Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 3 of 240
Found at i:999663 original size:32 final size:32
Alignment explanation
Indices: 999626--999689 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
999616 GTTGCTTGCC
999626 TGCATTGCTTTTGGTTG-ATTTGCCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTG-CTTCCTATT
* *
999658 TGCATTGGTTTTGGTTGTTTTTGCTTCCTATT
1 TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
999690 ATATGCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.56
Consensus pattern (32 bp):
TGCATTGCTTTTGGTTGTATTTGCTTCCTATT
Found at i:1000017 original size:218 final size:218
Alignment explanation
Indices: 999639--1000067 Score: 750
Period size: 218 Copynumber: 2.0 Consensus size: 218
999629 ATTGCTTTTG
* ** **
999639 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTGCTTCCTATTATATGCATATGATG
1 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACACATACAATG
*
999704 AACTCTACTCGGATTCCCCTTCAAGACTTCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
66 AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
999769 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
*
999834 TCATTCTTTCTTCAATTTGGTTT
196 TCATTCATTCTTCAATTTGGTTT
999857 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACACATACAATG
1 GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACACATACAATG
* * * *
999922 AACTCTACTTGGATTCCTCTTCAAGACATCATGGGTGATGCTAACTTGAGTTTCTGATGGAAACA
66 AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
*
999987 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGGAAGTATAAAAAATGTGTTTCT
131 TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
1000052 TCATTCATTCTTCAAT
196 TCATTCATTCTTCAAT
1000068 CCTCTAATAA
Statistics
Matches: 199, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
218 199 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (218 bp):
GTTGATTTGCCTTCCTATTTGCATTGGTTTTGGTTGTTTTTCCTTCCTATTATACACATACAATG
AACTCTACTCGGATTCCCCTTCAAGACATCATGGGTGATGCTAACTCGAGTTTCTGATGCAAACA
TTAAGTGATCAATTTTACATAGTTCACAAATTTGGTTTGTATGAAAGTATAAAAAATGTGTTTCT
TCATTCATTCTTCAATTTGGTTT
Found at i:1007367 original size:13 final size:13
Alignment explanation
Indices: 1007349--1007373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1007339 AGTTTGACAA
1007349 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1007362 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1007374 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1008043 original size:3 final size:3
Alignment explanation
Indices: 1008035--1008060 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1008025 ATAGGAAAAA
1008035 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1008061 AATCTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1028400 original size:31 final size:30
Alignment explanation
Indices: 1028343--1028400 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
1028333 CATAAAAAAG
* * *
1028343 GTTTAAACCTCAATATCAGAACAATTGGCT
1 GTTTAAACCCCAAAATAAGAACAATTGGCT
*
1028373 GTTTCAAACCCCAAAATAAGAATAATTG
1 GTTT-AAACCCCAAAATAAGAACAATTG
1028401 TCAAACCCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 4 0.17
31 19 0.83
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (30 bp):
GTTTAAACCCCAAAATAAGAACAATTGGCT
Found at i:1032761 original size:19 final size:18
Alignment explanation
Indices: 1032720--1032763 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1032710 TAGTTAAGAA
*
1032720 ATTATTAAAATAAATTTT
1 ATTATTAAAATAAATTAT
* *
1032738 TTTATATAAAATAAGTTAT
1 ATTAT-TAAAATAAATTAT
1032757 ATTATTA
1 ATTATTA
1032764 CAAGTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTATTAAAATAAATTAT
Found at i:1037351 original size:25 final size:25
Alignment explanation
Indices: 1037321--1037370 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1037311 TTCCACTCTT
1037321 GAAATCATTTTTTTTCTTCAATTGC
1 GAAATCATTTTTTTTCTTCAATTGC
1037346 GAAATCATTTTTTTTCTTCAATTGC
1 GAAATCATTTTTTTTCTTCAATTGC
1037371 ATCCAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (25 bp):
GAAATCATTTTTTTTCTTCAATTGC
Found at i:1061069 original size:33 final size:33
Alignment explanation
Indices: 1061027--1061092 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1061017 ACATTTTGTG
1061027 CTTATTTCAGGCAAAATATTATTCAGAAAGAGA
1 CTTATTTCAGGCAAAATATTATTCAGAAAGAGA
1061060 CTTATTTCAGGCAAAATATTATTCAGAAAGAGA
1 CTTATTTCAGGCAAAATATTATTCAGAAAGAGA
1061093 AAGTAAGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (33 bp):
CTTATTTCAGGCAAAATATTATTCAGAAAGAGA
Found at i:1061081 original size:17 final size:17
Alignment explanation
Indices: 1061028--1061082 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
1061018 CATTTTGTGC
1061028 TTATTTCAGGCAAAATA
1 TTATTTCAGGCAAAATA
*
1061045 TTA-TTCA-G-AAAGAGA
1 TTATTTCAGGCAAA-ATA
1061060 CTTATTTCAGGCAAAATA
1 -TTATTTCAGGCAAAATA
1061078 TTATT
1 TTATT
1061083 CAGAAAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 7 0.23
17 12 0.39
18 3 0.10
19 3 0.10
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
TTATTTCAGGCAAAATA
Found at i:1063945 original size:9 final size:10
Alignment explanation
Indices: 1063916--1063943 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1063906 ATTTTTTAAA
1063916 TTTCAAAAAT
1 TTTCAAAAAT
1063926 TTTCAAAAAT
1 TTTCAAAAAT
1063936 TTTCAAAA
1 TTTCAAAA
1063944 TTCAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (10 bp):
TTTCAAAAAT
Found at i:1067655 original size:15 final size:15
Alignment explanation
Indices: 1067637--1067674 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1067627 TATACAAGTT
1067637 AAATTAAAAAATTAA
1 AAATTAAAAAATTAA
**
1067652 AAATT-AAAAATTTC
1 AAATTAAAAAATTAA
1067666 AAATTAAAA
1 AAATTAAAA
1067675 TCTTGTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAAAAATTAA
Found at i:1070759 original size:24 final size:24
Alignment explanation
Indices: 1070731--1070790 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1070721 TGTCAAGATG
*
1070731 AAAATTTTCAAA-TCTGAAATATAA
1 AAAATTTT-AAATTCTGAAAAATAA
* *
1070755 AAAATTTTAAATTTTTAAAAATAA
1 AAAATTTTAAATTCTGAAAAATAA
1070779 AAAA-TTTAAATT
1 AAAATTTTAAATT
1070791 TAAATGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATTTTAAATTCTGAAAAATAA
Found at i:1076847 original size:22 final size:22
Alignment explanation
Indices: 1076805--1076847 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1076795 ATCTAAATTT
*
1076805 AGATGATTAATTAGTTAGTTAG
1 AGATGATTAATTAATTAGTTAG
1076827 AGATGAGTTAATTAATT-GTTA
1 AGATGA-TTAATTAATTAGTTA
1076848 AAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (22 bp):
AGATGATTAATTAATTAGTTAG
Found at i:1077961 original size:17 final size:17
Alignment explanation
Indices: 1077936--1077980 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1077926 CAAATATAAT
*
1077936 AAATATTTTTATTTTTA
1 AAATATTTTTAATTTTA
*
1077953 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
1077970 AAATACTTTTT
1 AAATA-TTTTT
1077981 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:1078015 original size:33 final size:31
Alignment explanation
Indices: 1077946--1078015 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
1077936 AAATATTTTT
*
1077946 ATTTTTAAAATTTTTTTAATTTTAAAATACT
1 ATTTTTAAAATTTTTTTAATTTTAAAATACA
* *
1077977 TTTTTTAAATTTTTGTTTTAATTTTTAAAATA-A
1 ATTTTTAAA-ATTT-TTTTAA-TTTTAAAATACA
1078010 ATTTTT
1 ATTTTT
1078016 GGTATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 8 0.25
32 3 0.09
33 11 0.34
34 10 0.31
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (31 bp):
ATTTTTAAAATTTTTTTAATTTTAAAATACA
Found at i:1080744 original size:47 final size:47
Alignment explanation
Indices: 1080693--1080788 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
1080683 ACATAATTTA
