
12769 -AAA-ATTGGTAACCGCACTATGAAAATTTTGATAATCTC-TTCAT
1 GAAATTTTGATAACCACACTATG-AAATTTTGATAATCTCACT-AT
* *
12812 AAAATTTTGATAACCACACTAT-AAAGTTTCGATAA
1 GAAATTTTGATAACCACACTATGAAA-TTTTGATAA
12847 GTACCTCCCT
Statistics
Matches: 166, Mismatches: 29, Indels: 22
0.76 0.13 0.10
Matches are distributed among these distances:
40 32 0.19
41 3 0.02
42 13 0.08
43 28 0.17
44 76 0.46
45 14 0.08
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAATTTTGATAATCTCACTAT
Found at i:12823 original size:65 final size:65
Alignment explanation
Indices: 12655--12836 Score: 199
Period size: 65 Copynumber: 2.8 Consensus size: 65
12645 TTTCGATAAC
* * * * * *
12655 CTATGAAAATTTGATAATCACAC-TGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCT
1 CTATGAAATTTTGATAATCTC-CTTATAAAATTTTGATAACCACACTAT-AAATATTGATAACCG
*
12719 TA
64 CA
* * * * *
12721 GTGTGAAATTTTGATAATCTCCTTATGAAATTTTGATAATCACACTATAAA-ATTGGTAACCGCA
1 CTATGAAATTTTGATAATCTCCTTATAAAATTTTGATAACCACACTATAAATATTGATAACCGCA
12785 CTATGAAAATTTTGATAATCT-CTTCATAAAATTTTGATAACCACACTATAAA
1 CTATG-AAATTTTGATAATCTCCTT-ATAAAATTTTGATAACCACACTATAAA
12837 GTTTCGATAA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 15 0.15
65 44 0.44
66 40 0.40
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (65 bp):
CTATGAAATTTTGATAATCTCCTTATAAAATTTTGATAACCACACTATAAATATTGATAACCGCA
Found at i:12955 original size:22 final size:22
Alignment explanation
Indices: 12930--12971 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12920 ACCTTGCTAT
* *
12930 GAAATTTTGTTAACCTCCCTGA
1 GAAACTTTGATAACCTCCCTGA
12952 GAAACTTTGATAACCTCCCT
1 GAAACTTTGATAACCTCCCT
12972 CTCTATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (22 bp):
GAAACTTTGATAACCTCCCTGA
Found at i:13070 original size:44 final size:43
Alignment explanation
Indices: 12909--13072 Score: 118
Period size: 44 Copynumber: 3.7 Consensus size: 43
12899 CCTCTCCATA
** * * *
12909 AAATTTTTGTAACCTTGCTATGAAATTTTGTTAACCTCCCTGAG
1 AAATTTTCATAACCTTTCTATGAAATTTTGTTAACCACTCT-AG
* * * * *
12953 AAACTTTGATAACCTCCCTCTCTATGAAATTTTGATAA-CAATACTAT
1 AAATTTTCATAACCT---T-TCTATGAAATTTTGTTAACCACT-CTAG
*
13000 AAA-TTTCAATAACC-TTCATATAAAATTTTGTTAACCACTCTAAG
1 AAATTTTC-ATAACCTTTC-TATGAAATTTTGTTAACCACTCT-AG
*
13044 AAATTTTCATAACCTTTTTATGAAATTTT
1 AAATTTTCATAACCTTTCTATGAAATTTT
13073 AGTAACGTCT
Statistics
Matches: 93, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
42 2 0.02
43 17 0.18
44 35 0.38
45 6 0.06
46 3 0.03
47 12 0.13
48 18 0.19
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (43 bp):
AAATTTTCATAACCTTTCTATGAAATTTTGTTAACCACTCTAG
Found at i:23533 original size:22 final size:23
Alignment explanation
Indices: 23480--23692 Score: 163
Period size: 22 Copynumber: 9.6 Consensus size: 23
23470 TATCAGGCCT
*
23480 AGTATGAAATTTTGATAACC-AC
1 AGTATGAAATTTTGATAACCTTC
* * *
23502 ACTATAAAATTTCGATAACCTTC
1 AGTATGAAATTTTGATAACCTTC
*
23525 -GTATGAAATTTTGTTAACCTTC
1 AGTATGAAATTTTGATAACCTTC
* * *
23547 -CTAAGAAATTTTGATAACCTTT
1 AGTATGAAATTTTGATAACCTTC
** *
23569 TCTATGAAATTTTGGTAACC-TC
1 AGTATGAAATTTTGATAACCTTC
* *
23591 TGTATGAAATTTTGATAA-CTAC
1 AGTATGAAATTTTGATAACCTTC
* *
23613 ATTATGAAATTTTGATAACCTCC
1 AGTATGAAATTTTGATAACCTTC
* * **
23636 A-TATAAAATTTTGGTAA-CAAC
1 AGTATGAAATTTTGATAACCTTC
* *
23657 ACTATTAAATTTTGATAACCTTC
1 AGTATGAAATTTTGATAACCTTC
* *
23680 -CTATGTAATTTTG
1 AGTATGAAATTTTG
23693 GTTTGATTGT
Statistics
Matches: 154, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
21 4 0.03
22 126 0.82
23 24 0.16
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
AGTATGAAATTTTGATAACCTTC
Found at i:23675 original size:111 final size:110
Alignment explanation
Indices: 23481--23694 Score: 277
Period size: 111 Copynumber: 1.9 Consensus size: 110
23471 ATCAGGCCTA
* * * * **
23481 GTATGAAATTTTGATAACCACACTATAAAATTTCGATAACCTTCGTATGAAATTTTGTTAACCTT
1 GTATGAAATTTTGATAACCACACTATAAAATTTCGATAACCTCCATATAAAATTTTGGTAACCAA
*
23546 CCTAAGAAATTTTGATAACCTTTTCTATGAAATTTTGGTAACCTCT
66 CCTAAGAAATTTTGATAACC-TTCCTATGAAATTTTGGTAACCTCT
* * * *
23592 GTATGAAATTTTGATAACTACATTATGAAATTTTGATAACCTCCATATAAAATTTTGGTAA-CAA
1 GTATGAAATTTTGATAACCACACTATAAAATTTCGATAACCTCCATATAAAATTTTGGTAACCAA
** *
23656 CACTATTAAATTTTGATAACCTTCCTATGTAATTTTGGT
66 C-CTAAGAAATTTTGATAACCTTCCTATGAAATTTTGGT
23695 TTGATTGTCA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 18 0.20
111 70 0.80
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (110 bp):
GTATGAAATTTTGATAACCACACTATAAAATTTCGATAACCTCCATATAAAATTTTGGTAACCAA
CCTAAGAAATTTTGATAACCTTCCTATGAAATTTTGGTAACCTCT
Found at i:23690 original size:66 final size:66
Alignment explanation
Indices: 23482--23692 Score: 189
Period size: 66 Copynumber: 3.2 Consensus size: 66
23472 TCAGGCCTAG
* * * * *
23482 TATGAAATTTTGATAACC-ACACTATAAAATTTCGATAAC--CTTCGTATGAAATTTTGTTAACC
1 TATGAAATTTTGATAACCTTC-CTATAAAATTTTGGTAACAAC-AC-TATGAAATTTTGATAACC
23544 TTCC
63 TTCC
* * * ** ** *
23548 TAAGAAATTTTGATAACCTTTTCTATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAA-CTA
1 TATGAAATTTTGATAACC-TTCCTATAAAATTTTGGTAACAACACTATGAAATTTTGATAACCTT
*
23612 CAT
65 C-C
*
23615 TATGAAATTTTGATAACC-TCCATATAAAATTTTGGTAACAACACTATTAAATTTTGATAACCTT
1 TATGAAATTTTGATAACCTTCC-TATAAAATTTTGGTAACAACACTATGAAATTTTGATAACCTT
23679 CC
65 CC
*
23681 TATGTAATTTTG
1 TATGAAATTTTG
23693 GTTTGATTGT
Statistics
Matches: 117, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
65 2 0.02
66 63 0.54
67 50 0.43
68 1 0.01
69 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (66 bp):
TATGAAATTTTGATAACCTTCCTATAAAATTTTGGTAACAACACTATGAAATTTTGATAACCTTC
C
Found at i:33577 original size:246 final size:244
Alignment explanation
Indices: 33145--33623 Score: 854
Period size: 246 Copynumber: 2.0 Consensus size: 244
33135 AAAGGGGGGG
*
33145 TTAGGGTTTAGAAGCAATTAATTAAAAGTCTTAAACATTGATTAAAAACAATTAAGGAAGGGAAA
1 TTAGGGTTTAGAAGCAATTAATTAAAAGACTTAAACATTGATTAAAAACAATTAAGGAAGGGAAA
* *
33210 TGTGTAATTAAAAAAGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTTTTGTCAT
66 TGTGTAATTAAAAAAGGTAGAAGGAAAAGGAATGGGGAAAACTCATAGAGGGGCTTTTTAGTCAT
33275 CCGAAAAGTGGGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTGACT-
131 CCGAAAAGTGGGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTT-ACTC
