Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_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: 2456583
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 6 of 9
Found at i:1449692 original size:143 final size:143
Alignment explanation
Indices: 1449434--1449726 Score: 577
Period size: 143 Copynumber: 2.0 Consensus size: 143
1449424 TGGAAAGTGG
1449434 AAACCGTTTTAGAGATTTGGAGTTTTCCGAGGGAGAGAAAACGGAACCTTTAGTAACGAAAGTCC
1 AAACCGTTTTAGAGATTTGGAGTTTTCCGAGGGAGAGAAAACGGAACCTTTAGTAACGAAAGTCC
1449499 GTTACACGTGCGGATGGTCCCAACACGTGTGCGCATGTTTGTGCTCTCTGTTTATTTTGTAACGG
66 GTTACACGTGCGGATGGTCCCAACACGTGTGCGCATGTTTGTGCTCTCTGTTTATTTTGTAACGG
1449564 AAGCCAAAAAGAA
131 AAGCCAAAAAGAA
1449577 AAACCGTTTTAGAGATTTGGAGTTTTCCGAGGGAGAGAAAACGGAACCTTTAGTAACGAAAGTCC
1 AAACCGTTTTAGAGATTTGGAGTTTTCCGAGGGAGAGAAAACGGAACCTTTAGTAACGAAAGTCC
1449642 GTTACACGTGCGGATGGTCCCAACACGTGTGCGCATGTTTGTGCTCTCTGTTTATTTTGTAACGG
66 GTTACACGTGCGGATGGTCCCAACACGTGTGCGCATGTTTGTGCTCTCTGTTTATTTTGTAACGG
*
1449707 AAGCCAAAAAGCA
131 AAGCCAAAAAGAA
1449720 AAACCGT
1 AAACCGT
1449727 AGTAACCATC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 149 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (143 bp):
AAACCGTTTTAGAGATTTGGAGTTTTCCGAGGGAGAGAAAACGGAACCTTTAGTAACGAAAGTCC
GTTACACGTGCGGATGGTCCCAACACGTGTGCGCATGTTTGTGCTCTCTGTTTATTTTGTAACGG
AAGCCAAAAAGAA
Found at i:1450062 original size:60 final size:60
Alignment explanation
Indices: 1449960--1450072 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1449950 ATAGTTGAGT
* * *
1449960 GATCATTTTATAACTTTTAATAGTCAAAAAACTCAATGAAATAATATCTTATAGTCTTAG
1 GATCATTTTATAACTTTTAATAGTCAAAAAACTCAATAAAATAACATCCTATAGTCTTAG
* *** *
1450020 GATCATTTTGTAACTTTTAATAGTTGGAGAACTC-ATCAAAATAACATCCTATA
1 GATCATTTTATAACTTTTAATAGTCAAAAAACTCAAT-AAAATAACATCCTATA
1450073 ATTGGAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 2 0.05
60 42 0.95
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAATAGTCAAAAAACTCAATAAAATAACATCCTATAGTCTTAG
Found at i:1451136 original size:30 final size:30
Alignment explanation
Indices: 1451100--1451157 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1451090 ACAGTGATCA
*
1451100 CCATAGGTCTCCAGGAGTATACGGCGACTT
1 CCATAGGTCTCCAGGAGTACACGGCGACTT
*
1451130 CCATAGGTCTTCAGGAGTACACGGCGAC
1 CCATAGGTCTCCAGGAGTACACGGCGAC
1451158 CTATGACGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (30 bp):
CCATAGGTCTCCAGGAGTACACGGCGACTT
Found at i:1451879 original size:17 final size:17
Alignment explanation
Indices: 1451857--1451900 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1451847 ATGTAAAAAT
1451857 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
1451874 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
1451891 AAATATTTAA
1 AAATATTTAA
1451901 TCAAGTAGGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:1453662 original size:20 final size:20
Alignment explanation
Indices: 1453637--1453682 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1453627 CGTCTGCGCG
1453637 TGGTCTGCGTGGCGCAGCCA
1 TGGTCTGCGTGGCGCAGCCA
*
1453657 TGGTCTGCGTGGCGCAGCCG
1 TGGTCTGCGTGGCGCAGCCA
1453677 TGGTCT
1 TGGTCT
1453683 TATGTCTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (20 bp):
TGGTCTGCGTGGCGCAGCCA
Found at i:1453818 original size:60 final size:62
Alignment explanation
Indices: 1453737--1453883 Score: 244
Period size: 60 Copynumber: 2.4 Consensus size: 62
1453727 TTAATTTTAC
1453737 ATTATATTTGATTTTAATTTTAATATT-AATTTTTAAATAAATTAAATAAT-ATTTTTTAAT
1 ATTATATTTGATTTTAATTTTAATATTAAATTTTTAAATAAATTAAATAATAATTTTTTAAT
*
1453797 ATTATATTTGATTTTAATTTTAATATTAAATTTTTAAATAAATTAAATATTAATTTTTTAAT
1 ATTATATTTGATTTTAATTTTAATATTAAATTTTTAAATAAATTAAATAATAATTTTTTAAT
1453859 ATTATATTATAGATATTTAATTTTA
1 ATTATATT-T-GAT-TTTAATTTTA
1453884 TATCATATAA
Statistics
Matches: 81, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
60 27 0.33
61 22 0.27
62 18 0.22
63 1 0.01
64 3 0.04
65 10 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (62 bp):
ATTATATTTGATTTTAATTTTAATATTAAATTTTTAAATAAATTAAATAATAATTTTTTAAT
Found at i:1453938 original size:20 final size:19
Alignment explanation
Indices: 1453878--1453939 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1453868 TAGATATTTA
*
1453878 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1453897 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1453915 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1453935 ATTTT
1 ATTTT
1453940 GATTTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1462086 original size:17 final size:17
Alignment explanation
Indices: 1462053--1462086 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1462043 AAACCTTGAC
* *
1462053 CATACCCGTGTCGGATA
1 CATACCCGTATCCGATA
1462070 CATACCCGTATCCGATA
1 CATACCCGTATCCGATA
1462087 GTCACAACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (17 bp):
CATACCCGTATCCGATA
Found at i:1463542 original size:23 final size:23
Alignment explanation
Indices: 1463511--1463600 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
1463501 TTTTTATTTA
* * *
1463511 TGTTAGTTTATGTTCATTTATTG
1 TGTTCGTTTACGTTCGTTTATTG
* *
1463534 TGTTCGTTTACATTCGTTTGTTTG
1 TGTTCGTTTACGTTCGTTT-ATTG
* *
1463558 TGTTCGTTAACGTTTGTTTATTG
1 TGTTCGTTTACGTTCGTTTATTG
* *
1463581 TGTTCATTTATGTTCGTTTA
1 TGTTCGTTTACGTTCGTTTA
1463601 CATCAGTTCA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 34 0.64
24 19 0.36
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTACGTTCGTTTATTG
Found at i:1463576 original size:24 final size:23
Alignment explanation
Indices: 1463527--1463585 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
1463517 TTTATGTTCA
*
1463527 TTTATTGTGTTCGTTTACATTCG
1 TTTATTGTGTTCGTTAACATTCG
* * *
1463550 TTTGTTTGTGTTCGTTAACGTTTG
1 TTT-ATTGTGTTCGTTAACATTCG
1463574 TTTATTGTGTTC
1 TTTATTGTGTTC
1463586 ATTTATGTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.59
Consensus pattern (23 bp):
TTTATTGTGTTCGTTAACATTCG
Found at i:1463632 original size:14 final size:14
Alignment explanation
Indices: 1463606--1463640 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1463596 GTTTACATCA
1463606 GTTCATTTATATTC
1 GTTCATTTATATTC
* *
1463620 GTTCATTTGTATTT
1 GTTCATTTATATTC
1463634 GTTCATT
1 GTTCATT
1463641 ATTTAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (14 bp):
GTTCATTTATATTC
Found at i:1468291 original size:31 final size:32
Alignment explanation
Indices: 1468229--1468301 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
1468219 TTTCGACTTA
*
1468229 GGTTGATTTTGATTCAAGTTATATTTTGTTTG
1 GGTTGCTTTTGATTCAAGTTATATTTTGTTTG
* *
1468261 TGTTGCTTTTG-TTCTAGTTA-ATTTTGGTTTG
1 GGTTGCTTTTGATTCAAGTTATATTTT-GTTTG
*
1468292 GGTTTCTTTT
1 GGTTGCTTTT
1468302 AATTTGGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 5 0.14
31 21 0.60
32 9 0.26
ACGTcount: A:0.12, C:0.05, G:0.22, T:0.60
Consensus pattern (32 bp):
GGTTGCTTTTGATTCAAGTTATATTTTGTTTG
Found at i:1468595 original size:22 final size:21
Alignment explanation
Indices: 1468557--1468598 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1468547 ATATGATTTT
1468557 TGAAAAAAATAATTAAATAAC
1 TGAAAAAAATAATTAAATAAC
1468578 TGAAATAAAA-AATCTAAATAA
1 TGAAA-AAAATAAT-TAAATAA
1468599 ATGAGCTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
TGAAAAAAATAATTAAATAAC
Found at i:1470746 original size:5 final size:5
Alignment explanation
Indices: 1470736--1470765 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1470726 AAAACACTAC
*
1470736 TATTT TATTT TATTT TAATT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT
1470766 ATGTTCGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:1472360 original size:30 final size:29
Alignment explanation
Indices: 1472326--1472384 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1472316 TTTAATTTTT
1472326 TTAAAAATCAATAAAAATGTAATAAAAAAA
1 TTAAAAATCAAT-AAAATGTAATAAAAAAA
* * *
1472356 TTAAAAGTGAATAAAATTTAATAAAAAAA
1 TTAAAAATCAATAAAATGTAATAAAAAAA
1472385 GAATGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (29 bp):