1080693 CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
1 CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
1080740 CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
1 CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
1080787 CT
1 CT
1080789 CTATATCCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.55
Consensus pattern (47 bp):
CTTAAACTAATTTATTTTTGTTGTATTTAATTTTTAGTTTGTAACAC
Found at i:1081473 original size:25 final size:23
Alignment explanation
Indices: 1081453--1081519 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 23
1081443 CACTATTAAG
*
1081453 CAGATAGCACTAAAGTGCTAT-A
1 CAGAAAGCACTAAAGTGCTATAA
1081475 CAGAAAGCAC-AAATGTGCTAATAA
1 CAGAAAGCACTAAA-GTGCT-ATAA
* * *
1081499 TCATAGAGCACTAACGTGCTA
1 -CAGAAAGCACTAAAGTGCTA
1081520 ATAATTAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
23 2 0.06
24 2 0.06
25 13 0.36
26 2 0.06
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (23 bp):
CAGAAAGCACTAAAGTGCTATAA
Found at i:1081478 original size:22 final size:22
Alignment explanation
Indices: 1081453--1081494 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1081443 CACTATTAAG
*
1081453 CAGATAGCACTAAA-GTGCTATA
1 CAGAAAGCAC-AAATGTGCTATA
1081475 CAGAAAGCACAAATGTGCTA
1 CAGAAAGCACAAATGTGCTA
1081495 ATAATCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
CAGAAAGCACAAATGTGCTATA
Found at i:1081531 original size:25 final size:25
Alignment explanation
Indices: 1081475--1081532 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1081465 AAGTGCTATA
* *
1081475 CAGAAAGCACAAATGTGCTAATAAT
1 CAGAGAGCACAAACGTGCTAATAAT
* *
1081500 CATAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACAAACGTGCTAATAAT
*
1081525 TAGAGAGC
1 CAGAGAGC
1081533 GCGCTAAGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (25 bp):
CAGAGAGCACAAACGTGCTAATAAT
Found at i:1085149 original size:18 final size:19
Alignment explanation
Indices: 1085105--1085156 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1085095 CTTCAAATTT
* *
1085105 TATATAATAATTTAT-TAA
1 TATAAAATAATTTTTATAA
*
1085123 TATATAATAATTTTTATAA
1 TATAAAATAATTTTTATAA
*
1085142 TA-AAAATAATGTTTA
1 TATAAAATAATTTTTA
1085157 ATATTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATAAAATAATTTTTATAA
Found at i:1088828 original size:17 final size:19
Alignment explanation
Indices: 1088794--1088840 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1088784 TATGCATGGT
*
1088794 AAATAATAAAAGTTAACAA
1 AAATAATAAAAGTAAACAA
1088813 AAATAA-AAAA-TAAACAA
1 AAATAATAAAAGTAAACAA
*
1088830 ACAAGAATAAA
1 A-AATAATAAA
1088841 GACATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.15
Consensus pattern (19 bp):
AAATAATAAAAGTAAACAA
Found at i:1089123 original size:20 final size:20
Alignment explanation
Indices: 1089086--1089144 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1089076 TATGCACGTG
* **
1089086 TATTATATTGTAGGTATAAA
1 TATTATATAGTATATATAAA
1089106 TATTATATAGTATATATATAA
1 TATTATATAGTATATATA-AA
1089127 -A-TATATAG-ATAT-TAAA
1 TATTATATAGTATATATAAA
1089143 TA
1 TA
1089145 AATAAAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 4 0.12
19 7 0.21
20 16 0.47
21 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TATTATATAGTATATATAAA
Found at i:1089133 original size:19 final size:19
Alignment explanation
Indices: 1089109--1089148 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1089099 GTATAAATAT
*
1089109 TATATAG-TATATATATAAA
1 TATATAGATAT-TAAATAAA
1089128 TATATAGATATTAAATAAA
1 TATATAGATATTAAATAAA
1089147 TA
1 TA
1089149 AAAAGCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TATATAGATATTAAATAAA
Found at i:1090414 original size:15 final size:16
Alignment explanation
Indices: 1090388--1090417 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1090378 TAGTGTTTAG
1090388 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
1090404 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
1090418 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:1091088 original size:87 final size:87
Alignment explanation
Indices: 1090972--1091133 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
1090962 AGACTTGATG
* * * * *
1090972 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTA-TTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGAT-CTCTAGCTTCAATCCGCTCCACTGTAACC
1091036 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * *
1091059 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTAGCTTCAATCCGCTCCACTGTAACCT
1091124 CAGGGAGATA
66 CAGGGAGATA
1091134 AGATCCGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
86 4 0.06
87 61 0.94
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTAGCTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:1091301 original size:44 final size:43
Alignment explanation
Indices: 1090984--1091352 Score: 213
Period size: 44 Copynumber: 8.5 Consensus size: 43
1090974 ATCTACTCTG
* * * * *
1090984 CTGTAACCTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATAC--TATCTTTGATCTGCTCCA
* * * * *
1091028 CTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATACTATCTTTGATCTGCTCCA
* * **
1091071 CTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT-ACTATCTTTGATCTGCTCCA
* * * * **
1091115 CTGTAACCTCAGGGAGATAAGATCCGAAATTCTTTGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATAC--TA-TCTTTGATCTGCTCCA
* * * *
1091161 CTGTAATCTCAGGGAGATAAGA-CCTGA--TGTGATTTTC-CCTA
1 CTGTAATCTCAGGGAGATAAGATACT-ATCTTTGATCTGCTCC-A
* * *
1091202 CTGTAA-CTTCAGAGAGATAAGAT-C---CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATACTATCTTTGATCTGCTCCA
* * * *
1091241 TTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGA-TACTATCTTTGATCTGCTCCA
* *
1091285 CTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATACT---A-TCTTTGATCTGCTCCA
*
1091331 CTGTATTCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
1091353 CCTGTATAAT
Statistics
Matches: 250, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
39 22 0.09
40 7 0.03
41 27 0.11
42 4 0.02
43 33 0.13
44 88 0.35
45 4 0.02
46 65 0.26
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
CTGTAATCTCAGGGAGATAAGATACTATCTTTGATCTGCTCCA
Found at i:1103618 original size:20 final size:20
Alignment explanation
Indices: 1103581--1103641 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1103571 TATGCACGTG
* **
1103581 TATTATATTGTAGGTATAAA
1 TATTATATAGTATATATAAA
*
1103601 TATTATATAGTATATATATA
1 TATTATATAGTATATATAAA
*
1103621 TAAATATATAG-ATAT-TAAA
1 T-ATTATATAGTATATATAAA
1103640 TA
1 TA
1103642 AATAAAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 21 0.62
21 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TATTATATAGTATATATAAA
Found at i:1103619 original size:16 final size:16
Alignment explanation
Indices: 1103594--1103641 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1103584 TATATTGTAG
*
1103594 GTATAAATATTATATA
1 GTATAAATATTAAATA
*
1103610 GTATATATATATAAATA
1 GTATAAATAT-TAAATA
*
1103627 -TATAGATATTAAATA
1 GTATAAATATTAAATA
1103642 AATAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
GTATAAATATTAAATA
Found at i:1103642 original size:19 final size:21
Alignment explanation
Indices: 1103595--1103645 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1103585 ATATTGTAGG
*
1103595 TATAAAT-ATTATATAGTATA
1 TATAAATAAATATATAGTATA
*
1103615 TATATATAAATATATAG-ATA
1 TATAAATAAATATATAGTATA
1103635 T-TAAATAAATA
1 TATAAATAAATA
1103646 AAAAGCAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAAATAAATATATAGTATA
Found at i:1104901 original size:15 final size:16
Alignment explanation
Indices: 1104875--1104904 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1104865 TAGTGTTTAG
1104875 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
1104891 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