*
33339 TTTTAGTGATTTCCATTGTAGTTAAAAATAATATATAGTTAATTAAGAGT
195 TTTTAGTAATTTCCATTGTAGTTAAAAATAATATATAGTTAATTAAGAGT
33389 TTAGGGTTTAGAAGCAATTAATTAAAAGACTTAAACATTGATTAAAAACAATTAAGGAAGGGAAA
1 TTAGGGTTTAGAAGCAATTAATTAAAAGACTTAAACATTGATTAAAAACAATTAAGGAAGGGAAA
33454 TGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAAT-GGGAAAACTCATAGAGGGGCTTTTTAGT
66 TGTGTAATT--AAAAAA-GGTAGAAGGAAAAGGAATGGGGAAAACTCATAGAGGGGCTTTTTAGT
* *
33518 CATCCGAAAAGTGTGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTAG
128 CATCCGAAAAGTGGGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTAC
33583 TCTTTTAGTAATTTCCATTGTAGTTAAAAATAATATATAGT
193 TCTTTTAGTAATTTCCATTGTAGTTAAAAATAATATATAGT
33624 ATATATAAGT
Statistics
Matches: 225, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
244 73 0.32
245 2 0.01
246 132 0.59
247 18 0.08
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (244 bp):
TTAGGGTTTAGAAGCAATTAATTAAAAGACTTAAACATTGATTAAAAACAATTAAGGAAGGGAAA
TGTGTAATTAAAAAAGGTAGAAGGAAAAGGAATGGGGAAAACTCATAGAGGGGCTTTTTAGTCAT
CCGAAAAGTGGGAAAAGACCAAAAATAACCAAAAGGTGGCACCACATTAATCCTCAATTTACTCT
TTTAGTAATTTCCATTGTAGTTAAAAATAATATATAGTTAATTAAGAGT
Found at i:34442 original size:18 final size:17
Alignment explanation
Indices: 34414--34447 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
34404 ACTCAAACTT
34414 AAACTAACTGACTCAAA
1 AAACTAACTGACTCAAA
34431 AAACTGAACTGACTCAA
1 AAACT-AACTGACTCAA
34448 CTGACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.18
Consensus pattern (17 bp):
AAACTAACTGACTCAAA
Found at i:34475 original size:27 final size:27
Alignment explanation
Indices: 34419--34475 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
34409 AACTTAAACT
* * *
34419 AACTGACTCAAAAAACTGAACTGACTC
1 AACTGACTAAAAAAACTGAACTAACCC
34446 AACTGACTAAAAAAACTG-ACTAAACCC
1 AACTGACTAAAAAAACTGAACT-AACCC
34473 AAC
1 AAC
34476 AGATCAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.16
Consensus pattern (27 bp):
AACTGACTAAAAAAACTGAACTAACCC
Found at i:37953 original size:64 final size:64
Alignment explanation
Indices: 37852--37979 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
37842 TGCAACCCTC
37852 CTTCTTCCTTCCATGATAAACCCAAATCAAGAGGTAAATCATGAAAAAGGAAGAGGCAAAGGGA
1 CTTCTTCCTTCCATGATAAACCCAAATCAAGAGGTAAATCATGAAAAAGGAAGAGGCAAAGGGA
37916 CTTCTTCCTTCCATGATAAACCCAAATCAAGAGGTAAATCATGAAAAAGGAAGAGGCAAAGGGA
1 CTTCTTCCTTCCATGATAAACCCAAATCAAGAGGTAAATCATGAAAAAGGAAGAGGCAAAGGGA
37980 GAGAGAGTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (64 bp):
CTTCTTCCTTCCATGATAAACCCAAATCAAGAGGTAAATCATGAAAAAGGAAGAGGCAAAGGGA
Found at i:38527 original size:6 final size:6
Alignment explanation
Indices: 38513--38543 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
38503 CATCTTCTGC
*
38513 TGCTCT TGCTGT TGCTGT TGCTGT TGCTGT T
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT T
38544 ACCCCTCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.29, T:0.52
Consensus pattern (6 bp):
TGCTGT
Found at i:41347 original size:23 final size:23
Alignment explanation
Indices: 41316--41366 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
41306 AGACAATAGA
* *
41316 AAAAACTCTCACAGAGGAGTCTC
1 AAAAACTCTCACAAAGGAGTCCC
*
41339 AAAAGCTCTCACAAAGGAGTCCC
1 AAAAACTCTCACAAAGGAGTCCC
41362 AAAAA
1 AAAAA
41367 AAACAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (23 bp):
AAAAACTCTCACAAAGGAGTCCC
Found at i:41918 original size:20 final size:21
Alignment explanation
Indices: 41894--41948 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
41884 CATAGTATTA
*
41894 AAATTATTATATATTA-ATAAC
1 AAATTATTATATATTATA-AAT
* *
41915 AATTTTTTA-ATATTATAAAT
1 AAATTATTATATATTATAAAT
41935 AAATTATTATATAT
1 AAATTATTATATAT
41949 ATGATAACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATTATATATTATAAAT
Found at i:42071 original size:22 final size:22
Alignment explanation
Indices: 42029--42072 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42019 TATTCATATG
*
42029 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
42051 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
42073 TTTCTGATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:42111 original size:22 final size:22
Alignment explanation
Indices: 42086--42647 Score: 235
Period size: 22 Copynumber: 25.7 Consensus size: 22
42076 CTGATCCCAT
*
42086 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
42108 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
42130 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
42152 TAT-AAATTATTTTTAACCTTCT
1 TATGAAATT-TTGATAACCTTCC
* *
42174 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
42196 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
42218 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
42240 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * * *
42263 CATGAGATGTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* * * *
42285 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-C
* * *
42307 TATGAAAATTT-AAAAACTTCC
1 TATGAAATTTTGATAACCTTCC
* *
42328 GTATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * ***
42351 TCTGAAATTTTGATAATCAGAC
1 TATGAAATTTTGATAACCTTCC
*
42373 TATGAAATTGTGATAACC-TCAC
1 TATGAAATTTTGATAACCTTC-C
*
42395 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
42418 TATAAAATTTTTATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * **
42441 TATAAAATTTTGATAACTTTAT
1 TATGAAATTTTGATAACCTTCC
*
42463 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
42480 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
42501 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
42523 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
42545 TATGAAATTTAGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
42567 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
42589 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
42611 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
42633 TATGAAATTTTGATA
1 TATGAAATTTTGATA
42648 TCCTCCCCGA
Statistics
Matches: 397, Mismatches: 110, Indels: 66
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 23 0.06
22 283 0.71
23 76 0.19
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:42425 original size:23 final size:23