TTAAAAATCAATAAAATGTAATAAAAAAA
Found at i:1472499 original size:36 final size:34
Alignment explanation
Indices: 1472434--1472502 Score: 84
Period size: 36 Copynumber: 2.0 Consensus size: 34
1472424 TTTTCTAATA
*
1472434 TTAATTTTAAAAAAATATTAAAAAATATTAAATT
1 TTAATTTTAAAAAAATAATAAAAAATATTAAATT
* * *
1472468 TTAATTTTATTAAAAATGAATAAATATTATTAAAT
1 TTAATTTTA-AAAAAAT-AATAAAAAATATTAAAT
1472503 ATTGTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 9 0.31
35 6 0.21
36 14 0.48
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
TTAATTTTAAAAAAATAATAAAAAATATTAAATT
Found at i:1474152 original size:60 final size:59
Alignment explanation
Indices: 1474048--1474207 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 59
1474038 GTATAACTTG
* * *
1474048 GGATGAGATTTGAATGTTCAAAAAGTTT-GGGAACCAATTTAGAATGA-AGATCATAATTTAG
1 GGATGA-ATTAGAATATTCAAAAA-TTTAGGG-ACCAATTTAGAATGATAG-TCATAATTTAA
* *
1474109 GGATGAAATT-GAAATATTCAAAAATTTATGGACTAATTTAGAATGATAGTCATAATTTAA
1 GGATG-AATTAG-AATATTCAAAAATTTAGGGACCAATTTAGAATGATAGTCATAATTTAA
* *
1474169 GGATGAATTAGAATATTTAAAAGTTTAGGGACCAATTTA
1 GGATGAATTAGAATATTCAAAAATTTAGGGACCAATTTA
1474208 AAATAAGGGT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
59 28 0.33
60 34 0.40
61 23 0.27
62 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (59 bp):
GGATGAATTAGAATATTCAAAAATTTAGGGACCAATTTAGAATGATAGTCATAATTTAA
Found at i:1474220 original size:59 final size:59
Alignment explanation
Indices: 1474068--1474221 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 59
1474058 TGAATGTTCA
* *
1474068 AAAAGTTT-GGGAACCAATTTAGAATGAAGATCATAATTTAGGGATGAAATTGAAATATTC
1 AAAAGTTTAGGG-ACCAATTTAGAAT-AAGGTCATAATTTAAGGATGAAATTGAAATATTC
* * * *
1474128 AAAAATTTATGGACTAATTTAGAATGATA-GTCATAATTTAAGGATG-AATT-AGAATATTT
1 AAAAGTTTAGGGACCAATTTAGAAT-A-AGGTCATAATTTAAGGATGAAATTGA-AATATTC
*
1474187 AAAAGTTTAGGGACCAATTTAAAATAAGGGTCATA
1 AAAAGTTTAGGGACCAATTTAGAATAA-GGTCATA
1474222 CTTTGATGAC
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 2 0.03
59 37 0.47
60 36 0.46
61 3 0.04
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (59 bp):
AAAAGTTTAGGGACCAATTTAGAATAAGGTCATAATTTAAGGATGAAATTGAAATATTC
Found at i:1474930 original size:6 final size:6
Alignment explanation
Indices: 1474919--1474960 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1474909 ACCCTCATAG
1474919 GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA
1 GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA GCCTCA
1474961 CCTTTACCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
GCCTCA
Found at i:1487387 original size:44 final size:45
Alignment explanation
Indices: 1487301--1487391 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 45
1487291 GCTATTGAGT
* *
1487301 ACAAAGTCTCAATCAGCAAAAAAAAAAGTGACGAAGACCAATTGC
1 ACAAAGTCTCAATCAGCAAAAAAAAAAGTGACCAAGAACAATTGC
** *
1487346 ACAAAGTCTCCCTCAGC-AAAAGAAAAGTGACCAAGAACAATTGC
1 ACAAAGTCTCAATCAGCAAAAAAAAAAGTGACCAAGAACAATTGC
1487390 AC
1 AC
1487392 GTCCTTCGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 26 0.63
45 15 0.37
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.13
Consensus pattern (45 bp):
ACAAAGTCTCAATCAGCAAAAAAAAAAGTGACCAAGAACAATTGC
Found at i:1496336 original size:51 final size:51
Alignment explanation
Indices: 1496256--1496355 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
1496246 ATGTTAGTCT
*
1496256 GAATACATAGCATAAAGTCCGAAATCGATATTTAACATAATCAAATATTCC
1 GAATACATAGCATAAAGTCCGAAATCGATAATTAACATAATCAAATATTCC
* *
1496307 GAATGCATAGCATAAAGTCCGAAGTCGATAATTAACATAATCAAATATT
1 GAATACATAGCATAAAGTCCGAAATCGATAATTAACATAATCAAATATT
1496356 AAAAATACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (51 bp):
GAATACATAGCATAAAGTCCGAAATCGATAATTAACATAATCAAATATTCC
Found at i:1497016 original size:17 final size:18
Alignment explanation
Indices: 1496982--1497016 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1496972 GAGTCAAAAA
1496982 GAAAAGAAAAAGGAAGAG
1 GAAAAGAAAAAGGAAGAG
*
1497000 GAAAAGATAAA-GAAGAG
1 GAAAAGAAAAAGGAAGAG
1497017 TGCGGCCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
GAAAAGAAAAAGGAAGAG
Found at i:1498432 original size:2 final size:2
Alignment explanation
Indices: 1498425--1498456 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1498415 TTTCACCCTA
1498425 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
1498457 GGATCTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1503875 original size:18 final size:19
Alignment explanation
Indices: 1503852--1503887 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1503842 TGAACCAAAA
*
1503852 GGAAAAGA-AAAAGGAAGG
1 GGAAAAGATAAAAAGAAGG
1503870 GGAAAAGATAAAAAGAAG
1 GGAAAAGATAAAAAGAAG
1503888 CTGCGCGATG
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:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (19 bp):
GGAAAAGATAAAAAGAAGG
Found at i:1513919 original size:2 final size:2
Alignment explanation
Indices: 1513912--1513953 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1513902 ACATACATAC
1513912 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
1513954 GATGTCATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1514825 original size:3 final size:3
Alignment explanation
Indices: 1514819--1514851 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1514809 TCTAAAAAAA
1514819 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1514852 TACATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1515155 original size:21 final size:21
Alignment explanation
Indices: 1515129--1515169 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1515119 CCTAATATAT
* *
1515129 CAACACCAGCTCAATCGCCGC
1 CAACACCAACTCAACCGCCGC
1515150 CAACACCAACTCAACCGCCG
1 CAACACCAACTCAACCGCCG
1515170 TCGCTCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.49, G:0.12, T:0.07
Consensus pattern (21 bp):
CAACACCAACTCAACCGCCGC
Found at i:1518373 original size:31 final size:32
Alignment explanation
Indices: 1518335--1518394 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1518325 CGGTTGAAGG
* *
1518335 ACAAAATATAATTGATCA-ATAAAATGAGAGA
1 ACAAAATATAATTAATCATAGAAAATGAGAGA
1518366 ACAAAATATAATTAATCATAGAAAATGAG
1 ACAAAATATAATTAATCATAGAAAATGAG
1518395 GAGGCATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (32 bp):
ACAAAATATAATTAATCATAGAAAATGAGAGA
Found at i:1519431 original size:22 final size:20
Alignment explanation
Indices: 1519394--1519434 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1519384 TTTAGATTGT
*
1519394 TTTTTTCTTGGTATTTGTGA
1 TTTTTTCTTGGAATTTGTGA
1519414 TTTTTTCTAATGGAATTTGTG
1 TTTTTTCT--TGGAATTTGTG
1519435 GCTCATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.15, C:0.05, G:0.20, T:0.61
Consensus pattern (20 bp):
TTTTTTCTTGGAATTTGTGA
Found at i:1522958 original size:18 final size:17
Alignment explanation
Indices: 1522935--1522994 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
1522925 AACATTCCCA
1522935 GTAATCTTATTCTCACGG
1 GTAATCTTATTCTCAC-G
*
1522953 GTAATCTTACATTC-C-CA
1 GTAATCTT--ATTCTCACG
1522970 GTAATCTTATTCTCACCG
1 GTAATCTTATTCTCA-CG
1522988 GTAATCT
1 GTAATCT
1522995 AATATTCCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 4 0.11
16 1 0.03
17 8 0.23
18 17 0.49
19 1 0.03
20 4 0.11
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (17 bp):
GTAATCTTATTCTCACG
Found at i:1522975 original size:17 final size:17
Alignment explanation
Indices: 1522926--1522978 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1522916 ACAAAATACA
1522926 ACATTCCCAGTAATCTT
1 ACATTCCCAGTAATCTT
*
1522943 --ATTCTCACGGGTAATCTT
1 ACATTC-C-C-AGTAATCTT
1522961 ACATTCCCAGTAATCTT
1 ACATTCCCAGTAATCTT
1522978 A
1 A
1522979 TTCTCACCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 4 0.14
16 1 0.03
17 10 0.34
18 9 0.31
19 1 0.03
20 4 0.14
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (17 bp):
ACATTCCCAGTAATCTT
Found at i:1523002 original size:35 final size:35
Alignment explanation
Indices: 1522925--1523002 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