1104905 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:1106458 original size:23 final size:22
Alignment explanation
Indices: 1106432--1106474 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1106422 AGGCCCATTT
*
1106432 ATAATTTATAAAATTTTATATTA
1 ATAA-TTATAAAATTATATATTA
*
1106455 ATAATTGTAAAATTATATAT
1 ATAATTATAAAATTATATAT
1106475 AAACTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAATTATAAAATTATATATTA
Found at i:1118660 original size:19 final size:20
Alignment explanation
Indices: 1118626--1118666 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1118616 AAAATAAATA
1118626 TTTAACACAAATTTTTA-AT
1 TTTAACACAAATTTTTATAT
1118645 TTTATACACAAA-TTTTATAT
1 TTTA-ACACAAATTTTTATAT
1118665 TT
1 TT
1118667 CTTTAGGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAACACAAATTTTTATAT
Found at i:1120132 original size:24 final size:25
Alignment explanation
Indices: 1120082--1120133 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1120072 TTTTGGTGTT
* **
1120082 AATTTGATACTTACTTTCTTGTATC
1 AATTTGATACCTAAGTTCTTGTATC
*
1120107 AATTTGATACCTAAGTT-TTGTTTC
1 AATTTGATACCTAAGTTCTTGTATC
1120131 AAT
1 AAT
1120134 GTTTCTTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (25 bp):
AATTTGATACCTAAGTTCTTGTATC
Found at i:1128252 original size:21 final size:20
Alignment explanation
Indices: 1128226--1128265 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1128216 ATACGCGACA
1128226 TTGATATTGTTGATTATTGTC
1 TTGATATTGTTGA-TATTGTC
1128247 TTGATATTGTTGATATTGT
1 TTGATATTGTTGATATTGT
1128266 TGTTTCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (20 bp):
TTGATATTGTTGATATTGTC
Found at i:1128261 original size:9 final size:9
Alignment explanation
Indices: 1128226--1128267 Score: 57
Period size: 9 Copynumber: 4.3 Consensus size: 9
1128216 ATACGCGACA
1128226 TTGATATTG
1 TTGATATTG
1128235 TTGATTATTG
1 TTGA-TATTG
1128245 TCTTGATATTG
1 --TTGATATTG
1128256 TTGATATTG
1 TTGATATTG
1128265 TTG
1 TTG
1128268 TTTCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 16 0.53
10 5 0.17
11 5 0.17
12 4 0.13
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.57
Consensus pattern (9 bp):
TTGATATTG
Found at i:1134337 original size:19 final size:20
Alignment explanation
Indices: 1134298--1134335 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1134288 CTGATTAATT
1134298 AATTTCAAATTATATTTTTA
1 AATTTCAAATTATATTTTTA
1134318 AATTT-AAATTAATATTTT
1 AATTTCAAATT-ATATTTT
1134336 AACGTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTCAAATTATATTTTTA
Found at i:1177473 original size:19 final size:19
Alignment explanation
Indices: 1177446--1177488 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1177436 ATATTTTCCG
1177446 TTTTCTCATTTATT-TAATAA
1 TTTTCTCATTT-TTCTAAT-A
1177466 TTTT-TCATTTTTCTAATA
1 TTTTCTCATTTTTCTAATA
1177484 TTTTC
1 TTTTC
1177489 AAGTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTCTCATTTTTCTAATA
Found at i:1183655 original size:19 final size:19
Alignment explanation
Indices: 1183631--1183676 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1183621 TATGATGAAT
1183631 ATATTTTAG-TTTAGTATTA
1 ATATTTTAGATTT-GTATTA
*
1183650 ATATTTTAGATTTTTATTA
1 ATATTTTAGATTTGTATTA
*
1183669 AAATTTTA
1 ATATTTTA
1183677 AATATAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
ATATTTTAGATTTGTATTA
Found at i:1199994 original size:29 final size:30
Alignment explanation
Indices: 1199931--1199996 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1199921 AGAATTGGAT
**
1199931 CTAAATTTTGAAATCTAAAAAATAAGAGAA
1 CTAAATTTTGAAAAATAAAAAATAAGAGAA
* *
1199961 TTAAATTTTTAAAAATAAAAATATAA-A-AA
1 CTAAATTTTGAAAAATAAAAA-ATAAGAGAA
1199990 CTAAATT
1 CTAAATT
1199997 CTAAATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.27
30 18 0.60
31 4 0.13
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (30 bp):
CTAAATTTTGAAAAATAAAAAATAAGAGAA
Found at i:1205045 original size:23 final size:24
Alignment explanation
Indices: 1205002--1205047 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1204992 TAAATATTCT
* *
1205002 ACAATATTTTAGTTTTATTTAATG
1 ACAATATATTAGTATTATTTAATG
1205026 ACAATATATTA-TATTATTTAAT
1 ACAATATATTAGTATTATTTAAT
1205048 ATGATACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ACAATATATTAGTATTATTTAATG
Found at i:1221233 original size:9 final size:8
Alignment explanation
Indices: 1221214--1221300 Score: 52
Period size: 9 Copynumber: 10.4 Consensus size: 8
1221204 TAAAATTAGA
1221214 AAAAATA-
1 AAAAATAT
1221221 AAAAATCAT
1 AAAAAT-AT
1221230 AAAAATAT
1 AAAAATAT
** *
1221238 AAATTTGT
1 AAAAATAT
*
1221246 AAAATTTTAT
1 AAAA--ATAT
*
1221256 AAAAATCGT
1 AAAAAT-AT
1221265 AAAAATAT
1 AAAAATAT
1221273 AAAAATTAT
1 AAAAA-TAT
*
1221282 AGAAATA-
1 AAAAATAT
1221289 AAAAAGTAT
1 AAAAA-TAT
1221298 AAA
1 AAA
1221301 TTTATAAAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
7 10 0.16
8 22 0.35
9 23 0.37
10 7 0.11
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:1221287 original size:17 final size:17
Alignment explanation
Indices: 1221205--1221300 Score: 63
Period size: 17 Copynumber: 5.6 Consensus size: 17
1221195 AAATTTTATT
*
1221205 AAAATTAGAAAAA-ATAA
1 AAAATTATAAAAATAT-A
*
1221222 AAAATCATAAAAATAT-
1 AAAATTATAAAAATATA
* * *
1221238 AAATTTGTAAAATTTTATA
1 AAAATTATAAAA--ATATA
**
1221257 AAAATCGTAAAAATATA
1 AAAATTATAAAAATATA
*
1221274 AAAATTATAGAAATA-A
1 AAAATTATAAAAATATA
*
1221290 AAAAGTATAAA
1 AAAATTATAAA
1221301 TTTATAAAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
16 19 0.31
17 27 0.44
18 5 0.08
19 10 0.16
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAATTATAAAAATATA
Found at i:1221747 original size:89 final size:87
Alignment explanation
Indices: 1221643--1221834 Score: 233
Period size: 88 Copynumber: 2.2 Consensus size: 87
1221633 TAAGAGCAAG
* *
1221643 GGCTTAATTGTTTTTTTGAAAATTTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
1 GGCTTAATTGATTTTTTGAAAA-GTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
*
1221708 AATTGAGTGGAAAAAGAAA-GAAGA
65 AATTGAGTAGAAAAA-AAATG-AGA
* * * * * **
1221732 GGCTTAATTGATTTTTTGAGAAGTTTGAGGGTCTTTTTGATGGATTTTGAAAGTTTAAGTGCTTA
1 GGCTTAATTGATTTTTTGAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
* *
1221797 ATTGAGTATAAAAAAAATGAGG
66 ATTGAGTAGAAAAAAAATGAGA
*
1221819 GGCTTAATTGCTTTTT
1 GGCTTAATTGATTTTT
1221835 CTTTTTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 20 0.22
88 49 0.55
89 20 0.22
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (87 bp):
GGCTTAATTGATTTTTTGAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
ATTGAGTAGAAAAAAAATGAGA
Found at i:1221864 original size:92 final size:93
Alignment explanation
Indices: 1221752--1221945 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 93
1221742 ATTTTTTGAG
* * * *
1221752 AAGTTTGAGGGTCTTTTTGATGGATTTTGAAAGTTTAAGTGCTTAATTGAGT-ATAAAAAAAATG
1 AAGTTTGAGGGCCTTTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGTCA-AAAAAAAAAG
*
1221816 AGGGGCTTAATTGCTTTT-TCT-TTTTTTT
65 AGGGGCTTAATT-ATTTTATCTCTTTTTTT
*
1221844 AAGTTTGAGGGCCTTTTTGATGTATTTTAAAAGTTTAAGTGCTCAATTGAGTGCAAAAAAAAAAG
1 AAGTTTGAGGGCCTTTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGT-CAAAAAAAAAAG
* *
1221909 ATGGGCTTAATTATTTTATTTCTTTTTTT
65 AGGGGCTTAATTATTTTATCTCTTTTTTT
1221938 AAGTTTGA
1 AAGTTTGA
1221946 AGACTTTTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
92 52 0.58
93 22 0.24
94 16 0.18
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.44
Consensus pattern (93 bp):
AAGTTTGAGGGCCTTTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGTCAAAAAAAAAAGA
GGGGCTTAATTATTTTATCTCTTTTTTT
Found at i:1226087 original size:20 final size:21
Alignment explanation
Indices: 1226043--1226094 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