Alignment explanation
Indices: 42372--42456 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
42362 GATAATCAGA
* * *
42372 CTATGAAATTGTGAT-AACCTCA
1 CTATAAAATTTTGATAAACCTCC
* * *
42394 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
*
42417 CTATAAAATTTTTATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
42440 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
42457 CTTTATTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 14 0.26
23 39 0.74
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:42717 original size:20 final size:20
Alignment explanation
Indices: 42692--42739 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
42682 GTTCAATAAC
42692 ATTTTGATATCCTCCCTGAA
1 ATTTTGATATCCTCCCTGAA
*
42712 ATTTTGATATCCTCTCTGAA
1 ATTTTGATATCCTCCCTGAA
42732 ATTTTGAT
1 ATTTTGAT
42740 TACTCCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTTTGATATCCTCCCTGAA
Found at i:42906 original size:44 final size:44
Alignment explanation
Indices: 42814--42983 Score: 148
Period size: 44 Copynumber: 3.9 Consensus size: 44
42804 GAAATACCAC
* * *
42814 TATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCTT
1 TATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCTCCT
* * * *
42858 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACC-CCT
1 TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCCT
* * * *
42901 CTATGAAATTCTGATAATCACATTATATAATTTTGATAACCTCGT
1 -TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCCT
* * * * *
42946 TTTGAAATTTTGATAACAACACTATGAAATTTCGATAA
1 TATGAAATTTTGATAACCACATTATAAAATTTTGATAA
42984 TCACTCTATG
Statistics
Matches: 99, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
43 11 0.11
44 86 0.87
45 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCCT
Found at i:42971 original size:66 final size:66
Alignment explanation
Indices: 42863--42987 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
42853 CTCTTTATGA
* * ** *
42863 AATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAA-TTCTGATAATCACATTAT
1 AATTTTGATAACCTCTTTATAAAATTTTGATAACAACACTATGAAATTTC-GATAATCACATTAT
42927 AT
65 AT
*
42929 AATTTTGATAACCTCGTTT-TGAAATTTTGATAACAACACTATGAAATTTCGATAATCAC
1 AATTTTGATAACCTC-TTTATAAAATTTTGATAACAACACTATGAAATTTCGATAATCAC
42988 TCTATGAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
66 45 0.88
67 6 0.12
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (66 bp):
AATTTTGATAACCTCTTTATAAAATTTTGATAACAACACTATGAAATTTCGATAATCACATTATA
T
Found at i:42973 original size:22 final size:21
Alignment explanation
Indices: 42811--43005 Score: 78
Period size: 22 Copynumber: 9.0 Consensus size: 21
42801 CCAGAAATAC
42811 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAA-CA
* * *
42833 CATTTTGAAAATTTGATAAC-
1 CACTATGAAATTTTGATAACA
*
42853 CTCTTTATGAAATTTTGATAAC-
1 CAC--TATGAAATTTTGATAACA
* * * * *
42875 CTCTTTATAAAATTTTGTTGACCC
1 CAC--TATGAAATTTTGAT-AACA
* *
42899 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAA-CA
*
42921 CATTAT-ATAATTTTGATAAC-
1 CACTATGA-AATTTTGATAACA
* *
42941 CTCGTTTTGAAATTTTGATAACAA
1 CAC--TATGAAATTTTGATAAC-A
*
42965 CACTATGAAATTTCGATAATCA
1 CACTATGAAATTTTGATAA-CA
* *
42987 CTCTATGAGA-TTTGATAAC
1 CACTATGAAATTTTGATAAC
43006 CTTCTATCAA
Statistics
Matches: 133, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
20 3 0.02
21 15 0.11
22 106 0.80
23 4 0.03
24 5 0.04
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
CACTATGAAATTTTGATAACA
Found at i:42976 original size:88 final size:88
Alignment explanation
Indices: 42813--42977 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
42803 AGAAATACCA
* * **
42813 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
**
42878 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
*
42901 CTATGAAA-TTCTGATAATCACATTAT-ATAATTTTGATAACCTCGTTT-TGAAATTTTGATAAC
1 CTATGAAATTTCTG-TAATCACATTATGA-AAATTTGATAACCTC-TTTATGAAATTTTGATAAC
*
42963 AACACTATGAAATTT
63 AACACTATAAAATTT
42978 CGATAATCAC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
87 5 0.08
88 58 0.88
89 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:43075 original size:22 final size:21
Alignment explanation
Indices: 42838--43183 Score: 141
Period size: 22 Copynumber: 15.7 Consensus size: 21
42828 AATCACATTT
* *
42838 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-ATA
*
42860 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-ATA
* * *
42882 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-A-ACCTCATA
* * *
42904 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCA-TA
* *
42926 T-ATAATTTTGATAACCTCGTTT
1 TGA-AATTTTGATAACCTC-ATA
**
42948 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCA-TA
*
42970 TGAAATTTCGATAATCACTC-TA
1 TGAAATTTTGATAA-C-CTCATA
*
42992 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACC-TCATA
* * * *
43012 TCAAATTTTGGTACTCCTTATAAAA
1 TGAAATTTTGATA-ACCTCAT---A
43037 TGGAGAATTTT-ATAACCTTCATA
1 T-GA-AATTTTGATAACC-TCATA
*
43060 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCA-TA
* * **
43082 TAAAATTTGGATAACCTCCCCA
1 TGAAATTTTGATAACCT-CATA
* *
43104 TGAAATATT-AGTAACCTCCTAA
1 TGAAATTTTGA-TAACCTCAT-A
* *
43126 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCA-TA
*
43148 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-ATA
*
43170 TGACATTTTGATAA
1 TGAAATTTTGATAA
43184 TCTCTTTGAT
Statistics
Matches: 243, Mismatches: 51, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.00
20 10 0.04
21 29 0.12
22 173 0.71
23 9 0.04
24 5 0.02
25 4 0.02
26 6 0.02
27 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCATA
Found at i:43251 original size:22 final size:22
Alignment explanation
Indices: 43219--43266 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43209 TTGTGATAAT
*
43219 TAACCACCCTATA-AAATTTCAA
1 TAACCAACCTA-AGAAATTTCAA
*
43241 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
43263 TAAC
1 TAAC
43267 ATGATCCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:43291 original size:46 final size:45
Alignment explanation
Indices: 43241--43336 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 45
43231 AAAATTTCAA
*
43241 TAACCAAC-CTAAGAAATTTTAATAACATGATCCTACGAAATTTTGG
