Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 1 of 352
Found at i:1796 original size:21 final size:21
Alignment explanation
Indices: 1754--1796 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1744 TTCACTATAC
*
1754 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
1775 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
1796 A
1 A
1797 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:2907 original size:39 final size:37
Alignment explanation
Indices: 2840--2932 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
2830 ACCAGAATGG
* *
2840 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
2879 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
2916 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
2933 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3295 original size:3 final size:3
Alignment explanation
Indices: 3287--3322 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3277 ATTCCCACTC
* *
3287 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3323 CTTACCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3304 original size:12 final size:12
Alignment explanation
Indices: 3287--3322 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3277 ATTCCCACTC
*
3287 ATAATAATAATA
1 ATAATACTAATA
3299 ATAATACTAATA
1 ATAATACTAATA
3311 ATAATACTAATA
1 ATAATACTAATA
3323 CTTACCTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:3990 original size:11 final size:11
Alignment explanation
Indices: 3974--3999 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3964 CTTTTTCTTC
3974 TTTCTCCCCTG
1 TTTCTCCCCTG
3985 TTTCTCCCCTG
1 TTTCTCCCCTG
3996 TTTC
1 TTTC
4000 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:4381 original size:21 final size:21
Alignment explanation
Indices: 4357--4399 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4347 AATAATAACT
4357 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
4378 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
4399 A
1 A
4400 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:13515 original size:127 final size:127
Alignment explanation
Indices: 13302--13585 Score: 392
Period size: 127 Copynumber: 2.2 Consensus size: 127
13292 GCAAAGTTTG
* * *
13302 ATGTTTGAAAATTCGAGGAATCATGCCCTATCGTGCTGGGTTTCAATTTCCCGTTCATTCAAGAT
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTCATTCAAAAT
* * *
13367 AATCGAATATTCCTTTAGAATTTCACTCGTGTTTT-TCAAATTCTGAAA-CAAGGCAATGTTCA
66 AATCGAATATTCCTTAAGAATTTCACTCGTGTTTTAT-AAATTCT-AAAGCAAGACAATGTCCA
* * * * **
13429 ATGTTTGGAAATTCGGGGAGTCGTGCCCTATCGTGCTGGGTTTCGATTTCCGGTTTGTTCAAAAT
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTCATTCAAAAT
* *
13494 AATTGAATATTCCTTAAGAATTTCATTCGTGTTTTATAAATTCTAAAGCAAGACAATGTCCA
66 AATCGAATATTCCTTAAGAATTTCACTCGTGTTTTATAAATTCTAAAGCAAGACAATGTCCA
* *
13556 GTGTTTGGAAATTCGAGGAATCGTACCCTA
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTA
13586 CCTGCAAGGT
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
126 3 0.02
127 133 0.97
128 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (127 bp):
ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTCATTCAAAAT
AATCGAATATTCCTTAAGAATTTCACTCGTGTTTTATAAATTCTAAAGCAAGACAATGTCCA
Found at i:15676 original size:105 final size:104
Alignment explanation
Indices: 15528--15720 Score: 291
Period size: 105 Copynumber: 1.8 Consensus size: 104
15518 TCCTCATTGA
*
15528 AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACGTTTCACAACTCGGTAT
1 AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGTAT
*
15593 GGGA-AATGCCATACCTACATTTCTTAACTCAGTATGGAT
66 -GGATAATACCATACCTACATTTCTTAACTCAGTATGGAT
* ** *
15632 AATACCATACCTATATTTCTCA-ACTCGGTATGGATGATACCATACTTACATTTCACAACTCGGT
1 AATACCATACCTACATTT-T-ATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGT
15696 ATGGATAATACCATACCTACATTTC
64 ATGGATAATACCATACCTACATTTC
15721 GCACTTTGCC
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
104 20 0.25
105 59 0.74
106 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (104 bp):
AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGTAT
GGATAATACCATACCTACATTTCTTAACTCAGTATGGAT
Found at i:15736 original size:35 final size:35
Alignment explanation
Indices: 15528--15720 Score: 255
Period size: 35 Copynumber: 5.5 Consensus size: 35
15518 TCCTCATTGA
* * *
15528 AATACCATACCTACATTTTA-TACTCGGTATGGAA
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
*
15562 AATACCATACCTACGTTTCACAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCGGTAT-GGAT
* ** *
15597 AATGCCATACCTACATTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
* *
15632 AATACCATACCTATATTTCTCAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
* *
15667 GATACCATACTTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
15702 AATACCATACCTACATTTC
1 AATACCATACCTACATTTC
15721 GCACTTTGCC
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
34 21 0.15
35 114 0.83
36 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCGGTATGGAT
Found at i:18521 original size:46 final size:46
Alignment explanation
Indices: 18471--18558 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
18461 TCTTTGAATT
* *
18471 ATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAGCC
1 ATGGTCTTACTCA-TTTCACGTCATGTTACCATGGTATCTTTCAGCC
** *
18517 ATGGTCTTGTTCATTTCACGTCATGTTATCATGGTATCTTTC
1 ATGGTCTTACTCATTTCACGTCATGTTACCATGGTATCTTTC
18559 TGTAACAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 4 0.11
46 32 0.89
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (46 bp):
ATGGTCTTACTCATTTCACGTCATGTTACCATGGTATCTTTCAGCC
Found at i:20738 original size:16 final size:16
Alignment explanation
Indices: 20717--20773 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
20707 TGTCATGCTG
20717 CCATGGTATCTTTCAA
1 CCATGGTATCTTTCAA
* *
20733 CCATGGTCT-TATTCATTG
1 CCATGGTATCT-TTCA--A
20751 CCATGGTATCTTTCAA
1 CCATGGTATCTTTCAA
20767 CCATGGT
1 CCATGGT
20774 CTTATTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 1 0.03
16 19 0.58
18 12 0.36
19 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (16 bp):
CCATGGTATCTTTCAA
Found at i:20758 original size:34 final size:34
Alignment explanation
Indices: 20715--20780 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
20705 CATGTCATGC
20715 TGCCATGGTATCTTTCAACCATGGTCTTATTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCAT
20749 TGCCATGGTATCTTTCAACCATGGTCTTATTC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTC
20781 TTTTCATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (34 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCAT
Found at i:20800 original size:46 final size:46
Alignment explanation
Indices: 20748--20876 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
20738 GTCTTATTCA
** * *
20748 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACG
*
20794 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACG
*
20840 TTGCCATGGTATCTTTCAACCATGGTCTTACAAATTT
1 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
20877 TATTTCAGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACG
Found at i:22343 original size:16 final size:16
Alignment explanation
Indices: 22322--22363 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
22312 TTTAAGAAAA
22322 TATTATTATAGTATAT
1 TATTATTATAGTATAT
*
22338 TATTATTATATTATAT
1 TATTATTATAGTATAT
* *
22354 GACTATTATA
1 TATTATTATA
22364 ATTAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (16 bp):
TATTATTATAGTATAT
Found at i:23120 original size:25 final size:25
Alignment explanation
Indices: 23092--23171 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
23082 ACTTTAGCAC
**
23092 GCTCTCTGATTATTAGCACATCGGT
1 GCTCTCTGATTATTAGCACATAAGT
*
23117 GCTCTCTGATTATTAGCACATTAGT
1 GCTCTCTGATTATTAGCACATAAGT
* *
23142 GCTCTCCG--T-TTAGCACATATGT
1 GCTCTCTGATTATTAGCACATAAGT
23164 GCTCTCTG
1 GCTCTCTG
23172 TTCATTAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 18 0.37
23 1 0.02
25 30 0.61
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATAAGT
Found at i:25583 original size:18 final size:18
Alignment explanation
