Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008667.1 Hibiscus syriacus cultivar Beakdansim tig00111670_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: 235496
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1214 original size:32 final size:31
Alignment explanation
Indices: 1140--1216 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1130 CTAATGTGAC
* *
1140 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
1171 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
1203 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1217 CGTGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:14036 original size:96 final size:95
Alignment explanation
Indices: 13868--14149 Score: 354
Period size: 95 Copynumber: 3.0 Consensus size: 95
13858 AATTATCATC
** * * * * * *
13868 AAAAATTGAAAAAAAT-AATAAGGAAAGAAAGACTAAGGACTTCTCCACTCTTAATCAATTATTA
1 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTC
* *
13932 TTATTATCTTTCTTTGATTTTAATTTAATA
66 TTACTATCTTTCTTTGATTTTAGTTTAATA
13962 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTCAAGGACCTCTCAAGTCTTTATCAATTATT
1 AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACT-AAGGACCTCTCAAGTCTTTATCAATTATT
14027 CTTACTATCTTTCTTT-AGTTTTAGTTTAATA
65 CTTACTATCTTTCTTTGA-TTTTAGTTTAATA
* * * * * *
14058 AAAGAATTGAAAAGTGTAAATAAATAAA-AAAGACAAAGGTCCTCTCAAGCCTTTATCAATGATT
1 AAA-AATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATT
* *
14122 CTTACTATGTTTCTTTGCTTTTAGTTTA
65 CTTACTATCTTTCTTTGATTTTAGTTTA
14150 GGCTCAGATA
Statistics
Matches: 165, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
94 14 0.08
95 69 0.42
96 60 0.36
97 22 0.13
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (95 bp):
AAAAATTGAAAAGTATAAATAAAGAAAGAAAGACTAAGGACCTCTCAAGTCTTTATCAATTATTC
TTACTATCTTTCTTTGATTTTAGTTTAATA
Found at i:14547 original size:21 final size:22
Alignment explanation
Indices: 14508--14548 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14498 ACCAAGAAAG
*
14508 AAAATATAATTACTTATTTAAA
1 AAAATATAATTACTAATTTAAA
14530 AAAATATAATTA-TAATTTA
1 AAAATATAATTACTAATTTA
14549 TAATAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATAATTACTAATTTAAA
Found at i:16534 original size:17 final size:16
Alignment explanation
Indices: 16510--16558 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
16500 AGGATGTAAC
16510 AAAAATAATAT-TTAT
1 AAAAATAATATATTAT
16525 AATTAAATAAATGATATTAT
1 AA--AAAT-AAT-ATATTAT
16545 AAAAATAATATATT
1 AAAAATAATATATT
16559 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 7 0.24
18 7 0.24
19 2 0.07
20 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAATAATATATTAT
Found at i:21639 original size:21 final size:21
Alignment explanation
Indices: 21580--21642 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
21570 CTACATTGCG
* *
21580 TGAAGAGATGTGATGTCAACG
1 TGAAGAGATGTGATGTTAACA
* *
21601 T-AAAAGAATTTGTTATGTTAACA
1 TGAAGAG-A--TGTGATGTTAACA
21624 TGAAGAGATGTGATGTTAA
1 TGAAGAGATGTGATGTTAA
21643 TATGGATTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.12
21 12 0.38
23 12 0.38
24 4 0.12
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (21 bp):
TGAAGAGATGTGATGTTAACA
Found at i:26389 original size:24 final size:24
Alignment explanation
Indices: 26333--26381 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
26323 ACATGGTTTC
* *
26333 TGTTCTGATATCTGATCTGGATTA
1 TGTTCTGATATCTGACCTGAATTA
26357 TGTTCTGATATCTGACCTGAATTA
1 TGTTCTGATATCTGACCTGAATTA
26381 T
1 T
26382 TTTTTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (24 bp):
TGTTCTGATATCTGACCTGAATTA
Found at i:26703 original size:154 final size:154
Alignment explanation
Indices: 26416--26719 Score: 432
Period size: 154 Copynumber: 2.0 Consensus size: 154
26406 TACGGACTGA
* * * * *
26416 AAATATTTTATTTGGGGGTATTGTTGGAGGAAGAATACTTGTAGGCTCCTCGGCTTTGTGCTCGG
1 AAATATTTTATTTGGGGGTATTATTGGAGGAAGAATACTTGCAGGCTCCTCGACTTTATGCTCGA
** * * * *
26481 GCCTTACTTGATGTGATGGTGGGTGTATGGTTCTGGGGAATCTACACATTATGATGTGTTTGGTT
66 GCCTTACTCAATGTGACGGTGGGTGTATGGTTATGGGGAATCTACACATTATGATGTGTTGGGCT
*
26546 GGAAGGATTATTATGGTTTTTGAT
131 GGAAGGATTACTATGGTTTTTGAT
* * *
26570 AAATGTTTTATTT-GGGGTATTATTGGAGGAAGTATACTTGCAGGTTCCTCGACTTTATGCTCAG
1 AAATATTTTATTTGGGGGTATTATTGGAGGAAGAATACTTGCAGGCTCCTCGACTTTATGCTC-G
26634 AGCCTTACTCAATGTGACGGTGGGTGTATGGTTATGGGGAA-CATACACATTATGATGTGTTGGG
65 AGCCTTACTCAATGTGACGGTGGGTGTATGGTTATGGGGAATC-TACACATTATGATGTGTTGGG
*
26698 CTGGAAGGTTTACTATGGTTTT
129 CTGGAAGGATTACTATGGTTTT
26720 CTGAATTTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
153 44 0.33
154 88 0.67
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (154 bp):
AAATATTTTATTTGGGGGTATTATTGGAGGAAGAATACTTGCAGGCTCCTCGACTTTATGCTCGA
GCCTTACTCAATGTGACGGTGGGTGTATGGTTATGGGGAATCTACACATTATGATGTGTTGGGCT
GGAAGGATTACTATGGTTTTTGAT
Found at i:32249 original size:21 final size:22
Alignment explanation
Indices: 32204--32246 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32194 TTAATTTCTG
32204 TTTGGGTGCTATTTGTGTAAAA
1 TTTGGGTGCTATTTGTGTAAAA
*
32226 TTTGGGTGTTAGTTTG-GTAAA
1 TTTGGGTGCTA-TTTGTGTAAA
32247 TTTTTTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTGGGTGCTATTTGTGTAAAA
Found at i:38544 original size:11 final size:11
Alignment explanation
Indices: 38518--38550 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38508 AATAGAAACA
*
38518 AGAATCAACA-
1 AGAATCAAGAG
38528 AGAATCAAGAG
1 AGAATCAAGAG
38539 AGAATCAAGAG
1 AGAATCAAGAG
38550 A
1 A
38551 AAGCAGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.58, C:0.12, G:0.21, T:0.09
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:39064 original size:129 final size:129
Alignment explanation
Indices: 38839--39102 Score: 494
Period size: 129 Copynumber: 2.0 Consensus size: 129
38829 TGTGGAAAAT
38839 TCTTAGTGTGGATAGCTAAGGTAGTTGACGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAAT
1 TCTT-GTGTGGATAGCTAAGGTAGTTGACGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAAT
38904 CGCGCGCAATTACTTTCAATTTTCTGCAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCCCC
65 CGCGCGCAATTACTTTCAATTTTCTGCAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCCCC
38969 TCTTGTGTGGATAGCTAAGGTAGTTGACGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAATC
1 TCTTGTGTGGATAGCTAAGGTAGTTGACGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAATC
*
39034 GC-TGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCCCC
66 GCGCGCAATTACTTTCAATTTTCTGC-AAAGCTTCCACCGAAATTTTAATTGCCAATTCACCCCC
39098 TCTTG
1 TCTTG
39103 GTCATATTCA
Statistics
Matches: 132, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
128 22 0.17
129 106 0.80
130 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (129 bp):
TCTTGTGTGGATAGCTAAGGTAGTTGACGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAATC
GCGCGCAATTACTTTCAATTTTCTGCAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCCCC
Found at i:39880 original size:19 final size:18
Alignment explanation
Indices: 39843--39881 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39833 ACTTCTTCTA
* *
39843 AAAATGAAATGAATTTTG
1 AAAATCAAATGAATCTTG
39861 AAAATCAAATGAAATCTTG
1 AAAATCAAATG-AATCTTG
39880 AA
1 AA
39882 GAAGGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (18 bp):
AAAATCAAATGAATCTTG
Found at i:43796 original size:23 final size:22
Alignment explanation
Indices: 43754--43837 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
43744 TTGGTGCAGA
* *
43754 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
43776 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
* *
43799 GGGAACCGATTCCTCCC-CGTAG
1 GGGAACCGATTCC-CCCTTGAAG
* *
43821 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