1226033 AAATCTAAAT
1226043 TTTTTATTT-T-AATATCATA
1 TTTTTATTTCTAAATATCATA
*
1226062 -TGTTATTTCTAAATA-CATA
1 TTTTTATTTCTAAATATCATA
1226081 TTTTTA-TTCTAAAT
1 TTTTTATTTCTAAAT
1226095 TTATGATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 13 0.46
20 8 0.29
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTATTTCTAAATATCATA
Found at i:1238427 original size:33 final size:33
Alignment explanation
Indices: 1238322--1238428 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
1238312 GAGTAATCGA
* *
1238322 CGGTCGTCGGTGGTGGTTGAGGGTGAATAGCGA
1 CGGTCGTCGGTGGTGGTTGAGGGTGAACAGCGG
*
1238355 CGGTCGTCGGTGGTGGTTAAGGGTGAACAGCGG
1 CGGTCGTCGGTGGTGGTTGAGGGTGAACAGCGG
* ** * *
1238388 CAGTCGTCGGCAGTGGTTGAGAGTGAACCGCGG
1 CGGTCGTCGGTGGTGGTTGAGGGTGAACAGCGG
*
1238421 TGGTCGTC
1 CGGTCGTC
1238429 AAGGTTGCCT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.15, C:0.17, G:0.46, T:0.22
Consensus pattern (33 bp):
CGGTCGTCGGTGGTGGTTGAGGGTGAACAGCGG
Found at i:1238762 original size:13 final size:14
Alignment explanation
Indices: 1238737--1238772 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1238727 AATTTCATTT
1238737 TTTTCATTT-AATA
1 TTTTCATTTAAATA
1238750 TTTT-ATTTAAATA
1 TTTTCATTTAAATA
1238763 TTTTCATTTA
1 TTTTCATTTA
1238773 TTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 12 0.57
14 5 0.24
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCATTTAAATA
Found at i:1238778 original size:14 final size:14
Alignment explanation
Indices: 1238737--1238778 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1238727 AATTTCATTT
1238737 TTTTCATTTA-ATA
1 TTTTCATTTATATA
*
1238750 TTTT-ATTTAAATA
1 TTTTCATTTATATA
*
1238763 TTTTCATTTATTTA
1 TTTTCATTTATATA
1238777 TT
1 TT
1238779 ATTTTTGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 9 0.36
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTCATTTATATA
Found at i:1238913 original size:12 final size:12
Alignment explanation
Indices: 1238892--1238923 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1238882 TTTCAAATTT
1238892 AAAGGC-AAAAA
1 AAAGGCAAAAAA
1238903 AAAGGCAAAAAA
1 AAAGGCAAAAAA
1238915 AAAGGCAAA
1 AAAGGCAAA
1238924 TGAGTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.72, C:0.09, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAGGCAAAAAA
Found at i:1238956 original size:5 final size:5
Alignment explanation
Indices: 1238946--1239040 Score: 73
Period size: 5 Copynumber: 17.6 Consensus size: 5
1238936 ACCTCTTTTT
* * *
1238946 TTTCA TTTCA TTTCCT TTTCA TTTTCA TTTCA TTTTA TTTTTA TTTCA
1 TTTCA TTTCA TTT-CA TTTCA -TTTCA TTTCA TTTCA -TTTCA TTTCA
* * *
1238994 TTTCA TTCTAA TTTCA TTTCCA TTACCA TTTCCC TTTCA TTTCA TTT
1 TTTCA TT-TCA TTTCA TTT-CA TT-TCA TTT-CA TTTCA TTTCA TTT
1239041 AAAAAAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
5 43 0.59
6 30 0.41
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:1238966 original size:16 final size:16
Alignment explanation
Indices: 1238945--1239040 Score: 70
Period size: 17 Copynumber: 5.9 Consensus size: 16
1238935 AACCTCTTTT
1238945 TTTTCATTTCATTTCC
1 TTTTCATTTCATTTCC
*
1238961 TTTTCATTTTCATTTCA
1 TTTTCA-TTTCATTTCC
*
1238978 TTTT-ATTTTTATTT-C
1 TTTTCA-TTTCATTTCC
* * *
1238993 ATTTCATTCTAATTTCA
1 TTTTCATT-TCATTTCC
* *
1239010 TTTCCATTACCATTTCC
1 TTTTCATT-TCATTTCC
*
1239027 CTTTCATTTCATTT
1 TTTTCATTTCATTT
1239041 AAAAAAATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
15 5 0.08
16 26 0.43
17 30 0.49
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCATTTCATTTCC
Found at i:1239091 original size:22 final size:22
Alignment explanation
Indices: 1239050--1239098 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
1239040 TAAAAAAATA
1239050 TTTTTCAATTTCAATTTATT-T
1 TTTTTCAATTTCAATTTATTAT
*
1239071 TTTTCTCAA-TTCATTTATATTAT
1 TTTT-TCAATTTCAATT-TATTAT
1239094 TTTTT
1 TTTTT
1239099 AATGTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTCAATTTCAATTTATTAT
Found at i:1241179 original size:91 final size:91
Alignment explanation
Indices: 1241024--1241205 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
1241014 AGACTGTGTC
1241024 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1241089 TTTTTTGTTATCAAATTGTTGTCTTA
66 TTTTTTGTTATCAAATTGTTGTCTTA
1241115 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1 GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
1241180 TTTTTTGTTATCAAATTGTTGTCTTA
66 TTTTTTGTTATCAAATTGTTGTCTTA
1241206 CACACAACTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.43
Consensus pattern (91 bp):
GACTTCGTTACTTTATAATCCACACCTAACTTCAAGCTAAGTTATTTTATAGCATGTAAACAGTC
TTTTTTGTTATCAAATTGTTGTCTTA
Found at i:1242077 original size:12 final size:12
Alignment explanation
Indices: 1242060--1242125 Score: 109
Period size: 12 Copynumber: 5.7 Consensus size: 12
1242050 GATTTTTGAT
1242060 AAATGGAACATA
1 AAATGGAACATA
1242072 AAATGGAACAT-
1 AAATGGAACATA
1242083 AAATGGAACAT-
1 AAATGGAACATA
1242094 AAATGGAACATA
1 AAATGGAACATA
1242106 AAATGGAACATA
1 AAATGGAACATA
*
1242118 AAAAGGAA
1 AAATGGAA
1242126 AAAAAAATTC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
11 22 0.42
12 30 0.58
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (12 bp):
AAATGGAACATA
Found at i:1242086 original size:11 final size:11
Alignment explanation
Indices: 1242058--1242119 Score: 106
Period size: 11 Copynumber: 5.5 Consensus size: 11
1242048 TTGATTTTTG
1242058 ATAAATGGAAC
1 ATAAATGGAAC
1242069 ATAAAATGGAAC
1 AT-AAATGGAAC
1242081 ATAAATGGAAC
1 ATAAATGGAAC
1242092 ATAAATGGAAC
1 ATAAATGGAAC
1242103 ATAAAATGGAAC
1 AT-AAATGGAAC
1242115 ATAAA
1 ATAAA
1242120 AAGGAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
11 27 0.55
12 22 0.45
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.18
Consensus pattern (11 bp):
ATAAATGGAAC
Found at i:1242131 original size:23 final size:23
Alignment explanation
Indices: 1242060--1242131 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
1242050 GATTTTTGAT
* *
1242060 AAATGGAACATAAAATGGAACAT
1 AAATGGAACATAAAATGGAAAAA
*
1242083 AAATGGAACAT-AAATGGAACATA
1 AAATGGAACATAAAATGGAA-AAA
*
1242106 AAATGGAACATAAAAAGGAAAAA
1 AAATGGAACATAAAATGGAAAAA
1242129 AAA
1 AAA
1242132 ATTCAAACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 8 0.19
23 27 0.64
24 7 0.17
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (23 bp):
AAATGGAACATAAAATGGAAAAA
Found at i:1244888 original size:51 final size:50
Alignment explanation
Indices: 1244744--1244887 Score: 148
Period size: 50 Copynumber: 2.9 Consensus size: 50
1244734 TTTTCGTAGA
* * * * *
1244744 CTGGTGCCGCCCATTGACAAGCTAACACCCCAAGA-TTTTTTTTCCGTACTG
1 CTGGTGCCGACCATTGACAGGCCAACA-CCCAA-ATTTTTTTTTTCATACTG
* * * *
1244795 CTGGTGTCGGCCATTTTA-AGGCCAACACCAAAATTTTTTTTTTCATACTG
1 CTGGTGCCGACCA-TTGACAGGCCAACACCCAAATTTTTTTTTTCATACTG
* *
1244845 CTGGTGCCGACCATTGACAGGCCAGCACCCAATTTTTTTTTTT
1 CTGGTGCCGACCATTGACAGGCCAACACCCAAATTTTTTTTTT
1244888 TAATTTTTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
49 4 0.05
50 51 0.67
51 18 0.24
52 3 0.04
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (50 bp):
CTGGTGCCGACCATTGACAGGCCAACACCCAAATTTTTTTTTTCATACTG
Found at i:1249740 original size:7 final size:8
Alignment explanation
Indices: 1249723--1249785 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
1249713 AATTTATTTT
1249723 AAAAATAA
1 AAAAATAA
1249731 AAAAATAA
1 AAAAATAA
**
1249739 AAAAGTATTT
1 AAAA--ATAA
*
1249749 TAAAAT--
1 AAAAATAA
1249755 AAAAATAA
1 AAAAATAA
1249763 AAAAAT-A
1 AAAAATAA
1249770 AAAAAT-A
1 AAAAATAA
1249777 AAAAATAA
1 AAAAATAA
1249785 A
1 A
1249786 TATTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
6 5 0.11
7 14 0.30
8 22 0.48
10 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (8 bp):
