Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008525.1 Hibiscus syriacus cultivar Beakdansim tig00111394_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: 732385
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1060 original size:21 final size:20
Alignment explanation
Indices: 968--1057 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 20
958 TATGCCATCT
*
968 CCGCATGGTTACAT-CCGAGC
1 CCGCA-GGTTACATGCCTAGC
*
988 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
1009 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
1030 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
1051 CCGCAGG
1 CCGCAGG
1058 GTTTTATACC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
20 17 0.26
21 46 0.71
22 2 0.03
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.19
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:1633 original size:32 final size:33
Alignment explanation
Indices: 1577--1658 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
1567 AATACAAATT
1577 ATATTATTCGAAATTTAAAATAAAA-ATAAAAA
1 ATATTATTCGAAATTTAAAATAAAATATAAAAA
* **
1609 ATATTATTC-AAATTTAAATTTAAAATAT-AATT
1 ATATTATTCGAAATTTAAA-ATAAAATATAAAAA
*
1641 ATAGTATTCGAAATTTAA
1 ATATTATTCGAAATTTAA
1659 CATTAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
31 9 0.21
32 24 0.56
33 10 0.23
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (33 bp):
ATATTATTCGAAATTTAAAATAAAATATAAAAA
Found at i:2527 original size:126 final size:126
Alignment explanation
Indices: 2046--2762 Score: 1182
Period size: 126 Copynumber: 5.7 Consensus size: 126
2036 CTGAGGGACA
2046 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAAAATAATGGAAGGCGCG-CCCCGGGA
1 TGACATAATAGGGCAATGATAATATTCTCTGACG-----AAATAATGGAAGGCGCGCCCCCGGGA
* *
2110 ACGCGCCTTCACGTGAATAGTGAAA-AATAGGTACTGATATATCTAGTGT-CCCGAGGGACATGG
61 ACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGA
2173 G
126 G
*
2174 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAA-G-GCGCCCCCAGGAACGCG
1 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
*
2237 CCTTCATGTGAATAGTGAAATAATA-GTACAT-ATATATCTAGTGT-CCCGAGGGACATGAA
66 CCTTCATGTGAATAGTGAAATAATAGGTAC-TGATATATCTAGTGTCCCCGAGGGACATGAG
2296 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAAAAATAATGGAA-GCGCGCCCCCGGG
1 TGACATAATAGGGCAATGATAATATTCTCTGACG------AAATAATGGAAGGCGCGCCCCCGGG
*
2360 AACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATG
60 AACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATG
2425 AG
125 AG
2427 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
1 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
*
2492 CCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAA
66 CCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAG
2553 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
1 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
*
2618 CGTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAG
66 CCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAG
* *
2679 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAATGCGCGCCCCCGGGAACGCT
1 TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
2744 CCTTCATGTGAATAGTGAA
66 CCTTCATGTGAATAGTGAA
2763 CCGATTATAG
Statistics
Matches: 561, Mismatches: 14, Indels: 30
0.93 0.02 0.05
Matches are distributed among these distances:
121 3 0.01
122 96 0.17
123 16 0.03
125 11 0.02
126 283 0.50
128 46 0.08
129 41 0.07
130 17 0.03
131 48 0.09
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (126 bp):
TGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCG
CCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAG
Found at i:2844 original size:8 final size:8
Alignment explanation
Indices: 2831--2871 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2821 TCACAATCTT
2831 TCAAATTC
1 TCAAATTC
2839 TCAAATTC
1 TCAAATTC
* *
2847 CCAAACTC
1 TCAAATTC
2855 T-AAATTC
1 TCAAATTC
2862 TCAAATTC
1 TCAAATTC
2870 TC
1 TC
2872 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:5878 original size:13 final size:13
Alignment explanation
Indices: 5860--5899 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
5850 TACATAAATA
5860 TATTTAATATAAT
1 TATTTAATATAAT
5873 TATTTAATATAA-
1 TATTTAATATAAT
*
5885 TATTTAATATTAT
1 TATTTAATATAAT
5898 TA
1 TA
5900 GTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTAATATAAT
Found at i:6778 original size:5 final size:5
Alignment explanation
Indices: 6768--6810 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
6758 AAATATGTCA
6768 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAA
1 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAA
6811 GTAGCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:7900 original size:2 final size:2
Alignment explanation
Indices: 7893--7927 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7883 CAAAAAGTAC
*
7893 AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7928 TGGGTCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:8824 original size:52 final size:52
Alignment explanation
Indices: 8746--8850 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
8736 TCCCAAAAAT
8746 GTTAGTCAATTATTAGAAGTCTGGTTCGCTCAGAGTATTAGGAGGTGTGTGG
1 GTTAGTCAATTATTAGAAGTCTGGTTCGCTCAGAGTATTAGGAGGTGTGTGG
8798 GTTAGTCAATTATTAGAAGTCTGGTTCGCTCAGAGTATTAGGAGGTGTGTGG
1 GTTAGTCAATTATTAGAAGTCTGGTTCGCTCAGAGTATTAGGAGGTGTGTGG
8850 G
1 G
8851 GGCGCTTTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.34
Consensus pattern (52 bp):
GTTAGTCAATTATTAGAAGTCTGGTTCGCTCAGAGTATTAGGAGGTGTGTGG
Found at i:8838 original size:25 final size:25
Alignment explanation
Indices: 8756--8838 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
8746 GTTAGTCAAT
8756 TATTAGAAGTCTGGTTCGCTCAGAG
1 TATTAGAAGTCTGGTTCGCTCAGAG
* * * *
8781 TATTAGGAGGTGTGTGGGTTAG-TCA-AT
1 TATTA-GA--AGTCT-GGTTCGCTCAGAG
8808 TATTAGAAGTCTGGTTCGCTCAGAG
1 TATTAGAAGTCTGGTTCGCTCAGAG
8833 TATTAG
1 TATTAG
8839 GAGGTGTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
23 5 0.11
24 6 0.14
25 12 0.27
26 4 0.09
27 6 0.14
28 6 0.14
29 5 0.11
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (25 bp):
TATTAGAAGTCTGGTTCGCTCAGAG
Found at i:12135 original size:25 final size:24
Alignment explanation
Indices: 12107--12157 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
12097 TTTAATATAT
12107 TGATACATG-ATGACATTCCATATTA
1 TGATACATGAATGA-ATT-CATATTA
12132 TGATACATGACATGAATTCATATTA
1 TGATACATGA-ATGAATTCATATTA
12157 T
1 T
12158 ATGCATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 17 0.71
26 3 0.12
27 4 0.17
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (24 bp):
TGATACATGAATGAATTCATATTA
Found at i:13204 original size:19 final size:20
Alignment explanation
Indices: 13161--13210 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
13151 TAATGTTCAT
* *
13161 TACTATTCACACAGTATCGA
1 TACTATTCATACAGTATCAA
13181 TACTATTCATACAGTAT-AA
1 TACTATTCATACAGTATCAA
13200 TACTATTCATA
1 TACTATTCATA
13211 AAAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:20142 original size:60 final size:59
Alignment explanation
Indices: 20063--20228 Score: 183
Period size: 59 Copynumber: 2.8 Consensus size: 59
20053 ATATGAATGG
* **
20063 TCGAGTGATCATTTTGTAACTTTTAATAGTCGGGAGACTCAACAAAACGACGCCCTATAAC
1 TCGAGGGATCATTTTGTAACTTTTAATAGTCAAG-GACTCAACAAAACGACGCCCTAT-AC
* * ** *
20124 -CG-GGGAATCATTTTGTAACTTTTAATAATTAAGGACTCAACAAAGGGACGCCTTATAC
1 TCGAGGG-ATCATTTTGTAACTTTTAATAGTCAAGGACTCAACAAAACGACGCCCTATAC
* * *
20182 TCGAGGGATTATTTTGTAACTTTTAATAGTCAGAGTACTCAATAAAA
1 TCGAGGGATCATTTTGTAACTTTTAATAGTCA-AGGACTCAACAAAA
20229 TAACGTTATA
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.02
59 46 0.53
60 39 0.45
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (59 bp):
TCGAGGGATCATTTTGTAACTTTTAATAGTCAAGGACTCAACAAAACGACGCCCTATAC
Found at i:23333 original size:3 final size:3
Alignment explanation
Indices: 23325--23394 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
23315 GCCTGATTCT
* * *
23325 TCA TCA TCA TCG TCA CCA TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* *
23373 TCA TCA TCA TCC TCG TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA T
