Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold136
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: 1039917
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.32
Warning! 114553 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:971169 original size:11 final size:11
Alignment explanation
Indices: 971150--971232 Score: 53
Period size: 11 Copynumber: 7.2 Consensus size: 11
971140 TTGATAATTT
*
971150 TAAATATAATA
1 TAAAAATAATA
971161 TAAAAATAAT-
1 TAAAAATAATA
*
971171 TAAAATTAATA
1 TAAAAATAATA
971182 TTAAATATAATAATA
1 -T-AA-A-AATAATA
*
971197 TAATAAT-ATA
1 TAAAAATAATA
971207 TTAAAAATATATA
1 -TAAAAATA-ATA
* *
971220 TAATATTAATA
1 TAAAAATAATA
971231 TA
1 TA
971233 TTAAATTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 12 0.21
11 23 0.40
12 7 0.12
13 7 0.12
14 2 0.04
15 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:971186 original size:33 final size:37
Alignment explanation
Indices: 971144--971212 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 37
971134 TTACCTTTGA
*
971144 TAATTTTAAATATAAT-ATA-AA-AATA-ATTAAAAT
1 TAATATTAAATATAATAATATAATAATATATTAAAAT
971177 TAATATTAAATATAATAATATAATAATATATTAAAA
1 TAATATTAAATATAATAATATAATAATATATTAAAA
971213 ATATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 15 0.48
34 3 0.10
35 2 0.06
36 4 0.13
37 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
TAATATTAAATATAATAATATAATAATATATTAAAAT
Found at i:971225 original size:36 final size:37
Alignment explanation
Indices: 971155--971230 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
971145 AATTTTAAAT
*
971155 ATAATATAAAAATAATTAAAATTAATATTAAATA-TA
1 ATAATATAAAAATAATTAAAAATAATATTAAATATTA
*
971191 ATAATATAATAATATATTAAAAAT-ATA-TATAATATTA
1 ATAATATAAAAATA-ATTAAAAATAATATTA-AATATTA
971228 ATA
1 ATA
971231 TATTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 2 0.06
36 20 0.57
37 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
ATAATATAAAAATAATTAAAAATAATATTAAATATTA
Found at i:971231 original size:13 final size:13
Alignment explanation
Indices: 971177--971257 Score: 51
Period size: 13 Copynumber: 5.9 Consensus size: 13
971167 TAATTAAAAT
971177 TAATATTAAATATAA
1 TAATATT-AATAT-A
971192 TAATATAATAATATA
1 TAATAT--TAATATA
* *
971207 TTAAAAAT-ATATA
1 -TAATATTAATATA
971220 TAATATTAATATA
1 TAATATTAATATA
*
971233 TTAA-ATTTATATA
1 -TAATATTAATATA
971246 T-ATATTTAATAT
1 TAATA-TTAATAT
971258 TTTAAAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
11 1 0.02
12 7 0.13
13 24 0.45
14 4 0.08
15 7 0.13
16 9 0.17
17 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATTAATATA
Found at i:971273 original size:28 final size:27
Alignment explanation
Indices: 971179--971278 Score: 111
Period size: 26 Copynumber: 3.9 Consensus size: 27
971169 ATTAAAATTA
* *
971179 ATATTAAATATA-ATA-ATATAATAAT
1 ATATTAAAAATATATATATATATTAAT
971204 ATATTAAAAATATATATA-ATATTAAT
1 ATATTAAAAATATATATATATATTAAT
**
971230 ATATTAAATTTATATATATAT-TTAAT
1 ATATTAAAAATATATATATATATTAAT
*
971256 ATTTTAAAAATA-ATTATATATAT
1 ATATTAAAAATATA-TATATATAT
971279 CCGATTATCG
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
25 12 0.19
26 47 0.75
27 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTAAAAATATATATATATATTAAT
Found at i:975398 original size:8 final size:9
Alignment explanation
Indices: 975372--975438 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 9
975362 TTAAAAATAA
975372 ATATTTTAT
1 ATATTTTAT
975381 AATATTTTAT
1 -ATATTTTAT
975391 AT-TTTTAT
1 ATATTTTAT
** *
975399 ATATTAAAA
1 ATATTTTAT
*
975408 AAATTATTATT
1 ATATT-TTA-T
975419 ATATTTT-T
1 ATATTTTAT
975427 ATA-TTTAT
1 ATATTTTAT
975435 ATAT
1 ATAT
975439 AATAATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
7 3 0.07
8 16 0.36
9 9 0.20
10 12 0.27
11 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTTTAT
Found at i:975438 original size:38 final size:40
Alignment explanation
Indices: 975360--975439 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 40
975350 TTTAGATACG
*
975360 TATTAAAAATAAATATTTTATAATATTTTATATTTTTATA
1 TATTAAAAATAAATATTTTATAATATTTTATATTTATATA
*
975400 TATTAAAAA-AATTATTATTAT-AT-TTTTATATTTATATA