1522915 CACAAAATAC
*
1522925 AACATTCCCAGTAATCTTATTCTCACGGGTAATCT
1 AACATTCCCAGTAATCTTATTCTCACCGGTAATCT
*
1522960 TACATTCCCAGTAATCTTATTCTCACCGGTAATCT
1 AACATTCCCAGTAATCTTATTCTCACCGGTAATCT
*
1522995 AATATTCC
1 AACATTCC
1523003 GTGAACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (35 bp):
AACATTCCCAGTAATCTTATTCTCACCGGTAATCT
Found at i:1526091 original size:34 final size:33
Alignment explanation
Indices: 1526034--1526097 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
1526024 TATTTTAATC
* *
1526034 AAAATATAATATATAAATGAAATCATAATTATA
1 AAAATATAATATATAAATAAAATCAAAATTATA
* *
1526067 AAAATATATCTATATAATTAAAATCAAAATT
1 AAAATATA-ATATATAAATAAAATCAAAATT
1526098 TTATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 8 0.31
34 18 0.69
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAATATAATATATAAATAAAATCAAAATTATA
Found at i:1531420 original size:96 final size:96
Alignment explanation
Indices: 1531252--1531439 Score: 333
Period size: 96 Copynumber: 2.0 Consensus size: 96
1531242 TATACTCACG
1531252 TGAGCTTCTTGCTTGTATGATGAGTAACCTTAAAGGCTGAACTTGTTGAAATTTAGCATTCAAAG
1 TGAGCTTCTTGCTTGTATGATGAGTAACCTTAAAGGCTGAACTTGTTGAAATTTAGCATTCAAAG
*
1531317 TTCCTTTTTTTATACGTTTCTCTTATACACA
66 TTACTTTTTTTATACGTTTCTCTTATACACA
1531348 TGAGCTTCTTGCTTGTATGATGAGTAACCTTAAAGGCTGAACTTGTTGAAATTTCA-CATTCAAA
1 TGAGCTTCTTGCTTGTATGATGAGTAACCTTAAAGGCTGAACTTGTTGAAATTT-AGCATTCAAA
* *
1531412 TTTACTTTTTTTCTACGTTTCTCTTATA
65 GTTACTTTTTTTATACGTTTCTCTTATA
1531440 AATGAGTTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 87 0.99
97 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (96 bp):
TGAGCTTCTTGCTTGTATGATGAGTAACCTTAAAGGCTGAACTTGTTGAAATTTAGCATTCAAAG
TTACTTTTTTTATACGTTTCTCTTATACACA
Found at i:1544917 original size:59 final size:60
Alignment explanation
Indices: 1544804--1544917 Score: 135
Period size: 59 Copynumber: 1.9 Consensus size: 60
1544794 TACATCACTC
* * * *
1544804 AATTATGATATTTATTTTAATTTAATTTTTAAAATTTTGAATATTTTAGTTTTATTCTTG
1 AATTATGATATTTATTCTAAATTAATTCTTAAAATTTTGAATATTTTAGATTTATTCTTG
* *
1544864 AATTATGAT-TTTCATTCTAAATTAA-TCTTAAATTTTTTAATATTTT-GAATTTAT
1 AATTATGATATTT-ATTCTAAATTAATTCTTAAAATTTTGAATATTTTAG-ATTTAT
1544918 ATCAAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
58 1 0.02
59 26 0.57
60 19 0.41
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (60 bp):
AATTATGATATTTATTCTAAATTAATTCTTAAAATTTTGAATATTTTAGATTTATTCTTG
Found at i:1549936 original size:26 final size:26
Alignment explanation
Indices: 1549907--1549980 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 26
1549897 AAAGTCCAAC
**
1549907 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAAAAATT
* *
1549933 AAA-TGAGA-AATAATAAA-AAAAAATT
1 AAATTTA-ACAA-AATAAAGTAAAAATT
1549958 ACAATTTAACAAAATAAAGTAAA
1 A-AATTTAACAAAATAAAGTAAA
1549981 TACAAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
25 10 0.28
26 19 0.53
27 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (26 bp):
AAATTTAACAAAATAAAGTAAAAATT
Found at i:1552245 original size:110 final size:111
Alignment explanation
Indices: 1552025--1552235 Score: 370
Period size: 110 Copynumber: 1.9 Consensus size: 111
1552015 ATTACAAAAA
* *
1552025 TTAATTCTTAATATAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
1552090 AATTAAAACGTTAAAATGTTACTGTATCAGTAAAGTATCAAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTATCAAGATAT
*
1552136 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1552200 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGT
66 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGT
1552236 GTAGAGATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 61 0.64
111 34 0.36
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTATCAAGATAT
Found at i:1552970 original size:2 final size:2
Alignment explanation
Indices: 1552963--1553003 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1552953 AAGGAAAGTG
1552963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1553004 GAACGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1556118 original size:29 final size:28
Alignment explanation
Indices: 1556071--1556149 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
1556061 GTATGGGCAT
* *
1556071 TATTATTTTAAAAAT--CCCCAATA-AT
1 TATTATTTGAAAAATAACCCCAATACAA
1556096 TAATTATTTGAAAAATTAACCCCAA-ACAA
1 T-ATTATTTGAAAAA-TAACCCCAATACAA
* *
1556125 TATTGTTTGAAAAATAACTCCAATA
1 TATTATTTGAAAAATAACCCCAATA
1556150 GTTTTTTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 1 0.02
26 12 0.27
27 9 0.20
28 14 0.32
29 8 0.18
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (28 bp):
TATTATTTGAAAAATAACCCCAATACAA
Found at i:1562767 original size:15 final size:15
Alignment explanation
Indices: 1562737--1562770 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1562727 TGAGAATTTA
**
1562737 TAAAATTTTATGGGG
1 TAAAATTTTAAAGGG
1562752 TAAAATTTTAAAGGG
1 TAAAATTTTAAAGGG
1562767 TAAA
1 TAAA
1562771 GCATACGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TAAAATTTTAAAGGG
Found at i:1562842 original size:11 final size:11
Alignment explanation
Indices: 1562826--1562853 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1562816 ATTCAACTTC
1562826 TAAATAATTAT
1 TAAATAATTAT
1562837 TAAATAATTAT
1 TAAATAATTAT
1562848 TAAATA
1 TAAATA
1562854 TATCAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAATAATTAT
Found at i:1569402 original size:17 final size:18
Alignment explanation
Indices: 1569363--1569409 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
1569353 TTCATTTTCT
* *
1569363 ATATTTTGATTTTTTAGTT
1 ATATTTTG-TTTTATAGTC
1569382 ATATTTTGTTTTATA-TC
1 ATATTTTGTTTTATAGTC
1569399 ATA-TTTGTTTT
1 ATATTTTGTTTT
1569410 GTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 6 0.23
19 8 0.31
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (18 bp):
ATATTTTGTTTTATAGTC
Found at i:1579615 original size:42 final size:42
Alignment explanation
Indices: 1579556--1579640 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1579546 GGCTCACTAC
1579556 CTCCTTTCTTTGAATTAATGGTCTTTTTAGGTGTTTCAAAGG
1 CTCCTTTCTTTGAATTAATGGTCTTTTTAGGTGTTTCAAAGG
1579598 CTCCTTTCTTTGAATTAATGGTCTTTTTAGGTGTTTCAAAGG
1 CTCCTTTCTTTGAATTAATGGTCTTTTTAGGTGTTTCAAAGG
1579640 C
1 C
1579641 AGAGCTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (42 bp):
CTCCTTTCTTTGAATTAATGGTCTTTTTAGGTGTTTCAAAGG
Found at i:1586420 original size:3 final size:3
Alignment explanation
Indices: 1586412--1586465 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
1586402 AACACTTGTT
*
1586412 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TCTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC
1586457 TTC TTC TTC
1 TTC TTC TTC
1586466 ATTTATCTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 45 0.96
4 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1587648 original size:43 final size:43
Alignment explanation
Indices: 1587594--1587678 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
1587584 TTATTTTATC
1587594 AACACCCCATATGAACAAATCTATTTTCACACTACATTATTCG
1 AACACCCCATATGAACAAATCTATTTTCACACTACATTATTCG
1587637 AACACCCCATATGAACAAATCTATTTTCACACTACATTATTC
1 AACACCCCATATGAACAAATCTATTTTCACACTACATTATTC
1587679 AGACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.31
Consensus pattern (43 bp):
AACACCCCATATGAACAAATCTATTTTCACACTACATTATTCG
Found at i:1587992 original size:31 final size:31
Alignment explanation
Indices: 1587954--1588047 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
1587944 AAATGATCAT
* *
1587954 TAACGTTATCT-ATTTATAATAAATCGGTTAC
1 TAACGTTAT-TGATTTATAACAAATCGGTCAC
*
1587985 TAACGTTATTGATTTATAACAAATCGATCAC
1 TAACGTTATTGATTTATAACAAATCGGTCAC
*
1588016 TAACGCTATTGATTTATAACAAATCGGTCAC
1 TAACGTTATTGATTTATAACAAATCGGTCAC
1588047 T
1 T
1588048 CACCACTAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 56 0.98
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
TAACGTTATTGATTTATAACAAATCGGTCAC
Found at i:1595017 original size:4 final size:4
Alignment explanation