43838 GGAGGTTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.06
22 28 0.53
23 19 0.36
24 3 0.06
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:47851 original size:21 final size:22
Alignment explanation
Indices: 47825--47882 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
47815 AGGGTGTCAA
47825 AGTGCATCCATGCACCCCTG-C-
1 AGTGCATCCATGCA-CCCTGACT
47846 AGTGCATCCATGCA-CCTGCACT
1 AGTGCATCCATGCACCCTG-ACT
47868 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
47883 TCCATTTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.12
21 15 0.45
22 14 0.42
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
AGTGCATCCATGCACCCTGACT
Found at i:50650 original size:19 final size:20
Alignment explanation
Indices: 50610--50667 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
50600 AGGGTGTCAA
50610 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
50631 AGTGGATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
50652 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
50668 TCCATTTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 4 0.13
21 14 0.45
22 13 0.42
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:50754 original size:20 final size:20
Alignment explanation
Indices: 50695--50759 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
50685 TAGTGGATCG
*
50695 ATGCATCCTAT-TGTGCATCG
1 ATGCATCCT-TCTGTGCATCC
*
50715 ATGCATCCTTCTGTGAATCC
1 ATGCATCCTTCTGTGCATCC
*
50735 ATGCATCCTTCTGTTCATCC
1 ATGCATCCTTCTGTGCATCC
50755 ATGCA
1 ATGCA
50760 CAAAGGCTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGCATCCTTCTGTGCATCC
Found at i:50910 original size:20 final size:22
Alignment explanation
Indices: 50872--50911 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
50862 TTTGAGTAGA
50872 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
50894 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
50912 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:52568 original size:22 final size:22
Alignment explanation
Indices: 52543--52589 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
52533 GGACAAATAC
* *
52543 AATACATAGGTCCTTTGGGACA
1 AATACAGAGGTCCTTCGGGACA
52565 AATACAGAGGTCCTTCGGGACA
1 AATACAGAGGTCCTTCGGGACA
52587 AAT
1 AAT
52590 TTCATAGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (22 bp):
AATACAGAGGTCCTTCGGGACA
Found at i:53262 original size:21 final size:21
Alignment explanation
Indices: 53236--53275 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53226 AGCAGTATTG
53236 TAGCAGGGTATCGGTACCCTA
1 TAGCAGGGTATCGGTACCCTA
53257 TAGCAGGGTATCGGTACCC
1 TAGCAGGGTATCGGTACCC
53276 CTCTGGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (21 bp):
TAGCAGGGTATCGGTACCCTA
Found at i:53325 original size:12 final size:12
Alignment explanation
Indices: 53305--53372 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
53295 TTTAACATTC
53305 GGTATTGTTCAT
1 GGTATTGTTCAT
*
53317 GGTAATGTTCA-
1 GGTATTGTTCAT
* *
53328 -GTATTATTCAC
1 GGTATTGTTCAT
53339 GGTATTGTTCAT
1 GGTATTGTTCAT
53351 --TATTGTTCAT
1 GGTATTGTTCAT
*
53361 GGTACTGTTCAT
1 GGTATTGTTCAT
53373 ACCGTATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 18 0.39
12 28 0.61
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (12 bp):
GGTATTGTTCAT
Found at i:53372 original size:22 final size:22
Alignment explanation
Indices: 53307--53372 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
53297 TAACATTCGG
*
53307 TATTGTTCATGGTAATGTTCAG
1 TATTGTTCATGGTAATGTTCAT
* * *
53329 TATTATTCACGGTATTGTTCAT
1 TATTGTTCATGGTAATGTTCAT
*
53351 TATTGTTCATGGTACTGTTCAT
1 TATTGTTCATGGTAATGTTCAT
53373 ACCGTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (22 bp):
TATTGTTCATGGTAATGTTCAT
Found at i:60978 original size:16 final size:16
Alignment explanation
Indices: 60957--60989 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60947 TACTATTCAT
*
60957 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
60973 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
60989 G
1 G
60990 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:70479 original size:15 final size:15
Alignment explanation
Indices: 70453--70502 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
70443 CGCCCCGCAT
*
70453 CCGCCCCACATCCAC
1 CCGCCCCACATCCGC
* *
70468 CCGCGCCGCATCCGC
1 CCGCCCCACATCCGC
70483 CCGCCCCACATCCGC
1 CCGCCCCACATCCGC
70498 CCGCC
1 CCGCC
70503 TAGCTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.12, C:0.66, G:0.16, T:0.06
Consensus pattern (15 bp):
CCGCCCCACATCCGC
Found at i:72543 original size:22 final size:23
Alignment explanation
Indices: 72518--72576 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
72508 AATATTATTT
72518 TTATAATTATATTAAT-GTATAA
1 TTATAATTATATTAATGGTATAA
* * *
72540 TTATTATT-TATAAATGGTATCA
1 TTATAATTATATTAATGGTATAA
*
72562 TT-TATTTATATTAAT
1 TTATAATTATATTAAT
72577 TTTCTAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
TTATAATTATATTAATGGTATAA
Found at i:80031 original size:27 final size:24
Alignment explanation
Indices: 79993--80059 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
79983 AAAAAAAAAT
79993 TCCAGATAAGTTTACCTCACCATCTTC
1 TCCAGATAAGTTTACCT--CCA-CTTC
80020 TCCAGATAAGTTTA-CT-CACTTC
1 TCCAGATAAGTTTACCTCCACTTC
*
80042 TCCGGATAAGTTTACCTC
1 TCCAGATAAGTTTACCTC
80060 GTAATTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 17 0.46
23 4 0.11
26 2 0.05
27 14 0.38
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.34
Consensus pattern (24 bp):
TCCAGATAAGTTTACCTCCACTTC
Found at i:90901 original size:18 final size:18
Alignment explanation
Indices: 90866--90908 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
90856 GTTGTTTTTA
* *
90866 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
90884 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
*
90902 AATTAAA
1 AAATAAA
90909 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:95501 original size:12 final size:12
Alignment explanation
Indices: 95486--95555 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
95476 GATAAATGAC
95486 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
95498 CTGATTTCTGAT
1 CTGAATTCTGTT
*
95510 CTGGATTCTGTT
1 CTGAATTCTGTT
*
95522 ATGATATT-TGTT
1 CTGA-ATTCTGTT
95534 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
95546 TTGATTTCTG
1 CTGAATTCTG
95556 ATATCTTCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 3 0.07
12 40 0.87
13 3 0.07
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:95505 original size:48 final size:48
Alignment explanation
Indices: 95449--95553 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
95439 AAATATTTTA
*
95449 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTATGATAAATGACCTGAATTCTGT
* * ** **
95497 TCTGATTTCTGATCTGGATTCTGTTATGATATTTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTATGATAAATGACCTGAATTCTGT
*
95545 TTTGATTTC
1 TCTGATTTC
95554 TGATATCTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 47 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTATGATAAATGACCTGAATTCTGT
Found at i:95517 original size:24 final size:24
Alignment explanation
Indices: 95449--95557 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
95439 AAATATTTTA
*
95449 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
95473 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
95497 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
95521 TATGATATT-TGTTCTGAATTCTGT
1 TCTGAT-TTCTGATCTGAATTCTGT
*
95545 TTTGATTTCTGAT
1 TCTGATTTCTGAT
95558 ATCTTCGTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:100165 original size:12 final size:12
Alignment explanation
Indices: 100144--100208 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