AAAAATAA
Found at i:1249748 original size:27 final size:25
Alignment explanation
Indices: 1249717--1249767 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1249707 ACCAAAAATT
1249717 TATTTTAAAAATAAAAAAATAAAAAAG
1 TATTTT-AAAATAAAAAAA-AAAAAAG
*
1249744 TATTTTAAAATAAAAATAAAAAAA
1 TATTTTAAAATAAAAAAAAAAAAA
1249768 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 11 0.48
27 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
TATTTTAAAATAAAAAAAAAAAAAG
Found at i:1249759 original size:6 final size:7
Alignment explanation
Indices: 1249750--1249785 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
1249740 AAAGTATTTT
1249750 AAAAT-A
1 AAAATAA
1249756 AAAATAAA
1 AAAAT-AA
1249764 AAAATAA
1 AAAATAA
1249771 AAAATAA
1 AAAATAA
1249778 AAAATAA
1 AAAATAA
1249785 A
1 A
1249786 TATTTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.18
7 17 0.61
8 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1249787 original size:32 final size:32
Alignment explanation
Indices: 1249722--1249787 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1249712 AAATTTATTT
****
1249722 TAAAAATAAAAAAATAAAAAAGTATTTTAAAA
1 TAAAAATAAAAAAATAAAAAAGTAAAAAAAAA
1249754 TAAAAATAAAAAAATAAAAAA-TAAAAAATAAA
1 TAAAAATAAAAAAATAAAAAAGTAAAAAA-AAA
1249786 TA
1 TA
1249788 TTTATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (32 bp):
TAAAAATAAAAAAATAAAAAAGTAAAAAAAAA
Found at i:1253670 original size:23 final size:22
Alignment explanation
Indices: 1253643--1253697 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
1253633 ATTTTTATAA
1253643 TTTAAAATATCACA-ATAAAAAAT
1 TTTAAAATAT-A-ATATAAAAAAT
*
1253666 TTTAAAAAAAATAATATAAAAAAT
1 TTT--AAAATATAATATAAAAAAT
1253690 TTTAAAAT
1 TTTAAAAT
1253698 GTAAGTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 13 0.48
25 6 0.22
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATATAATATAAAAAAT
Found at i:1263066 original size:16 final size:17
Alignment explanation
Indices: 1263035--1263079 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1263025 AATTTAAAAT
1263035 AATATATATAAAAATCA
1 AATATATATAAAAATCA
*
1263052 AATATA-ATCAAAATCA
1 AATATATATAAAAATCA
*
1263068 AGTAT-TATAAAA
1 AATATATATAAAA
1263080 CACAAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (17 bp):
AATATATATAAAAATCA
Found at i:1269410 original size:112 final size:113
Alignment explanation
Indices: 1269225--1269431 Score: 303
Period size: 112 Copynumber: 1.8 Consensus size: 113
1269215 GACGTGAGCT
* *
1269225 AGAACCCCACTAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCG
1 AGAACCCCACCAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCA
* * *
1269290 ATGTACTCTCAATTTTGTAAACCAAGCCCTCACAAAGGGATGTGGGCG
66 AGGTACTCTCAATTCTGTAAACCAAACCCTCACAAAGGGATGTGGGCG
* * *
1269338 AGAACCCCACCAGGGACGAGATGCTTATGT-CCCTTGGTGGGTGG-TGTGTGCTC-ATGTACGGT
1 AGAACCCCACCA-GGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGC-CAATGTACGGT
1269400 CAAGGTACTCTCAATTCTGTAAACCAAACCCT
64 CAAGGTACTCTCAATTCTGTAAACCAAACCCT
1269432 TAAGGCAACT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
112 44 0.52
113 25 0.30
114 15 0.18
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (113 bp):
AGAACCCCACCAGGACGAGACGCTCATGTCCCCTTGATGGGTGGTTGTGTGCCAATGTACGGTCA
AGGTACTCTCAATTCTGTAAACCAAACCCTCACAAAGGGATGTGGGCG
Found at i:1270104 original size:32 final size:31
Alignment explanation
Indices: 1270059--1270154 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
1270049 CTTAGATAAT
1270059 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1270090 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
** *
1270122 TCGAAAGAGTTGTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1270153 TT
1 TT
1270155 GTAATTTGCC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:1277992 original size:12 final size:12
Alignment explanation
Indices: 1277950--1277990 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1277940 TTCCCACTCA
*
1277950 TAATAATAATAC
1 TAATAATAATAT
*
1277962 TAATAATTATAT
1 TAATAATAATAT
*
1277974 TAATACTAATAT
1 TAATAATAATAT
1277986 TAATA
1 TAATA
1277991 CTTACTTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:1278758 original size:19 final size:19
Alignment explanation
Indices: 1278713--1278752 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1278703 TTTGTTTTGT
*
1278713 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
1278731 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
1278750 TTT
1 TTT
1278753 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:1278912 original size:5 final size:5
Alignment explanation
Indices: 1278904--1278955 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
1278894 TATTTAGTTT
* * * *
1278904 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATAAA ATATC ATATA
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
1278956 TAAAACATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 33 0.89
7 4 0.11
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1278940 original size:27 final size:27
Alignment explanation
Indices: 1278902--1278956 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1278892 TCTATTTAGT
*
1278902 TTATATAATATAATACAATATAATATA
1 TTATATAATATAATAAAATATAATATA
* *
1278929 TTATATTATATAATAAAATATCATATA
1 TTATATAATATAATAAAATATAATATA
1278956 T
1 T
1278957 AAAACATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
TTATATAATATAATAAAATATAATATA
Found at i:1278955 original size:17 final size:17
Alignment explanation
Indices: 1278903--1278958 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1278893 CTATTTAGTT
1278903 TATATAATATAATA-CA
1 TATATAATATAATATCA
*
1278919 -ATATAATATATTAT-A
1 TATATAATATAATATCA
*
1278934 TTATATAATAAAATATCA
1 -TATATAATATAATATCA
1278952 TATATAA
1 TATATAA
1278959 AACATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 13 0.39
17 19 0.58
18 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATAATATAATATCA
Found at i:1279364 original size:20 final size:20
Alignment explanation
Indices: 1279320--1279370 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1279310 AAATTACAAA
*
1279320 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTAT
*
1279340 TAAAAATTCAAAAT-ATCTAT
1 AAAAAATTCAAAATAAT-TAT
1279360 AAAAAATTCAA
1 AAAAAATTCAA
1279371 TTTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTAT
Found at i:1280924 original size:6 final size:6
Alignment explanation
Indices: 1280913--1280948 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1280903 AATGAGTACA
*
1280913 TATATT TATATT TATATG TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
1280949 GAATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:1280936 original size:18 final size:18
Alignment explanation
Indices: 1280913--1280947 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1280903 AATGAGTACA
1280913 TATATTTATATTTATATG
1 TATATTTATATTTATATG
1280931 TATATTTATATTTATAT
1 TATATTTATATTTATAT
1280948 TGAATTAATA
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:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATATTTATATTTATATG
Found at i:1283978 original size:26 final size:27
Alignment explanation
Indices: 1283948--1284005 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1283938 CTTTAACAGG
1283948 TTCTTGCAAAGTTTG-TTTCCCCATTT
1 TTCTTGCAAAGTTTGTTTTCCCCATTT
*
1283974 TTCTTGCCAAGTTTGTTTTCCCCATTT
1 TTCTTGCAAAGTTTGTTTTCCCCATTT
1284001 TTCTT
1 TTCTT
1284006 TGTTGAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.53
Consensus pattern (27 bp):
TTCTTGCAAAGTTTGTTTTCCCCATTT
Found at i:1284676 original size:21 final size:21
Alignment explanation
Indices: 1284652--1284694 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1284642 ACCCTTACTC
1284652 CTTATATGGTATCTGACGGTA
1 CTTATATGGTATCTGACGGTA