Indices: 1595008--1595038 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1594998 GATTGAAGAA
1595008 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1595039 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1595172 original size:22 final size:22
Alignment explanation
Indices: 1595133--1595179 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1595123 CCAAAAATGC
* *
1595133 ATATTTATCATATATAATGTAT
1 ATATATATCATATATAATATAT
1595155 ATATATAT-ATATATTAATATAT
1 ATATATATCATATA-TAATATAT
1595177 ATA
1 ATA
1595180 CACAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATATATCATATATAATATAT
Found at i:1597091 original size:23 final size:23
Alignment explanation
Indices: 1597061--1597109 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1597051 TTGATAATCA
1597061 AGTCTTTGATGAGTTCGAGTTCG
1 AGTCTTTGATGAGTTCGAGTTCG
1597084 AGTCTTTGATGAGTTCGAGTTCG
1 AGTCTTTGATGAGTTCGAGTTCG
1597107 AGT
1 AGT
1597110 TCAAGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.39
Consensus pattern (23 bp):
AGTCTTTGATGAGTTCGAGTTCG
Found at i:1597889 original size:121 final size:125
Alignment explanation
Indices: 1597663--1597964 Score: 434
Period size: 121 Copynumber: 2.4 Consensus size: 125
1597653 CGGTTACTGA
1597663 TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATCCTTCTTAAAATAATATTTTTGGATCG
1 TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATCCTTCTTAAAATAATATTTTTGGATCG
* *
1597728 AAAAATAATATGAAATGCACCTTTTATTTAATAACCG-A-T-A-TTTTTAACGGTTGTTG
66 AAAAATAATACGAAATGCACCTTTTATTTAATAACCGAATTAACTTTTTAACGGTTGTGG
*
1597784 TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATTCTTCTTAAAATAATATTTTTGGATCG
1 TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATCCTTCTTAAAATAATATTTTTGGATCG
* * * *
1597849 AAAAATAATACGAAATGCACCTTTTGTTTAGTATCTGATATTTTTAACTTTTTAACGGTTGTGG
66 AAAAATAATACGAAATGCACCTTTTATTTAATAACCGA-A---TTAACTTTTTAACGGTTGTGG
* * *
1597913 TCTTGATCAGTGTGTAAACTTTATTATTTTGTACTTATCCTT-TCTAAAATAA
1 TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATCCTTCT-TAAAATAA
1597965 AATAAACGCG
Statistics
Matches: 161, Mismatches: 11, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
121 96 0.60
123 1 0.01
127 1 0.01
128 2 0.01
129 61 0.38
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (125 bp):
TCTTGATCAATGTGTAAACTTTATTCTTTTGTGCTTATCCTTCTTAAAATAATATTTTTGGATCG
AAAAATAATACGAAATGCACCTTTTATTTAATAACCGAATTAACTTTTTAACGGTTGTGG
Found at i:1598780 original size:17 final size:17
Alignment explanation
Indices: 1598738--1598781 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1598728 GTCGCGGTTA
*
1598738 CGGATGTTACGATGTTG
1 CGGATGTTACGATGTAG
*
1598755 CGGGTGTTACGATGTAG
1 CGGATGTTACGATGTAG
*
1598772 CGGACGTTAC
1 CGGATGTTAC
1598782 AGCTTGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (17 bp):
CGGATGTTACGATGTAG
Found at i:1603727 original size:43 final size:43
Alignment explanation
Indices: 1603624--1603833 Score: 136
Period size: 43 Copynumber: 4.8 Consensus size: 43
1603614 AGTTTAGATA
* * *
1603624 TTTTGCGGCGTTTGTAACAAAAAACGCCGCTATATACCAGATC
1 TTTTGCGGCGTTTGTATCAGAAAACGCCGCTATATACCAGACC
** * * * *
1603667 TTTTGCAACGTTAGTATCTGAAAACGCCGTTATATACCATACC
1 TTTTGCGGCGTTTGTATCAGAAAACGCCGCTATATACCAGACC
* * * ** *
1603710 TTTTGCGGCGTTTGTATCCGAACAACGCAGCTATAGATGTAGACA
1 TTTTGCGGCGTTTGTATCAGAA-AACGCCGCTATATA-CCAGACC
* * * ** * **
1603755 TTTTGCGGCGTTTATATCCAAAAAAACACCATTAAATATTTAGA-C
1 TTTTGCGGCGTTTGTAT-C-AGAAAACGCCGCTATATA-CCAGACC
* *
1603800 TTTTGCGGCGTTTAT-TCAAAAAACGCCGCTATAT
1 TTTTGCGGCGTTTGTATCAGAAAACGCCGCTATAT
1603834 CTCTTCACCT
Statistics
Matches: 128, Mismatches: 35, Indels: 9
0.74 0.20 0.05
Matches are distributed among these distances:
42 13 0.10
43 53 0.41
44 12 0.09
45 34 0.27
46 14 0.11
47 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (43 bp):
TTTTGCGGCGTTTGTATCAGAAAACGCCGCTATATACCAGACC
Found at i:1614298 original size:5 final size:5
Alignment explanation
Indices: 1614288--1614317 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1614278 CAAACATATT
1614288 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1614318 CCCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1636087 original size:49 final size:49
Alignment explanation
Indices: 1636015--1636115 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
1636005 AAACCGCTTC
1636015 CCACATAAAACCCTCTTTCATGGCGGCTTCCTTACACCGCCACGATTCT
1 CCACATAAAACCCTCTTTCATGGCGGCTTCCTTACACCGCCACGATTCT
* *
1636064 CCACATAGAACCCTCTTTCATGGCGGCTTCCTTGCACCGCCACGATTCT
1 CCACATAAAACCCTCTTTCATGGCGGCTTCCTTACACCGCCACGATTCT
1636113 CCA
1 CCA
1636116 ATTATCTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.26
Consensus pattern (49 bp):
CCACATAAAACCCTCTTTCATGGCGGCTTCCTTACACCGCCACGATTCT
Found at i:1639015 original size:23 final size:22
Alignment explanation
Indices: 1638952--1639016 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
1638942 AATAATTTTG
* *
1638952 CCTTTATGACAAGTCTTCTTCTA
1 CCTTTATGACACGT-TTTTTCTA
* * * *
1638975 TCTTTGTGACACAATTTTATCTA
1 CCTTTATGACAC-GTTTTTTCTA
1638998 CCTTTATGACACGTTTTTT
1 CCTTTATGACACGTTTTTT
1639017 TGTTTGGTCG
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
22 5 0.16
23 25 0.81
24 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (22 bp):
CCTTTATGACACGTTTTTTCTA
Found at i:1643253 original size:8 final size:8
Alignment explanation
Indices: 1643240--1643406 Score: 113
Period size: 8 Copynumber: 20.9 Consensus size: 8
1643230 TGGGATATAA
*
1643240 AATGACAG
1 AATGACCG
*
1643248 AATGACCT
1 AATGACCG
*
1643256 AATGGCCG
1 AATGACCG
*
1643264 AATGATCG
1 AATGACCG
***
1643272 AATGATAA
1 AATGACCG
1643280 AATGACCG
1 AATGACCG
1643288 AATGACCG
1 AATGACCG
*
1643296 AATGACCT
1 AATGACCG
*
1643304 AATGACTG
1 AATGACCG
*
1643312 AATGACCT
1 AATGACCG
*
1643320 AATGATCG
1 AATGACCG
**
1643328 AATGACAT
1 AATGACCG
*
1643336 AATGACTG
1 AATGACCG
* *
1643344 AATGGCTG
1 AATGACCG
*
1643352 AATGACCT
1 AATGACCG
**
1643360 AATGATTG
1 AATGACCG
1643368 AATGACCTG
1 AATGACC-G
*
1643377 -ATGACTG
1 AATGACCG
1643384 AATGACTC-
1 AATGAC-CG
*
1643392 AATGATCG
1 AATGACCG
1643400 AATGACC
1 AATGACC
1643407 TGATGATCTA
Statistics
Matches: 119, Mismatches: 36, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
7 2 0.02
8 116 0.97
9 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (8 bp):
AATGACCG
Found at i:1643266 original size:16 final size:16
Alignment explanation
Indices: 1643240--1643503 Score: 111
Period size: 16 Copynumber: 16.0 Consensus size: 16
1643230 TGGGATATAA
*
1643240 AATGACAGAATGACCT
1 AATGACCGAATGACCT
* * *
1643256 AATGGCCGAATGATCG
1 AATGACCGAATGACCT
*** *
1643272 AATGATAAAATGACCG
1 AATGACCGAATGACCT
1643288 AATGACCGAATGACCT
1 AATGACCGAATGACCT
*
1643304 AATGACTGAATGACCT
1 AATGACCGAATGACCT
* *
1643320 AATGATCGAATGACAT
1 AATGACCGAATGACCT
1643336 AATGACTGAATGGCTGAATGACCT
1 AATGAC-------C-GAATGACCT
**
1643360 AATGATTGAATGACCT
1 AATGACCGAATGACCT
* *
1643376 GATGACTGAATGA-CT
1 AATGACCGAATGACCT
*
1643391 CAATGATCGAATGACCT
1 -AATGACCGAATGACCT
* * * *
1643408 GATGATCTAACGA-CT
1 AATGACCGAATGACCT
*** *
1643423 GAATGGTTGAATGACTT
1 -AATGACCGAATGACCT
* * *
1643440 AATGATC-AGATGTCCG
1 AATGACCGA-ATGACCT
* * *
1643456 AATGACCGAACGCCCA
1 AATGACCGAATGACCT
*
1643472 AATGACCAAATGACCT
1 AATGACCGAATGACCT
**
1643488 AATGATTGAATGACCT
1 AATGACCGAATGACCT
1643504 CACACTTGTA
Statistics
Matches: 183, Mismatches: 51, Indels: 28
0.70 0.19 0.11
Matches are distributed among these distances:
15 5 0.03
16 160 0.87
17 4 0.02
23 1 0.01
24 13 0.07
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (16 bp):
AATGACCGAATGACCT
Found at i:1643333 original size:32 final size:32
Alignment explanation
Indices: 1643240--1643503 Score: 142
Period size: 32 Copynumber: 8.0 Consensus size: 32
1643230 TGGGATATAA
* ** * *
1643240 AATGACAGAATGACCTAATGGCCGAATGATCG
1 AATGACTGAATGACCTAATGATCGAATGACCT
* * *
1643272 AATGA-TAAAATGACCGAATGACCGAATGACCT
1 AATGACT-GAATGACCTAATGATCGAATGACCT
1643304 AATGACTGAATGACCTAATGATCGAATGACATAATGACT