100134 ATGACCGGAA
100144 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
100156 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
*
100168 TTCTTTTCTGAT
1 TTCTGTTCTGAT
* *
100180 ATCTGTTCTGAA
1 TTCTGTTCTGAT
*
100192 TTCTGTTTTGAT
1 TTCTGTTCTGAT
100204 TTCTG
1 TTCTG
100209 ATATATTCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.55
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:100170 original size:24 final size:24
Alignment explanation
Indices: 100102--100210 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
100092 AAATATTTTA
*
100102 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** * *
100126 TCTGATAAATGACCGGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
100150 TCTGATTTCTGATCTGGATTCTTT
1 TCTGATTTCTGATCTGAATTCTGT
* *
100174 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
100198 TTTGATTTCTGAT
1 TCTGATTTCTGAT
100211 ATATTCGTTT
Statistics
Matches: 65, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:101257 original size:25 final size:25
Alignment explanation
Indices: 101223--101271 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
101213 TGCACTATGG
101223 GTGCATCGATACACAGAATAGCTTA
1 GTGCATCGATACACAGAATAGCTTA
101248 GTGCATCGATACACAGAATAGCTT
1 GTGCATCGATACACAGAATAGCTT
101272 CGAAAGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (25 bp):
GTGCATCGATACACAGAATAGCTTA
Found at i:102429 original size:21 final size:22
Alignment explanation
Indices: 102382--102429 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
102372 AAAAATAAAA
102382 ATAAAAACAAAGTAAAACTTTG
1 ATAAAAACAAAGTAAAACTTTG
*
102404 A-AAAAGA-AAAG-AAAACTTTT
1 ATAAAA-ACAAAGTAAAACTTTG
102424 ATAAAA
1 ATAAAA
102430 CTATAGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 9 0.39
21 12 0.52
22 2 0.09
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (22 bp):
ATAAAAACAAAGTAAAACTTTG
Found at i:103467 original size:27 final size:27
Alignment explanation
Indices: 103428--103481 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
103418 GATGAAGATC
*
103428 TTGATGCTGTGGACTTTCAAGTTCAAA
1 TTGATGCTATGGACTTTCAAGTTCAAA
* *
103455 TTGATGTTATGGAGTTTCAAGTTCAAA
1 TTGATGCTATGGACTTTCAAGTTCAAA
103482 GTGGTGATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (27 bp):
TTGATGCTATGGACTTTCAAGTTCAAA
Found at i:114645 original size:24 final size:23
Alignment explanation
Indices: 114589--114646 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
114579 ATCGTCTTTC
114589 ATCACTTTTCATATAAACATATAT
1 ATCAC-TTTCATATAAACATATAT
* *
114613 TTCAC-TTCATATGGACACATATA-
1 ATCACTTTCATAT--AAACATATAT
114636 ATCACTTTCAT
1 ATCACTTTCAT
114647 TATTTCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 17 0.61
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (23 bp):
ATCACTTTCATATAAACATATAT
Found at i:115182 original size:19 final size:18
Alignment explanation
Indices: 115158--115228 Score: 97
Period size: 19 Copynumber: 3.8 Consensus size: 18
115148 TTTAAGTAGG
115158 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACT-CTTA
115177 TGCATCGATGCACTCTTCA
1 TGCATCGATGCACTCTT-A
**
115196 TGCATCGATGCACTTCTGG
1 TGCATCGATGCAC-TCTTA
115215 TGCATCGATGCACT
1 TGCATCGATGCACT
115229 AATTGCATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.08
19 41 0.85
20 3 0.06
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (18 bp):
TGCATCGATGCACTCTTA
Found at i:116142 original size:35 final size:35
Alignment explanation
Indices: 116096--116233 Score: 145
Period size: 35 Copynumber: 3.9 Consensus size: 35
116086 CTTAGATCCG
* *
116096 TAAGGACTTACCAGTTCGATC-AGTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTATA
* ***
116131 TAAGGAATTACCAGTTTGATCGAGCTGAACATGCCG
1 TAAGGAATTACCAGTTTGATCGAGCTGAACCT-ATA
* * * *
116167 CAAGGAATTACCAATTTTATCG-GTCTGAAACTATA
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTATA
116202 TAAGGAATTACCAGTTTGATCGAGCTGAACCT
1 TAAGGAATTACCAGTTTGATCGAGCTGAACCT
116234 GCAGAGACTT
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
35 53 0.65
36 28 0.35
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCGAGCTGAACCTATA
Found at i:117393 original size:9 final size:9
Alignment explanation
Indices: 117361--117468 Score: 99
Period size: 10 Copynumber: 11.3 Consensus size: 9
117351 CTGCTGGAAA
*
117361 ACCGGTTTA
1 ACCGGTTTG
*
117370 ACCAGTTTTG
1 ACC-GGTTTG
117380 AACCGGTTTG
1 -ACCGGTTTG
*
117390 ACCGGTTCG
1 ACCGGTTTG
117399 AACCGGTTTG
1 -ACCGGTTTG
*
117409 ACCGGTTCG
1 ACCGGTTTG
117418 AACCGGTTTG
1 -ACCGGTTTG
*
117428 ACCGGTCTG
1 ACCGGTTTG
117437 AACCGGTTTG
1 -ACCGGTTTG
*
117447 ACCGGTCTG
1 ACCGGTTTG
*
117456 AACCGGGTTG
1 -ACCGGTTTG
117466 ACC
1 ACC
117469 CGACCCGACT
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
9 38 0.47
10 40 0.49
11 3 0.04
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:117403 original size:19 final size:19
Alignment explanation
Indices: 117360--117468 Score: 141
Period size: 19 Copynumber: 5.7 Consensus size: 19
117350 GCTGCTGGAA
* * *
117360 AACCGGTTTAACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
117380 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
117399 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
117418 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
117437 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
117456 AACCGGGTTGACC
1 AACCGGTTTGACC
117469 CGACCCGACT
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
18 2 0.02
19 70 0.83
20 12 0.14
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:117484 original size:17 final size:17
Alignment explanation
Indices: 117462--117520 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
117452 TCTGAACCGG
*
117462 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
117479 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
117496 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
117513 GTTG-CCCG
1 GTTGACCCG
117521 TGACCGTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
16 4 0.10
17 37 0.90
ACGTcount: A:0.15, C:0.44, G:0.25, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:117521 original size:7 final size:7
Alignment explanation
Indices: 117509--117551 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
117499 GACCCGACCC
117509 GACCGTT
1 GACCGTT
*
117516 GCCCG-T
1 GACCGTT
117522 GACCGTT
1 GACCGTT
117529 GACCG-T
1 GACCGTT
117535 GACCGTT
1 GACCGTT
117542 GACCGTT
1 GACCGTT
117549 GAC
1 GAC
117552 TTTCTTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:117527 original size:13 final size:13
Alignment explanation
Indices: 117509--117547 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
117499 GACCCGACCC
*
117509 GACCGTTGCCCGT
1 GACCGTTGACCGT
117522 GACCGTTGACCGT
1 GACCGTTGACCGT
117535 GACCGTTGACCGT
1 GACCGTTGACCGT
117548 TGACTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:124775 original size:9 final size:9
Alignment explanation
Indices: 124743--124831 Score: 79
Period size: 10 Copynumber: 9.3 Consensus size: 9
124733 CTGCTGGAAA
*
124743 ACCGGTTTA
1 ACCGGTTTG
*
124752 ACCAGTTTTG
1 ACC-GGTTTG
124762 AACCGGTTTG
1 -ACCGGTTTG
*
124772 ACCGGTTCG
1 ACCGGTTTG
124781 AACCGGTTTG
1 -ACCGGTTTG
*
124791 ACCGGTCTG
1 ACCGGTTTG
124800 AACCGGTTTG
1 -ACCGGTTTG
*
124810 ACCGGTCTG
1 ACCGGTTTG
*
124819 AACCGGGTTG
1 -ACCGGTTTG
124829 ACC
1 ACC
124832 CGACCCGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.46
10 32 0.49
11 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:124785 original size:19 final size:19
Alignment explanation
Indices: 124760--124831 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
124750 TAACCAGTTT
124760 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
124778 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