1 TATTAAAAATAAATATT-TTATAATATTTTATATTTATATA
975438 TA
1 TA
975440 ATAATATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 16 0.43
39 8 0.22
40 13 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (40 bp):
TATTAAAAATAAATATTTTATAATATTTTATATTTATATA
Found at i:979330 original size:14 final size:14
Alignment explanation
Indices: 979296--979337 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
979286 TCAGTTTTTT
*
979296 TTTAAATATTTATG
1 TTTAAATATTTATA
979310 TTT-AATATTTATA
1 TTTAAATATTTATA
*
979323 TTTAAATATTAATA
1 TTTAAATATTTATA
979337 T
1 T
979338 AAAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTTAAATATTTATA
Found at i:983586 original size:14 final size:14
Alignment explanation
Indices: 983569--983612 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
983559 TATTATATTT
983569 ATATTAAAATATAA
1 ATATTAAAATATAA
*
983583 ATATT--ACTATAA
1 ATATTAAAATATAA
*
983595 ATTTTAAAATATAA
1 ATATTAAAATATAA
983609 ATAT
1 ATAT
983613 CATTATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:983605 original size:26 final size:26
Alignment explanation
Indices: 983572--983627 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
983562 TATATTTATA
*
983572 TTAAAATATAAATATTACTATAAATT
1 TTAAAATATAAATATCACTATAAATT
*
983598 TTAAAATATAAATATCATTATAAATT
1 TTAAAATATAAATATCACTATAAATT
983624 TTAA
1 TTAA
983628 TCTTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAAATATAAATATCACTATAAATT
Found at i:985612 original size:2 final size:2
Alignment explanation
Indices: 985605--985645 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
985595 TTTGGTGATA
* *
985605 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
985646 CACACACACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:987804 original size:17 final size:17
Alignment explanation
Indices: 987782--987818 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
987772 AATCCTATAA
*
987782 AAAATTTTTAAAATTTT
1 AAAATTTATAAAATTTT
*
987799 AAAATTTATAATATTTT
1 AAAATTTATAAAATTTT
987816 AAA
1 AAA
987819 TAACATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTTATAAAATTTT
Found at i:988245 original size:17 final size:17
Alignment explanation
Indices: 988205--988246 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
988195 AAAAAATAAA
*
988205 ATAATTATAATTTGTAT
1 ATAATTTTAATTTGTAT
988222 ATAATTTTAATTT-TAT
1 ATAATTTTAATTTGTAT
988238 ATTAATTTT
1 A-TAATTTT
988247 TTGATGTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATAATTTTAATTTGTAT
Found at i:988616 original size:21 final size:24
Alignment explanation
Indices: 988541--988628 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 24
988531 TAAATAGTAA
*
988541 TATTAACATAATTGTTAAGATATTTAT
1 TATTAAAAT-ATT-TTAA-ATATTTAT
* *
988568 TTTTAAAATATTTTAAATATCTAT
1 TATTAAAATATTTTAAATATTTAT
*
988592 TATTAAAA-A-TTT-AATATTTAA
1 TATTAAAATATTTTAAATATTTAT
988613 TATTAAAATATATTTA
1 TATTAAAATAT-TTTA
988629 TTATTAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 15 0.29
22 4 0.08
23 1 0.02
24 17 0.33
25 4 0.08
26 3 0.06
27 7 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTAAAATATTTTAAATATTTAT
Found at i:990212 original size:16 final size:18
Alignment explanation
Indices: 990181--990214 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
990171 TATTAATATT
990181 TTAAAATATATTTTAAAA
1 TTAAAATATATTTTAAAA
990199 TTAAAAT-T-TTTTAAAA
1 TTAAAATATATTTTAAAA
990215 AACAATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATATATTTTAAAA
Found at i:991778 original size:19 final size:18
Alignment explanation
Indices: 991729--991780 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
991719 AATTTTAAAA
*
991729 TTTATATTATAAATAATAT
1 TTTATATTA-AAATATTAT
* *
991748 TTAAAATT-AAATATTATT
1 TTTATATTAAAATATTA-T
991766 TTTATATTAAAATAT
1 TTTATATTAAAATAT
991781 AATTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 7 0.27
18 7 0.27
19 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATATTAAAATATTAT
Found at i:991822 original size:35 final size:35
Alignment explanation
Indices: 991737--991822 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 35