1 AATGACTGAATGACCTAATGATCGAATGAC-------CT
* *
1643343 GAATGGCTGAATGACCTAATGATTGAATGACCT
1 -AATGACTGAATGACCTAATGATCGAATGACCT
*
1643376 GATGACTGAATGA-CTCAATGATCGAATGACCT
1 AATGACTGAATGACCT-AATGATCGAATGACCT
* * * * *
1643408 GATGATCT-AACGA-CTGAATGGTTGAATGACTT
1 AATGA-CTGAATGACCT-AATGATCGAATGACCT
* * * * * * *
1643440 AATGA-TCAGATGTCCGAATGACCGAACGCCCA
1 AATGACTGA-ATGACCTAATGATCGAATGACCT
** *
1643472 AATGACCAAATGACCTAATGATTGAATGACCT
1 AATGACTGAATGACCTAATGATCGAATGACCT
1643504 CACACTTGTA
Statistics
Matches: 177, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
30 1 0.01
31 3 0.02
32 136 0.77
33 7 0.04
39 2 0.01
40 28 0.16
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (32 bp):
AATGACTGAATGACCTAATGATCGAATGACCT
Found at i:1643340 original size:40 final size:40
Alignment explanation
Indices: 1643247--1643446 Score: 172
Period size: 40 Copynumber: 5.0 Consensus size: 40
1643237 TAAAATGACA
* * *** *
1643247 GAATGACCTAATGGCCGAATGA-TCGAATGATAAAATGACC
1 GAATGACCTAATGACTGAATGACT-GAATGACCTAATGATC
*
1643287 GAATGACCGAATGACCT-AATGACTGAATGACCTAATGATC
1 GAATGACCTAATGA-CTGAATGACTGAATGACCTAATGATC
* * *
1643327 GAATGACATAATGACTGAATGGCTGAATGACCTAATGATT
1 GAATGACCTAATGACTGAATGACTGAATGACCTAATGATC
* * * * *
1643367 GAATGACCTGATGACTGAATGACTCAATGATCGAATGACC
1 GAATGACCTAATGACTGAATGACTGAATGACCTAATGATC
* * ** *
1643407 TG-ATGATCTAACGACTGAATGGTTGAATGACTTAATGATC
1 -GAATGACCTAATGACTGAATGACTGAATGACCTAATGATC
1643447 AGATGTCCGA
Statistics
Matches: 127, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
39 2 0.02
40 122 0.96
41 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (40 bp):
GAATGACCTAATGACTGAATGACTGAATGACCTAATGATC
Found at i:1644590 original size:8 final size:8
Alignment explanation
Indices: 1644577--1644642 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
1644567 TAATAATATT
1644577 TATAATAA
1 TATAATAA
*
1644585 TATAATAT
1 TATAATAA
*
1644593 TAT-AT-T
1 TATAATAA
*
1644599 TATAATAT
1 TATAATAA
1644607 TATAATAA
1 TATAATAA
*
1644615 AATAATCAA
1 TATAAT-AA
*
1644624 T-T-ATAT
1 TATAATAA
1644630 TATAATAA
1 TATAATAA
1644638 TATAA
1 TATAA
1644643 GATATTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
6 6 0.13
7 7 0.15
8 32 0.68
9 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (8 bp):
TATAATAA
Found at i:1644594 original size:53 final size:53
Alignment explanation
Indices: 1644546--1644654 Score: 132
Period size: 53 Copynumber: 2.0 Consensus size: 53
1644536 ATATTAATGA
* * *
1644546 TTAAAATATT-TAA-AATATATTTAATAATATTTATAATAATATAATATTATAT
1 TTAAAATATTATAATAAAATAATCAATAATA-TTATAATAATATAATATTATAT
* *
1644598 TTATAATATTATAATAAAATAATCAATTATATTATAATAATATAAGATATTATAT
1 TTAAAATATTATAATAAAATAATCAATAATATTATAATAATAT-A-ATATTATAT
1644653 TT
1 TT
1644655 TTATTTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
52 9 0.19
53 15 0.31
54 13 0.27
55 11 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (53 bp):
TTAAAATATTATAATAAAATAATCAATAATATTATAATAATATAATATTATAT
Found at i:1644597 original size:22 final size:20
Alignment explanation
Indices: 1644550--1644614 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 20
1644540 TAATGATTAA
* *
1644550 AATATTTAAAATATATTTAAT
1 AATATTTATAATA-ATATAAT
1644571 AATATTTATAATAATATAAT
1 AATATTTATAATAATATAAT
*
1644591 ATTATATTTATAATATTATAAT
1 A--ATATTTATAATAATATAAT
1644613 AA
1 AA
1644615 AATAATCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 8 0.21
21 12 0.31
22 19 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTATAATAATATAAT
Found at i:1644604 original size:14 final size:14
Alignment explanation
Indices: 1644561--1644610 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
1644551 ATATTTAAAA
1644561 TATATTTAATAATATT
1 TATATTT-ATAATA-T
*
1644577 TATAATAATATAATAT
1 TAT-AT-TTATAATAT
1644593 TATATTTATAATAT
1 TATATTTATAATAT
1644607 TATA
1 TATA
1644611 ATAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.40
15 2 0.07
16 7 0.23
17 8 0.27
18 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTTATAATAT
Found at i:1644737 original size:23 final size:25
Alignment explanation
Indices: 1644698--1644751 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
1644688 ATTATATTAT
*
1644698 TTATTAATTTCATAT-A-AATAATA
1 TTATTAAATTCATATAAGAATAATA
1644721 TTATTAAATT-ATAATAATGAATAATA
1 TTATTAAATTCAT-ATAA-GAATAATA
1644747 TTATT
1 TTATT
1644752 TATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 11 0.42
24 1 0.04
26 12 0.46
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TTATTAAATTCATATAAGAATAATA
Found at i:1644757 original size:35 final size:36
Alignment explanation
Indices: 1644718--1644788 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
1644708 CATATAAATA
* *
1644718 ATATTATTAA-ATTA-TAATAATGAA-TAATATTATTT
1 ATATT-TTAATATTAGT-ATAATAAACTAATAATATTT
1644753 ATATTTTAATATTAGTATAATAAACTAATAATATTT
1 ATATTTTAATATTAGTATAATAAACTAATAATATTT
1644789 TAATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 4 0.13
35 16 0.52
36 11 0.35
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (36 bp):
ATATTTTAATATTAGTATAATAAACTAATAATATTT
Found at i:1644808 original size:23 final size:23
Alignment explanation
Indices: 1644789--1644833 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1644779 AATAATATTT
1644789 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
1644812 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
1644834 ATATAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:1644840 original size:21 final size:21
Alignment explanation
Indices: 1644789--1644841 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
1644779 AATAATATTT
1644789 TAATA-AATATATTTAAAATA
1 TAATATAATATATTTAAAATA
* *
1644809 TACTAATTAATATTTTTAAAATA
1 TAAT-A-TAATATATTTAAAATA
1644832 TAATATAATA
1 TAATATAATA
1644842 CTGTTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 6 0.22
22 1 0.04
23 17 0.63
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATAATATATTTAAAATA
Found at i:1646783 original size:14 final size:14
Alignment explanation
Indices: 1646764--1646794 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1646754 AATTTATTAT
1646764 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
1646778 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
1646792 GTT
1 GTT
1646795 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1648756 original size:14 final size:15
Alignment explanation
Indices: 1648737--1648765 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1648727 AAGATTTGAT
1648737 GAGAATTT-ATAAAA
1 GAGAATTTAATAAAA
1648751 GAGAATTTAATAAAA
1 GAGAATTTAATAAAA
1648766 AATATGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (15 bp):
GAGAATTTAATAAAA
Found at i:1651830 original size:48 final size:49
Alignment explanation
Indices: 1651775--1651872 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
1651765 ACCGACGAAG
*
1651775 ACCCACATGTTATCCATTACTCATTAATGTTATTTAATT-AACACTGAA
1 ACCCACATGTTATCCATTACTCATTAATGTTATTCAATTCAACACTGAA
1651823 ACCCACATGTTATCCATTACTCATTAATGTTATTCAATTCAACACTGAA
1 ACCCACATGTTATCCATTACTCATTAATGTTATTCAATTCAACACTGAA
1651872 A
1 A
1651873 TTAATTATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 38 0.79
49 10 0.21
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (49 bp):
ACCCACATGTTATCCATTACTCATTAATGTTATTCAATTCAACACTGAA
Found at i:1652068 original size:2 final size:2
Alignment explanation
Indices: 1652063--1652106 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1652053 AACGTGTGTG
1652063 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
1652105 TA
1 TA
1652107 AGATTATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1653180 original size:31 final size:30
Alignment explanation
Indices: 1653111--1653223 Score: 86
Period size: 31 Copynumber: 3.7 Consensus size: 30
1653101 AAAAAGATTT
** *
1653111 AATACTTTAAGTA-TCTATTTTGACCAAAAT
1 AATACTTTAAGTACT-TATTTTGAAAAAAAA
*
1653141 GATAACTTTAAGTACTTATTTTGATAAAAAAA
1 AAT-ACTTTAAGTACTTATTTTGA-AAAAAAA
* **
1653173 AATACTTTAATTACTTAGATT-AAAAATATAA