124798 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
124817 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
124832 CGACCCGACT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 1 0.02
19 49 0.96
20 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:124806 original size:38 final size:39
Alignment explanation
Indices: 124742--124831 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
124732 GCTGCTGGAA
* * *
124742 AACCGGTTTAACCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCT-G
124781 AACCGGTTTGACC-GGTCTGAACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
*
124819 AACCGGGTTGACC
1 AACCGGTTTGACC
124832 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (39 bp):
AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
Found at i:124847 original size:17 final size:17
Alignment explanation
Indices: 124825--124882 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
124815 TCTGAACCGG
*
124825 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
124842 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
124859 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
124876 GTTGACC
1 GTTGACC
124883 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:124882 original size:7 final size:7
Alignment explanation
Indices: 124872--124914 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
124862 GACCCGACCC
124872 GACCGTT
1 GACCGTT
124879 GACCG-T
1 GACCGTT
124885 GACCGTT
1 GACCGTT
124892 GACCG-T
1 GACCGTT
124898 GACCGTT
1 GACCGTT
124905 GACCGTT
1 GACCGTT
124912 GAC
1 GAC
124915 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:124890 original size:13 final size:13
Alignment explanation
Indices: 124872--124910 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
124862 GACCCGACCC
124872 GACCGTTGACCGT
1 GACCGTTGACCGT
124885 GACCGTTGACCGT
1 GACCGTTGACCGT
124898 GACCGTTGACCGT
1 GACCGTTGACCGT
124911 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:124897 original size:20 final size:20
Alignment explanation
Indices: 124872--124914 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
124862 GACCCGACCC
124872 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
124892 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
124912 GAC
1 GAC
124915 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:129089 original size:22 final size:21
Alignment explanation
Indices: 129041--129082 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
129031 ATATGAAATT
129041 TGTCCCAAAGGACCTCATGTA
1 TGTCCCAAAGGACCTCATGTA
*
129062 TGTCCCAAATGACCT-ATGTA
1 TGTCCCAAAGGACCTCATGTA
129082 T
1 T
129083 ATGTCCCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (21 bp):
TGTCCCAAAGGACCTCATGTA
Found at i:132819 original size:37 final size:37
Alignment explanation
Indices: 132743--132819 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
132733 TTTTTATATT
*
132743 TTTAATTTTGTAAAAAATATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
* *
132780 TTTAATTTTTTAAAGAAA-A-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATATTATATAAATATTAT-CAA
132817 TTT
1 TTT
132820 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 19 0.54
38 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
Found at i:139174 original size:21 final size:21
Alignment explanation
Indices: 139148--139189 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
139138 CCCGCTACAC
* *
139148 CCGCAATAGTGTCCGTGACGG
1 CCGCAATAGCGCCCGTGACGG
139169 CCGCAATAGCGCCCGTGACGG
1 CCGCAATAGCGCCCGTGACGG
139190 TCACAATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.14
Consensus pattern (21 bp):
CCGCAATAGCGCCCGTGACGG
Found at i:139196 original size:21 final size:21
Alignment explanation
Indices: 139151--139196 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
139141 GCTACACCCG
* * *
139151 CAATAGTGTCCGTGACGGCCG
1 CAATAGCGCCCGTGACGGCCA
*
139172 CAATAGCGCCCGTGACGGTCA
1 CAATAGCGCCCGTGACGGCCA
139193 CAAT
1 CAAT
139197 CACGGTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.17
Consensus pattern (21 bp):
CAATAGCGCCCGTGACGGCCA
Found at i:146733 original size:16 final size:15
Alignment explanation
Indices: 146712--146744 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
146702 GTTTAAAATA
146712 AATTAAAATAATGAAT
1 AATTAAAATAAT-AAT
146728 AATTAAAATAATAAT
1 AATTAAAATAATAAT
146743 AA
1 AA
146745 AGACATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AATTAAAATAATAAT
Found at i:148282 original size:46 final size:48
Alignment explanation
Indices: 148192--148288 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 48
148182 CTTAATTTAC
* * *
148192 TTTATTTTCCTAATAAATGTATGCGAACTAGAAATCATGCGGTTA-GA
1 TTTATTTTCCAAATAAATGCATGCGAACTAGAAATCATGAGGTTAGGA
*
148239 TTTATTTCTCCAAATAAA-GCATG-GAACTAG-ATTACATGAGGTTAGGA
1 TTTATTT-TCCAAATAAATGCATGCGAACTAGAAAT-CATGAGGTTAGGA
148286 TTT
1 TTT
148289 TTATGATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
45 2 0.05
46 16 0.37
47 16 0.37
48 9 0.21
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (48 bp):
TTTATTTTCCAAATAAATGCATGCGAACTAGAAATCATGAGGTTAGGA
Found at i:148621 original size:20 final size:20
Alignment explanation
Indices: 148582--148621 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
148572 GCATTTTTTA
*
148582 CATTCACATCTTTGCATTTG
1 CATTCACATCTTTACATTTG
* *
148602 CATTCGCATCTTTACGTTTG
1 CATTCACATCTTTACATTTG
148622 TATTTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.45
Consensus pattern (20 bp):
CATTCACATCTTTACATTTG
Found at i:151078 original size:12 final size:12
Alignment explanation
Indices: 151061--151104 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
151051 AAAAAGAAAA
151061 AAAATGAAAATG
1 AAAATGAAAATG
151073 AAAATGAAAATG
1 AAAATGAAAATG
*
151085 -AAA-GAAAAAG
1 AAAATGAAAATG
*
151095 AAAAAGAAAA
1 AAAATGAAAA
151105 AATAGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 6 0.21
11 6 0.21
12 17 0.59
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAAATGAAAATG
Found at i:151105 original size:12 final size:11
Alignment explanation
Indices: 151029--151106 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 11
151019 CTCATCCATC
151029 AGAAAAAAAAA
1 AGAAAAAAAAA
151040 AGAAAACAATAAA
1 AGAAAA-AA-AAA
151053 A-AAGAAAAAAA
1 AGAA-AAAAAAA
*
151064 ATGAAAATGAAAA
1 A-GAAAA-AAAAA
* **
151077 TG-AAAATGAA
1 AGAAAAAAAAA
151087 AGAAAAAGAAAA
1 AGAAAAA-AAAA
151099 AGAAAAAA
1 AGAAAAAA
151107 TAGAAAATAG
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
10 3 0.06
11 18 0.35
12 18 0.35
13 12 0.24
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:151118 original size:16 final size:16
Alignment explanation
Indices: 151035--151120 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 16
151025 CATCAGAAAA
*
151035 AAAAAAGAAAACAATA-
1 AAAATAGAAAA-AATAG
*
151051 AAAA-AGAAAAAAAATG
1 AAAATAGAAAAAATA-G
151067 AAAAT-G--AAAAT-G
1 AAAATAGAAAAAATAG
*
151079 AAAAT-GAAAGAAAAAG
1 AAAATAGAAA-AAATAG
151095 AAAA-AGAAAAAATAG
1 AAAATAGAAAAAATAG
151110 AAAATAGAAAA
1 AAAATAGAAAA
151121 TATAAAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
12 7 0.12
14 8 0.14
15 18 0.32
16 24 0.42
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (16 bp):
AAAATAGAAAAAATAG
Found at i:151121 original size:7 final size:7
Alignment explanation
Indices: 151061--151148 Score: 60
Period size: 7 Copynumber: 12.6 Consensus size: 7
151051 AAAAAGAAAA
151061 AAAAT-G
1 AAAATAG
151067 AAAAT-G
1 AAAATAG
151073 AAAAT-G
1 AAAATAG
151079 AAAATGAAAG
1 AAAAT---AG
151089 AAAA-AG
1 AAAATAG
151095 AAAA-AG
1 AAAATAG
151101 AAAAAATAG
1 --AAAATAG
151110 AAAATAG
1 AAAATAG
*
151117 AAAATAT
1 AAAATAG
*
151124 AAAATAT
1 AAAATAG
*
151131 AAAATAT
1 AAAATAG
*
151138 AAAATAT