991727 AATTTATATT
* *
991737 ATAAATAAT-ATTTAAAATTAAATATTATTTTTATA
1 ATAAA-AATAATTTAAAATTAAATACTATTTTAATA
* *
991772 TTAAAATATAA-TTAAATTTAAATACT-TTTTAATA
1 ATAAAA-ATAATTTAAAATTAAATACTATTTTAATA
991806 CATAAAAATAATTTAAA
1 -ATAAAAATAATTTAAA
991823 CTATAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
34 12 0.29
35 29 0.69
36 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (35 bp):
ATAAAAATAATTTAAAATTAAATACTATTTTAATA
Found at i:994578 original size:30 final size:30
Alignment explanation
Indices: 994544--994602 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
994534 TATTTATTAT
*
994544 ATAAAATTAATAATTAAT-AATTAAATTTAA
1 ATAAAAATAA-AATTAATAAATTAAATTTAA
* *
994574 ATAAAAATAAAATTATTAAATTTAATTTA
1 ATAAAAATAAAATTAATAAATTAAATTTA
994603 TTTATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATAAAAATAAAATTAATAAATTAAATTTAA
Found at i:995307 original size:11 final size:11
Alignment explanation
Indices: 995272--995309 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
995262 TCAAGATACA
995272 ATGAAACTTTT
1 ATGAAACTTTT
*
995283 ATAAAACTTTT
1 ATGAAACTTTT
995294 ATGAAACTTTT
1 ATGAAACTTTT
995305 ATGAA
1 ATGAA
995310 TTTTGCAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (11 bp):
ATGAAACTTTT
Found at i:996825 original size:49 final size:50
Alignment explanation
Indices: 996714--996945 Score: 247
Period size: 49 Copynumber: 4.7 Consensus size: 50
996704 GCACCTCAAC
* * ** * *
996714 CATCTTTAAGCCCAATATCGCTGGCCTTGAGTCAATATATTGGCA--TAT
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTAT
*
996762 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCT-T
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTAT
* * * * *
996811 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGAATATTGGCGCCTTCGT
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACC-T-AT
* * * *
996863 CATCTTTAAGTTCAATGTCGCTGGCCTTGAATCAGCACATCGGCA-TTTT
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTAT
* * *
996912 CATCTTTAAATCCGATATCGTTGGCCTTGAATCA
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
996946 ACATATTAGC
Statistics
Matches: 154, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
48 38 0.25
49 73 0.47
50 3 0.02
52 40 0.26
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (50 bp):
CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATCGGCACCTAT
Found at i:996899 original size:101 final size:97
Alignment explanation
Indices: 996714--996957 Score: 328
Period size: 101 Copynumber: 2.5 Consensus size: 97
996704 GCACCTCAAC
* *
996714 CATCTTTAAGCCCAATATCGCTGGCCTTGAGTCAATATATTGGCATATCATCTTTAAGTCCAATG
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCATATCATCTTTAAGTCCAATG
996779 TCGCTGGCCTTGAATCAGCACATCGGCACCTT
66 TCGCTGGCCTTGAATCAGCACATCGGCACCTT
* * *
996811 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGA-ATATTGGCGCCTTCGTCATCTTTAAGTT
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCA-ATATATT-G-G-CAT-ATCATCTTTAAGTC
**
996875 CAATGTCGCTGGCCTTGAATCAGCACATCGGCATTTT
61 CAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTT
* * * * *
996912 CATCTTTAAATCCGATATCGTTGGCCTTGAATCAACATATTAGCAT
1 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCAT
996958 CTTTAACATC
Statistics
Matches: 129, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
97 37 0.29
98 4 0.03
99 2 0.02
100 3 0.02
101 83 0.64
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (97 bp):
CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCATATCATCTTTAAGTCCAATG
TCGCTGGCCTTGAATCAGCACATCGGCACCTT
Found at i:996980 original size:101 final size:99
Alignment explanation
Indices: 996773--997042 Score: 290
Period size: 101 Copynumber: 2.7 Consensus size: 99
996763 ATCTTTAAGT
* *
996773 CCAATGTCGCTGGCCTTGAATCAGCACATCGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATCGGCA--TTCATCTTTAAATCCAATATCGTTGGCCT
* * ** *** *
996838 TGAATCAGAATATTGGCGCCTTCGTCATCTTTAAGT
64 TGAATCAGAATATTAGCACCTTCAACATCCCGAAGC
* *
996874 TCAATGTCGCTGGCCTTGAATCAGCACATCGGCATTTTCATCTTTAAATCCGATATCGTTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATCGGCA--TTCATCTTTAAATCCAATATCGTTGGCCT
* *