1 TAACCAACACTAAGAAATTTTAATAAC-T-ATCATACGAAATTTTGG
* * * *
43287 TAACC-ACACTATGAAATTTTGATAACTTTCATATGAAATTTTGG
1 TAACCAACACTAAGAAATTTTAATAACTATCATACGAAATTTTGG
43331 TAACCA
1 TAACCA
43337 CATTATGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 19 0.44
45 3 0.07
46 21 0.49
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (45 bp):
TAACCAACACTAAGAAATTTTAATAACTATCATACGAAATTTTGG
Found at i:43305 original size:22 final size:21
Alignment explanation
Indices: 43277--43406 Score: 107
Period size: 22 Copynumber: 6.0 Consensus size: 21
43267 ATGATCCTAC
*
43277 GAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCACA-TAT
**
43299 GAAATTTTGATAACTTTCATAT
1 GAAATTTTGATAAC-CACATAT
*
43321 GAAATTTTGGTAACCACATTAT
1 GAAATTTTGATAACCACA-TAT
* ***
43343 GGAATTTTGATAACCTTTTCAT
1 GAAATTTTGATAACCACAT-AT
* * **
43365 GAAATTATAATAACCATTTTAT
1 GAAATTTTGATAACCA-CATAT
43387 GAAATTTTGATAACCACATA
1 GAAATTTTGATAACCACATA
43407 GAGACAAGAA
Statistics
Matches: 85, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
21 5 0.06
22 75 0.88
23 5 0.06
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (21 bp):
GAAATTTTGATAACCACATAT
Found at i:43338 original size:44 final size:43
Alignment explanation
Indices: 43277--43400 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 43
43267 ATGATCCTAC
*
43277 GAAATTTTGGTAACCACACTATGAAATTTTGATAAC-TTTCATAT
1 GAAATTTTGGTAACCACATTATGAAATTTTGATAACTTTTC--AT
*
43321 GAAATTTTGGTAACCACATTATGGAATTTTGATAACCTTTTCAT
1 GAAATTTTGGTAACCACATTATGAAATTTTGATAA-CTTTTCAT
* ** **
43365 GAAATTATAATAACCATTTTATGAAATTTTGATAAC
1 GAAATTTTGGTAACCACATTATGAAATTTTGATAAC
43401 CACATAGAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.01
44 64 0.91
45 1 0.01
46 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (43 bp):
GAAATTTTGGTAACCACATTATGAAATTTTGATAACTTTTCAT
Found at i:44237 original size:70 final size:70
Alignment explanation
Indices: 44154--44300 Score: 258
Period size: 70 Copynumber: 2.1 Consensus size: 70
44144 AATCCTATTG
* * * *
44154 AAATGAGAACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAAGCTCAGAAA
1 AAATGAGAACTTCACAAAAGCAGCTTTGGAAGAAAATTCATAACTTTTGATCCAAAACTCAGAAA
44219 AATGC
66 AATGC
44224 AAATGAGAACTTCACAAAAGCAGCTTTGGAAGAAAATTCATAACTTTTGATCCAAAACTCAGAAA
1 AAATGAGAACTTCACAAAAGCAGCTTTGGAAGAAAATTCATAACTTTTGATCCAAAACTCAGAAA
44289 AATGC
66 AATGC
44294 AAATGAG
1 AAATGAG
44301 GTACCGTTGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (70 bp):
AAATGAGAACTTCACAAAAGCAGCTTTGGAAGAAAATTCATAACTTTTGATCCAAAACTCAGAAA
AATGC
Found at i:44894 original size:37 final size:37
Alignment explanation
Indices: 44805--44900 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 37
44795 ATCTAAGCCC
* *** *
44805 AAATAGGATGTCGGAGGTAAAGACAAAAAGTAAAATT
1 AAATAGGATGTTGGAAACAAAGACAAAAAGCAAAATT
** * *
44842 AAATACAACGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGATG-TTGGAAACAAAGACAAAAAGCAAAATT
44880 AAATAGGATGTTGGAAACAAA
1 AAATAGGATGTTGGAAACAAA
44901 AAACAAATTG
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
37 18 0.39
38 28 0.61
ACGTcount: A:0.54, C:0.08, G:0.21, T:0.17
Consensus pattern (37 bp):
AAATAGGATGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:45209 original size:12 final size:12
Alignment explanation
Indices: 45187--45217 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
45177 CTACTTGGTT
45187 TATTT-GATATA
1 TATTTGGATATA
45198 TATTTGGATATA
1 TATTTGGATATA
45210 TATTTGGA
1 TATTTGGA
45218 AAATGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TATTTGGATATA
Found at i:45746 original size:11 final size:11
Alignment explanation
Indices: 45703--45740 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
45693 TTCCTATATA
*
45703 AAATAAATTAT
1 AAATTAATTAT
45714 CAAA-TAATTAT
1 -AAATTAATTAT
45725 AAATTAATTAT
1 AAATTAATTAT
45736 AAATT
1 AAATT
45741 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:51439 original size:162 final size:163
Alignment explanation
Indices: 51160--51488 Score: 570
Period size: 162 Copynumber: 2.0 Consensus size: 163
51150 GCAAGATAAC
*
51160 GCAGTTGCACGTAAAGACATCCATATTCTGATGTAAACTCTATCAGGCTTAGTCCTTCTGGGTTT
1 GCAGTTGCACGTAAAGACATCCATATTCTGATGTAAACTCTAT----CTTAGTCCTTCTGGGTTC
*
51225 AGGTTATTTGAAATATCCAGTCATTAAATGTGCAAGTTCAGTCATCTTCAGTTTAGTTAGACAGG
62 AGGTTATTTGAAATATCCAGTCATTAAATGTGCAAATTCAGTCATCTTCAGTTTAGTTAGACAGG
51290 ATAATGGAGAATGATCTATGTATAGCGTCATTTTTTA
127 ATAATGGAGAATGATCTATGTATAGCGTCATTTTTTA
* *
51327 GCAGTTTCACGTAAAGACATCCATATTCTGATGTAAACTCTAT-TTAGTCCTTTTGGGTTCAGGT
1 GCAGTTGCACGTAAAGACATCCATATTCTGATGTAAACTCTATCTTAGTCCTTCTGGGTTCAGGT
51391 TATTTGAAATATCCAGTCATTAAATGTGCAAATTCAGTCATCTTCAGTTTAGTTAGACAGGATAA
66 TATTTGAAATATCCAGTCATTAAATGTGCAAATTCAGTCATCTTCAGTTTAGTTAGACAGGATAA
*
51456 TGGAGAATGATCTATGTATAGCGTCTTTTTTTA
131 TGGAGAATGATCTATGTATAGCGTCATTTTTTA
51489 ATTATGAATA
Statistics
Matches: 157, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
162 115 0.73
167 42 0.27
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (163 bp):
GCAGTTGCACGTAAAGACATCCATATTCTGATGTAAACTCTATCTTAGTCCTTCTGGGTTCAGGT
TATTTGAAATATCCAGTCATTAAATGTGCAAATTCAGTCATCTTCAGTTTAGTTAGACAGGATAA
TGGAGAATGATCTATGTATAGCGTCATTTTTTA
Found at i:51521 original size:4 final size:4
Alignment explanation
Indices: 51512--51539 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
51502 ACCTACATTG
51512 ATGA ATGA ATGA ATGA ATGA ATGA ATGA
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA
51540 TCTAACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATGA
Found at i:59621 original size:2 final size:2
Alignment explanation
Indices: 59614--59667 Score: 81
Period size: 2 Copynumber: 25.5 Consensus size: 2
59604 CACCCATCAG
59614 TA TA TA TA CTA 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
59657 CTA TA CTA TA T
1 -TA TA -TA TA T
59668 TCTAAAGGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 43 0.88
3 6 0.12
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:65079 original size:51 final size:51
Alignment explanation
Indices: 65020--65117 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
65010 TAGTATTTGA
*
65020 TGCATGTACCTAATCAAGAGTTTGAAGGTTATAGCATGGATTAGTTCTAGT
1 TGCATGTACCTAATCAAGAGTTTGAAGGTTATAGCATGGATCAGTTCTAGT