1 AAAATAG
151145 AAAA
1 AAAA
151149 GAAAATAAGG
Statistics
Matches: 74, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
6 25 0.34
7 38 0.51
8 4 0.05
9 2 0.03
10 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (7 bp):
AAAATAG
Found at i:151127 original size:21 final size:21
Alignment explanation
Indices: 151103--151155 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
151093 AGAAAAAGAA
151103 AAAATAGAAAATAGAAAATAT
1 AAAATAGAAAATAGAAAATAT
* *
151124 AAAATATAAAATATAAAATAT
1 AAAATAGAAAATAGAAAATAT
151145 -AAA-AGAAAATA
1 AAAATAGAAAATA
151156 AGGAAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 3 0.10
21 19 0.66
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (21 bp):
AAAATAGAAAATAGAAAATAT
Found at i:151142 original size:14 final size:14
Alignment explanation
Indices: 151103--151148 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
151093 AGAAAAAGAA
* *
151103 AAAATAGAAAATAG
1 AAAATATAAAATAT
151117 AAAATATAAAATAT
1 AAAATATAAAATAT
151131 AAAATATAAAATAT
1 AAAATATAAAATAT
151145 AAAA
1 AAAA
151149 GAAAATAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAATATAAAATAT
Found at i:152661 original size:24 final size:22
Alignment explanation
Indices: 152626--152669 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
152616 TTGGCATAGT
152626 TACATCTACATTCTTCAAAGATGA
1 TACATCTACA-T-TTCAAAGATGA
152650 TACATTCT-CATTTCAAAGAT
1 TACA-TCTACATTTCAAAGAT
152670 AAGAGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.47
23 1 0.05
24 6 0.32
25 3 0.16
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (22 bp):
TACATCTACATTTCAAAGATGA
Found at i:153572 original size:311 final size:310
Alignment explanation
Indices: 153008--153612 Score: 960
Period size: 311 Copynumber: 1.9 Consensus size: 310
152998 GAATCAATTT
* * * * ** **
153008 TTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAGTAGAGTCAATTTCTG
1 TTGACTTCATCATGAAGAGAAGTCAACCTTTATTATTCCTAACTCCCCAACAGAGTCAATTTCTG
153073 ACTTCCTCGTGAAGAGAAGTCAACCTATATTATTTATGACTCCTCAGTAGAGTCAATATTTAACT
66 ACTTCCTCGTGAAGAGAAGTCAACCTATATTATTTATGACTCCTCAGTAGAGTCAATATTTAACT
* *
153138 CCCTCGTGAAGAGAATTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTTGACTTTC
131 CCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTTGACTTCC
* * *
153203 TCGTGAAGAGAAGCCAACCTTTATTATTTCTGACTCCTCAGTAGAGTTAATATTTGACTCCCTCA
196 TCGTGAAGAGAAGCCAACCTTTATTATTCCTGACTCCCCAGTAGAGTAAATATTTGACTCCCTCA
* * *
153268 TGAAGAGAAGTCAACATTTGTTATTTTTGACTCCTCAATAGAGTCAATCC
261 TGAAGAGAAATCAACATTTATTATTTCTGACTCCTCAATAGAGTCAATCC
*
153318 TTGACTTCATCATGAAGAGAAGTCAACCTTTATTATTCCTAACTCCCCAACAGAGTCAAATTTTT
1 TTGACTTCATCATGAAGAGAAGTCAACCTTTATTATTCCTAACTCCCCAACAGAGTC-AATTTCT
* * *
153383 GACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGAGTCAATATTTGAC
65 GACTTCCTCGTGAAGAGAAGTCAACCTATATTATTTATGACTCCTCAGTAGAGTCAATATTTAAC
153448 TCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTTGACTTC
130 TCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTTGACTTC
* ** *
153513 CTTGTGAAGAGAAGTTAACCTTTATTATTCCTGACTCCCCAGTAGAGTCAAAT-TTTGACTTCCT
195 CTCGTGAAGAGAAGCCAACCTTTATTATTCCTGACTCCCCAGTAGAGT-AAATATTTGACTCCCT
*
153577 CATGAAGAGAAATCAACCTTTATTATTTCTGACTCC
259 CATGAAGAGAAATCAACATTTATTATTTCTGACTCC
153613 CCAAATGAAC
Statistics
Matches: 268, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
310 49 0.18
311 216 0.81
312 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (310 bp):
TTGACTTCATCATGAAGAGAAGTCAACCTTTATTATTCCTAACTCCCCAACAGAGTCAATTTCTG
ACTTCCTCGTGAAGAGAAGTCAACCTATATTATTTATGACTCCTCAGTAGAGTCAATATTTAACT
CCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTTGACTTCC
TCGTGAAGAGAAGCCAACCTTTATTATTCCTGACTCCCCAGTAGAGTAAATATTTGACTCCCTCA
TGAAGAGAAATCAACATTTATTATTTCTGACTCCTCAATAGAGTCAATCC
Found at i:153632 original size:62 final size:62
Alignment explanation
Indices: 152996--153612 Score: 815
Period size: 62 Copynumber: 9.9 Consensus size: 62
152986 TCTTGTTTCC
* * *
152996 TAGAATCAATTTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTTAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* *
153058 TAGAGTCAAT-TTCTGACTTCCTCGTGAAGAGAAGTCAACCTATATTATTTATGACTCCTCAG
1 TAGAGTCAATCTT-TGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * * *
153120 TAGAGTCAATATTTAACTCCCTCGTGAAGAGAATTCAACATTTGTTATTTCTGACTCCTCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * *
153182 TAGAGTCAATCCTTGACTTTCTCGTGAAGAGAAGCCAACCTTTATTATTTCTGACTCCTCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * * * * *
153244 TAGAGTTAATATTTGACTCCCTCATGAAGAGAAGTCAACATTTGTTATTTTTGACTCCTCAA
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * * * *
153306 TAGAGTCAATCCTTGACTTCATCATGAAGAGAAGTCAACCTTTATTATTCCTAACTCCCCAA
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* *
153368 CAGAGTCAAATTTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
1 TAGAGTC-AATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * *
153431 TAGAGTCAATATTTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCTCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* * * * *
153493 TAGAGTCAATCCTTGACTTCCTTGTGAAGAGAAGTTAACCTTTATTATTCCTGACTCCCCAG
1 TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
* *
153555 TAGAGTCAAAT-TTTGACTTCCTCATGAAGAGAAATCAACCTTTATTATTTCTGACTCC
1 TAGAGTC-AATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCC
153613 CCAAATGAAC
Statistics
Matches: 480, Mismatches: 71, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
61 2 0.00
62 420 0.88
63 58 0.12
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (62 bp):
TAGAGTCAATCTTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
Found at i:153854 original size:36 final size:36
Alignment explanation
Indices: 153794--154148 Score: 523
Period size: 36 Copynumber: 9.9 Consensus size: 36
153784 TTATTTTAAA
* *
153794 CTTAACCTCCACAGAAGAGTAGTGAAGCAAAGCCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
* *
153830 CTTAGCCTCTACGGAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
* *
153866 CTTAGCCTCCACGGAATAGTAGTGAAGCAAATCCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
* *
153902 CTTAGCCTCCACGAAAGAGTAGT-AATGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAA-GCAAAGCCAT
*
153938 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGTCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
* * *
153974 CTTAGCCTCCATGGAAGAGTAGTGAAGCAAAACAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
** *
154010 CTTAGCCTCCACAAAAGAGTAGTGAAGCAAAGCAAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
*
154046 CTTAGCCTCCACTGAAGAGTAGTGAAGCAAAGCCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
* *
154082 CTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGTCAT
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
*
154118 CTTAGCCTCCACAGAAGAGTAGTGAAGCAAA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAA
154149 AACAGATCAA
Statistics
Matches: 286, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
35 2 0.01
36 282 0.99
37 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (36 bp):
CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCAT
Found at i:155562 original size:16 final size:15
Alignment explanation
Indices: 155541--155570 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
155531 TAAAATAAAA
155541 TAAAATAATGAATAAT
1 TAAAATAAT-AATAAT
155557 TAAAATAATAATAA
1 TAAAATAATAATAA
155571 AGACATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAATAATAATAAT
Found at i:156774 original size:35 final size:34
Alignment explanation
Indices: 156698--156791 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
156688 TTATAAAAAT
156698 ATATATTTTA-AAATTATAATTTTTGAATTCATA
1 ATATATTTTATAAATTATAATTTTTGAATTCATA
* * *