1 AATACTTTAAGTACTTATTTTGAAAAA-A-AA
* *
1653204 TATACTTTAAGTATTTATTT
1 AATACTTTAAGTACTTATTT
1653224 ATGATATAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
29 4 0.06
30 4 0.06
31 50 0.77
32 7 0.11
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.42
Consensus pattern (30 bp):
AATACTTTAAGTACTTATTTTGAAAAAAAA
Found at i:1653364 original size:2 final size:2
Alignment explanation
Indices: 1653353--1653409 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1653343 ATTTAAATCA
1653353 AT AT -T 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
1653394 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1653410 GCATGCATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1653778 original size:23 final size:23
Alignment explanation
Indices: 1653752--1653804 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1653742 GTGGTATTCC
1653752 TTTTCCTCATTTTTTGAACGTTA
1 TTTTCCTCATTTTTTGAACGTTA
* ** * *
1653775 TTTTGCAGATTTTTTTAACTTTA
1 TTTTCCTCATTTTTTGAACGTTA
1653798 TTTTCCT
1 TTTTCCT
1653805 GATCGAGGTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (23 bp):
TTTTCCTCATTTTTTGAACGTTA
Found at i:1655803 original size:102 final size:101
Alignment explanation
Indices: 1655634--1656033 Score: 543
Period size: 102 Copynumber: 3.9 Consensus size: 101
1655624 TTGTGTCTGG
* * *
1655634 GGGAGTGTCTCCTCAGGGCCAGCATTT-TGGACTGTTGGGGACTGCCTCTGGGTTAGTCAAGCAG
1 GGGAGTGTCTCCTCAGGGCCA-AATTTCTGGACTGTTGGGCACTGCCTCT-GGTTCGTCAAGCAG
* *
1655698 GTCTCATCTGATGTCATCTCGGCTGCCCAAATGTCTCC
64 GTCTCATCCGATGCCATCTCGGCTGCCCAAATGTCTCC
1655736 GGGAGTGTCTCCTCAGGGCCAAATTTCTGGACTGTTGGGCACTGCCTCTGGACTT-GTCAAGCAG
1 GGGAGTGTCTCCTCAGGGCCAAATTTCTGGACTGTTGGGCACTGCCTCTGG--TTCGTCAAGCAG
* *
1655800 GTCTCATCCGATGCCATCTCGGCTGTCCAAATGTCCCC
64 GTCTCATCCGATGCCATCTCGGCTGCCCAAATGTCTCC
* * * * * * *
1655838 GGGAGGGTCTCCTCAGGGTCAACTTTTTGGACTGGTGGGCAATGCCTCTGGATTCGTCAAGCAGA
1 GGGAGTGTCTCCTCAGGGCCAAATTTCTGGACTGTTGGGCACTGCCTCTGG-TTCGTCAAGCAGG
*
1655903 TCTCATCCGATGCCATCTCGGCTGCTCAAATGTCTCC
65 TCTCATCCGATGCCATCTCGGCTGCCCAAATGTCTCC
* * ** *
1655940 GGGTGTGTCTCCTCAGGGTCAACCTTCTGGACTGTTGGGCACTGCCTCTGGTTTCGTCAAGCAGC
1 GGGAGTGTCTCCTCAGGGCCAAATTTCTGGACTGTTGGGCACTGCCTCTGG-TTCGTCAAGCAGG
*
1656005 TCTCATCCGATGCCATCTCAGCTGCCCAA
65 TCTCATCCGATGCCATCTCGGCTGCCCAA
1656034 GGTGTGGCTA
Statistics
Matches: 267, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
101 8 0.03
102 257 0.96
103 2 0.01
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.28
Consensus pattern (101 bp):
GGGAGTGTCTCCTCAGGGCCAAATTTCTGGACTGTTGGGCACTGCCTCTGGTTCGTCAAGCAGGT
CTCATCCGATGCCATCTCGGCTGCCCAAATGTCTCC
Found at i:1658684 original size:18 final size:18
Alignment explanation
Indices: 1658661--1658802 Score: 162
Period size: 18 Copynumber: 7.9 Consensus size: 18
1658651 TTATTGCAGG
1658661 TTGGCGATTTGAGTAAAC
1 TTGGCGATTTGAGTAAAC
**
1658679 TTGGCGATTTGAGTAGGC
1 TTGGCGATTTGAGTAAAC
**
1658697 TTGGCGATTTGAGTAGGC
1 TTGGCGATTTGAGTAAAC
**
1658715 TTGGCGATTTGAGTAGGC
1 TTGGCGATTTGAGTAAAC
1658733 TTGGCGATTTGAGTAAAC
1 TTGGCGATTTGAGTAAAC
* *
1658751 TTGGAGATTTGAGTAATC
1 TTGGCGATTTGAGTAAAC
* *
1658769 TTGGAGAGTTGAGTAAGA-
1 TTGGCGATTTGAGTAA-AC
1658787 TTGGC-AGTTTGAGTAA
1 TTGGCGA-TTTGAGTAA
1658803 GATCGATGCA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
17 1 0.01
18 111 0.99
ACGTcount: A:0.24, C:0.08, G:0.34, T:0.34
Consensus pattern (18 bp):
TTGGCGATTTGAGTAAAC
Found at i:1658708 original size:36 final size:36
Alignment explanation
Indices: 1658661--1658801 Score: 187
Period size: 36 Copynumber: 3.9 Consensus size: 36
1658651 TTATTGCAGG
1658661 TTGGCGATTTGAGTAAACTTGGCGATTTGAGTAGGC
1 TTGGCGATTTGAGTAAACTTGGCGATTTGAGTAGGC
**
1658697 TTGGCGATTTGAGTAGGCTTGGCGATTTGAGTAGGC
1 TTGGCGATTTGAGTAAACTTGGCGATTTGAGTAGGC
* **
1658733 TTGGCGATTTGAGTAAACTTGGAGATTTGAGTAATC
1 TTGGCGATTTGAGTAAACTTGGCGATTTGAGTAGGC
* *
1658769 TTGGAGAGTTGAGTAAGA-TTGGC-AGTTTGAGTA
1 TTGGCGATTTGAGTAA-ACTTGGCGA-TTTGAGTA
1658802 AGATCGATGC
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
35 1 0.01
36 91 0.98
37 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.34, T:0.34
Consensus pattern (36 bp):
TTGGCGATTTGAGTAAACTTGGCGATTTGAGTAGGC
Found at i:1661565 original size:19 final size:19
Alignment explanation
Indices: 1661541--1661578 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1661531 GCTTCTGGAG
1661541 ATGTTAGACTCATATCTTT
1 ATGTTAGACTCATATCTTT
1661560 ATGTTAGACTCATATCTTT
1 ATGTTAGACTCATATCTTT
1661579 GTTATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (19 bp):
ATGTTAGACTCATATCTTT
Found at i:1665456 original size:60 final size:60
Alignment explanation
Indices: 1665363--1665480 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
1665353 CACATTTACA
* * * * *
1665363 GTAGAGTCGCGACCCCATAGGAGGACTTCGAGATGTGCTGCAGCCATAAACTCTTACCAC
1 GTAGAGTCGCAACCCCACAGGACGACTACGAGATGTGCTGCAGCCATAAAATCTTACCAC
*
1665423 GTAGAGTCGCAACCCCACCGGACGACTACGAGATGTGCTGCAGCCATAAAATCTTACC
1 GTAGAGTCGCAACCCCACAGGACGACTACGAGATGTGCTGCAGCCATAAAATCTTACC
1665481 GGGACATGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (60 bp):
GTAGAGTCGCAACCCCACAGGACGACTACGAGATGTGCTGCAGCCATAAAATCTTACCAC
Found at i:1667082 original size:18 final size:18
Alignment explanation
Indices: 1667051--1667092 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1667041 AAAATATTTA
1667051 TAAATAAAATTAAACATT
1 TAAATAAAATTAAACATT
*
1667069 TAAA-AAAATATAAATATTT
1 TAAATAAAAT-TAAACA-TT
1667088 TAAAT
1 TAAAT
1667093 TTTCTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATAAAATTAAACATT
Found at i:1668051 original size:2 final size:2
Alignment explanation
Indices: 1668044--1668069 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1668034 GTCATGAACT
1668044 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
1668070 AATAATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1672098 original size:14 final size:14
Alignment explanation
Indices: 1672079--1672108 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1672069 TCAATGTTTA
1672079 TTTTTTTATT-AAT
1 TTTTTTTATTAAAT
1672092 TTTTTTTATTAAAT
1 TTTTTTTATTAAAT
1672106 TTT
1 TTT
1672109 ATCTCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTATTAAAT
Found at i:1673549 original size:69 final size:69
Alignment explanation
Indices: 1673468--1673621 Score: 299
Period size: 69 Copynumber: 2.2 Consensus size: 69
1673458 CGACGTTCAT
1673468 CATGGTAGCATAATCGCCATGCCTGTCAATCGGTAGCTCTTTTCCTTGAGGTAAAGGATGTTTCT
1 CATGGTAGCATAATCGCCATGCCTGTCAATCGGTAGCTCTTTTCCTTGAGGTAAAGGATGTTTCT
1673533 CTAG
66 CTAG
*
1673537 CATGGTAGCATAATCGCCATGCCTGTCAATTGGTAGCTCTTTTCCTTGAGGTAAAGGATGTTTCT
1 CATGGTAGCATAATCGCCATGCCTGTCAATCGGTAGCTCTTTTCCTTGAGGTAAAGGATGTTTCT
1673602 CTAG
66 CTAG
1673606 CATGGTAGCATAATCG
1 CATGGTAGCATAATCG
1673622 TCGTTTCCAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 84 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (69 bp):
CATGGTAGCATAATCGCCATGCCTGTCAATCGGTAGCTCTTTTCCTTGAGGTAAAGGATGTTTCT
CTAG
Found at i:1676025 original size:17 final size:18
Alignment explanation
Indices: 1675998--1676031 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1675988 ATAACATGTT
*
1675998 TAAATATAAAACTTAAAA
1 TAAATATAAAAATTAAAA
1676016 TAAA-ATAAAAATTAAA
1 TAAATATAAAAATTAAA
1676032 TCTTGAAATT
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:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATATAAAAATTAAAA
Found at i:1676031 original size:24 final size:25
Alignment explanation
Indices: 1675999--1676050 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1675989 TAACATGTTT
*
1675999 AAATATAAAACTTAAAATAAAATAA
1 AAATATAAAACTTAAAATAAAAGAA
* * *
1676024 AAAT-TAAATCTTGAAATTAAAGAA
1 AAATATAAAACTTAAAATAAAAGAA
1676048 AAA
1 AAA
1676051 AGAACTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
AAATATAAAACTTAAAATAAAAGAA
Found at i:1678502 original size:40 final size:41
Alignment explanation
Indices: 1678447--1678535 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
1678437 ATTTACTGAA
1678447 ATAATTTTTATTTAATAT-AGTGATTAACATTTTTTATTAT