65071 TGCATGTACCTAATCAAGAGTTTGAAGGTTATAGCATGGATCAGTTC
1 TGCATGTACCTAATCAAGAGTTTGAAGGTTATAGCATGGATCAGTTC
65118 AGCATTCCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (51 bp):
TGCATGTACCTAATCAAGAGTTTGAAGGTTATAGCATGGATCAGTTCTAGT
Found at i:74867 original size:12 final size:13
Alignment explanation
Indices: 74849--74881 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
74839 GTGGATTTAG
74849 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
74862 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
74874 TAGTTTGT
1 TAGTTTGT
74882 AATTAGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:82942 original size:19 final size:18
Alignment explanation
Indices: 82918--82959 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
82908 GCATTAAATA
*
82918 AAAAAAAACAAACAAAAGG
1 AAAAAAAA-AAACAAAAAG
*
82937 AAAAAAAAAAAGAAAAAG
1 AAAAAAAAAAACAAAAAG
82955 AAAAA
1 AAAAA
82960 CCCTACTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAG
Found at i:85480 original size:156 final size:155
Alignment explanation
Indices: 84997--85548 Score: 613
Period size: 156 Copynumber: 3.5 Consensus size: 155
84987 TGTAGGTCAT
* * *** * *
84997 CTTGGCCAAGTTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAATTAAGGA
1 CTTGGCAAAGTTTCAGCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGA
* *
85062 CAGTTTGGGGTGTGAAACCAACTTCACTATGATAGGAAGTTCGGTTTTACTTAGAATTTTTTCCA
66 CAGTTT-GGGTGTGAAACCAACTTCACTATGATAGGGAGCTCGGTTTTACTTAGAATTTTTTCCA
* * *
85127 TAGTCTTATGGAGATAGTCTAAGTCT
130 TAGTCTTATGGAGATAATCTAAATCC
* * * *
85153 CGTGGCCAAGTTTCATCTCAATTGGACTT-AGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGG
1 CTTGGCAAAGTTTCAGCTCAATTGGACTTAAG-ATGAAAAACTTATGCTAGTTTTTCATTTAAGG
85217 ACAGTTTGGGTGTGAAACCAACTTCACTATGATAGGGAGCTCGGTTTTACTTAGAATTTTTTCCA
65 ACAGTTTGGGTGTGAAACCAACTTCACTATGATAGGGAGCTCGGTTTTACTTAGAATTTTTTCCA
** *
85282 TAGAATTATGG-GAATAATCT-AAGCC
130 TAGTCTTATGGAG-ATAATCTAAATCC
*
85307 TACTGGTGG-AAA--ATCAGCTTC-ATTGGACTT-AGAATGAAAAACTTATGCTAGTTTTTCATT
1 --CT--TGGCAAAGTTTCAGC-TCAATTGGACTTAAG-ATGAAAAACTTATGCTAGTTTTTCATT
* * * * * *
85367 TAAGGACAATTTAGGGAGAGAAACCAAGTTCA-TCATCA-AGGCGAGCTCGGTTTTACTTATAAT
60 TAAGGACAGTTT-GGGTGTGAAACCAACTTCACT-ATGATAGG-GAGCTCGGTTTTACTTAGAAT
* *
85430 TTTTTCCATAGTCTTGTGGAGAGAATCTAAATCC
122 TTTTTCCATAGTCTTATGGAGATAATCTAAATCC
** *
85464 CTTGGCAAAGTTTCAGCTCAATCAGACTTAAGGTGAAAAACTTATGC-ATGTTTTTCATTTAAGG
1 CTTGGCAAAGTTTCAGCTCAATTGGACTTAAGATGAAAAACTTATGCTA-GTTTTTCATTTAAGG
85528 ACAGTTTGGGGGTGTGAAACC
65 ACAGTTT--GGGTGTGAAACC
85549 TAGTTCACCA
Statistics
Matches: 338, Mismatches: 39, Indels: 37
0.82 0.09 0.09
Matches are distributed among these distances:
153 3 0.01
154 6 0.02
155 134 0.40
156 173 0.51
157 19 0.06
158 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (155 bp):
CTTGGCAAAGTTTCAGCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGA
CAGTTTGGGTGTGAAACCAACTTCACTATGATAGGGAGCTCGGTTTTACTTAGAATTTTTTCCAT
AGTCTTATGGAGATAATCTAAATCC
Found at i:85902 original size:17 final size:17
Alignment explanation
Indices: 85876--85941 Score: 114
Period size: 17 Copynumber: 3.9 Consensus size: 17
85866 GATACAGCAG
*
85876 ATGCTGCCTGGTACCTC
1 ATGCTACCTGGTACCTC
85893 ATGCTACCTGGTACCTC
1 ATGCTACCTGGTACCTC
*
85910 ATGCTACCTAGTACCTC
1 ATGCTACCTGGTACCTC
85927 ATGCTACCTGGTACC
1 ATGCTACCTGGTACC
85942 ACAAGGAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.18, C:0.35, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGCTACCTGGTACCTC
Found at i:88138 original size:17 final size:17
Alignment explanation
Indices: 88118--88176 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
88108 ATATTACATG
88118 TATTATCTAATTATTAT
1 TATTATCTAATTATTAT
*
88135 TATTAAT-TAA-TATTACAAG
1 TATT-ATCTAATTATT---AT
*
88154 TATTATCTAATTATAAT
1 TATTATCTAATTATTAT
88171 TATTAT
1 TATTAT
88177 AAATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 4 0.12
19 8 0.24
20 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTATCTAATTATTAT
Found at i:88143 original size:36 final size:36
Alignment explanation
Indices: 88089--88175 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
88079 TAATATTTTT
* *
88089 ATTATGAATATATAAATTAATATTACATGTATTATCTA
1 ATTAT-AAT-TATTAATTAATATTACAAGTATTATCTA
*
88127 ATTATTATTATTAATTAATATTACAAGTATTATCTA
1 ATTATAATTATTAATTAATATTACAAGTATTATCTA
88163 ATTATAATTATTA
1 ATTATAATTATTA
88176 TAAATTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 38 0.84
37 2 0.04
38 5 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (36 bp):
ATTATAATTATTAATTAATATTACAAGTATTATCTA
Found at i:88164 original size:19 final size:19
Alignment explanation
Indices: 88106--88164 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
88096 ATATATAAAT
*
88106 TAATATTACATGTATTATC
1 TAATATTACAAGTATTATC
*
88125 TAATTATT---ATTATTAAT-
1 TAA-TATTACAAGTATT-ATC
88142 TAATATTACAAGTATTATC
1 TAATATTACAAGTATTATC
88161 TAAT
1 TAAT
88165 TATAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 4 0.13
19 12 0.39
20 4 0.13
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (19 bp):
TAATATTACAAGTATTATC
Found at i:88184 original size:39 final size:36
Alignment explanation
Indices: 88099--88184 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 36
88089 ATTATGAATA
*
88099 TATAAATTAATATTACATGTATTATCTAATTATTAT
1 TATAAATTAATATTACAAGTATTATCTAATTATTAT
*
88135 TATTAATTAATATTACAAGTATTATCTAATTATAATTAT
1 TATAAATTAATATTACAAGTATTATCTAA-T-T-ATTAT
88174 TATAAATTAAT
1 TATAAATTAAT
88185 TTTTATGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 27 0.61
37 1 0.02
38 1 0.02
39 15 0.34
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (36 bp):
TATAAATTAATATTACAAGTATTATCTAATTATTAT
Found at i:104209 original size:174 final size:173
Alignment explanation
Indices: 103919--104282 Score: 568
Period size: 174 Copynumber: 2.1 Consensus size: 173
103909 CAATATCGAT
*
103919 CGAGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAAACGATCGAGCAT
1 CGAGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCATGTAATAAAAC-ATCGAGCAT
* * *
103984 CCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATTTAATAAATAAATCGAGCATCCCTCGG
65 CCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGG
* * * *
104049 TCACACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGAAAAC
130 TCACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAA
*
104093 CGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAGATAA-ATCGAGCA
1 CGAGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCATGTAATA-A-AACATCGAGCA
*
104157 TCCCTTGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCG
64 TCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCG
* *
104222 GTCACATGGCCCAATGGGCATCCCCCACACGTGCAAGAAGAAAAA
129 GTCACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAA
* *
104267 CAAGCATCCCTTGGTC
1 CGAGCATCCCTCGGTC
104283 GCACAACCTA
Statistics
Matches: 174, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 171 0.98
175 1 0.01
176 2 0.01
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.18
Consensus pattern (173 bp):
CGAGCATCCCTCGGTCACACGACCAAGTGGGCATCCCCCACTCATGTAATAAAACATCGAGCATC
CCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAATAAATCAAGCATCCCTCGGT
CACACGGCCCAATGGGCATCCCCCACACATGCAAGAAGAAAAA
Found at i:104277 original size:58 final size:59
Alignment explanation
Indices: 103917--104249 Score: 500
Period size: 58 Copynumber: 5.7 Consensus size: 59
103907 AGCAATATCG
* * *
103917 ATCGAGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAA-A-ACG
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATA-A
* *
103975 ATCGAGCATCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATTTAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
104033 ATCGAGCATCCCTCGGTCACACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGA-AA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
*
104091 ACCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAAT-AGATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
*
104149 ATCGAGCATCCCTTGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
104207 ATCAAGCATCCCTCGGTCACATGGCCCAA-TGGGCATCCCCCAC
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCAC
104250 ACGTGCAAGA
Statistics
Matches: 255, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
57 3 0.01
58 245 0.96
59 7 0.03
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (59 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
Found at i:104421 original size:48 final size:48
Alignment explanation
Indices: 104304--104492 Score: 299
Period size: 48 Copynumber: 4.0 Consensus size: 48
104294 AATGGGCACC
*
104304 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGTGTACAGCC-A
1 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCGTACAGCCTA
* *
104351 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGACGTATAGCCTA
1 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCGTACAGCCTA
* * * *
104399 CCCCAAAAGCATACAACCTAGATAAAATTTCCAAAGGCATACAACCTA
1 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCGTACAGCCTA
*
104447 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCATACAGCC
1 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCGTACAGCC
104493 AAAATAGAGC
Statistics
Matches: 129, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 43 0.33
48 86 0.67
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.17
Consensus pattern (48 bp):
CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGCGTACAGCCTA
Found at i:104454 original size:20 final size:20
Alignment explanation
Indices: 104429--104466 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
104419 GATAAAATTT
104429 CCAAAGGCATACAACCTACC
1 CCAAAGGCATACAACCTACC
*
104449 CCAAAGGCATACAGCCTA
1 CCAAAGGCATACAACCTA
104467 GATAAAATTT
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:0.39, C:0.37, G:0.13, T:0.11
Consensus pattern (20 bp):
CCAAAGGCATACAACCTACC
Found at i:104480 original size:96 final size:95
Alignment explanation
Indices: 104304--104482 Score: 304
Period size: 95 Copynumber: 1.9 Consensus size: 95
104294 AATGGGCACC
* * ** *
104304 CCCCAAAGGCATACAGCCTAGATAAAATTTCCAAAGGTGTACAGCCACCCCAAAGGCATACAGCC
1 CCCCAAAAGCATACAACCTAGATAAAATTTCCAAAGGCATACAACCACCCCAAAGGCATACAGCC
104369 TAGATAAAATTTCCAAAGACGTATAGCCTA
66 TAGATAAAATTTCCAAAGACGTATAGCCTA
104399 CCCCAAAAGCATACAACCTAGATAAAATTTCCAAAGGCATACAACCTACCCCAAAGGCATACAGC
1 CCCCAAAAGCATACAACCTAGATAAAATTTCCAAAGGCATACAACC-ACCCCAAAGGCATACAGC
104464 CTAGATAAAATTTCCAAAG
65 CTAGATAAAATTTCCAAAG
104483 GCATACAGCC
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 41 0.53
96 37 0.47
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.17
Consensus pattern (95 bp):
CCCCAAAAGCATACAACCTAGATAAAATTTCCAAAGGCATACAACCACCCCAAAGGCATACAGCC
TAGATAAAATTTCCAAAGACGTATAGCCTA
Found at i:104892 original size:29 final size:29
Alignment explanation
Indices: 104839--105319 Score: 488
Period size: 29 Copynumber: 16.3 Consensus size: 29
104829 AAAAAAAAAG
* *
104839 GTGGTAGTACGCCC-CCAAGGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
104867 GTGGTAGTACTCCCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
104896 GTGGTAGTACTCCCTCCAAAGCTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* *
104925 GTGGTAGTACTCCCTCCAAAGTTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* *
104954 GTGGTAGTA-TGCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACT-CCCTCCAAAGCTCACGAA
* *
104983 GTGGTAGTACTCCCTCCAAAGTTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105012 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105041 GTGGTAGTACTCCCTCCAAAGTTC-CTGAA
1 GTGGTAGTACTCCCTCCAAAGCTCAC-GAA
* *
105070 GTAGTAGTACTCCCTCCAAAGGCAAAAAAT-ACCAA
1 GTGGTAGTACTCCCTCCAAA-GC------TCACGAA
* * ****** **** **
105105 GTCATGGGA-AACTTTAAAAAAAAAAAATAAA
1 G---TGGTAGTACTCCCTCCAAAGCTCACGAA
* *
105136 GGTGGTAGTACGCCC-CCAAGGCTCACGAA
1 -GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105165 GTGGTAGTACTCCCTCCAAAGTTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105194 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* *
105223 GTGGTAGTACTCCCTCCAAAGTTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105252 GTGGTAGTACTACCTCCAAAGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
105281 GTGGTAGTACTCCCTCCAAAGTTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
105310 GTGGTAGTAC
1 GTGGTAGTAC
105320 ACCCCTTAGA
Statistics