996939 TGAATCA-ACATATTAGCATCTTTAACATCCCGAAGC
64 TGAATCAGA-ATATTAGCACCTTCAACATCCCGAAGC
* ** ** * * *
996975 CCAATGTTGCTGGCCTTGTCTCAGCACATTAGCATTCTTCTTTAAACCCAATGTCGTTGGCCTTG
1 CCAATGTCGCTGGCCTTGAATCAGCACATCGGCATTCATCTTTAAATCCAATATCGTTGGCCTTG
997040 AAT
66 AAT
997043 TAGCACATTG
Statistics
Matches: 142, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
99 30 0.21
100 1 0.01
101 111 0.78
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (99 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATCGGCATTCATCTTTAAATCCAATATCGTTGGCCTTG
AATCAGAATATTAGCACCTTCAACATCCCGAAGC
Found at i:997816 original size:13 final size:13
Alignment explanation
Indices: 997798--997854 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
997788 TTCAACAATT
997798 TGTATCGATACAA
1 TGTATCGATACAA
997811 TGTATCGATACATAA
1 TGTATCGATAC--AA
997826 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
997843 TGTATCGATACA
1 TGTATCGATACA
997855 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:997835 original size:19 final size:18
Alignment explanation
Indices: 997811--997873 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
997801 ATCGATACAA
997811 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
997830 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
997843 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
*
997862 TGTATCAATACA
1 TGTATCGATACA
997874 ATGTATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:997838 original size:32 final size:32
Alignment explanation
Indices: 997797--997881 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
997787 TTTCAACAAT
997797 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
997829 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
997861 TTGTATCAATACAATGTATCG
1 TTGTATCGATACAATGTATCG
997882 CTACGAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:997928 original size:21 final size:20
Alignment explanation
Indices: 997902--997978 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
997892 ATTGCCAAGG
997902 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTA-TC
997923 AAATGTATCGATACATTGATC
1 AAATGTATCGATACATT-ATC
** *
997944 -TTTGTATCGATACATTATA
1 AAATGTATCGATACATTATC
997963 AAATGTATCGATACAT
1 AAATGTATCGATACAT
997979 GCAGGCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.04
20 27 0.55
21 19 0.39
22 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
AAATGTATCGATACATTATC
Found at i:1000207 original size:1 final size:1
Alignment explanation
Indices: 1000201--1000286 Score: 91
Period size: 1 Copynumber: 86.0 Consensus size: 1
1000191 AAATCTTCAC
* * * *** * *
1000201 TTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTCTTCACTTTTTTTTTTGTTTTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1000266 TTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
1000287 CCAATTGCCA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.01, C:0.03, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:1000219 original size:12 final size:12
Alignment explanation
Indices: 1000202--1000286 Score: 118
Period size: 12 Copynumber: 6.9 Consensus size: 12
1000192 AATCTTCACT
1000202 TTTTTTTTTTTG
1 TTTTTTTTTTTG
1000214 TTTTTTTTTTTG
1 TTTTTTTTTTTG
*
1000226 TTTTTTTTTCTTCA
1 TTTTTTTTT-TT-G
*
1000240 CTTTTTTTTTTG
1 TTTTTTTTTTTG
1000252 TTTTTTTTTTTG
1 TTTTTTTTTTTG
1000264 TTTTTTTTTGTT-
1 TTTTTTTTT-TTG
1000276 TTTTTTTTTTT
1 TTTTTTTTTTT
1000287 CCAATTGCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
11 2 0.03
12 50 0.76
13 6 0.09
14 8 0.12
ACGTcount: A:0.01, C:0.04, G:0.06, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:1000254 original size:38 final size:39
Alignment explanation
Indices: 1000194--1000272 Score: 142
Period size: 38 Copynumber: 2.0 Consensus size: 39
1000184 AAGGAACAAA
1000194 TCTTCACTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1 TCTTCAC-TTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1000234 TCTTCAC-TTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1 TCTTCACTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1000272 T
1 T
1000273 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 32 0.82