*
1284673 CTTATATGGTATCTGAGGGTA
1 CTTATATGGTATCTGACGGTA
1284694 C
1 C
1284695 GTATGCTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (21 bp):
CTTATATGGTATCTGACGGTA
Found at i:1287095 original size:28 final size:29
Alignment explanation
Indices: 1287049--1287103 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1287039 GAATTTTAAG
* *
1287049 TTATTTTCATTATTTTAAATATAAAATAT
1 TTATTTTCATTATTATAAAAATAAAATAT
*
1287078 TTATTTTTA-TATTATAAAAATAAAAT
1 TTATTTTCATTATTATAAAAATAAAAT
1287104 TACTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTTCATTATTATAAAAATAAAATAT
Found at i:1287110 original size:29 final size:29
Alignment explanation
Indices: 1287049--1287110 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1287039 GAATTTTAAG
* * *
1287049 TTATTTTCATTATTTTAAATATAAAATAT
1 TTATTTTCATTATTATAAAAATAAAATAC
*
1287078 TTATTTTTA-TATTATAAAAATAAAATTAC
1 TTATTTTCATTATTATAAAAATAAAA-TAC
1287107 TTAT
1 TTAT
1287111 AAATTAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTTCATTATTATAAAAATAAAATAC
Found at i:1288254 original size:13 final size:13
Alignment explanation
Indices: 1288236--1288261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1288226 AGCCCTCCCT
1288236 TAATAAACAAAAA
1 TAATAAACAAAAA
1288249 TAATAAACAAAAA
1 TAATAAACAAAAA
1288262 GAGATTCAAC
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
TAATAAACAAAAA
Found at i:1295670 original size:21 final size:21
Alignment explanation
Indices: 1295644--1295684 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1295634 AGACGAGCAA
* *
1295644 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1295665 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1295685 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1310961 original size:14 final size:14
Alignment explanation
Indices: 1310935--1310978 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1310925 TATGTATAAG
*
1310935 TTATAAATTTAATCT
1 TTATAATTTTAAT-T
1310950 TTAT-ATTTTAATT
1 TTATAATTTTAATT
1310963 TTATCAATTTTAATT
1 TTAT-AATTTTAATT
1310978 T
1 T
1310979 AATCTGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 14 0.54
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATAATTTTAATT
Found at i:1316854 original size:236 final size:232
Alignment explanation
Indices: 1316336--1317000 Score: 736
Period size: 236 Copynumber: 2.8 Consensus size: 232
1316326 CACGATATAT
* * ** *
1316336 AAGGAAACTAAGACATGGATCATGAAAACCAGTCATTTCTCCTAGAACCTTATGGAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAG-ACAGTATGAAGCCAAAAGA
* * *
1316401 GAAAGAAAACGGAGTAACAGTAAAGAATCTGAGCATGCCATTAAA-CGAAATTACTCTCTGATAA
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACT-TCTGCTAA
* * ** * *** * *
1316465 TCATGAAAATGCAGGTA-GA-C-AGGATCC-TAAT--C-ATCCGTCCAAACCTCGAGCATAAAGC
129 TCAAGAAAATGCAGATAGGATCTAACATCCATGATGACTATGTATCCAAATCTCAAGCATAAAGC
*
1316523 ACATGTTAAAATTATTTCATGCATCCCCAACATGATATA
194 ACATGTTAAAATTATTTCATGCATCCCCAACATGATACA
* * * * * *
1316562 AAGAAAACCAAGTCATGGATCATGAAAACCGGTTATTCCTCCCAGATAGGTATGAAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGACA-GTATGAAGCCAAAAGA
*
1316627 GAAAGGAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTATCTGCTAA
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACT-TCTGCTAA
*
1316692 TCAAGAAAATGCAGATAGGATCTTAATCATCCATGATGACTATGTATCCTAATCTCAAGCATAAA
129 TCAAGAAAATGCAGATAGGATC-TAA-CATCCATGATGACTATGTATCCAAATCTCAAGCATAAA
* * ** * * *
1316757 GCGCATGTTACAATTATTTTGTGCATTCCCGACATGCTACA
192 GCACATGTTAAAATTATTTCATGCATCCCCAACATGATACA
* * *
1316798 AAGGAAACTAACTCATGGATCATGAAAATCAATTATTTCTCCTAGAGCAGTATGAAGCCAAAAGA
1 AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGA-CAGTATGAAGCCAAAAGA
* * * *
1316863 GAAAGAAAACACAGCAACAGTAAAGAATCCAAGTATGCCATTAAACCGAAATTAC-TCTGCTAAT
65 GAAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTTCTGCTAAT
* * * * *
1316927 CAAGAAAGTGCAGGTAGATAGAATCCTAACTATCCATGACGATTATGTATCCGAATCTCAAGCAT
130 CAAGAAAATGC----AGATAGGAT-CTAAC-ATCCATGATGACTATGTATCCAAATCTCAAGCAT
1316992 AAAGCACAT
189 AAAGCACAT
1317001 CTTGCAAAAT
Statistics
Matches: 366, Mismatches: 55, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
225 1 0.00
226 94 0.26
227 32 0.09
228 2 0.01
229 1 0.00
231 1 0.00
232 4 0.01
233 3 0.01
234 19 0.05
235 1 0.00
236 155 0.42
237 2 0.01
238 50 0.14
239 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (232 bp):
AAGGAAACTAAGTCATGGATCATGAAAACCAGTTATTTCTCCTAGACAGTATGAAGCCAAAAGAG
AAAGAAAACAGAGTAACAGTAAAGAATCCGAGCATGCCATTAAACCGAAATTACTTCTGCTAATC
AAGAAAATGCAGATAGGATCTAACATCCATGATGACTATGTATCCAAATCTCAAGCATAAAGCAC
ATGTTAAAATTATTTCATGCATCCCCAACATGATACA
Found at i:1317753 original size:12 final size:13
Alignment explanation
Indices: 1317725--1317770 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
1317715 CCGCTGTCAT
*
1317725 AAAACAAAAT-TA
1 AAAAAAAAATGTA
*
1317737 GAAAAAAAATG-A
1 AAAAAAAAATGTA
1317749 AAAAAAAAA-GTA
1 AAAAAAAAATGTA
1317761 AAAAAAAAAT
1 AAAAAAAAAT
1317771 ATTTTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 1 0.04
12 27 0.96
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATGTA
Found at i:1326086 original size:10 final size:10
Alignment explanation
Indices: 1326071--1326097 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1326061 ATTAATTTTT
1326071 AATATTTAAA
1 AATATTTAAA
1326081 AATATTTAAA
1 AATATTTAAA
1326091 AATATTT
1 AATATTT
1326098 TTATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATTTAAA
Found at i:1326916 original size:12 final size:11
Alignment explanation
Indices: 1326897--1326926 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1326887 GGTATACAAC
1326897 ATAATTATAAT
1 ATAATTATAAT
1326908 ATGAATTATAAT
1 AT-AATTATAAT
1326920 ATAATTA
1 ATAATTA
1326927 GGGTGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
ATAATTATAAT
Found at i:1328045 original size:18 final size:18
Alignment explanation
Indices: 1328019--1328061 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1328009 TTTAACCATT
*
1328019 TAAAATATTATAAA-AATA
1 TAAATTATTA-AAATAATA
1328037 TAAATTATTAAAATAATA
1 TAAATTATTAAAATAATA
1328055 -AAATTAT
1 TAAATTAT
1328062 ATTTTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATTATTAAAATAATA
Found at i:1328049 original size:15 final size:17
Alignment explanation
Indices: 1328025--1328062 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1328015 CATTTAAAAT
1328025 ATTATAAAAAT-AT-AA
1 ATTATAAAAATAATAAA
*
1328040 ATTATTAAAATAATAAA
1 ATTATAAAAATAATAAA
1328057 ATTATA
1 ATTATA
1328063 TTTTAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATAAAAATAATAAA
Found at i:1328506 original size:26 final size:26
Alignment explanation
Indices: 1328475--1328602 Score: 180
Period size: 26 Copynumber: 5.2 Consensus size: 26
1328465 ATAATAATTC
1328475 GAATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
1328501 GAATGCAATGGATATAATTGTAGTT-
1 GAATGCAATGGATATAATTGTAGTTA
*
1328526 --A-G-AATGGATATAATTG-A-TCA
1 GAATGCAATGGATATAATTGTAGTTA
**
1328546 TCATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
1328572 GAATGCAATGGATATAATTGTAGTTA
1 GAATGCAATGGATATAATTGTAGTTA
1328598 GAATG
1 GAATG
1328603 GATATAATTG
Statistics
Matches: 91, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 14 0.15
22 2 0.02
23 2 0.02
24 14 0.15
25 1 0.01
26 56 0.62
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (26 bp):
GAATGCAATGGATATAATTGTAGTTA
Found at i:1328554 original size:71 final size:71
Alignment explanation
Indices: 1328477--1328633 Score: 314
Period size: 71 Copynumber: 2.2 Consensus size: 71
1328467 AATAATTCGA
1328477 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
1 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
1328542 ATCATC
66 ATCATC
1328548 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