Matches: 376, Mismatches: 58, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
28 28 0.07
29 326 0.87
30 4 0.01
31 3 0.01
32 1 0.00
35 3 0.01
36 2 0.01
37 6 0.02
38 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (29 bp):
GTGGTAGTACTCCCTCCAAAGCTCACGAA
Found at i:105506 original size:29 final size:29
Alignment explanation
Indices: 105474--105820 Score: 422
Period size: 29 Copynumber: 12.4 Consensus size: 29
105464 ATCTTGAACG
*
105474 AGAGCGCTGTACATCCACCATTTTGGACA
1 AGAGCGCCGTACATCCACCATTTTGGACA
105503 AGAGCGCCGTACATCCACCATTTTGGAC-
1 AGAGCGCCGTACATCCACCATTTTGGACA
*
105531 -GAGCGCCGGACATCCACCATTTTGGAC-
1 AGAGCGCCGTACATCCACCATTTTGGACA
*
105558 -GAGCGCCGTACATCCACCATTTTAGACA
1 AGAGCGCCGTACATCCACCATTTTGGACA
* *
105586 CGAGCGCCGTACATCTACCATTTTGGAC-
1 AGAGCGCCGTACATCCACCATTTTGGACA
*
105614 -GAGCGCCGTACA---ACCATCTTGGA-A
1 AGAGCGCCGTACATCCACCATTTTGGACA
*
105638 GAGAGCGCCGTACA---ACCATTTTGGACT
1 -AGAGCGCCGTACATCCACCATTTTGGACA
*
105665 AGAGCGCCGTACATCCACCATCTTGGA-A
1 AGAGCGCCGTACATCCACCATTTTGGACA
105693 GAGAGCGCCGTACATCCACCATTTTGGAC-
1 -AGAGCGCCGTACATCCACCATTTTGGACA
* *
105722 -GAGCGCTGCACATCCACCATTTTGGACA
1 AGAGCGCCGTACATCCACCATTTTGGACA
* *
105750 AGAGCGTCGTACATCCACCATTTTGGACG
1 AGAGCGCCGTACATCCACCATTTTGGACA
* *
105779 AGAGCGCTGTACATCCACCATCTTGGA-A
1 AGAGCGCCGTACATCCACCATTTTGGACA
105807 GAGAGCGCCGTACA
1 -AGAGCGCCGTACA
105821 ACCATCTTGG
Statistics
Matches: 281, Mismatches: 23, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
24 10 0.04
26 35 0.12
27 88 0.31
29 148 0.53
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (29 bp):
AGAGCGCCGTACATCCACCATTTTGGACA
Found at i:105544 original size:56 final size:54
Alignment explanation
Indices: 105461--105820 Score: 381
Period size: 56 Copynumber: 6.4 Consensus size: 54
105451 GCGTCGTACA
* *
105461 ACCATCTTGAACGAGAGCGCTGTACATCCACCATTTTGGACAAGAGCGCCGTACATCC
1 ACCATCTTGGAC--GAGCGCCGTACATCCACCATTTTGGAC--GAGCGCCGTACATCC
* *
105519 ACCATTTTGGACGAGCGCCGGACATCCACCATTTTGGACGAGCGCCGTACATCC
1 ACCATCTTGGACGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACATCC
* * *
105573 ACCATTTTAGACACGAGCGCCGTACATCTACCATTTTGGACGAGCGCCGTACA---
1 ACCATCTT-G-GACGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACATCC
*
105626 ACCATCTTGGAAGAGAGCGCCGTACA---ACCATTTTGGACTAGAGCGCCGTACATCC
1 ACCATCTTGG-A-CGAGCGCCGTACATCCACCATTTTGGAC--GAGCGCCGTACATCC
* * *
105681 ACCATCTTGGAAGAGAGCGCCGTACATCCACCATTTTGGACGAGCGCTGCACATCC
1 ACCATCTTGG-A-CGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACATCC
* * *
105737 ACCATTTTGGACAAGAGCGTCGTACATCCACCATTTTGGACGAGAGCGCTGTACATCC
1 ACCATCTTGGAC--GAGCGCCGTACATCCACCATTTTGGAC--GAGCGCCGTACATCC
*
105795 ACCATCTTGGAAGAGAGCGCCGTACA
1 ACCATCTTGG-A-CGAGCGCCGTACA
105821 ACCATCTTGG
Statistics
Matches: 265, Mismatches: 19, Indels: 36
0.83 0.06 0.11
Matches are distributed among these distances:
50 12 0.05
52 14 0.05
53 19 0.07
54 23 0.09
55 28 0.11
56 112 0.42
58 56 0.21
59 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (54 bp):
ACCATCTTGGACGAGCGCCGTACATCCACCATTTTGGACGAGCGCCGTACATCC
Found at i:105979 original size:28 final size:28
Alignment explanation
Indices: 105947--106082 Score: 128
Period size: 28 Copynumber: 5.2 Consensus size: 28
105937 AAGATGGAGT
*
105947 GCTCCCAATGACCGCGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
*
105975 GCT-CCAAT----A-G-TG-G-TAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
* *
105994 ACTCCCAACGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
*
106022 GCTCCAAATGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
* * * *
106050 GCTCCCAATGACCGCAAAACGATAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
106078 GCTCC
1 GCTCC
106083 AAAAGCGGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
19 8 0.09
20 5 0.06
21 1 0.01
22 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 6 0.07
28 62 0.72
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (28 bp):
GCTCCCAATGACCACGAAGCGGTAGTAC
Found at i:109982 original size:255 final size:255
Alignment explanation
Indices: 109531--110043 Score: 882
Period size: 255 Copynumber: 2.0 Consensus size: 255
109521 TTCAGCAGAA
* *
109531 CTACTAGTATTGCAAATAATGTCATTATTAGAGCCATCTTCAAGAGTCTGGTGCAAATATTCGTG
1 CTACTAGTATTGCAAATAATGACATTATTAGAGCCACCTTCAAGAGTCTGGTGCAAATATTCGTG
*
109596 AGCTTCACTGGATACTTTTTGAGAAATAGGTATTTGCACTGGTTCTTGATCTTGTGTGGAGAATG
66 AGCTTCACTGGATACTTTTTGAGAAATAGGTATTTGCACTGGTTCTTGATCTTGTGTGGAGAACG
* * * *
109661 ACTTCTTGCTGCTATCAACATCACTAGAACCAGATGAATACCTTGCAAAGTAATTAGCTTTCTTA
131 ACTTCTTGCTGCTATCAACATCACCAGAACCAGAAGAATACCTTCCAAAATAATTAGCTTTCTTA
*
109726 AATGCGCCAGTATATTCACCATCAGGAGAAAGTCCAACATCAGATTGCTCATAAACATTT
196 AATGCACCAGTATATTCACCATCAGGAGAAAGTCCAACATCAGATTGCTCATAAACATTT
* * * * *
109786 CTACTAGTGTTGCAAATAATGACATTATTTGAGCCACCTTCGAGATTTTGGTGCAAATATTCGTG
1 CTACTAGTATTGCAAATAATGACATTATTAGAGCCACCTTCAAGAGTCTGGTGCAAATATTCGTG
109851 AGCTTCACTGGATACTTTTTGAGAAATAGGTATTTGCACTGGTTCTTGATCTTGTGTGGAGAACG
66 AGCTTCACTGGATACTTTTTGAGAAATAGGTATTTGCACTGGTTCTTGATCTTGTGTGGAGAACG
* *
109916 ACTTCTTGCTGTTATCAACATCACCAGAACCAGAAGAATACCTTCCAAAATAGTTAGCTTTCTTA
131 ACTTCTTGCTGCTATCAACATCACCAGAACCAGAAGAATACCTTCCAAAATAATTAGCTTTCTTA
*
109981 AATGCACCTGTATATTCACCATCAGGAGAAAGTCCAACATCAGATTGCTCATAAACATTT
196 AATGCACCAGTATATTCACCATCAGGAGAAAGTCCAACATCAGATTGCTCATAAACATTT
110041 CTA
1 CTA
110044 GTCTGTGGTT
Statistics
Matches: 242, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
255 242 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (255 bp):
CTACTAGTATTGCAAATAATGACATTATTAGAGCCACCTTCAAGAGTCTGGTGCAAATATTCGTG
AGCTTCACTGGATACTTTTTGAGAAATAGGTATTTGCACTGGTTCTTGATCTTGTGTGGAGAACG
ACTTCTTGCTGCTATCAACATCACCAGAACCAGAAGAATACCTTCCAAAATAATTAGCTTTCTTA
AATGCACCAGTATATTCACCATCAGGAGAAAGTCCAACATCAGATTGCTCATAAACATTT
Found at i:112565 original size:211 final size:212
Alignment explanation
Indices: 112200--112621 Score: 810
Period size: 211 Copynumber: 2.0 Consensus size: 212
112190 TTGTCATCAA
*
112200 TACTAGCAGTGTAAAAAACTACTATTTAGAAGATACATATATGACCAAAAGCTTAGCCTTGTCCT
1 TACTAGCAGTGTAAAAAACTACTATTTAGAAGATACATATATGAACAAAAGCTTAGCCTTGTCCT
*
112265 AAAATTAAATTTTGATTAATAACATTCATATATTAACTGCCACAAACTTGTGCAATTATCCATGG
66 AAAATTAAATTTTGATTAATAACATTCATATATTAACTGCCACAAACCTGTGCAATTATCCATGG