23395 AGGATACATC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:31621 original size:21 final size:21
Alignment explanation
Indices: 31583--31622 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31573 GATGGCAACT
*
31583 CAACCCGAATCCGACGGGTTC
1 CAACCCGAACCCGACGGGTTC
31604 CAACCCG-ACCCGATCGGGT
1 CAACCCGAACCCGA-CGGGT
31623 CGAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.40, G:0.25, T:0.12
Consensus pattern (21 bp):
CAACCCGAACCCGACGGGTTC
Found at i:31685 original size:35 final size:36
Alignment explanation
Indices: 31617--31696 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
31607 CCCGACCCGA
* *
31617 TCGGGTCGAATTTTTTTAAAAAAATTCGGGTTCGGG
1 TCGGGTCGGATTTTTTTAAAAAAATACGGGTTCGGG
* * *
31653 TCGGGTCGGATTTTTTTTAAAATATAC-TGTTCGGG
1 TCGGGTCGGATTTTTTTAAAAAAATACGGGTTCGGG
31688 TCGGGTCGG
1 TCGGGTCGG
31697 GTCGAGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 16 0.41
36 23 0.59
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38
Consensus pattern (36 bp):
TCGGGTCGGATTTTTTTAAAAAAATACGGGTTCGGG
Found at i:32994 original size:31 final size:31
Alignment explanation
Indices: 32954--33038 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
32944 GGATTTAATG
* * **
32954 ATTAGATTGATATTTTATTTAATGTTTA-AGA
1 ATTAAATTGATATTTTATCTAAAATTTATA-A
32985 ATTAAATTGATATTTTATCTAAAATTTATAA
1 ATTAAATTGATATTTTATCTAAAATTTATAA
*
33016 ATTAAATTAATATTTTATCTAAA
1 ATTAAATTGATATTTTATCTAAA
33039 TTTCAGAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (31 bp):
ATTAAATTGATATTTTATCTAAAATTTATAA
Found at i:33054 original size:31 final size:31
Alignment explanation
Indices: 32988--33056 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
32978 TTTAAGAATT
* * *
32988 AAATTGATATTTTATCTAAAATTTATAAATT
1 AAATTAATATTTTATCTAAAATTTAGAAATC
*
33019 AAATTAATATTTTATCT-AAATTTCAGAAGTC
1 AAATTAATATTTTATCTAAAATTT-AGAAATC
33050 AAATTAA
1 AAATTAA
33057 AAATTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (31 bp):
AAATTAATATTTTATCTAAAATTTAGAAATC
Found at i:33518 original size:21 final size:20
Alignment explanation
Indices: 33432--33589 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
33422 AAATGACTAA
**
33432 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
33451 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
33471 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
33491 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
33512 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
33533 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
33553 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* *
33574 GAAAATCACAACGCGA
1 CAAAATCGCAACGCGA
33590 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 47 0.46
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:33580 original size:20 final size:19
Alignment explanation
Indices: 33554--33608 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
33544 TGCGATTTTC
*
33554 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
* *
33573 TGAAAATCACAACGCGAACA
1 -CAAAATCGCAACGCGAACA
33593 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
33609 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.11
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:33618 original size:20 final size:20
Alignment explanation
Indices: 33595--33749 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
33585 CGCGAACACA
33595 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
33615 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
33635 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
33655 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
33675 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
33695 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
33715 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
33736 TAAATCGCAACGCG
1 TAAATCGCAACGCG
33750 ATATTTAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.85
21 15 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:33620 original size:40 final size:39
Alignment explanation
Indices: 33556--33750 Score: 192
Period size: 40 Copynumber: 4.9 Consensus size: 39
33546 CGATTTTCCA
* ** * *
33556 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * *
33596 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
33636 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* ** *
33676 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
33716 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
33751 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:33640 original size:60 final size:60
Alignment explanation
Indices: 33556--33749 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
33546 CGATTTTCCA
* ** * * *
33556 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
33616 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
33676 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
33737 AAATCGCAACGCG
1 AAATCGCAACGCG
33750 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:34169 original size:33 final size:33
Alignment explanation
Indices: 34130--34200 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
34120 TTCACTTAGA
*
34130 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
34163 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
34196 TTTCA
1 TTTCA
34201 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:34324 original size:20 final size:20
Alignment explanation
Indices: 34280--34389 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
34270 TGCAGAAGAG
*
34280 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
34301 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
34321 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
34342 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
34356 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
34375 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
34390 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:34337 original size:41 final size:38
Alignment explanation
Indices: 34273--34389 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
34263 TTCAATTTGC
* *
34273 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
34311 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
34352 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
34385 AGAAT
1 AGAAT
34390 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:34359 original size:14 final size:14
Alignment explanation
Indices: 34340--34396 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34330 GAGAAATGAA
34340 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34354 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
34373 AATCGCAACGAGAG
1 AATCGCAACGAGAG
34387 AATCGCAACG
1 AATCGCAACG
34397 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:34372 original size:33 final size:33
Alignment explanation
Indices: 34332--34412 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
34322 CGCAACGAGA
34332 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34365 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
34398 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
34413 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:34430 original size:19 final size:19
Alignment explanation
Indices: 34408--34491 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
34398 GAAACCAAAA
*
34408 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34427 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34446 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
34460 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
34479 TCGCGTTGCGATT
1 TCGCGTTGCGATT
34492 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 41 0.73
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:34468 original size:14 final size:14
Alignment explanation
Indices: 34449--34505 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34439 TTTCATTTCG
34449 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
34463 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