40 7 0.18
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.85
Consensus pattern (39 bp):
TCTTCACTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
Found at i:1000283 original size:38 final size:38
Alignment explanation
Indices: 1000200--1000286 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
1000190 CAAATCTTCA
1000200 CTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTCTT
1 CTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTCTT
** *
1000238 CACTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTGTT
1 CTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTCTT
1000276 -TTTTTTTTTTT
1 CTTTTTTTTTTT
1000287 CCAATTGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 9 0.20
38 35 0.80
ACGTcount: A:0.01, C:0.05, G:0.06, T:0.89
Consensus pattern (38 bp):
CTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTCTT
Found at i:1000315 original size:16 final size:16
Alignment explanation
Indices: 1000294--1000326 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1000284 TTTCCAATTG
1000294 CCATGCATCATTTTTC
1 CCATGCATCATTTTTC
1000310 CCATGCATCATTTTTC
1 CCATGCATCATTTTTC
1000326 C
1 C
1000327 TCTTGTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.42
Consensus pattern (16 bp):
CCATGCATCATTTTTC
Found at i:1013887 original size:13 final size:13
Alignment explanation
Indices: 1013869--1013895 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1013859 TCTTAAAAAG
1013869 TCTGCAGTACCCT
1 TCTGCAGTACCCT
1013882 TCTGCAGTACCCT
1 TCTGCAGTACCCT
1013895 T
1 T
1013896 TTTTGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (13 bp):
TCTGCAGTACCCT
Found at i:1015109 original size:20 final size:20
Alignment explanation
Indices: 1015080--1015121 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1015070 TTTGGTTATT
*
1015080 AAAAATTATATTTTTTATCC
1 AAAAAATATATTTTTTATCC
1015100 AAAAAATATATTTTTTATCC
1 AAAAAATATATTTTTTATCC
1015120 AA
1 AA
1015122 CCAATGCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAAATATATTTTTTATCC
Found at i:1015622 original size:28 final size:28
Alignment explanation
Indices: 1015569--1015623 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1015559 TTTTTAATTT
* *
1015569 TTAATTATAAAAATTTATATTGTAAATA
1 TTAATTATAAAAATTAATAATGTAAATA
*
1015597 TTAATTTTAAAAAATTAATAAT-TAAAT
1 TTAATTAT-AAAAATTAATAATGTAAAT
1015624 TTTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAATTATAAAAATTAATAATGTAAATA
Found at i:1016396 original size:16 final size:16
Alignment explanation
Indices: 1016355--1016400 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1016345 TTTTTGTTAT
1016355 AATTTATTATTT-TTAA
1 AATTTA-TATTTATTAA
*
1016371 TATATT-TATTTATTAA
1 AAT-TTATATTTATTAA
1016387 AATTTATATTTATT
1 AATTTATATTTATT
1016401 TATAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 16 0.64
17 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTATATTTATTAA
Found at i:1016396 original size:20 final size:19
Alignment explanation
Indices: 1016371--1016409 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1016361 TTATTTTTAA
1016371 TATATTTATTTATTAAAATT
1 TATATTTATTTA-TAAAATT
1016391 TATATTTATTTATAAAATT
1 TATATTTATTTATAAAATT
1016410 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTTATTTATAAAATT
Found at i:1016417 original size:19 final size:20
Alignment explanation
Indices: 1016372--1016417 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1016362 TATTTTTAAT
*
1016372 ATATTTATTTATTAAAATTT
1 ATATTTATTTATTAAAATTA
1016392 ATATTTATTTA-TAAAATTA
1 ATATTTATTTATTAAAATTA
*
1016411 ATTTTTA
1 ATATTTA
1016418 AATAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTATTTATTAAAATTA
Found at i:1017044 original size:26 final size:25
Alignment explanation
Indices: 1016982--1017044 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1016972 ATATATTGAT
* *
1016982 TTTTAAGTTTTTTTTATTATGTTAC
1 TTTTAAGTTTATTCTATTATGTTAC
*
1017007 TTTTATATTTTATTCTATTATGTT-C
1 TTTTA-AGTTTATTCTATTATGTTAC
1017032 TAGTTTAAGTTTA
1 T--TTTAAGTTTA
1017045 ATATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 7 0.23
26 20 0.65