156731 AAATTATTTTATAAATTATATTTTATTTAATT-ATA
1 ATA-TATTTTATAAATTATAATTT-TTGAATTCATA
156766 AT-TATATTTATAAAATTTATAATTTT
1 ATATAT-TTTAT-AAA-TTATAATTTT
156792 CATTATCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
33 5 0.10
34 12 0.24
35 19 0.38
36 14 0.28
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
ATATATTTTATAAATTATAATTTTTGAATTCATA
Found at i:156785 original size:21 final size:22
Alignment explanation
Indices: 156738--156789 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
156728 ATAAAATTAT
**
156738 TTTATAAATTATATTTTATTTAA
1 TTTAT-AATTATATTTTATAAAA
156761 -TTATAATTATA-TTTATAAAA
1 TTTATAATTATATTTTATAAAA
156781 TTTATAATT
1 TTTATAATT
156790 TTCATTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATAATTATATTTTATAAAA
Found at i:159686 original size:11 final size:11
Alignment explanation
Indices: 159662--159695 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
159652 AATTTTCATC
159662 CATATATAATAT
1 CATATAT-ATAT
159674 CATATATATAT
1 CATATATATAT
*
159685 CACATATATAT
1 CATATATATAT
159696 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:160501 original size:9 final size:9
Alignment explanation
Indices: 160489--160527 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
160479 TCCTTTTTTA
160489 TATTTTATT
1 TATTTTATT
160498 TATTTATTCATT
1 TA-TT-TT-ATT
160510 TATTTTATT
1 TATTTTATT
160519 TATTTTATT
1 TATTTTATT
160528 AATATTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 14 0.52
10 4 0.15
11 4 0.15
12 5 0.19
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:160562 original size:3 final size:3
Alignment explanation
Indices: 160549--160587 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
160539 ATATGTCCTT
* *
160549 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
160588 TTTTGGGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:160682 original size:22 final size:22
Alignment explanation
Indices: 160623--160705 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 22
160613 ATTATATATA
* *
160623 TTTTATTTA-TTTCTTTTATTT
1 TTTTACTTATTTTCTTTTGTTT
*
160644 TTATTACTTATTATCTTATTGTTT
1 TT-TTACTTATTTTCTT-TTGTTT
160668 TTTTAC-TATTTTCTTTTTGGTTT
1 TTTTACTTATTTTC-TTTT-GTTT
*
160691 TTATTATTTATTTTC
1 TT-TTACTTATTTTC
160706 CATACGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.04
22 14 0.28
23 17 0.34
24 10 0.20
25 7 0.14
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTACTTATTTTCTTTTGTTT
Found at i:162084 original size:16 final size:16
Alignment explanation
Indices: 162063--162106 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
162053 GAATAATAAG
162063 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
162079 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
*
162095 CATGTGGTGTAG
1 CATGTGGGGTAG
162107 GACTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.32
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:165279 original size:95 final size:95
Alignment explanation
Indices: 165115--165296 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
165105 ATATTATTTA
* * *
165115 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATGAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
* *
165180 ATTCAGCTAGCCTGATAAAGGTGATTATAC
66 ATTCAGCTAACATGATAAAGGTGATTATAC
*
165210 TATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAATGCCCCGACTTTATGGATAA
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGACTTTATGGATAA
165274 GATTCAGCTAACATGATAAAGGT
65 GATTCAGCTAACATGATAAAGGT
165297 ATTTACATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 79 0.99
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACATGATAAAGGTGATTATAC
Found at i:166610 original size:72 final size:72
Alignment explanation
Indices: 166510--166688 Score: 261
Period size: 72 Copynumber: 2.5 Consensus size: 72
166500 TAATGCAGAT
* * * * *
166510 GATTTATCTCACTTGAGATTGTTATTCTTAAAACAGACCGTGTCTCACTTGAGACTGTTTTATTC
1 GATTTATTTCCCTTAAGATTGTTTTTCTTAAAACAGACCGTGTCTCACTTGAGACTGTTTTACTC
166575 AAAAGAA
66 AAAAGAA
* **
166582 GATTTATTT-CCTTCAAGATTATTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACT
1 GATTTATTTCCCTT-AAGATTGTTTTTCTTAAAACAGACCGTGTCTCACTTGAGACTGTTTTACT
*
166646 CGAAAGAA
65 CAAAAGAA
166654 GATTTATTTCCCTTAAGATTGTTTTTCTTAAAACA
1 GATTTATTTCCCTTAAGATTGTTTTTCTTAAAACA
166689 ATATTTTATC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 3 0.03
72 88 0.93
73 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (72 bp):
GATTTATTTCCCTTAAGATTGTTTTTCTTAAAACAGACCGTGTCTCACTTGAGACTGTTTTACTC
AAAAGAA
Found at i:166725 original size:37 final size:37
Alignment explanation
Indices: 166684--166762 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
166674 GTTTTTCTTA
* * *
166684 AAACAATATTTTATCTCGCTTGAGATAGTTTCCCTTG
1 AAACAAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
* *
166721 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
166758 AAACA
1 AAACA
166763 TAAACATTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
AAACAAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
Found at i:166817 original size:65 final size:65
Alignment explanation
Indices: 166712--167103 Score: 392
Period size: 65 Copynumber: 5.8 Consensus size: 65
166702 CTTGAGATAG
** * * *
166712 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTGAAAAC
166777 A
65 A
* *
166778 TTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTGAAAACA
**
166843 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAATTTTGTCTCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTG------
*
166907 TAGAGACA
60 -A-AAACA
* * * * ** * *
166915 GTTTCTCTTGAAATGAATTTTTTCTCCCTTGAGAGAGTTTTTCTTCAAACATAAACATTGAAAAT
1 -TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTGAAAAC
166980 A
65 A
* **
166981 TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACA-AAATTTTGTCTCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTG------
*
167045 TAGAGACA
60 -A-AAACA
*
167053 TTTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 -TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
167104 AAATTTTGTC
Statistics
Matches: 274, Mismatches: 33, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
64 12 0.04
65 140 0.51
66 15 0.05
67 1 0.00
71 2 0.01
72 7 0.03
73 91 0.33
74 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (65 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACATAAACATTGAAAACA
Found at i:166967 original size:138 final size:138
Alignment explanation
Indices: 166778--167103 Score: 544
Period size: 138 Copynumber: 2.4 Consensus size: 138
166768 ATTGAAAACA
* * *
166778 TTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTCAAACATAAACATTGAAAACA
*
166843 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
66 TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
166908 AGAGACAG
131 AGAGACAG
* * * * *
166916 TTTCTCTTGAAATGAATTTTTTCTCCCTTGAGAGAGTTTTTCTTCAAACATAAACATTGAAAATA
1 TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTCAAACATAAACATTGAAAACA
166981 TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
66 TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
167046 AGAGACAT
131 AGAGACAG
* *
167054 TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTCAAACA
167104 AAATTTTGTC
Statistics
Matches: 172, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 172 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTCAAACATAAACATTGAAAACA
TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
AGAGACAG
Found at i:167105 original size:73 final size:73
Alignment explanation
Indices: 166981--167139 Score: 282
Period size: 73 Copynumber: 2.2 Consensus size: 73
166971 ATTGAAAATA
*
166981 TTTCCCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCTCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