34482 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34496 CGTTGCGATT
1 CGTTGCGATT
34506 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:34472 original size:33 final size:33
Alignment explanation
Indices: 34430--34513 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
34420 TTTCATTTCG
34430 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
34463 CGTTGCGATTGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
34496 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
34514 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:35409 original size:20 final size:20
Alignment explanation
Indices: 35384--35425 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35374 TTATAATTAA
35384 TTATTTAACAATTACTAATT
1 TTATTTAACAATTACTAATT
35404 TTATTTAACAATTACTAATT
1 TTATTTAACAATTACTAATT
35424 TT
1 TT
35426 GTTATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTTAACAATTACTAATT
Found at i:36622 original size:93 final size:93
Alignment explanation
Indices: 36224--36599 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
36214 TAGATTGCTT
*
36224 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
36289 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
36317 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
36382 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
36410 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
36475 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
36503 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
36568 TTTGTCTTTGTTTTGTCTTTTGGTT-AA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
36595 AGTAA
1 AGTAA
36600 TGTAATCCAT
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 7 0.03
93 273 0.98
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:36687 original size:19 final size:19
Alignment explanation
Indices: 36647--36775 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
36637 TAGTTTACTT
* *
36647 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
36667 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
36686 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
36705 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
36719 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
36738 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
*
36752 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAACCAAAA
36771 TCGCA
1 TCGCA
36776 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:36726 original size:33 final size:31
Alignment explanation
Indices: 36683--36775 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 31
36673 CGCGAAACCA
36683 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAAT-AAAATCGCAACGAC
*
36715 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAA-TAAAATCGCAACGAC
36748 AAGATCGCAACGCGAAACTAAAATCGCA
1 AA-ATCGCAACGCGAAA-TAAAATCGCA
36776 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (31 bp):
AAATCGCAACGCGAAATAAAATCGCAACGAC
Found at i:36773 original size:52 final size:51
Alignment explanation
Indices: 36647--36775 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 51
36637 TAGTTTACTT
36647 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
36699 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAACTA-A-AATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
36752 TCGCAACGCGAAACTAAAATCGCA
1 TCGCAACACGAAACTAAAATCGCA
36776 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
50 4 0.06
51 7 0.11
52 39 0.62
53 4 0.06
54 7 0.11
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:36793 original size:19 final size:18
Alignment explanation
Indices: 36771--36870 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
36761 GAAACTAAAA
36771 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
36790 TCGCGTTGC-A-ATTC-TT
1 TCGC-TTGCGATTTTCATT
36806 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
36823 TCGCATTGCGA--TTC-TG
1 TCGC-TTGCGATTTTCATT
36839 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
36856 TCGCGTTGCGATTTT
1 TCGC-TTGCGATTTT
36871 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 15 0.23
17 15 0.23
18 1 0.02
19 24 0.36
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:36865 original size:33 final size:33
Alignment explanation
Indices: 36776--36868 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
36766 TAAAATCGCA
* *
36776 TTGCGATTTTCATTTCGCGTTGCAATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
36809 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
36842 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
36869 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:36883 original size:20 final size:19
Alignment explanation
Indices: 36840--36886 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
36830 GCGATTCTGT
*
36840 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
36859 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAA-TTTCG
*
36879 TGTTGCGA
1 CGTTGCGA
36887 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:38817 original size:14 final size:14
Alignment explanation
Indices: 38798--38833 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38788 GATTGTTAAT
38798 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
38812 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
38826 TGATTTGT
1 TGATTTGT
38834 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:38952 original size:19 final size:19
Alignment explanation
Indices: 38936--39033 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
38926 AAAAATGACT
38936 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
38955 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
38974 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
38988 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39007 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
39027 ATCGCAA
1 ATCGCAA
39034 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:39065 original size:53 final size:53
Alignment explanation
Indices: 38936--39051 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
38926 AAAAATGACT
38936 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
38988 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
39041 ATCGCAATGCG
1 ATCGCAATGCG
39052 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:39085 original size:14 final size:14
Alignment explanation
Indices: 39066--39120 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
39056 TAATTTCGCA
39066 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
39080 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
39097 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
39113 TTGCGATT
1 TTGCGATT
39121 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:39104 original size:19 final size:19
Alignment explanation
Indices: 39080--39277 Score: 193
Period size: 19 Copynumber: 11.4 Consensus size: 19
39070 GATTCTCTCG
39080 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
39099 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
39113 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
39132 TTGCGATTTTCTTTTCGCA
1 TTGCGATTTTCATTTCGCA
*
39151 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
39165 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
39184 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
39203 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
39217 TTGCGATTTTTATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
39237 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
39251 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
39270 TTGCGATT
1 TTGCGATT
39278 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 11, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
14 29 0.20
16 22 0.15
17 20 0.14
18 3 0.02
19 62 0.42
20 11 0.07
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:39136 original size:52 final size:52
Alignment explanation
Indices: 39080--39249 Score: 313
Period size: 52 Copynumber: 3.2 Consensus size: 52
39070 GATTCTCTCG
39080 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