Indices: 25560--25680 Score: 57
Period size: 18 Copynumber: 6.7 Consensus size: 18
25550 TTTATCAGTT
25560 TCATTCAGTAACATTCAA
1 TCATTCAGTAACATTCAA
* *
25578 TCATTCAATAACAGTT-AG
1 TCATTCAGTAACA-TTCAA
* * * *
25596 TCGTTCAATAATATTCAG
1 TCATTCAGTAACATTCAA
* ** * * *
25614 TCACTCTTTAATAGTCAG
1 TCATTCAGTAACATTCAA
* *
25632 TTATTCAGTAACGA-TAAA
1 TCATTCAGTAAC-ATTCAA
* *
25650 TTATTCAGTAACAGTCAA
1 TCATTCAGTAACATTCAA
*
25668 TTATTCAGTAACA
1 TCATTCAGTAACA
25681 ATATTTTACT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
17 3 0.04
18 76 0.93
19 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (18 bp):
TCATTCAGTAACATTCAA
Found at i:25672 original size:36 final size:36
Alignment explanation
Indices: 25626--25785 Score: 146
Period size: 36 Copynumber: 4.4 Consensus size: 36
25616 ACTCTTTAAT
* * *
25626 AGTCAGTTATTCAGTAACGATAAATTATTCAGTAAC
1 AGTCAATTATTCAGTAACGATAAGTTATTCAGTAGC
* ** *
25662 AGTCAATTATTCAGTAACAATATTTTACTT-GGTAGC
1 AGTCAATTATTCAGTAACGATAAGTTA-TTCAGTAGC
* * *
25698 AGTCAGTTATCCAGTAAC-AGTCAGTTATTCAGTAGC
1 AGTCAATTATTCAGTAACGA-TAAGTTATTCAGTAGC
* * * *
25734 AGCCAATTATTCAGTAGAAG-TCAGTTATCCAGTAGC
1 AGTCAATTATTCAGTA-ACGATAAGTTATTCAGTAGC
25770 AGTCAATTATTCAGTA
1 AGTCAATTATTCAGTA
25786 CCTTTATTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
35 3 0.03
36 95 0.94
37 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (36 bp):
AGTCAATTATTCAGTAACGATAAGTTATTCAGTAGC
Found at i:25720 original size:18 final size:18
Alignment explanation
Indices: 25626--25785 Score: 130
Period size: 18 Copynumber: 8.9 Consensus size: 18
25616 ACTCTTTAAT
25626 AGTCAGTTATTCAGTAAC
1 AGTCAGTTATTCAGTAAC
* *
25644 -GATAAATTATTCAGTAAC
1 AG-TCAGTTATTCAGTAAC
*
25662 AGTCAATTATTCAGTAAC
1 AGTCAGTTATTCAGTAAC
* * * *
25680 AAT-ATTTTACTT-GGTAGC
1 AGTCA-GTTA-TTCAGTAAC
*
25698 AGTCAGTTATCCAGTAAC
1 AGTCAGTTATTCAGTAAC
*
25716 AGTCAGTTATTCAGTAGC
1 AGTCAGTTATTCAGTAAC
* *
25734 AGCCAATTATTCAGTAGA-
1 AGTCAGTTATTCAGTA-AC
* *
25752 AGTCAGTTATCCAGTAGC
1 AGTCAGTTATTCAGTAAC
*
25770 AGTCAATTATTCAGTA
1 AGTCAGTTATTCAGTA
25786 CCTTTATTTA
Statistics
Matches: 111, Mismatches: 23, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
17 3 0.03
18 104 0.94
19 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
AGTCAGTTATTCAGTAAC
Found at i:25963 original size:54 final size:54
Alignment explanation
Indices: 25899--26067 Score: 230
Period size: 54 Copynumber: 3.1 Consensus size: 54
25889 CACCGTAACG
* * *
25899 GTAACAGTAACAGTAGTGGTACACAGAGTACCTCATCGAAACAAATTCGGAACA
1 GTAACAGTAACAGTAGTGGTACACAAAGTACCTCATCGGAACAAATCCGGAACA
* ** * *
25953 GTAACAGTAACAATAGCCGTACATAAAGTACCTCATCGGAACAAATCCGAAACA
1 GTAACAGTAACAGTAGTGGTACACAAAGTACCTCATCGGAACAAATCCGGAACA
* * * *
26007 GTAACAGTAACAGTAGTGGTACACAAAGTACCACTTCGGAACGAATCCGGAATA
1 GTAACAGTAACAGTAGTGGTACACAAAGTACCTCATCGGAACAAATCCGGAACA
26061 GTAACAG
1 GTAACAG
26068 CAAGGCGACA
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (54 bp):
GTAACAGTAACAGTAGTGGTACACAAAGTACCTCATCGGAACAAATCCGGAACA
Found at i:27349 original size:24 final size:27
Alignment explanation
Indices: 27322--27375 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 27
27312 AGATTTATTC
27322 ATTATATAAATA-TTTTATAATATAATTA
1 ATTA-ATAAATACTTTTATAA-ATAATTA
27350 ATTAATAAATATCTTTTATAAATAAT
1 ATTAATAAATA-CTTTTATAAATAAT
27376 AAATATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.29
28 9 0.38
29 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTAATAAATACTTTTATAAATAATTA
Found at i:27386 original size:17 final size:17
Alignment explanation
Indices: 27352--27404 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
27342 TATAATTAAT
27352 TAATAAATATCTTTTATAAA
1 TAATAAATATC---TATAAA
27372 TAATAAATATCTATAAA
1 TAATAAATATCTATAAA
*
27389 TAATTAAATATATATA
1 TAA-TAAATATCTATA
27405 TTACAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.29
18 11 0.35
20 11 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAAATATCTATAAA
Found at i:29084 original size:82 final size:82
Alignment explanation