1 ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
1328613 ATCATC
66 ATCATC
1328619 ATGCAATGGATATAA
1 ATGCAATGGATATAA
1328634 CATGATGATC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 86 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (71 bp):
ATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTGTAGTTAGAATGGATATAATTG
ATCATC
Found at i:1328632 original size:45 final size:46
Alignment explanation
Indices: 1328476--1328633 Score: 148
Period size: 45 Copynumber: 3.3 Consensus size: 46
1328466 TAATAATTCG
1328476 AATGCAATGGATATAATTGTAGTTAGAATGCAATGGATATAATTG-TAGT
1 AATGCAATGGATATAATTGTAGTT---ATGCAATGGATATAATTGATA-T
* * *
1328525 TA-G-AATGGATATAATTGATCA-TCATGCAATGGATATAATTGTAGTTAG
1 AATGCAATGGATATAATTG-T-AGTTATGCAATGGATATAATTG-A--TAT
1328573 AATGCAATGGATATAATTGTAGTTA-G-AATGGATATAATTGATCAT
1 AATGCAATGGATATAATTGTAGTTATGCAATGGATATAATTGAT-AT
*
1328618 CATGCAATGGATATAA
1 AATGCAATGGATATAA
1328634 CATGATGATC
Statistics
Matches: 92, Mismatches: 7, Indels: 24
0.75 0.06 0.20
Matches are distributed among these distances:
44 1 0.01
45 34 0.37
46 1 0.01
47 28 0.30
48 6 0.07
49 8 0.09
50 14 0.15
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (46 bp):
AATGCAATGGATATAATTGTAGTTATGCAATGGATATAATTGATAT
Found at i:1333472 original size:43 final size:41
Alignment explanation
Indices: 1333331--1333494 Score: 161
Period size: 43 Copynumber: 3.9 Consensus size: 41
1333321 TAGGGTTACC
*
1333331 GAGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATAT
1 GAGATT-CGTGTAAGACCATGTCT-GGATATTGGCATCGATAT
* *
1333373 GAGACTTCGTCTAAGACCATGTCTAGGACATTGGCATCGATAT
1 GAGA-TTCGTGTAAGACCATGTCT-GGATATTGGCATCGATAT
* * *
1333416 GTGAATTCGTGTAAGACCATGGCTGGAATATTGGCATCGATAC
1 GAG-ATTCGTGTAAGACCATGTCTGG-ATATTGGCATCGATAT
* * *
1333459 AAGATTACATGTAAGACCATATCTGGGATA-TGGCAT
1 GAGATT-CGTGTAAGACCATGTCT-GGATATTGGCAT
1333495 TGTTACGGTA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
42 34 0.33
43 65 0.64
44 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (41 bp):
GAGATTCGTGTAAGACCATGTCTGGATATTGGCATCGATAT
Found at i:1338428 original size:11 final size:11
Alignment explanation
Indices: 1338406--1338438 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1338396 AATTAATCCT
1338406 CTCTCAAATTTC
1 CTCTC-AATTTC
1338418 CTCTCAATTTC
1 CTCTCAATTTC
1338429 CTCTCAATTT
1 CTCTCAATTT
1338439 GTTCTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:1343819 original size:14 final size:15
Alignment explanation
Indices: 1343800--1343842 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1343790 TTGATTGTCA
1343800 GTAAAATGTTTTAC-
1 GTAAAATGTTTTACT
*
1343814 GTAAAATGATTT-CT
1 GTAAAATGTTTTACT
*
1343828 GGAAAATGTTTTACT
1 GTAAAATGTTTTACT
1343843 TTTCTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 21 0.88
15 2 0.08
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (15 bp):
GTAAAATGTTTTACT
Found at i:1343848 original size:20 final size:20
Alignment explanation
Indices: 1343823--1343862 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1343813 CGTAAAATGA
*
1343823 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1343843 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1343863 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1344857 original size:31 final size:32
Alignment explanation
Indices: 1344797--1344861 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
1344787 TGCAATAGTT
1344797 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGTG-AAAGAGGAGCTGTGGAA
* *
1344830 AGGGTGAAGAGAGTG-GAGATGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAGAGGAGCTGTGGAA
1344861 A
1 A
1344862 ATGTCTTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.37, C:0.03, G:0.46, T:0.14
Consensus pattern (32 bp):
AGGGTGAAGAGAGTGAAAGAGGAGCTGTGGAA
Found at i:1348652 original size:18 final size:18
Alignment explanation
Indices: 1348631--1348671 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1348621 TGAGCGTGAT
1348631 CGTGACCATGATAGAGAC
1 CGTGACCATGATAGAGAC
* *
1348649 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAC
1348667 CGTGA
1 CGTGA
1348672 GCGTTATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAC
Found at i:1348680 original size:18 final size:18
Alignment explanation
Indices: 1348639--1348680 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1348629 ATCGTGACCA
*
1348639 TGATAGAGACCGTGATCG
1 TGATAGAGACCGTGAGCG
1348657 TGATAGAGACCGTGAGCG
1 TGATAGAGACCGTGAGCG
*
1348675 TTATAG
1 TGATAG
1348681 GGAGAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (18 bp):
TGATAGAGACCGTGAGCG
Found at i:1357144 original size:18 final size:18
Alignment explanation
Indices: 1357123--1357163 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1357113 TGAGCGTGAT
*
1357123 CGTGACCATGATAGAGAG
1 CGTGACCATGATAGAGAC
* *
1357141 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAC
1357159 CGTGA
1 CGTGA
1357164 GCGCTATAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAC
Found at i:1357172 original size:18 final size:18
Alignment explanation
Indices: 1357131--1357193 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
1357121 ATCGTGACCA
* *
1357131 TGATAGAGAGCGTGATCG
1 TGATAGAGACCGTGAGCG
1357149 TGATAGAGACCGTGAGCG
1 TGATAGAGACCGTGAGCG
* * *
1357167 CT-ATAGGGAGCGGGAGCG
1 -TGATAGAGACCGTGAGCG
*
1357185 TGATCGAGA
1 TGATAGAGA
1357194 GCGGGATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.41, T:0.17
Consensus pattern (18 bp):
TGATAGAGACCGTGAGCG
Found at i:1365833 original size:17 final size:16
Alignment explanation
Indices: 1365813--1365863 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1365803 TTGAATTTTT
1365813 ATTATTGTAATATTTAA
1 ATTATT-TAATATTTAA
* *
1365830 ATTATTAAAATAATTAA
1 ATTATT-TAATATTTAA
1365847 TATT-TTTAATATTTAA
1 -ATTATTTAATATTTAA
1365863 A
1 A
1365864 AAATAAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 1 0.04
16 8 0.29
17 16 0.57
18 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTATTTAATATTTAA
Found at i:1367854 original size:4 final size:4
Alignment explanation
Indices: 1367847--1367919 Score: 62
Period size: 4 Copynumber: 18.0 Consensus size: 4
1367837 TTTCTCCTTC
*
1367847 CTTT CTTT CCTT -TTT CTTTT CTTT CTTT CTTT CTTT C-TT -TTT CTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
* *
1367893 CTGTTT CGTTT CTAT ATTT CTTT CTTT
1 C--TTT C-TTT CTTT CTTT CTTT CTTT
1367920 TTATTTATTC
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.11
4 38 0.67
5 9 0.16
6 4 0.07
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:1367899 original size:16 final size:15
Alignment explanation
Indices: 1367847--1367921 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1367837 TTTCTCCTTC
*
1367847 CTTTCTTTCCTTTTT
1 CTTTCTTTTCTTTTT
1367862 CTTT-TCTTTC--TTT
1 CTTTCT-TTTCTTTTT
1367875 CTTTC-TTTCTTTTT
1 CTTTCTTTTCTTTTT
1367889 CTTTCTGTTTCGTTTCTAT
1 CTTTCT-TTTC-TTT-T-T
*
1367908 ATTTC-TTTCTTTTT
1 CTTTCTTTTCTTTTT
1367922 ATTTATTCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
12 4 0.08
13 7 0.14
14 10 0.20
15 8 0.16
16 7 0.14
17 7 0.14
18 1 0.02
19 5 0.10
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (15 bp):
CTTTCTTTTCTTTTT
Found at i:1367913 original size:33 final size:31
Alignment explanation
Indices: 1367859--1367921 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 31
1367849 TTCTTTCCTT
* *
1367859 TTTCTTTTCTTTCTTTCTTTCTTTCTTTTTC
1 TTTCTTTTCTTTCTATATTTCTTTCTTTTTC
1367890 TTTCTGTTTCGTTTCTATATTTCTTTCTTTTT
1 TTTCT-TTTC-TTTCTATATTTCTTTCTTTTT
1367922 ATTTATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 4 0.14
33 19 0.68
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTCTTTTCTTTCTATATTTCTTTCTTTTTC
Found at i:1367913 original size:37 final size:38