1 ATAATTTTTATTTAATATAAGTGATTAACATTTTTTATTAT
*
1678487 ATAATTTTTATTTAATATAAGTGATTAACGTTTTTTATTAT
1 ATAATTTTTATTTAATATAAGTGATTAACATTTTTTATTAT
1678528 ATAATTTT
1 ATAATTTT
1678536 CAAATAAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 18 0.38
41 29 0.62
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (41 bp):
ATAATTTTTATTTAATATAAGTGATTAACATTTTTTATTAT
Found at i:1680008 original size:23 final size:21
Alignment explanation
Indices: 1679978--1680025 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
1679968 ATTTTATTAA
*
1679978 TAATATATTAAATTATATAATTT
1 TAATATATTAAA-TATA-AATCT
1680001 TAATATATTAAATATAAATCT
1 TAATATATTAAATATAAATCT
1680022 TAAT
1 TAAT
1680026 TGAAAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 4 0.17
23 12 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATATTAAATATAAATCT
Found at i:1689471 original size:18 final size:19
Alignment explanation
Indices: 1689434--1689475 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1689424 TTATCAATAA
1689434 AAAATATATAGAAAATTTT
1 AAAATATATAGAAAATTTT
* *
1689453 AAAATATATA-TATATTTT
1 AAAATATATAGAAAATTTT
1689471 AAAAT
1 AAAAT
1689476 GAATTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATATATAGAAAATTTT
Found at i:1691685 original size:20 final size:20
Alignment explanation
Indices: 1691660--1691699 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1691650 GCGTAAAAAT
1691660 ATTTGACTT-TCGCGTTGCGA
1 ATTTGACTTAT-GCGTTGCGA
1691680 ATTTGACTTATGCGTTGCGA
1 ATTTGACTTATGCGTTGCGA
1691700 TTTACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTGACTTATGCGTTGCGA
Found at i:1691756 original size:20 final size:20
Alignment explanation
Indices: 1691706--1691760 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1691696 GCGATTTACA
*
1691706 AATTCGCGTTACGAAATTGG
1 AATTCGCGTTGCGAAATTGG
* *
1691726 AA-ACTGGGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
1691746 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
1691761 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:1692192 original size:11 final size:11
Alignment explanation
Indices: 1692176--1692203 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1692166 AGTCACTTAA
1692176 GATCATACGAG
1 GATCATACGAG
1692187 GATCATACGAG
1 GATCATACGAG
1692198 GATCAT
1 GATCAT
1692204 GTTAAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (11 bp):
GATCATACGAG
Found at i:1698941 original size:20 final size:20
Alignment explanation
Indices: 1698916--1698954 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1698906 CCGTTATACA
1698916 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCTCT
*
1698936 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
1698955 CGAGTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.41, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCTCT
Found at i:1699020 original size:20 final size:20
Alignment explanation
Indices: 1698991--1699032 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1698981 AAACCATTCA
1698991 GGGGGAATCTGTACCCCATG
1 GGGGGAATCTGTACCCCATG
* *
1699011 GGGGGTATCTGTACCCTATG
1 GGGGGAATCTGTACCCCATG
1699031 GG
1 GG
1699033 CAATCTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.24
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCATG
Found at i:1699274 original size:21 final size:19
Alignment explanation
Indices: 1699247--1699302 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
1699237 GTTTAGTGAT
1699247 AAAGATACCAATTGTTAACA
1 AAAGATACCAATTGTTAA-A
*
1699267 AAAGGATATCAATTGTT-AA
1 AAA-GATACCAATTGTTAAA
*
1699286 AAAGATACCTATTGTTA
1 AAAGATACCAATTGTTA
1699303 CCAATTGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 4 0.13
21 12 0.39
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAGATACCAATTGTTAAA
Found at i:1699292 original size:18 final size:19
Alignment explanation
Indices: 1699247--1699303 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
1699237 GTTTAGTGAT
1699247 AAAGATACCAATTGTTAACA
1 AAAGATACCAATTGTT-ACA
*
1699267 AAAGGATATCAATTGTTA-A
1 AAA-GATACCAATTGTTACA
*
1699286 AAAGATACCTATTGTTAC
1 AAAGATACCAATTGTTAC
1699304 CAATTGTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.38
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAGATACCAATTGTTACA
Found at i:1703547 original size:28 final size:29
Alignment explanation
Indices: 1703516--1703572 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
1703506 TAACACTAAC
1703516 ACTTCTCCCATTTATCA-TTTTTTAACTT
1 ACTTCTCCCATTTATCATTTTTTTAACTT
1703544 ACTTCTCCCATTTATCATTTTTTTAACTT
1 ACTTCTCCCATTTATCATTTTTTTAACTT
1703573 CTCCCCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (29 bp):
ACTTCTCCCATTTATCATTTTTTTAACTT
Found at i:1705449 original size:26 final size:26
Alignment explanation
Indices: 1705420--1705471 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1705410 CAAAACACGA
*
1705420 TAATTT-GAAAATTATCATTTTTTTTT
1 TAATTTCGAAAATT-TAATTTTTTTTT
1705446 TAATTTCGAAAATTTAATTTTTTTTT
1 TAATTTCGAAAATTTAATTTTTTTTT
1705472 GGAAAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TAATTTCGAAAATTTAATTTTTTTTT
Found at i:1711779 original size:20 final size:21
Alignment explanation
Indices: 1711741--1711784 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1711731 AAACCATTCA
*
1711741 GGGGGAATCGGTACCCCCTTTG
1 GGGGGAATCGGTA-CCCCTCTG
*
1711763 GGGGGAATCGGT-TCCCTCTG
1 GGGGGAATCGGTACCCCTCTG
1711783 GG
1 GG
1711785 CAATCTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.11, C:0.25, G:0.41, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCTCTG
Found at i:1712092 original size:21 final size:19
Alignment explanation
Indices: 1712067--1712118 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
1712057 TTTTTATACA
1712067 GGGGGAATCGGTACCCCCT
1 GGGGGAATCGGTACCCCCT
**
1712086 GGGGGGGAATCAATACCCCCT
1 --GGGGGAATCGGTACCCCCT
1712107 GGGGGAATCGGT
1 GGGGGAATCGGT
1712119 TCCCTCCGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.37
21 17 0.63
ACGTcount: A:0.19, C:0.25, G:0.40, T:0.15
Consensus pattern (19 bp):
GGGGGAATCGGTACCCCCT
Found at i:1712104 original size:20 final size:21
Alignment explanation
Indices: 1712067--1712111 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1712057 TTTTTATACA
**
1712067 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCAATACCCCCTGG
1712088 GGGGGAATCAATACCCCCTGG
1 GGGGGAATCAATACCCCCTGG
1712109 GGG
1 GGG
1712112 AATCGGTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.42, T:0.13
Consensus pattern (21 bp):
GGGGGAATCAATACCCCCTGG
Found at i:1713828 original size:20 final size:18
Alignment explanation
Indices: 1713803--1713841 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1713793 TCTAACATGC
1713803 AAACTATATAGTATATACTA
1 AAACTATATA--ATATACTA
*
1713823 AAACTATGTAATATACTA
1 AAACTATATAATATACTA
1713841 A
1 A
1713842 TGATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
AAACTATATAATATACTA
Found at i:1713894 original size:17 final size:18
Alignment explanation
Indices: 1713857--1713894 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1713847 TAATATCTAA
1713857 TATAATATGCAATACTATT
1 TATAATATGCAATA-TATT
1713876 TATAATATGCAAT-TATT
1 TATAATATGCAATATATT
1713893 TA
1 TA
1713895 ATATGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (18 bp):
TATAATATGCAATATATT
Found at i:1723014 original size:13 final size:13
Alignment explanation
Indices: 1722996--1723048 Score: 79
Period size: 13 Copynumber: 3.8 Consensus size: 13
1722986 GTAAACGAAC
1722996 ATAAATGAACACA
1 ATAAATGAACACA
1723009 ATAAATGAACACAA
1 ATAAATGAACAC-A
1723023 ATGTAAATGAACACA
1 A--TAAATGAACACA
1723038 ATAAATGAACA
1 ATAAATGAACA
1723049 TAAACGAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 22 0.59
14 2 0.05
15 2 0.05
16 11 0.30
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.17
Consensus pattern (13 bp):
ATAAATGAACACA
Found at i:1723096 original size:10 final size:10
Alignment explanation
Indices: 1723038--1723082 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1723028 AATGAACACA