27 4 0.13
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTTAAGTTTATTCTATTATGTTAC
Found at i:1017369 original size:17 final size:18
Alignment explanation
Indices: 1017329--1017370 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1017319 TTTATAATAT
1017329 TTTTAAAATACAACAAAA
1 TTTTAAAATACAACAAAA
* *
1017347 -TATAAAATATAA-AAAA
1 TTTTAAAATACAACAAAA
1017363 TTTTAAAA
1 TTTTAAAA
1017371 AAAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TTTTAAAATACAACAAAA
Found at i:1018501 original size:20 final size:21
Alignment explanation
Indices: 1018461--1018501 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1018451 TAGTTTGGCT
1018461 AATAATAATATTTTATATTAA
1 AATAATAATATTTTATATTAA
1018482 AATAAT-ATATTTGTAT-TTAA
1 AATAATAATATTT-TATATTAA
1018502 TTTTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATAATAATATTTTATATTAA
Found at i:1018573 original size:18 final size:19
Alignment explanation
Indices: 1018552--1018587 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1018542 TTTAGTAAAA
*
1018552 TAAAT-AATAATTTAAATC
1 TAAATAAATAAATTAAATC
1018570 TAAATAAATAAATTAAAT
1 TAAATAAATAAATTAAAT
1018588 TAGATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATAAATAAATTAAATC
Found at i:1020271 original size:18 final size:20
Alignment explanation
Indices: 1020244--1020282 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1020234 TATAAAAATC
1020244 TAAAATTATATATTT-TTTA
1 TAAAATTATATATTTATTTA
*
1020263 TAAAA-TATATTTTTATTTA
1 TAAAATTATATATTTATTTA
1020282 T
1 T
1020283 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAAATTATATATTTATTTA
Found at i:1020372 original size:15 final size:16
Alignment explanation
Indices: 1020338--1020379 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1020328 AAATTATAAC
*
1020338 TATTTTTTAGTTTTTAT
1 TATTTATTA-TTTTTAT
1020355 TATTTATTATTTTT-T
1 TATTTATTATTTTTAT
1020370 TATTTATTAT
1 TATTTATTAT
1020380 AATTATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 5 0.21
17 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TATTTATTATTTTTAT
Found at i:1020488 original size:10 final size:10
Alignment explanation
Indices: 1020473--1020535 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
1020463 AAATATAATA
1020473 TTAAATTTAT
1 TTAAATTTAT
1020483 TTAAATTTAAT
1 TTAAATTT-AT
* *
1020494 TT-AATTAAA
1 TTAAATTTAT
*
1020503 TT--ATTAAT
1 TTAAATTTAT
1020511 ATTAAATTTTAT
1 -TTAAA-TTTAT
1020523 TTAAATTTAT
1 TTAAATTTAT
1020533 TTA
1 TTA
1020536 TTTTGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 5 0.11
9 5 0.11
10 20 0.45
11 10 0.23
12 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:1020521 original size:25 final size:24
Alignment explanation
Indices: 1020472--1020535 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
1020462 TAAATATAAT
*
1020472 ATTAAATTTATTTAAATTTAATTTA
1 ATTAAA-TTATTTAAATTAAATTTA
1020497 ATTAAATTA-TTAATATTAAATTTTA
1 ATTAAATTATTTAA-ATTAAA-TTTA
*
1020522 TTTAAATTTATTTA
1 ATTAAA-TTATTTA
1020536 TTTTGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 15 0.45
26 3 0.09
27 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTAAATTATTTAAATTAAATTTA
Found at i:1021403 original size:23 final size:21
Alignment explanation
Indices: 1021377--1021420 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1021367 TAATATTTTT
*
1021377 ATTTAATAATAAATATTAAAAAA
1 ATTTAAGAATAAA-A-TAAAAAA
1021400 ATTTAAGAATAAAATAAAAAA
1 ATTTAAGAATAAAATAAAAAA
1021421 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
23 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATTTAAGAATAAAATAAAAAA
Found at i:1021493 original size:32 final size:32
Alignment explanation
Indices: 1021450--1021510 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1021440 TTTATTTATT
* * *
1021450 TTTAATTGTATTGAGATAAAT-ATTATTTTCAA
1 TTTAATAGTATTAAAATAAATGA-TATTTTCAA
1021482 TTTAATAGTATTAAAATAAATGATATTTT
1 TTTAATAGTATTAAAATAAATGATATTTT
1021511 TAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (32 bp):
TTTAATAGTATTAAAATAAATGATATTTTCAA
Found at i:1021579 original size:21 final size:21
Alignment explanation