39132 TTGCGATTTTCTTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
39184 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
39237 TTGCGATTTTCAT
1 TTGCGATTTTCAT
39250 GTTGGGATTT
Statistics
Matches: 114, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 97 0.85
53 17 0.15
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:39299 original size:33 final size:33
Alignment explanation
Indices: 39058--39291 Score: 269
Period size: 33 Copynumber: 6.9 Consensus size: 33
39048 TGCGTTTATA
39058 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
39091 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
39124 ATTTCGCATTGCGATTTTCTTTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
39164 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
*
39195 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
39228 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
39262 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
39292 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 18, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
31 9 0.05
32 6 0.04
33 94 0.56
34 28 0.17
35 6 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:41590 original size:12 final size:12
Alignment explanation
Indices: 41573--41597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41563 TCTTCGGGGA
41573 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41585 CTTTTTCTTCTT
1 CTTTTTCTTCTT
41597 C
1 C
41598 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:42529 original size:20 final size:20
Alignment explanation
Indices: 42501--42730 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
42491 AAATTTCAGT
* * *
42501 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
42521 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
42541 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
42561 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
42581 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
42601 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
42621 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
42641 GTTGCGATTTACGGATAT-AC
1 GTTGCGATTTACGGAT-TCGC
*
42661 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
42681 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
42701 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
42721 GTTGCGATTT
1 GTTGCGATTT
42731 TGGAAAATCG
Statistics
Matches: 179, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.02
20 171 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:42731 original size:20 final size:20
Alignment explanation
Indices: 42697--42794 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
42687 ATTTATGTGT
*
42697 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
42717 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
42738 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
42759 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
42780 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
42795 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:42790 original size:42 final size:43
Alignment explanation
Indices: 42697--42795 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
42687 ATTTATGTGT
* *
42697 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
42738 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
42780 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
42796 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:45944 original size:87 final size:88
Alignment explanation
Indices: 45787--45950 Score: 312
Period size: 87 Copynumber: 1.9 Consensus size: 88
45777 AGATTTTCCT
45787 TGTTAATGTAATGTATCTGTTTAATAAAAAATTAAAAAAAAAACTTACTTTAATTAGATTTTCAC
1 TGTTAATGTAATGTATCTGTTTAATAAAAAATTAAAAAAAAAACTTACTTTAATTAGATTTTCAC
45852 TAAATAAATTACTTTAATGTATC
66 TAAATAAATTACTTTAATGTATC
*
45875 TGTTAATGTAATGTATCTGTTTAATAAAAAATT-TAAAAAAAACTTACTTTAATTAGATTTTCAC
1 TGTTAATGTAATGTATCTGTTTAATAAAAAATTAAAAAAAAAACTTACTTTAATTAGATTTTCAC
45939 TAAATAAATTAC
66 TAAATAAATTAC
45951 ATCTGTAAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
87 42 0.56
88 33 0.44
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (88 bp):
TGTTAATGTAATGTATCTGTTTAATAAAAAATTAAAAAAAAAACTTACTTTAATTAGATTTTCAC
TAAATAAATTACTTTAATGTATC
Found at i:46467 original size:10 final size:10
Alignment explanation
Indices: 46452--46476 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46442 TATCGATGCA
46452 ATAATTAATG
1 ATAATTAATG
46462 ATAATTAATG
1 ATAATTAATG
46472 ATAAT
1 ATAAT
46477 AACAAACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
ATAATTAATG
Found at i:58096 original size:29 final size:27
Alignment explanation
Indices: 58022--58100 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
58012 AATTAGTCTT
*
58022 TAAACTTTTTAATATTCTAATTCACCCC
1 TAAA-TTTTTAATATTCTAATTAACCCC
* * * *
58050 TAAATTATGACTATTTCTAATCTAATCCC
1 TAAATTTTTAATA-TTCTAAT-TAACCCC
58079 TAAATTTTTAAATATTCTAATT
1 TAAATTTTT-AATATTCTAATT
58101 TCATTCCCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.15
28 12 0.30
29 19 0.47
30 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.01, T:0.46
Consensus pattern (27 bp):
TAAATTTTTAATATTCTAATTAACCCC
Found at i:58471 original size:3 final size:3
Alignment explanation
Indices: 58463--58540 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
58453 ATCACTGTTA
58463 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58511 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58541 GATTTTTAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:62039 original size:32 final size:32
Alignment explanation
Indices: 61901--62091 Score: 234
Period size: 31 Copynumber: 6.1 Consensus size: 32
61891 GCTCGTATAA
*
61901 TAATC-TGTCCATATGTCCTGAAGAACATAGG
1 TAATCATGTCCATATGTCCCGAAGAACATAGG
*
61932 TAAAC-TGTCCATATGTCCCGAAGAACATAGG
1 TAATCATGTCCATATGTCCCGAAGAACATAGG
* *
61963 TAA-AATGTCCATATGTCTCGAA-AGACATAGG
1 TAATCATGTCCATATGTCCCGAAGA-ACATAGG
61994 TAAT-ATGTCCATATGTCCCGAA-AGACATAGG
1 TAATCATGTCCATATGTCCCGAAGA-ACATAGG
*
62025 TAATCATGTCCATATATCCCGAA-AGACATAGG
1 TAATCATGTCCATATGTCCCGAAGA-ACATAGG
* * *
62057 TAATCTTGTTCATATGTTCCGAAGAACATAGG
1 TAATCATGTCCATATGTCCCGAAGAACATAGG
62089 TAA
1 TAA
62092 CCCTCGACTC
Statistics
Matches: 145, Mismatches: 10, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
30 1 0.01
31 88 0.61
32 55 0.38
33 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (32 bp):
TAATCATGTCCATATGTCCCGAAGAACATAGG
Found at i:83596 original size:15 final size:15
Alignment explanation
Indices: 83576--83606 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
83566 CGAATAATAT
*
83576 TTATTTTATTTTAAA
1 TTATTTTATATTAAA
83591 TTATTTTATATTAAA
1 TTATTTTATATTAAA
83606 T
1 T
83607 AATAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTTTATATTAAA
Found at i:85582 original size:31 final size:31
Alignment explanation
Indices: 85544--85603 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
85534 ACGGGTGAGG
85544 GACTAAAATCGAACGGATAAATAACGTTAAA
1 GACTAAAATCGAACGGATAAATAACGTTAAA
**
85575 GACTAAAATCGAACGGATTGATAACGTTA
1 GACTAAAATCGAACGGATAAATAACGTTA
85604 GGGAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (31 bp):
GACTAAAATCGAACGGATAAATAACGTTAAA
Found at i:85620 original size:49 final size:49
Alignment explanation
Indices: 85563--85656 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
85553 CGAACGGATA
85563 AATAACGTTAAAGACTAAAATCGAACGGATTGATAACGTTAGGGAAATG
1 AATAACGTTAAAGACTAAAATCGAACGGATTGATAACGTTAGGGAAATG
*
85612 AATAACGTTAAAGACTAAAATCGAACGGATTGATAAGGTTAGGGA
1 AATAACGTTAAAGACTAAAATCGAACGGATTGATAACGTTAGGGA
85657 CCATTTTCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (49 bp):
AATAACGTTAAAGACTAAAATCGAACGGATTGATAACGTTAGGGAAATG
Found at i:92290 original size:18 final size:18
Alignment explanation
Indices: 92262--92303 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
92252 TGAGCTTAAT
92262 ATATATATATATAATATTTA
1 ATATATATA-AT-ATATTTA
*
92282 ATATGTATAATATATTTA
1 ATATATATAATATATTTA
92300 ATAT
1 ATAT
92304 TTAACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 2 0.10