*
1723038 ATAAATGAAC
1 ATAAACGAAC
1723048 ATAAACGAAC
1 ATAAACGAAC
*
1723058 GTAAACGAAC
1 ATAAACGAAC
*
1723068 ATAAATGAAC
1 ATAAACGAAC
1723078 A-AAAC
1 ATAAAC
1723083 AAACGAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 3 0.10
10 27 0.90
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1723538 original size:33 final size:33
Alignment explanation
Indices: 1723501--1723569 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1723491 TAATAAGTAA
1723501 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1723534 CAAATGATACTGATTGATGAATATGTCTAATTC
1 CAAATGATACTGATTGATGAATATGTCTAATTC
1723567 CAA
1 CAA
1723570 TCAAAATTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (33 bp):
CAAATGATACTGATTGATGAATATGTCTAATTC
Found at i:1729522 original size:60 final size:60
Alignment explanation
Indices: 1729377--1729508 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 60
1729367 ACTTAAGAGT
* * *
1729377 AAAG-TACACAAATGGTCCCC-GACTATAGGGTGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACA-AAATAGTCCCCTGACTATAGCGTGTTGCTTTGTTGAGTCACTCGACTATTA
* *
1729436 AAAGTTACAAAATAGTCCCCTAACTATAGCGTGTTGCTTTGTTGAGTCATTCGACTATTA
1 AAAGTTACAAAATAGTCCCCTGACTATAGCGTGTTGCTTTGTTGAGTCACTCGACTATTA
1729496 AAAGTTACAAAAT
1 AAAGTTACAAAAT
1729509 GGTTGTCTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
59 14 0.21
60 52 0.79
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATAGTCCCCTGACTATAGCGTGTTGCTTTGTTGAGTCACTCGACTATTA
Found at i:1732681 original size:2 final size:2
Alignment explanation
Indices: 1732674--1732705 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1732664 AAAACCATTC
*
1732674 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1732706 TAAAAGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1736250 original size:64 final size:65
Alignment explanation
Indices: 1736116--1736272 Score: 178
Period size: 64 Copynumber: 2.4 Consensus size: 65
1736106 TTGAAGGTGT
* * *
1736116 ACCGATGCATAAGTAGTGCATCGATGCA-CTTCTTAATATTAGAAACATCGAATGTAATTAGTGC
1 ACCGATGCATAAGTAGTGCATCGATGCATCTCCTTAATAATAGAAACATCGAATGCAATTAGTGC
* *** * *
1736180 ATCGATGCATAAGGCTTGCATCGATGCATC-CCATTAATAATA-AAACATTGAATGCATTTTA-T
1 ACCGATGCATAAGTAGTGCATCGATGCATCTCC-TTAATAATAGAAACATCGAATGCA-ATTAGT
1736242 GC
64 GC
*
1736244 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ACCGATGCATAAGTAGTGCATCGATGCAT
1736273 ACCTTCATTA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
64 64 0.84
65 12 0.16
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (65 bp):
ACCGATGCATAAGTAGTGCATCGATGCATCTCCTTAATAATAGAAACATCGAATGCAATTAGTGC
Found at i:1736801 original size:22 final size:22
Alignment explanation
Indices: 1736776--1736831 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1736766 GGGTATTGTA
* *
1736776 GTCCTTCGGTACGTATCCAGTG
1 GTCCTTCGGGACGTATACAGTG
* *
1736798 GTCCTACGGGACGTATATAGTG
1 GTCCTTCGGGACGTATACAGTG
*
1736820 GTCATTCGGGAC
1 GTCCTTCGGGAC
1736832 ATAATAGTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATACAGTG
Found at i:1743085 original size:64 final size:65
Alignment explanation
Indices: 1743009--1743164 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 65
1742999 TTGAAGGTGT
* *
1743009 ATCGATGCATAAGTAGTGCATCGATGCAAT-TC-TTAATATTAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAGTGCATCGATGCAATCCCATTAATAATA-AAACATCGAATGCATATTA-T
1743071 GC
64 GC
* * *
1743073 ATCGATGCATAAGGCA-TGCATCGATGC-ATCCCATTAATAATAAAACATCGAATGTATTTTATG
1 ATCGATGCATAA-GTAGTGCATCGATGCAATCCCATTAATAATAAAACATCGAATGCATATTATG
1743136 C
65 C
* *
1743137 ACCGATGCACAAGTAGTGCATCGATGCA
1 ATCGATGCATAAGTAGTGCATCGATGCA
1743165 TACCTTCATT
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
63 4 0.05
64 61 0.78
65 13 0.17
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (65 bp):
ATCGATGCATAAGTAGTGCATCGATGCAATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:1743694 original size:22 final size:22
Alignment explanation
Indices: 1743669--1743724 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1743659 GGGTATTGTA
*
1743669 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATACAGTG
* *
1743691 GTCCTACGAGACGTATACAGTG
1 GTCCTTCGGGACGTATACAGTG
*
1743713 GTCCTTCCGGAC
1 GTCCTTCGGGAC
1743725 ATAATAGTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.25
Consensus pattern (22 bp):
GTCCTTCGGGACGTATACAGTG
Found at i:1744697 original size:12 final size:14
Alignment explanation
Indices: 1744676--1744713 Score: 62
Period size: 12 Copynumber: 2.9 Consensus size: 14
1744666 TGACTTTTTG
1744676 GTCAAAGTCAACA-
1 GTCAAAGTCAACAT
1744689 GTC-AAGTCAACAT
1 GTCAAAGTCAACAT
1744702 GTCAAAGTCAAC
1 GTCAAAGTCAAC
1744714 GGGTTGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 6 0.26
14 8 0.35
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (14 bp):
GTCAAAGTCAACAT
Found at i:1748626 original size:17 final size:18
Alignment explanation
Indices: 1748589--1748626 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1748579 TAATATCTAA
1748589 TATAATATGCAATACTATT
1 TATAATATGCAATA-TATT
1748608 TATAATATGCAAT-TATT
1 TATAATATGCAATATATT
1748625 TA
1 TA
1748627 ATATGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (18 bp):
TATAATATGCAATATATT
Found at i:1748813 original size:25 final size:26
Alignment explanation
Indices: 1748760--1748814 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1748750 TGTGCCAGAT
* *
1748760 GGGCGACGGCCCATGGCAGCATGTAG
1 GGGCGACGACCCAGGGCAGCATGTAG
1748786 GGGCGACGACCCAGGGCA-CATGTAG
1 GGGCGACGACCCAGGGCAGCATGTAG
1748811 GGGC
1 GGGC
1748815 ATCAGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.20, C:0.27, G:0.44, T:0.09
Consensus pattern (26 bp):
GGGCGACGACCCAGGGCAGCATGTAG
Found at i:1749884 original size:2 final size:2
Alignment explanation
Indices: 1749868--1749905 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1749858 TTGTTTCTTT
* *
1749868 TC TC -C TC TC TA TC TC TC TC TT TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1749906 TTTTAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1750727 original size:16 final size:15
Alignment explanation
Indices: 1750703--1750741 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1750693 TGATTATCTA
*
1750703 ATATGCATACTATACT
1 ATATACATACTATA-T
1750719 ATATACATACTATAT
1 ATATACATACTATAT
1750734 ATTATACA
1 A-TATACA
1750742 CATGCCCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATACATACTATAT
Found at i:1751045 original size:25 final size:26
Alignment explanation
Indices: 1750992--1751046 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1750982 TGTGCCAGAT
1750992 GGGCGACGACCCAGGGCAGCATGTAG
1 GGGCGACGACCCAGGGCAGCATGTAG
*
1751018 GGGCGACGGCCCAGGGCA-CATGTAG
1 GGGCGACGACCCAGGGCAGCATGTAG
1751043 GGGC
1 GGGC
1751047 ATCAGTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.20, C:0.27, G:0.45, T:0.07
Consensus pattern (26 bp):
GGGCGACGACCCAGGGCAGCATGTAG
Found at i:1752111 original size:2 final size:2
Alignment explanation
Indices: 1752100--1752145 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1752090 TTGTTTCTTT
*
1752100 TC TC -C TC TC TC TC TC TC TC TT 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
1752141 TC TC T
1 TC TC T
1752146 TTTTAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1753875 original size:6 final size:5
Alignment explanation
Indices: 1753856--1753889 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1753846 TTTTTTCACA
* *
1753856 AAAAT AAAAT AAATT AAAAT AAAAG AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1753890 GTGAAAAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1754760 original size:12 final size:12
Alignment explanation
Indices: 1754719--1754758 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1754709 ATACGGTATA
*
1754719 AACAATACCGTG
1 AACAATACCATG
1754731 AACAATACCATG
1 AACAATACCATG
*
1754743 AACAGTACCATG
1 AACAATACCATG
1754755 AACA
1 AACA
1754759 GTGAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.15
Consensus pattern (12 bp):
AACAATACCATG
Done.