Indices: 1021555--1021607 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1021545 TTGTTAAAAA
*
1021555 TAAAAATTATTTTAAAATTTT
1 TAAAAATAATTTTAAAATTTT
** *
1021576 TAAAAATAATTTTTTATTTTT
1 TAAAAATAATTTTAAAATTTT
1021597 TAAAAATAATT
1 TAAAAATAATT
1021608 ATTGATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAAATAATTTTAAAATTTT
Found at i:1021621 original size:24 final size:21
Alignment explanation
Indices: 1021572--1021622 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
1021562 TATTTTAAAA
1021572 TTTTTAAAAATAATTTTTTAT
1 TTTTTAAAAATAATTTTTTAT
1021593 TTTTTAAAAATAATTATTGATTAT
1 TTTTTAAAAATAATT-TT--TTAT
1021617 TTTTTA
1 TTTTTA
1021623 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.56
22 2 0.07
24 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTAAAAATAATTTTTTAT
Found at i:1021799 original size:35 final size:35
Alignment explanation
Indices: 1021744--1021850 Score: 101
Period size: 35 Copynumber: 2.9 Consensus size: 35
1021734 ATTTAAATAA
1021744 AATATTTTATAATTTAAATTATTTTTATATATTAAAAA-
1 AATA-TTTA-AATTT-AATTATTTTTATATA-TAAAAAT
* *
1021782 ATTATTTAAATTTAATTATATATTA-ATATAAAAAT
1 AATATTTAAATTTAATTAT-TTTTATATATAAAAAT
* *
1021817 AATATTTAATTTTAAATATTATTTATAATATAAA
1 AATATTTAAATTTAATTATT-TTTAT-ATATAAA
1021851 TTTTAAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
34 7 0.12
35 28 0.48
36 9 0.16
37 11 0.19
38 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
AATATTTAAATTTAATTATTTTTATATATAAAAAT
Found at i:1023649 original size:33 final size:32
Alignment explanation
Indices: 1023592--1023654 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
1023582 ATGTAATAAT
*
1023592 TGTAAACATAATAAAATTATAAATTTATATGA
1 TGTAAACATAATAAAATTATAAATTAATATGA
*
1023624 TGTAAACATGATAAAAATT-TAAAATTAATAT
1 TGTAAACATAAT-AAAATTAT-AAATTAATAT
1023655 AAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (32 bp):
TGTAAACATAATAAAATTATAAATTAATATGA
Found at i:1023707 original size:42 final size:43
Alignment explanation
Indices: 1023661--1023742 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
1023651 ATATAAAATA
*
1023661 ATAATATGAA-TATGCATAAATATATAAATTAT-TAAATTTTAT
1 ATAATATGAATTATGAATAAAT-TATAAATTATATAAATTTTAT
* *
1023703 ATAATATGAATTATTAATATATTATAAATTATATAAATTT
1 ATAATATGAATTATGAATAAATTATAAATTATATAAATTT
1023743 ATAATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 20 0.57
43 15 0.43
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (43 bp):
ATAATATGAATTATGAATAAATTATAAATTATATAAATTTTAT
Found at i:1023714 original size:24 final size:25
Alignment explanation
Indices: 1023682--1023728 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1023672 ATGCATAAAT
*
1023682 ATATAAATTATTAA-ATTTTATATA
1 ATATAAATTATTAATATATTATATA
*
1023706 ATATGAATTATTAATATATTATA
1 ATATAAATTATTAATATATTATA
1023729 AATTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATAAATTATTAATATATTATATA
Found at i:1023744 original size:42 final size:42
Alignment explanation
Indices: 1023609--1023745 Score: 113
Period size: 42 Copynumber: 3.3 Consensus size: 42
1023599 ATAATAAAAT
* * * * * *
1023609 TATAAATTTATATGATGTAAACATG-ATAAAAATTTAAAATTAA
1 TATAAATTTATATAATATGAATATGAATAAATATAT-AAATT-A
* *
1023652 TATAAA-ATA-ATAATATGAATATGCATAAATATATAAATTA
1 TATAAATTTATATAATATGAATATGAATAAATATATAAATTA
* *
1023692 T-TAAATTTTATATAATATGAATTATTAATATAT-TATAAATTA
1 TATAAA-TTTATATAATATGAA-TATGAATAAATATATAAATTA
1023734 TATAAATTTATA
1 TATAAATTTATA
1023746 ATATTTTAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
39 4 0.05
40 2 0.03
41 17 0.22
42 36 0.47
43 18 0.23
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (42 bp):
TATAAATTTATATAATATGAATATGAATAAATATATAAATTA
Found at i:1026507 original size:21 final size:21
Alignment explanation
Indices: 1026463--1026531 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1026453 GTATTGATAA
*
1026463 AAAATTAAAAAAATTATAAAT
1 AAAATTAAAAAAATAATAAAT
* **
1026484 AAAATTAATAAAATAATACGT
1 AAAATTAAAAAAATAATAAAT
*
1026505 AAAAAGT-AAAAAATAAATAAAT
1 -AAAATTAAAAAAAT-AATAAAT
1026527 AAAAT
1 AAAAT
1026532 ATATATTACT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 27 0.73
22 10 0.27