167046 AGAGACAT
66 AGAGACAG
*
167054 TTTCTCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCTCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
167119 AGAGACAG
66 AGAGACAG
*
167127 TTTCTCTTAAAAT
1 TTTCTCTTGAAAT
167140 TTTGTGTTGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (73 bp):
TTTCTCTTGAAATGAATTTTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
AGAGACAG
Found at i:167915 original size:64 final size:62
Alignment explanation
Indices: 167847--168026 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 62
167837 TTGGAACACT
* * *
167847 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCC
1 TGATGCATCGATGCA-CGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGA-AAAAAGCC
* * **
167911 TGATGCATCGATGCATG-GCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTC
1 TGATGCATCGATGCACGAG--TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAAAGCC
* * * * *
167975 AGAGTGCATCGATGCATGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCACGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
168027 CAATTAATTC
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 76 0.77
65 19 0.19
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (62 bp):
TGATGCATCGATGCACGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAAGCC
Found at i:167998 original size:18 final size:18
Alignment explanation
Indices: 167975--168024 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
167965 GAAAAAATTC
167975 AGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCATG
*
167993 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
*
168011 -GAATGCATTCGATG
1 AGAGTGCA-TCGATG
168025 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
AGAGTGCATCGATGCATG
Found at i:174531 original size:22 final size:21
Alignment explanation
Indices: 174489--174528 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
174479 GAGTTTGTTT
*
174489 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
174510 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
174529 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:176607 original size:19 final size:19
Alignment explanation
Indices: 176583--176633 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
176573 GAAAAAATTC
176583 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
176602 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
176621 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
176634 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:176675 original size:65 final size:64
Alignment explanation
Indices: 176477--176684 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 64
176467 GCACCAAGTG
* * * * ** *
176477 TGCATCGATGCATTAAATGCATTCGATGTTTGAGAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCA-AAAAATTCAGATGCATCGATGCATGGAC-TG
176541 -
64 A
* * *
176541 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAAAATTCAGA-TGCATCGATGCATGGACTG
176604 A
64 A
* **
176605 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCA--GATGCATCGATGCATGGACT
176669 GA
63 GA
176671 TGCATCGGTGCATG
1 TGCATCGGTGCATG
176685 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
63 11 0.09
64 50 0.40
65 61 0.49
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCAGATGCATCGATGCATGGACTGA
Found at i:177061 original size:42 final size:36
Alignment explanation
Indices: 176927--177114 Score: 216
Period size: 36 Copynumber: 5.0 Consensus size: 36
176917 TGTTTTCAAT
* * *
176927 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACTA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* * *
176963 ATTTCGTCTCCCTTGAGACAGTTTCT-TTTAGAACTAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGA-AAC-AA
* *
177000 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAGCAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
*
177036 ATTTTGTCTTTGTCTCTCTTGAGACAGTTTTTCTTGAAACAA
1 A-----T-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
177078 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
177114 A
1 A
177115 ATCTTTGAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
35 3 0.02
36 62 0.48
37 27 0.21
38 3 0.02
41 1 0.01
42 33 0.26
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
Found at i:177098 original size:78 final size:73
Alignment explanation
Indices: 176927--177114 Score: 229
Period size: 78 Copynumber: 2.5 Consensus size: 73
176917 TGTTTTCAAT
* * *
176927 ATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACTAATTTCGTCTCCCTTGAGACAGTTTCTTTT
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
176992 AGAACTAA
66 AGAACTAA
* * *
177000 GTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAGCAAATTTTGTCTTTGTCTCTCTTGAGACAGTT
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA--TT-TC---GTCTCCCTTGAGACAGTT
177065 T-TTCTT-GAAAC-AA
60 TCTT-TTAG-AACTAA
177078 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
177115 ATCTTTGAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
73 32 0.32
75 2 0.02
76 2 0.02
78 40 0.40
79 23 0.23
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (73 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
AGAACTAA
Found at i:177203 original size:37 final size:37
Alignment explanation
Indices: 177133--177250 Score: 143
Period size: 36 Copynumber: 3.2 Consensus size: 37
177123 ATATGTTTTC
* *
177133 CTTGAAACAAGTTTCGTCTCCCTTGAGACAGTTTCTT
1 CTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTT
* * *
177170 C-TGGAACTAAGTTTTGTCTCTCTTCAGATAGTTT-TT
1 CTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTT
* *
177206 CTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTC-T
1 CTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTT
177242 CTTGAAACA
1 CTTGAAACA
177251 CCAAAAAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
36 40 0.59
37 28 0.41
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (37 bp):
CTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:177884 original size:11 final size:11
Alignment explanation
Indices: 177860--177893 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
177850 AATTTTCATC
177860 CATATATAATAT
1 CATATAT-ATAT
177872 CATATATATAT
1 CATATATATAT
*
177883 CACATATATAT
1 CATATATATAT
177894 ATTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:178763 original size:9 final size:9
Alignment explanation
Indices: 178751--178785 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
178741 TCCTTTTTTA
178751 TATTTTATT
1 TATTTTATT
*
178760 TA-TTCATT
1 TATTTTATT
178768 TATTTTATT
1 TATTTTATT
178777 TATTTTATT
1 TATTTTATT
178786 AATATTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:178904 original size:16 final size:17
Alignment explanation
Indices: 178883--178916 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
178873 ATATATTTTA
*
178883 TTTATTTCTT-TTATTT
1 TTTATTACTTATTATTT
178899 TTTATTACTTATTATTT
1 TTTATTACTTATTATTT
178916 T
1 T
178917 ATTTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTACTTATTATTT
Found at i:180902 original size:32 final size:32
Alignment explanation
Indices: 180861--180925 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
180851 TTAAACTCCC
*
180861 TAGTGCTTGGGATGGAAGTTAGGGTAGATGAA
1 TAGTGCTTGGCATGGAAGTTAGGGTAGATGAA
180893 TAGTGCTTGGCATGGAAGTTAGGGTAGATGAA
1 TAGTGCTTGGCATGGAAGTTAGGGTAGATGAA
180925 T
1 T
180926 TGTATGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.29
Consensus pattern (32 bp):
TAGTGCTTGGCATGGAAGTTAGGGTAGATGAA
Found at i:191517 original size:14 final size:14
Alignment explanation
Indices: 191498--191526 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
191488 TATTCGTCGA
191498 CCCGATGGCACTTT
1 CCCGATGGCACTTT
191512 CCCGATGGCACTTT
1 CCCGATGGCACTTT