20 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATATATATAATATATTTA
Found at i:97690 original size:26 final size:26
Alignment explanation
Indices: 97657--97709 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
97647 CTTTGACAAA
97657 ATAGCAGTTGGAATTTTGTAGAAATC
1 ATAGCAGTTGGAATTTTGTAGAAATC
97683 ATAGCAGTTGGAATTTTGTAGAAATC
1 ATAGCAGTTGGAATTTTGTAGAAATC
97709 A
1 A
97710 CAGTCGTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.34
Consensus pattern (26 bp):
ATAGCAGTTGGAATTTTGTAGAAATC
Found at i:114161 original size:33 final size:33
Alignment explanation
Indices: 114124--114189 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
114114 CTTGTTATTA
*
114124 GGGGCTTAATTTTTATTTTTGCCCAAGGCCATT
1 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
114157 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
1 GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
114190 AAAATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (33 bp):
GGGGCTTAATTTTTATTTTCGCCCAAGGCCATT
Found at i:114747 original size:22 final size:22
Alignment explanation
Indices: 114719--114766 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
114709 AAAATTTAAA
*
114719 AAAAATTATA-AAAAATCTTTAG
1 AAAAATTA-AGAAAAATATTTAG
114741 AAAAATTAAGAAAAATATTTAG
1 AAAAATTAAGAAAAATATTTAG
114763 AAAA
1 AAAA
114767 CTTTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAAATTAAGAAAAATATTTAG
Found at i:114826 original size:18 final size:20
Alignment explanation
Indices: 114805--114850 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
114795 TTTTGGATTA
114805 TTTTAAAAAGTTTTAA-G-T
1 TTTTAAAAAGTTTTAAGGTT
** *
114823 TTTTAGTAATTTTTAAGGTT
1 TTTTAAAAAGTTTTAAGGTT
114843 TTTTAAAA
1 TTTTAAAA
114851 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
18 13 0.62
19 1 0.05
20 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTTAAAAAGTTTTAAGGTT
Found at i:115041 original size:158 final size:160
Alignment explanation
Indices: 114843--115151 Score: 572
Period size: 156 Copynumber: 1.9 Consensus size: 160
114833 TTTTAAGGTT
114843 TTTTAAAATTAAATTTATATTATTTATCACGTAGCACATTCTAGAGTGTAATATAGTTTTTTTAT
1 TTTTAAAATTAAATTTATATTATTTATCACGTAGCACATTCTAGAGTGT-ATATAGTTTTTTTAT
114908 AAATAGTAAAATGATTTGGGAGTGCTTTATAATGAGAAAATTTAAGGGTCAGATTGAATCAAT-A
65 AAATAGT-AAATGATTTGGGAGTGCTTTATAATGAGAAAATTTAAGGGTCAGATTGAATCAATAA
114972 TACTTGTAGATATTAAATTAATAGGACCATCC
129 TACTTGTAGATATTAAATTAATAGGACCATCC
115004 TTTTAAAATTAAA-TT-TA-TATTTATCACGTAGCACATTCTAGAGTGTATATAGTTTTTTTATA
1 TTTTAAAATTAAATTTATATTATTTATCACGTAGCACATTCTAGAGTGTATATAGTTTTTTTATA
115066 AATAGTAAATGATTTGGGAGTGCTTTATAATGAGAAAATTTAAGGGTCAGATTGAATCAATAATA
66 AATAGTAAATGATTTGGGAGTGCTTTATAATGAGAAAATTTAAGGGTCAGATTGAATCAATAATA
115131 CTTGTAGATATTAAATTAATA
131 CTTGTAGATATTAAATTAATA
115152 ATAAGGACCA
Statistics
Matches: 147, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
156 55 0.37
157 46 0.31
158 29 0.20
159 2 0.01
160 2 0.01
161 13 0.09
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (160 bp):
TTTTAAAATTAAATTTATATTATTTATCACGTAGCACATTCTAGAGTGTATATAGTTTTTTTATA
AATAGTAAATGATTTGGGAGTGCTTTATAATGAGAAAATTTAAGGGTCAGATTGAATCAATAATA
CTTGTAGATATTAAATTAATAGGACCATCC
Found at i:124450 original size:5 final size:5
Alignment explanation
Indices: 124440--124468 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
124430 AACTCTTGTT
124440 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
124469 TTCCCATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:130801 original size:2 final size:2
Alignment explanation
Indices: 130794--130827 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
130784 GCAAAGTAAC
130794 TA TA TA TA TA TA -A 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 T
130828 GAGTTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:131317 original size:2 final size:2
Alignment explanation
Indices: 131310--131353 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
131300 AATTAAAACC
131310 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
131352 AT
1 AT
131354 TAGGGGTTTG
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):
AT
Found at i:131682 original size:27 final size:28
Alignment explanation
Indices: 131652--131723 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
131642 TGATGACTAG
*
131652 AAAGTGTAGTGCCAAAGCAATCTATTT-
1 AAAGTTTAGTGCCAAAGCAATCTATTTA
*
131679 AAAGTTTAGTGTCAAAAGCAATCTATTTA
1 AAAGTTTAGTG-CCAAAGCAATCTATTTA
*
131708 AAAGTTTAGTGACAAA
1 AAAGTTTAGTGCCAAA
131724 ATCGATAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 10 0.26
28 18 0.46
29 11 0.28
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (28 bp):
AAAGTTTAGTGCCAAAGCAATCTATTTA
Found at i:131705 original size:28 final size:28
Alignment explanation
Indices: 131652--131724 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
131642 TGATGACTAG
* *
131652 AAAGTGTAGTGCCAAAGCAATCTATTT-
1 AAAGTTTAGTGCAAAAGCAATCTATTTA
131679 AAAGTTTAGTGTCAAAAGCAATCTATTTA
1 AAAGTTTAGTG-CAAAAGCAATCTATTTA
131708 AAAGTTTAGTGACAAAA
1 AAAGTTTAGTG-CAAAA
131725 TCGATAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.24
28 15 0.37
29 16 0.39
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (28 bp):
AAAGTTTAGTGCAAAAGCAATCTATTTA
Found at i:131735 original size:29 final size:28
Alignment explanation
Indices: 131652--131735 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 28
131642 TGATGACTAG
* * **
131652 AAAGTGTAGTG-CCAAAGCAATCTATTT
1 AAAGTTTAGTGACAAAAGCAATAAATTT
* **
131679 AAAGTTTAGTGTCAAAAGCAATCTATTT
1 AAAGTTTAGTGACAAAAGCAATAAATTT
* *
131707 AAAAGTTTAGTGACAAAATCGATAAATTT
1 -AAAGTTTAGTGACAAAAGCAATAAATTT
131736 CTAAAGTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 10 0.21
28 15 0.31
29 23 0.48
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (28 bp):
AAAGTTTAGTGACAAAAGCAATAAATTT
Found at i:133568 original size:27 final size:28
Alignment explanation
Indices: 133538--133613 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 28
133528 TATCGTTCGT
* *
133538 ATTAAAATTTAATGTTATAATTAAAA-A
1 ATTAAAATTTAATGATATAACTAAAATA
*
133565 ATTAAAATTCAAT-ACTATAACTAAAATA
1 ATTAAAATTTAATGA-TATAACTAAAATA
133593 ATTAAAAATTTAATGATATAA
1 ATT-AAAATTTAATGATATAA
133614 ACGAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 22 0.54
28 4 0.10
29 14 0.34
30 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (28 bp):
ATTAAAATTTAATGATATAACTAAAATA
Found at i:137955 original size:60 final size:60
Alignment explanation
Indices: 137861--137976 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
137851 TGGTCCCTTG
* ** *
137861 ACTATAGGATGTTGCTTTATTGAGTCCCTTAACTATTAAAAGTTATGAAATAGTCAATTT
1 ACTATAGGATGTTGCTTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCAATTT
*
137921 ACTATAGTG-TGTTGCTTTGTTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCA
1 ACTATAG-GATGTTGCTTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCA
137977 CCCAACTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (60 bp):
ACTATAGGATGTTGCTTTATTGAGTCCCTCAACTATTAAAAACTATAAAATAGTCAATTT
Found at i:138316 original size:33 final size:35
Alignment explanation
Indices: 138277--138349 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
138267 ACCTTACAAC
* *
138277 TCCCTAG-TTTTTC-CGGGCTAAACTATAACCTTT
1 TCCCTAGCTTTTACACGGGATAAACTATAACCTTT
138310 TCCCTAGCTTTTACACGGGATAAACTATAACCTTT
1 TCCCTAGCTTTTACACGGGATAAACTATAACCTTT
*
138345 CCCCT
1 TCCCT
138350 TTACAAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 7 0.20
34 5 0.14
35 23 0.66
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (35 bp):
TCCCTAGCTTTTACACGGGATAAACTATAACCTTT
Found at i:138655 original size:21 final size:21
Alignment explanation
Indices: 138630--138671 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
138620 CCAGAATTAG
*
138630 GGGAATCGGTACCACTTCATA
1 GGGAATCGATACCACTTCATA
*
138651 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCACTTCATA
138672 ATATTCAAAT
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:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCACTTCATA
Found at i:138792 original size:20 final size:20
Alignment explanation