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAATTAAAAAAATAATAAAT
Found at i:1029946 original size:20 final size:19
Alignment explanation
Indices: 1029896--1029946 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1029886 TAAAAAAATT
*
1029896 AATAATTAAATTTTAAACA
1 AATAATTATATTTTAAACA
*
1029915 AATAATTTTATTTTAATA-A
1 AATAATTATATTTTAA-ACA
1029934 AATTAATTATATT
1 AA-TAATTATATT
1029947 AAATATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATTATATTTTAAACA
Found at i:1034696 original size:21 final size:21
Alignment explanation
Indices: 1034672--1034715 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1034662 AGTCAAAAAG
1034672 AGATAGACAAATTGAAGGCTC
1 AGATAGACAAATTGAAGGCTC
1034693 AGATAGACAAATTGAAGGCTC
1 AGATAGACAAATTGAAGGCTC
1034714 AG
1 AG
1034716 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (21 bp):
AGATAGACAAATTGAAGGCTC
Found at i:1035761 original size:27 final size:26
Alignment explanation
Indices: 1035731--1035809 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
1035721 AAAAGCTACT
*
1035731 CTTTGTATTTATCAAAAATAGTGGTTC
1 CTTTGTATTTGT-AAAAATAGTGGTTC
* *
1035758 CTTTGTGTTTGTAAAAAATTGTGGTTC
1 CTTTGTATTTGT-AAAAATAGTGGTTC
* *
1035785 TTTTTTATTTGTAAAAATAGTGGTT
1 CTTTGTATTTGTAAAAATAGTGGTT
1035810 TGTTGTTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 12 0.27
27 32 0.73
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (26 bp):
CTTTGTATTTGTAAAAATAGTGGTTC
Found at i:1036700 original size:18 final size:19
Alignment explanation
Indices: 1036667--1036702 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1036657 TGGCTTTGAT
*
1036667 TTTTGGATTGGTTAGGTGA
1 TTTTGAATTGGTTAGGTGA
1036686 TTTTGAATT-GTTAGGTG
1 TTTTGAATTGGTTAGGTG
1036703 TTTGTGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (19 bp):
TTTTGAATTGGTTAGGTGA
Found at i:1038904 original size:14 final size:14
Alignment explanation
Indices: 1038881--1038913 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1038871 GGTTCAAGTC
1038881 GAAAAAGAAAGAAA
1 GAAAAAGAAAGAAA
*
1038895 GAAAAGGAAAGAAA
1 GAAAAAGAAAGAAA
1038909 -AAAAA
1 GAAAAA
1038914 ATATTTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAGAAA
Found at i:1038967 original size:18 final size:18
Alignment explanation
Indices: 1038930--1038967 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1038920 ATTCGTATTT
*
1038930 ATATTATTTTTATTTAAA
1 ATATTATATTTATTTAAA
1038948 ATATTATATTT-TTTATAA
1 ATATTATATTTATTTA-AA
1038966 AT
1 AT
1038968 TTTTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTATATTTATTTAAA
Found at i:1038983 original size:18 final size:18
Alignment explanation
Indices: 1038962--1038996 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1038952 TATATTTTTT
1038962 ATAAATTTTTATATATTA
1 ATAAATTTTTATATATTA
1038980 ATAAATTTTTATATATT
1 ATAAATTTTTATATATT
1038997 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAAATTTTTATATATTA
Found at i:1039076 original size:27 final size:27
Alignment explanation
Indices: 1039041--1039093 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1039031 TATTATTTTT
*
1039041 ATATTATATTT-TAAATATTTTTTATAA
1 ATATCATATTTAT-AATATTTTTTATAA
*
1039068 ATATCATATTTATATTATTTTTTATA
1 ATATCATATTTATAATATTTTTTATA
1039094 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
ATATCATATTTATAATATTTTTTATAA
Found at i:1039293 original size:23 final size:23
Alignment explanation
Indices: 1039264--1039322 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1039254 CATGCCGTAT
1039264 TTATTTTTTATATTATATTTTAA
1 TTATTTTTTATATTATATTTTAA
* * *
1039287 TTATTTTTTATGTCATATTTTTA
1 TTATTTTTTATATTATATTTTAA
*
1039310 TT-TTTTGTATATT
1 TTATTTTTTATATT
1039323 TAAAGTAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (23 bp):
TTATTTTTTATATTATATTTTAA
Found at i:1039295 original size:11 final size:12
Alignment explanation
Indices: 1039264--1039297 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1039254 CATGCCGTAT
1039264 TTATTTTTTATA
1 TTATTTTTTATA
*
1039276 TTATATTTTA-A
1 TTATTTTTTATA
1039287 TTATTTTTTAT
1 TTATTTTTTAT
1039298 GTCATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTTTATA
Done.