191526 C
1 C
191527 AATCGTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.28
Consensus pattern (14 bp):
CCCGATGGCACTTT
Found at i:197714 original size:31 final size:31
Alignment explanation
Indices: 197628--197714 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 31
197618 GGTCAAATTG
* * *
197628 ATATTTTGTC-AAAGTTTAAAGATTAAATTA
1 ATATTTTGTCTAAAGTTTTAAGGTTAAACTA
* * * *
197658 ATATTTTATTTAAA-ATTTATGGTTAAACTA
1 ATATTTTGTCTAAAGTTTTAAGGTTAAACTA
*
197688 GTATTTTGTCTAAAGTTTTAAGGTTAA
1 ATATTTTGTCTAAAGTTTTAAGGTTAA
197715 GTTAGAATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.47
Consensus pattern (31 bp):
ATATTTTGTCTAAAGTTTTAAGGTTAAACTA
Found at i:197828 original size:31 final size:31
Alignment explanation
Indices: 197793--197856 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
197783 ATAAATTCAT
197793 AATAAGAC-A-AATAAAAAATAAAAGTGACCAA
1 AATAAGACAAGAAT-AAAAATAAAA-TGACCAA
*
197824 AATAAGACAAGAATAAAAATAAAATGATCAA
1 AATAAGACAAGAATAAAAATAAAATGACCAA
197855 AA
1 AA
197857 CATATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 16 0.53
32 11 0.37
33 3 0.10
ACGTcount: A:0.69, C:0.08, G:0.09, T:0.14
Consensus pattern (31 bp):
AATAAGACAAGAATAAAAATAAAATGACCAA
Found at i:198044 original size:21 final size:21
Alignment explanation
Indices: 198020--198059 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
198010 TTTATCATTT
198020 ATTAATAT-TAAAATTAAATTA
1 ATTAAT-TCTAAAATTAAATTA
*
198041 ATTAATTCTAAATTTAAAT
1 ATTAATTCTAAAATTAAAT
198060 ATTAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAATTCTAAAATTAAATTA
Found at i:198505 original size:60 final size:60
Alignment explanation
Indices: 198411--198525 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
198401 ATGAATTTAT
* * * *
198411 GGATGAAATTGGAAGATCTAAAAGTTTGGAGACCAATTTAGAATGAGAGTCATAGGTTGA
1 GGATGAAATTAGAAGATCCAAAAGTTTGGAGACCAATTTAAAATGAGAATCATAGGTTGA
198471 GGATGAAATTAGAATG-TCCAAAAGTTTAGG-GACCAATTTAAAATGAGAATCATAG
1 GGATGAAATTAGAA-GATCCAAAAGTTT-GGAGACCAATTTAAAATGAGAATCATAG
198526 TTTGGGGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (60 bp):
GGATGAAATTAGAAGATCCAAAAGTTTGGAGACCAATTTAAAATGAGAATCATAGGTTGA
Found at i:202116 original size:13 final size:13
Alignment explanation
Indices: 202098--202132 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
202088 TATGATATAC
202098 TCGTTATGATGGG
1 TCGTTATGATGGG
202111 TCGTTATGATGGG
1 TCGTTATGATGGG
*
202124 TCGTGATGA
1 TCGTTATGA
202133 CATTCCGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (13 bp):
TCGTTATGATGGG
Found at i:202673 original size:2 final size:2
Alignment explanation
Indices: 202666--202697 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
202656 GGAGTTGATC
202666 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
202698 TTACTGATGC
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:204443 original size:4 final size:4
Alignment explanation
Indices: 204434--205633 Score: 2192
Period size: 4 Copynumber: 301.0 Consensus size: 4
204424 GATCTCCATC
204434 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204482 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204530 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204578 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204626 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204674 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204722 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204770 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
204818 TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
204864 TACA TACA TGCA TGCA TACA TACA TGCA TACA TACA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
204912 TGCA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
204958 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205006 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205054 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205102 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205150 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205198 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205246 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205294 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205342 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205390 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
205438 TACA TACA TACA TACA TACA TGCA TGCA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
205486 TACA TGCA TACA TGCA TACA TACA TACA TACA TGCA TACA TGCA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
205534 TACA TGCA TACA TACA TGCA TACA TACA TGCA TACA TACA TGCA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
205582 TACA TGCA TACA TACA TGCA TACA TACA TGCA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
205630 TACA
1 TACA
205634 GTATTTATCA
Statistics
Matches: 1158, Mismatches: 34, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
2 4 0.00
4 1154 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:206236 original size:18 final size:18
Alignment explanation
Indices: 206193--206230 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
206183 GTGAAGTATG
*
206193 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
206211 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
206229 AA
1 AA
206231 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:209942 original size:16 final size:16
Alignment explanation
Indices: 209921--209956 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
209911 TGGGCTAAGG
209921 CTTTCCCTCACGTAGC
1 CTTTCCCTCACGTAGC
209937 CTTTCCCTCACGTAGC
1 CTTTCCCTCACGTAGC
209953 CTTT
1 CTTT
209957 TTCCATCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.42, G:0.11, T:0.36
Consensus pattern (16 bp):
CTTTCCCTCACGTAGC
Found at i:212717 original size:18 final size:18
Alignment explanation
Indices: 212674--212711 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
212664 GTGAAGTATG
*
212674 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
212692 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
212710 AA
1 AA
212712 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:216123 original size:28 final size:28
Alignment explanation
Indices: 216092--216148 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
216082 ACTCTCCGTC
* *
216092 ATATTATGTCGTCGATCTC-ATACTTGAA
1 ATATTATATCGTCGAGC-CAATACTTGAA
216120 ATATTATATCGTCGAGCCAATACTTGAA
1 ATATTATATCGTCGAGCCAATACTTGAA
216148 A
1 A
216149 GCAATGACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (28 bp):
ATATTATATCGTCGAGCCAATACTTGAA
Found at i:216609 original size:2 final size:2
Alignment explanation
Indices: 216602--216635 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
216592 GGTGTGGATG
216602 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
216636 TAAGGCATCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219203 original size:31 final size:31
Alignment explanation
Indices: 219165--219246 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
219155 TTAGTCACCC
* * * **
219165 AACTATTCATGCGTTTGCGTTTTGGTTTTCA
1 AACTATTCATGAGGTTACGTTTTGGTCGTCA
219196 AACTATTCATGAGGTTACGTTTTGGTCGTCA
1 AACTATTCATGAGGTTACGTTTTGGTCGTCA
*
219227 AACTATTCATGTGGTTACGT
1 AACTATTCATGAGGTTACGT
219247 ATTAATCACC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (31 bp):
AACTATTCATGAGGTTACGTTTTGGTCGTCA
Found at i:225306 original size:5 final size:5
Alignment explanation
Indices: 225298--225324 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
225288 TATTATTAAA
225298 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
225325 TCACGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Done.