Indices: 138764--138840 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
138754 AACCATACAG
138764 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
* *
138784 GGGGAGAATCTGT----TCT
1 GGGGGGAATCTGTACCCCCT
* *
138800 -CGGGGAA-CCGATACCCCCT
1 GGGGGGAATCTG-TACCCCCT
138819 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
138839 GG
1 GG
138841 ACAATCTGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
14 2 0.05
15 6 0.14
16 2 0.05
19 2 0.05
20 28 0.67
21 2 0.05
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:141853 original size:13 final size:13
Alignment explanation
Indices: 141835--141860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
141825 ATCTTAATAC
141835 TCAAATCCTTAAA
1 TCAAATCCTTAAA
141848 TCAAATCCTTAAA
1 TCAAATCCTTAAA
141861 ACCCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TCAAATCCTTAAA
Found at i:150601 original size:19 final size:19
Alignment explanation
Indices: 150577--150614 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
150567 CTACAGGTGC
150577 CACTTATTCCTTTCTTCCA
1 CACTTATTCCTTTCTTCCA
150596 CACTTATTCCTTTCTTCCA
1 CACTTATTCCTTTCTTCCA
150615 TATGTTCTGG
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:0.16, C:0.37, G:0.00, T:0.47
Consensus pattern (19 bp):
CACTTATTCCTTTCTTCCA
Found at i:160183 original size:24 final size:23
Alignment explanation
Indices: 160139--160183 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
160129 AATAAAATAC
* * *
160139 AAAAATTCTATTTTTTTATTTAT
1 AAAAATTCAATTTTATAATTTAT
160162 AAAAACTTCAATTTTATAATTT
1 AAAAA-TTCAATTTTATAATTT
160184 TTCGCAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
AAAAATTCAATTTTATAATTTAT
Found at i:162505 original size:2 final size:2
Alignment explanation
Indices: 162498--162554 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
162488 AGATGCATGT
162498 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
162540 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
162555 GCACGAACTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168681 original size:4 final size:4
Alignment explanation
Indices: 168674--168724 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
168664 TATATATATT
*
168674 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
168722 TAT
1 TAT
168725 ACTTATAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:169144 original size:18 final size:17
Alignment explanation
Indices: 169118--169164 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
169108 AATTTTGTAT
169118 AAAAATATTAAAAATAA
1 AAAAATATTAAAAATAA
*
169135 AAATAATATTTAAAACTAA
1 AAA-AATA-TTAAAAATAA
*
169154 TAAAATATTAA
1 AAAAATATTAA
169165 CTATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 11 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATATTAAAAATAA
Found at i:169175 original size:18 final size:17
Alignment explanation
Indices: 169154--169192 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
169144 TTAAAACTAA
* *
169154 TAAAATATTAACTATTAT
1 TAAAATATAAAATATT-T
169172 TAAAATATAAAATATTT
1 TAAAATATAAAATATTT
169189 TAAA
1 TAAA
169193 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATATAAAATATTT
Found at i:170056 original size:2 final size:2
Alignment explanation
Indices: 170049--170078 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
170039 ATTCATTTTA
170049 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
170079 TAATTAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171090 original size:3 final size:3
Alignment explanation
Indices: 171082--171128 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
171072 AACCAATCCA
171082 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
171129 GAAATGAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:174860 original size:15 final size:16
Alignment explanation
Indices: 174836--174868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
174826 GCTCTTTTCT
174836 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
174851 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
174867 TT
1 TT
174869 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:176718 original size:76 final size:76
Alignment explanation
Indices: 176584--176993 Score: 691
Period size: 76 Copynumber: 5.4 Consensus size: 76
176574 GAAATGTTGA
* *
176584 AAACATCATGCACTGAAGGGCTTACAGATGA-CCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
176648 AGGCTTTTTGG
66 AGGCTTTTTGG
*
176659 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
176724 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
176735 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
176800 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
176811 AAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
176876 AGGCTTTTTGG
66 AGGCTTTTTGG
*
176887 AAACATCATGCACTGAAGGACTTACAGATGA-CCTGAAGGCTTT-AAGAACATCAAAAAGCTCTC
1 AAACATCATGCACTGAAGGACTTACAGATGACCCT-AAGGCTTTGAA-AACATCAAAAAGCTCCC
176950 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
*
176963 AAACATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
176994 GGGAAATAGT
Statistics
Matches: 321, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
75 33 0.10
76 288 0.90
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:177655 original size:113 final size:114
Alignment explanation
Indices: 177393--178029 Score: 905
Period size: 113 Copynumber: 5.6 Consensus size: 114
177383 ATAGAATTAT
* * *
177393 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCCC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
177458 ATTATGAA-CTTCTCTAGAAAAGTTGTTCCATCAAGTGATGTATT-TGA
66 ATTATGAACCTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGA
* *
177505 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
177570 ATTATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTCAGA
66 ATTATGAACCTTCTCTGG-AAATGATGATCCATCAAATGATGAATTCAGA
177619 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
177683 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATAAT-AGATTCA-A
66 ATTATGAACCTTCTCTGGAAATGATGATCCATCAAATGATGA-ATTCAGA
* *
177731 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
177796 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCA-A
66 ATTATGAACCTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGA
* *
177844 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *** * * *
177909 ATTATGAA-CTTCTATAGAAATGCCAATCCATCGAATGATGGATT-GGA
66 ATTATGAACCTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGA
*
177956 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
178021 ATTATGAAC
66 ATTATGAAC
178030 TCGACCTGGA
Statistics
Matches: 482, Mismatches: 34, Indels: 17
0.90 0.06 0.03
Matches are distributed among these distances:
112 175 0.36
113 302 0.63
114 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACCTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAGA
Found at i:177898 original size:24 final size:23
Alignment explanation
Indices: 177863--177907 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
177853 TGAACAAATT
177863 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
177887 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
177908 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:178491 original size:22 final size:22
Alignment explanation
Indices: 178466--178520 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
178456 CATAAAGTTT
*
178466 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
178488 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
178510 TCATCTTTGAA
1 TCATCTTTGAA
178521 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:178966 original size:54 final size:54
Alignment explanation
Indices: 178884--179053 Score: 286
Period size: 54 Copynumber: 3.1 Consensus size: 54
178874 AGAATAGCAG
* *** *
178884 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
*
178938 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
178992 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
179046 GTTCGTAA
1 GTTCGTAA
179054 TTATTGAAGT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 109 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