Alignment explanation
Indices: 1367848--1367919 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
1367838 TTCTCCTTCC
* * * *
1367848 TTTCTTTCCTTTTTCTTTTCTTTCTTTCTTTCTTTCTT
1 TTTCTTTCCTGTTTCGTTTCTATATTTCTTTCTTTCTT
1367886 TTTCTTT-CTGTTTCGTTTCTATATTTCTTTCTTT
1 TTTCTTTCCTGTTTCGTTTCTATATTTCTTTCTTT
1367920 TTATTTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 23 0.77
38 7 0.23
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (38 bp):
TTTCTTTCCTGTTTCGTTTCTATATTTCTTTCTTTCTT
Found at i:1369118 original size:14 final size:14
Alignment explanation
Indices: 1369099--1369125 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1369089 ACTCAATTGA
1369099 ATTTTTTTTAAAAT
1 ATTTTTTTTAAAAT
1369113 ATTTTTTTTAAAA
1 ATTTTTTTTAAAA
1369126 ATAATACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTTTTAAAAT
Found at i:1375299 original size:29 final size:29
Alignment explanation
Indices: 1375249--1375314 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
1375239 ATATGAACTA
* *
1375249 CTAAAATAGTAAAATTATATTTCTATCATC
1 CTAAAA-ATTAAAATTATATTTCGATCATC
* *
1375279 GTAAAAATTAAAATT-TAATTTCGATCCTC
1 CTAAAAATTAAAATTAT-ATTTCGATCATC
1375308 CTAAAAA
1 CTAAAAA
1375315 ACATTTTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (29 bp):
CTAAAAATTAAAATTATATTTCGATCATC
Found at i:1379015 original size:16 final size:16
Alignment explanation
Indices: 1378996--1379028 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1378986 TTGATATATG
*
1378996 TACATTTCTATTCCAT
1 TACATTTCTACTCCAT
1379012 TACATTTCTACTCCAT
1 TACATTTCTACTCCAT
1379028 T
1 T
1379029 TCAGTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (16 bp):
TACATTTCTACTCCAT
Found at i:1388600 original size:19 final size:18
Alignment explanation
Indices: 1388578--1388620 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1388568 AAATTACAAA
* *
1388578 AAAAATCAAAATAATTTTT
1 AAAAATAAAAAT-ATTTAT
*
1388597 AAAATTAAAAATATTTAT
1 AAAAATAAAAATATTTAT
1388615 AAAAAT
1 AAAAAT
1388621 TCCAAAATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATAAAAATATTTAT
Found at i:1388815 original size:16 final size:16
Alignment explanation
Indices: 1388794--1388825 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1388784 CTTTGAAAAA
1388794 AATTTCAAATATATAT
1 AATTTCAAATATATAT
*
1388810 AATTTCAAATTTATAT
1 AATTTCAAATATATAT
1388826 GCTCTAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTCAAATATATAT
Found at i:1393441 original size:17 final size:18
Alignment explanation
Indices: 1393406--1393442 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1393396 AATCCATTTG
1393406 AAAGAGTAAAAAGAAGAA
1 AAAGAGTAAAAAGAAGAA
1393424 AAAGAG-AAAGAA-AAGAA
1 AAAGAGTAAA-AAGAAGAA
1393441 AA
1 AA
1393443 CCCCACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (18 bp):
AAAGAGTAAAAAGAAGAA
Found at i:1400000 original size:28 final size:28
Alignment explanation
Indices: 1399959--1400029 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
1399949 TTAATGAAAA
1399959 AAAATTTAATAAAA-TTTGAGAG-TCTAATT
1 AAAATTT--TAAAATTTTGAGAGCT-TAATT
*
1399988 AAAACTTTTAAAATTTTGTGAGCTTAATT
1 AAAA-TTTTAAAATTTTGAGAGCTTAATT
1400017 AAAATTTTCAAAA
1 AAAATTTT-AAAA
1400030 AAAAAAAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
28 9 0.24
29 24 0.65
30 4 0.11
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (28 bp):
AAAATTTTAAAATTTTGAGAGCTTAATT
Found at i:1408101 original size:3 final size:3
Alignment explanation
Indices: 1408095--1408123 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1408085 AATACAAAAC
1408095 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1408124 GTTTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1408156 original size:41 final size:40
Alignment explanation
Indices: 1408093--1408188 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 40
1408083 ATAATACAAA
* * **
1408093 ACTAATAATAATAA-TAA-TAATAATAATAA-TAGTTTTTT
1 ACTAAAAATAATAACTAACT-ACAATAATAATTAGGGTTTT
*
1408131 ACTCAAAATAAT-ACTAACTACAATAATAATTAGGGTTTT
1 ACTAAAAATAATAACTAACTACAATAATAATTAGGGTTTT
1408170 ACTAAAAATAATAACTAAC
1 ACTAAAAATAATAACTAAC
1408189 AATAATATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
37 1 0.02
38 22 0.46
39 19 0.40
40 6 0.12
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.34
Consensus pattern (40 bp):
ACTAAAAATAATAACTAACTACAATAATAATTAGGGTTTT
Found at i:1416918 original size:25 final size:27
Alignment explanation
Indices: 1416880--1416932 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
1416870 TATAAAAAAT
*
1416880 TATTCTTAATAAAATAATATATAATTA
1 TATTCTTAATAAAATAAAATATAATTA
*
1416907 TATT-TTAA-AAAATAAAATATATTTA
1 TATTCTTAATAAAATAAAATATAATTA
1416932 T
1 T
1416933 GTGCAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.67
26 4 0.17
27 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTCTTAATAAAATAAAATATAATTA
Found at i:1421710 original size:19 final size:19
Alignment explanation
Indices: 1421652--1421710 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
1421642 TACCTTGTTC
*
1421652 TAACATACAAATATCAATTTT
1 TAACATA-AAAAAT-AATTTT
* * *
1421673 TAAGGATAAAAATTTATTTT
1 TAA-CATAAAAAATAATTTT
1421693 TAACATAAAAAATAATTT
1 TAACATAAAAAATAATTT
1421711 ACTATTTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 12 0.40
20 8 0.27
21 7 0.23
22 3 0.10
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (19 bp):
TAACATAAAAAATAATTTT
Found at i:1434328 original size:19 final size:20
Alignment explanation
Indices: 1434290--1434331 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1434280 ACTTAATATG
1434290 TTTTAAAATATATCAAAAAA
1 TTTTAAAATATATCAAAAAA
*
1434310 TTTTAAAA-ATCATAAAAAAA
1 TTTTAAAATAT-ATCAAAAAA
1434330 TT
1 TT
1434332 CAAAAGAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTTAAAATATATCAAAAAA
Found at i:1435067 original size:3 final size:3
Alignment explanation
Indices: 1435059--1435083 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1435049 ATAAATTATA
1435059 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1435084 TGATTATGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1447355 original size:19 final size:19
Alignment explanation
Indices: 1447328--1447370 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1447318 ATATTTTCCG
1447328 TTTTCTCATTTATT-TAATAA
1 TTTTCTCATTT-TTCTAAT-A
1447348 TTTT-TCATTTTTCTAATA
1 TTTTCTCATTTTTCTAATA
1447366 TTTTC
1 TTTTC
1447371 AAGTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTCTCATTTTTCTAATA
Found at i:1453545 original size:19 final size:19
Alignment explanation
Indices: 1453521--1453563 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1453511 TGAAATATAT
*
1453521 TTTTAG-TTTAGTATTAATA
1 TTTTAGATTT-GTATTAAAA
*
1453540 TTTTAGATTTTTATTAAAA
1 TTTTAGATTTGTATTAAAA
1453559 TTTTA
1 TTTTA
1453564 AATATAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTAGATTTGTATTAAAA
Found at i:1484324 original size:16 final size:16
Alignment explanation
Indices: 1484303--1484336 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1484293 TTAATTAATT
**
1484303 AATTAAAATTTATAAA
1 AATTAAAAAATATAAA
1484319 AATTAAAAAATATAAA
1 AATTAAAAAATATAAA
1484335 AA
1 AA
1484337 ATTTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAAAAAATATAAA
Found at i:1491089 original size:29 final size:27
Alignment explanation
Indices: 1491049--1491111 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
1491039 TTAAATCAAT
1491049 AAAATTATAAATATTATTAAATTTTAATA
1 AAAATTATAAATATTA--AAATTTTAATA
*
1491078 AAAATT-TCAAATATTAAAATTTTATTA
1 AAAATTAT-AAATATTAAAATTTTAATA
1491105 AAAATTA
1 AAAATTA
1491112 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 16 0.52
28 1 0.03
29 14 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AAAATTATAAATATTAAAATTTTAATA
Done.