112330 CAATAGAGAATAGCTATTGTTTGTTGTTGATACAAGCATAAAACACATGTCTCAATCCTGACCAC
131 CAATAGAGAATAGCTATTGTTTGTTGTTGATACAAGCATAAAACACATGTCTCAATCCTGACCAC
112395 TTTATTATCTCTTTCAG
196 TTTATTATCTCTTTCAG
112412 TACTAGCAGTGTAAAAAACTACTATTTAGAAGATACATATAT-AACAAAAGCTTAGCCTTGTCCT
1 TACTAGCAGTGTAAAAAACTACTATTTAGAAGATACATATATGAACAAAAGCTTAGCCTTGTCCT
112476 AAAATTAAATTTTGATTAATAACATTCATATATTAACTGCCACAAACCTGTGCAATTATCCATGG
66 AAAATTAAATTTTGATTAATAACATTCATATATTAACTGCCACAAACCTGTGCAATTATCCATGG
*
112541 CAATAGAGAATAGCTATTGTTTGTTGTTGATACAAGCATAAAACACATTTCTCAATCCTGACCAC
131 CAATAGAGAATAGCTATTGTTTGTTGTTGATACAAGCATAAAACACATGTCTCAATCCTGACCAC
112606 TTTATTATCTCTTTCA
196 TTTATTATCTCTTTCA
112622 AACTAAATCT
Statistics
Matches: 207, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
211 165 0.80
212 42 0.20
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (212 bp):
TACTAGCAGTGTAAAAAACTACTATTTAGAAGATACATATATGAACAAAAGCTTAGCCTTGTCCT
AAAATTAAATTTTGATTAATAACATTCATATATTAACTGCCACAAACCTGTGCAATTATCCATGG
CAATAGAGAATAGCTATTGTTTGTTGTTGATACAAGCATAAAACACATGTCTCAATCCTGACCAC
TTTATTATCTCTTTCAG
Found at i:117691 original size:2 final size:2
Alignment explanation
Indices: 117686--117719 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
117676 ACAAAAGTTT
117686 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
117720 TAGTTCAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:134055 original size:30 final size:29
Alignment explanation
Indices: 133978--134056 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
133968 TTCTTTTTTG
*
133978 AAACTTAAGGGATTAATTTGTCCAAAAAA
1 AAACTTAAGGGATTATTTTGTCCAAAAAA
* * *
134007 AAATCATAAGGAATTATTTTGTCCCAAACCAA
1 AAA-CTTAAGGGATTATTTTGT-CCAAA-AAA
134039 AAACTTAAGGGA-TATTTT
1 AAACTTAAGGGATTATTTT
134057 TGGGTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 3 0.07
30 21 0.51
31 12 0.29
32 5 0.12
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (29 bp):
AAACTTAAGGGATTATTTTGTCCAAAAAA
Found at i:134297 original size:2 final size:2
Alignment explanation
Indices: 134292--134321 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
134282 TGGATAAATC
*
134292 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134322 GTTCATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:134543 original size:22 final size:21
Alignment explanation
Indices: 134479--134550 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
134469 ATCAAGATTA
134479 GGGTTTGACCATTAAGATTTG
1 GGGTTTGACCATTAAGATTTG
* ** * * *
134500 GGGTTTCATAATCGATGATTGG
1 GGGTTTGACCAT-TAAGATTTG
134522 GGGTTTGACCATTAAGATTTG
1 GGGTTTGACCATTAAGATTTG
134543 GGGTTTGA
1 GGGTTTGA
134551 TCCCATTACA
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.38
Consensus pattern (21 bp):
GGGTTTGACCATTAAGATTTG
Found at i:134606 original size:88 final size:87
Alignment explanation
Indices: 134514--134811 Score: 264
Period size: 88 Copynumber: 3.4 Consensus size: 87
134504 TTCATAATCG
* *
134514 ATGATTGGGGGTTTGACCATTAAGATTTGGGGTTTGATCCCATTACATCATTGGGTTTGCGTAAT
1 ATGATTTGGAGTTTGACCATTAAGATTTGGGGTTTGATCCCATTACAT-ATTGGGTTTGCGTAAT
134579 CATGCTTTACAATTTCACCATAC
65 CATGCTTTACAATTTCACCATAC
** * * * *** * *
134602 ATGATTTACAGTTTGATCATTACGGTTCT-AATTTTGATCCCATTAC-TAGTAGGGTTTAG-GGA
1 ATGATTTGGAGTTTGACCATTAAGATT-TGGGGTTTGATCCCATTACATA-TTGGGTTT-GCGTA
** *
134664 ATCATGCTTTA-AAGTTTCGTCGTAC
63 ATCATGCTTTACAA-TTTCACCATAC
* * * * * * *
134689 ATGATTTGGGGTTTGACCATTACGATTTGGGCTTTGATTCCATTACTAGTAAT-GGTTTGCCTAT
1 ATGATTTGGAGTTTGACCATTAAGATTTGGGGTTTGATCCCATTAC-A-TATTGGGTTTGCGTAA
* *
134753 TCATGCTTTACATTTTGACCATAC
64 TCATGCTTTACAATTTCACCATAC
* *
134777 ATAATTTGTAGTTTGACCATTAAGATTTGGGGTTT
1 ATGATTTGGAGTTTGACCATTAAGATTTGGGGTTT
134812 CACAATGGAT
Statistics
Matches: 161, Mismatches: 39, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
86 4 0.02
87 65 0.40
88 88 0.55
89 2 0.01
90 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (87 bp):
ATGATTTGGAGTTTGACCATTAAGATTTGGGGTTTGATCCCATTACATATTGGGTTTGCGTAATC
ATGCTTTACAATTTCACCATAC
Found at i:134703 original size:87 final size:88
Alignment explanation
Indices: 134546--134712 Score: 198
Period size: 87 Copynumber: 1.9 Consensus size: 88
134536 AGATTTGGGG
* *
134546 TTTGATCCCATTACATCATTGGGTTTGCGTAATCATGCTTTACAATTTCACCATACATGATTTAC
1 TTTGATCCCATTACATCATAGGGTTTGCGGAATCATGCTTTACAATTTCACCATACATGATTTAC
*
134611 AGTTTGATCATTACGGTTCTAAT
66 AGTTTGACCATTACGGTTCTAAT
** *
134634 TTTGATCCCATTAC-T-AGTAGGGTTTAG-GGAATCATGCTTTA-AAGTTTCGTCGTACATGATT
1 TTTGATCCCATTACATCA-TAGGGTTT-GCGGAATCATGCTTTACAA-TTTCACCATACATGATT
***
134695 TGGGGTTTGACCATTACG
63 TACAGTTTGACCATTACG
134713 ATTTGGGCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
86 3 0.04
87 49 0.73
88 15 0.22
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (88 bp):
TTTGATCCCATTACATCATAGGGTTTGCGGAATCATGCTTTACAATTTCACCATACATGATTTAC
AGTTTGACCATTACGGTTCTAAT
Found at i:134715 original size:21 final size:22
Alignment explanation
Indices: 134691--134734 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
134681 CGTCGTACAT
*
134691 GATTTGGGGTTTGA-CCATTAC
1 GATTTGGGCTTTGATCCATTAC
134712 GATTTGGGCTTTGATTCCATTAC
1 GATTTGGGCTTTGA-TCCATTAC
134735 TAGTAATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (22 bp):
GATTTGGGCTTTGATCCATTAC
Found at i:134811 original size:21 final size:21
Alignment explanation
Indices: 134787--134863 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
134777 ATAATTTGTA
134787 GTTTGACCATTAAGATTTGGG
1 GTTTGACCATTAAGATTTGGG
* * * * *
134808 GTTTCACAATGGATGCTTTGGG
1 GTTTGACCAT-TAAGATTTGGG
*
134830 GTTTGACCATTAATATTTGGG
1 GTTTGACCATTAAGATTTGGG
134851 GTTTGACCATTAA
1 GTTTGACCATTAA
134864 ACTAATAGTC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 28 0.64
22 16 0.36
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (21 bp):
GTTTGACCATTAAGATTTGGG
Found at i:137243 original size:20 final size:19
Alignment explanation
Indices: 137211--137249 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
137201 ACCGATCGAT
*
137211 TATATTATTATATATATAA
1 TATATTATGATATATATAA
137230 TATATTTATGATATATATAA
1 TATA-TTATGATATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTATGATATATATAA
Done.