Found at i:180196 original size:40 final size:35
Alignment explanation
Indices: 180150--180245 Score: 104
Period size: 35 Copynumber: 2.6 Consensus size: 35
180140 AGTGAGCTCT
* *
180150 AAAATGCCCCAATATTGCTTCTTGTTAAGATGAGCCTAC
1 AAAATGCCCCAATATT-CATATTGTT--G-TGAGCCTAC
* *
180189 AAGAATGCCCAAATATTCATATTGTTGTGAGCCTTC
1 AA-AATGCCCCAATATTCATATTGTTGTGAGCCTAC
180225 AAAATGCCCCAATATTC-TATT
1 AAAATGCCCCAATATTCATATT
180246 TCTGGTTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 4 0.08
35 14 0.27
36 10 0.20
37 1 0.02
39 9 0.18
40 13 0.25
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (35 bp):
AAAATGCCCCAATATTCATATTGTTGTGAGCCTAC
Found at i:181305 original size:83 final size:83
Alignment explanation
Indices: 181166--181421 Score: 476
Period size: 83 Copynumber: 3.1 Consensus size: 83
181156 CTTATTTCTC
*
181166 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
181231 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
181249 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
181314 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
181332 CTATGAGCAGATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
181397 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
181415 CTATGAG
1 CTATGAG
181422 TCTCTTTCAG
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 169 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:188383 original size:18 final size:17
Alignment explanation
Indices: 188335--188385 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
188325 AAATACTTGC
*
188335 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
188353 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
188371 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
188386 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:188950 original size:15 final size:16
Alignment explanation
Indices: 188926--188958 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
188916 GCTCTTTTCT
188926 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
188941 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
188957 TT
1 TT
188959 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:189433 original size:2 final size:2
Alignment explanation
Indices: 189426--189450 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
189416 GATATTTACC
189426 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 T
189451 TCTGATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190514 original size:3 final size:3
Alignment explanation
Indices: 190506--190546 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
190496 ATTTTTTATT
*
190506 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
190547 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:202791 original size:12 final size:12
Alignment explanation
Indices: 202774--202805 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
202764 CTCTGTAATT
202774 TCTCTCTCTTTC
1 TCTCTCTCTTTC
202786 TCTCTCTCTTTC
1 TCTCTCTCTTTC
*
202798 TCACTCTC
1 TCTCTCTC
202806 AATTCGCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:206479 original size:29 final size:29
Alignment explanation
Indices: 206425--206630 Score: 143
Period size: 29 Copynumber: 7.0 Consensus size: 29
206415 TTCAATTTGG
* *
206425 TATTATTATCTT-CACTTAAAACTATATTT
1 TATTATTATCTTAAATTTAAAA-TATATTT
* *
206454 TATTCTTATTTTAAATTTAAAATATATATTT
1 TATTATTATCTTAAATTT-AAA-ATATATTT
* * * *
206485 TATTTTTGTCTT-AACTTATAAATCTATTT
1 TATTATTATCTTAAATTTA-AAATATATTT
* * *
206514 TATTCTTAT-TTTAATATAAAA-ATATTT
1 TATTATTATCTTAAATTTAAAATATATTT
* * * * *
206541 TATTATTGTCTTCACTTAAAAATATCTTT
1 TATTATTATCTTAAATTTAAAATATATTT
*
206570 TATTATTATTTTAAA-TTAAATATATATTT
1 TATTATTATCTTAAATTTAAA-ATATATTT
* *
206599 TATTAGTATCTTAACTTTTTAAAATATATTT
1 TATTATTATCTTAA--ATTTAAAATATATTT
206630 T
1 T
206631 TAAAATATAT
Statistics
Matches: 136, Mismatches: 30, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
27 12 0.09
28 17 0.12
29 64 0.47
30 9 0.07
31 28 0.21
32 6 0.04
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.56
Consensus pattern (29 bp):
TATTATTATCTTAAATTTAAAATATATTT
Found at i:206571 original size:56 final size:58
Alignment explanation
Indices: 206425--206630 Score: 229
Period size: 60 Copynumber: 3.5 Consensus size: 58
206415 TTCAATTTGG
* * *
206425 TATTATTATCTTCACTTAAAACTATATTTTATTCTTATTTTAAATTTAAAATATATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTT-AATAT-AAATATATATTT
* * * *
206485 TATTTTTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATATAAA-A-ATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATATAAATATATATTT
* *
206541 TATTATTGTCTTCACTTAAAAATATCTTTTATTATTATTTTAA-ATTAAATATATATTT
1 TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATA-TAAATATATATTT
* * * *
206599 TATTAGTATCTTAACTTTTTAAAATATATTTT
1 TATTATTGTCTTCAC--TTAAAAATATATTTT
206631 TAAAATATAT
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
55 1 0.01
56 47 0.38
57 2 0.02
58 21 0.17
59 4 0.03
60 48 0.39
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.56
Consensus pattern (58 bp):
TATTATTGTCTTCACTTAAAAATATATTTTATTCTTATTTTAATATAAATATATATTT
Found at i:206632 original size:13 final size:13
Alignment explanation
Indices: 206614--206641 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
206604 GTATCTTAAC
206614 TTTTTAAAATATA
1 TTTTTAAAATATA
206627 TTTTTAAAATATA
1 TTTTTAAAATATA
206640 TT
1 TT
206642 AATTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:206644 original size:116 final size:118
Alignment explanation
Indices: 206425--206660 Score: 284
Period size: 116 Copynumber: 2.0 Consensus size: 118
206415 TTCAATTTGG
* * *
206425 TATTATTATCTTCACTTAAAACTATATTTTATTCTTATTTTAAATTTAAAATATATATTTTATTT
1 TATTATTATCTTCACTTAAAAATATATTTTATTATTATTTTAAATTTAAAATATATATTTTATTA
* * * *** *
206490 TTGTCTTAACTTATAAATCTATTTTATTCTTATTTTAATAT-AAAA-ATATTT
66 GTATCTTAACTTATAAATATATTTTATAAATATATTAATATCAAAAGATATTT
* *
206541 TATTATTGTCTTCACTTAAAAATATCTTTTATTATTATTTTAAA-TT-AAATATATATTTTATTA
1 TATTATTATCTTCACTTAAAAATATATTTTATTATTATTTTAAATTTAAAATATATATTTTATTA
* *
206604 GTATCTTAACTTTTTAAAATATATTTT-TAAAATATATTAATTTCAAAAGATATTT
66 GTATCTTAAC-TTAT-AAATATATTTTAT-AAATATATTAATATCAAAAGATATTT
206659 TA
1 TA
206661 ACTTAAGAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
114 24 0.24
115 6 0.06
116 59 0.58
117 4 0.04
118 8 0.08
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (118 bp):
TATTATTATCTTCACTTAAAAATATATTTTATTATTATTTTAAATTTAAAATATATATTTTATTA
GTATCTTAACTTATAAATATATTTTATAAATATATTAATATCAAAAGATATTT
Found at i:206674 original size:23 final size:23
Alignment explanation
Indices: 206648--206691 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
206638 TATTAATTTC
206648 AAAAGATATTTTAACTTAAGAAT
1 AAAAGATATTTTAACTTAAGAAT
* *
206671 AAAATATATTTTAAGTTAAGA
1 AAAAGATATTTTAACTTAAGA
206692 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAAGATATTTTAACTTAAGAAT
Found at i:206756 original size:30 final size:29
Alignment explanation
Indices: 206664--206868 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 29
206654 TATTTTAACT
*
206664 TAAGAATAAAATATA-TTTTAAGTTAAGA
1 TAAGAATAAAATATATTTTTAAGTTAATA
***
206692 T-ATTTTAAAATCAT-TTTTTAAAGGTTAATA
1 TAAGAATAAAAT-ATATTTTT-AA-GTTAATA
*
206722 TAAGAATAAAATATAATTTTTAAGTTAATG
1 TAAGAATAAAATAT-ATTTTTAAGTTAATA
* * *
206752 TAAGAATAAAATATACTTTTAAGTGAAGA
1 TAAGAATAAAATATATTTTTAAGTTAATA
* *
206781 TAAGATAAAAACATATATTTTTATA-TTAAAA
1 TAAGA-ATAAA-ATATATTTTTA-AGTTAATA
* * *
206812 TTAA-AATAAAATAGATTTATAAGTTAAGA
1 -TAAGAATAAAATATATTTTTAAGTTAATA
* * *
206841 CAAAAATAAAATATATTTTAAAAGTTAA
1 TAAGAATAAAATATATTTT-TAAGTTAA
206869 GAATATAAGA
Statistics
Matches: 139, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
27 7 0.05
28 10 0.07
29 45 0.32
30 44 0.32
31 24 0.17
32 9 0.06
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (29 bp):
TAAGAATAAAATATATTTTTAAGTTAATA
Found at i:206784 original size:29 final size:28
Alignment explanation
Indices: 206664--206870 Score: 152
Period size: 30 Copynumber: 7.0 Consensus size: 28
206654 TATTTTAACT
206664 TAAGAATAAAATATATTTTAAGTTAAGA
1 TAAGAATAAAATATATTTTAAGTTAAGA
*** * *
206692 T-ATTTTAAAATCATTTTTTAAAGGTTAATA
1 TAAGAATAAAAT-ATATTTT-AA-GTTAAGA
206722 TAAGAATAAAATATAATTTTTAAGTTAATG-
1 TAAGAATAAAATAT-A-TTTTAAGTTAA-GA
*
206752 TAAGAATAAAATATACTTTTAAGTGAAGA
1 TAAGAATAAAATATA-TTTTAAGTTAAGA
* *
206781 TAAGATAAAAACATATATTTTTATA-TTAAAA
1 TAAGA-ATAAA-ATATA-TTTTA-AGTTAAGA
*
206812 TTAA-AATAAAATAGATTTATAAGTTAAGA
1 -TAAGAATAAAATATATTT-TAAGTTAAGA
* *
206841 CAAAAATAAAATATATTTTAAAAGTTAAGA
1 TAAGAATAAAATATATTTT--AAGTTAAGA
206871 ATATAAGATA
Statistics
Matches: 141, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
27 7 0.05
28 15 0.11
29 42 0.30
30 45 0.32
31 24 0.17
32 8 0.06
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (28 bp):
TAAGAATAAAATATATTTTAAGTTAAGA
Found at i:209202 original size:2 final size:2
Alignment explanation
Indices: 209195--209247 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
209185 TGTACCATGC
209195 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
209237 AT AT AT AT AT A
1 AT AT AT AT AT A
209248 AGGACAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:209311 original size:25 final size:23
Alignment explanation
Indices: 209279--209341 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
209269 GTTACGGGTG
209279 AATTTATAAAATTTTAAGAGTGATA
1 AATTTATAAAATTTTAA-AG-GATA
*
209304 AATTTAT-AAATTTTCAAGGATA
1 AATTTATAAAATTTTAAAGGATA
*
209326 AATTTGTAAAATTTTA
1 AATTTATAAAATTTTA
209342 GGGATAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.29
23 9 0.26
24 8 0.24
25 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.43
Consensus pattern (23 bp):
AATTTATAAAATTTTAAAGGATA
Found at i:210515 original size:25 final size:26
Alignment explanation
Indices: 210464--210526 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
210454 TTAATTTTAC
*
210464 ATCTTTTAAAATTTTCAAAATTCTAT
1 ATCTTTTAAAATTTTCAAAATTATAT
210490 ATCTTTT-AAA-TTTCAATATATATATAT
1 ATCTTTTAAAATTTTCAA-A-AT-TATAT
210517 AT-TTTTAAAA
1 ATCTTTTAAAA
210527 ATTGTACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 6 0.19
25 4 0.12
26 13 0.41
27 9 0.28
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (26 bp):
ATCTTTTAAAATTTTCAAAATTATAT
Found at i:215635 original size:21 final size:21
Alignment explanation
Indices: 215588--215636 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
215578 CTGGTCATCC
**
215588 AATTTTTTAAACCCCAGACTG
1 AATTTTTTAAACCCCAGACCA
* *
215609 GA-TTTTTAAACCCCATACCA
1 AATTTTTTAAACCCCAGACCA
215629 AATTTTTT
1 AATTTTTT
215637 TCCGAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (21 bp):
AATTTTTTAAACCCCAGACCA
Found at i:216022 original size:15 final size:15
Alignment explanation
Indices: 215998--216029 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
215988 TAACCGATTT
*
215998 CGGTTTTAAAAAAAC
1 CGGTTATAAAAAAAC
216013 CGGTTATAAAAAAAC
1 CGGTTATAAAAAAAC
216028 CG
1 CG
216030 ATTTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (15 bp):
CGGTTATAAAAAAAC
Found at i:216178 original size:32 final size:33
Alignment explanation
Indices: 216078--216180 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
216068 ACAAAGTTTA
* *
216078 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
216110 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
216143 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
216175 CGATAA
1 CGATAA
216181 TTGAAACAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
32 15 0.23
33 51 0.77
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:216199 original size:21 final size:21
Alignment explanation
Indices: 216175--216216 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
216165 ACTTCAAGTT
216175 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
216196 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
216217 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:218676 original size:27 final size:28
Alignment explanation
Indices: 218645--218702 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
218635 AAAAAACCGG
*
218645 TTTTTC-CCAAATCCGAT-TTCGGATATT
1 TTTTTCGCAAAATCCGATATTCGGAT-TT
*
218672 TTTTTCGCAAAATCGGATATTCGGATTT
1 TTTTTCGCAAAATCCGATATTCGGATTT
218700 TTT
1 TTT
218703 GTGACCCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 6 0.22
28 14 0.52
29 7 0.26
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTTTCGCAAAATCCGATATTCGGATTT
Found at i:236019 original size:7 final size:7
Alignment explanation
Indices: 236009--236061 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
235999 TATATATATA
236009 ATATTTT
1 ATATTTT
236016 ATATTTT
1 ATATTTT
* *
236023 TTATATT
1 ATATTTT
*
236030 A-ATTAT
1 ATATTTT
* *
236036 ATATATA
1 ATATTTT
236043 ATATTTT
1 ATATTTT
236050 ATATTTT
1 ATATTTT
236057 ATATT
1 ATATT
236062 AATTATATAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:236038 original size:34 final size:32
Alignment explanation
Indices: 235999--236081 Score: 139
Period size: 32 Copynumber: 2.5 Consensus size: 32
235989 ATTATATATA
235999 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATA--TTTTATATTAAT
236033 TATATATATAATATTTTATATTTTATATTAAT
1 TATATATATAATATTTTATATTTTATATTAAT
*
236065 TATATATAAAATATTTT
1 TATATATATAATATTTT
236082 CGGGTTTGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 28 0.58
34 20 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATATATAATATTTTATATTTTATATTAAT
Found at i:241453 original size:11 final size:11
Alignment explanation
Indices: 241437--241461 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
241427 TTGTTTATTC
241437 GAATAGCAGAG
1 GAATAGCAGAG
241448 GAATAGCAGAG
1 GAATAGCAGAG
241459 GAA
1 GAA
241462 AACAACTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.36, T:0.08
Consensus pattern (11 bp):
GAATAGCAGAG
Found at i:245572 original size:24 final size:24
Alignment explanation
Indices: 245545--245611 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
245535 TTTTATACTT
* *
245545 ATTCGTTTATGTTCGTTTACGCTC
1 ATTCATTTGTGTTCGTTTACGCTC
* *
245569 ATTCATTTGTGTTTGTTTACGTTC
1 ATTCATTTGTGTTCGTTTACGCTC
*
245593 ATTAATTTGTGTTCGTTTA
1 ATTCATTTGTGTTCGTTTA
245612 TCATTTTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.15, C:0.13, G:0.16, T:0.55
Consensus pattern (24 bp):
ATTCATTTGTGTTCGTTTACGCTC
Found at i:245897 original size:16 final size:16
Alignment explanation
Indices: 245876--245919 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
245866 AATAAATAAG
245876 CGAACATAAACGAACA
1 CGAACATAAACGAACA
* *
245892 CGAACATAAATGAGCA
1 CGAACATAAACGAACA
245908 CGAACATAAACG
1 CGAACATAAACG
245920 TTGGAGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.52, C:0.23, G:0.16, T:0.09
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:247021 original size:14 final size:14
Alignment explanation
Indices: 247002--247030 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
246992 AAACATAAAT
247002 GAACATAACCGAAC
1 GAACATAACCGAAC
247016 GAACATAACCGAAC
1 GAACATAACCGAAC
247030 G
1 G
247031 TTCACGAACG
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:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:256826 original size:18 final size:19
Alignment explanation
Indices: 256785--256828 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
256775 TTTGGTTCAC
*
256785 GGAATATAAGATTATCAGTT
1 GGAATAAAAGATTATCAG-T
*
256805 GGAATAAAAGATTATTAG-
1 GGAATAAAAGATTATCAGT
256823 GGAATA
1 GGAATA
256829 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (19 bp):
GGAATAAAAGATTATCAGT
Found at i:261451 original size:13 final size:13
Alignment explanation
Indices: 261433--261460 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
261423 TGATTATGGG
261433 AAGTTTATGGCTT
1 AAGTTTATGGCTT
261446 AAGTTTATGGCTT
1 AAGTTTATGGCTT
261459 AA
1 AA
261461 TTGATATCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (13 bp):
AAGTTTATGGCTT
Found at i:262304 original size:3 final size:3
Alignment explanation
Indices: 262296--262325 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
262286 GTTCTAATTC
262296 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
262326 GAAAATGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.