Indices: 28947--29194 Score: 451
Period size: 82 Copynumber: 3.0 Consensus size: 82
28937 CTCCATCAAA
* *
28947 CTCTCTGCCAAAACAACACATGAAAATAGAAGGAGATAATGAAATTTTAAAATAAACATAAACAT
1 CTCTCTGCCCAAACAACACATGAAAATAGAAGAAGATAATGAAATTTTAAAATAAACATAAACAT
29012 AGAAAGAAAGTGGAAAG
66 AGAAAGAAAGTGGAAAG
29029 CTCTCTGCCCAAACAACACATGAAAATAGAAGAAGATAATGAAATTTTAAAATAAACATAAACAT
1 CTCTCTGCCCAAACAACACATGAAAATAGAAGAAGATAATGAAATTTTAAAATAAACATAAACAT
29094 AGAAAGAAAGTGGAAAG
66 AGAAAGAAAGTGGAAAG
* *
29111 CTCTCTGCCCAAACAACAAATGAAAATAGAAGTAGATAATGAAATTTTAAAATAAACATAAACAT
1 CTCTCTGCCCAAACAACACATGAAAATAGAAGAAGATAATGAAATTTTAAAATAAACATAAACAT
*
29176 AGAAAGAAAGTGAAAAG
66 AGAAAGAAAGTGGAAAG
29193 CT
1 CT
29195 TTGTTATTAA
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 161 1.00
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.19
Consensus pattern (82 bp):
CTCTCTGCCCAAACAACACATGAAAATAGAAGAAGATAATGAAATTTTAAAATAAACATAAACAT
AGAAAGAAAGTGGAAAG
Found at i:29334 original size:11 final size:11
Alignment explanation
Indices: 29318--29358 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
29308 TATGCATCTT
29318 TTCCACTCACA
1 TTCCACTCACA
29329 TTCCACTC-CA
1 TTCCACTCACA
29339 TTCTCACTCACA
1 TTC-CACTCACA
*
29351 TCCCACTC
1 TTCCACTC
29359 TGCATTCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 18 0.67
12 4 0.15
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (11 bp):
TTCCACTCACA
Found at i:31357 original size:20 final size:20
Alignment explanation
Indices: 31332--31372 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
31322 AGGCACATCA
31332 GAAATCAAGAGCAAAAAAAG
1 GAAATCAAGAGCAAAAAAAG
31352 GAAATCAAGAGCAAAAAAAG
1 GAAATCAAGAGCAAAAAAAG
31372 G
1 G
31373 GTTGATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.22, T:0.05
Consensus pattern (20 bp):
GAAATCAAGAGCAAAAAAAG
Found at i:32471 original size:14 final size:14
Alignment explanation
Indices: 32454--32487 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
32444 TTATACATTG
32454 ATATTTATATACAT
1 ATATTTATATACAT
*
32468 ATATATATATACAT
1 ATATTTATATACAT
32482 A-ATTTA
1 ATATTTA
32488 ATTGAATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTTATATACAT
Found at i:35779 original size:46 final size:44
Alignment explanation
Indices: 35762--36021 Score: 192
Period size: 37 Copynumber: 6.3 Consensus size: 44
35752 GACAAGTGGA
* * * * *
35762 AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAA
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
* *
35807 AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
35852 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 -AAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGAC
*
35898 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
35935 AAAGTGATAA--G-T-G----GCTACACTTATCTGATCAAGAAAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
*
35972 AAAGTGAT-AG-G-T-G----GCTACACTTATCTGATC-AGGGAC
1 -AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
36008 AAGTGATAAGTGAT
1 AAGTGATAAGTGAT
36022 CATACGTAAG
Statistics
Matches: 201, Mismatches: 8, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
35 7 0.03
36 7 0.03
37 89 0.44
38 1 0.00
42 1 0.00
43 1 0.00
44 1 0.00
45 42 0.21
46 50 0.25
47 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (44 bp):
AAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGAGAC
Found at i:35780 original size:52 final size:47
Alignment explanation
Indices: 35695--35910 Score: 244
Period size: 46 Copynumber: 4.6 Consensus size: 47
35685 TTTGAGTACT
* * * *
35695 TCTGATCAAGTGA-TAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
35741 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGAC-A----AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
35793 TCTGATCAAGTG--AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGAGACAAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
35838 TCTGATCAAGAGAC-AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAAGTGATAAGTGATAGCTTCAGCTACACTTA
35884 TCTGATCAAGAGAC-AAAGTGATAAGTG
1 TCTGATCAAGAGACAAAAGTGATAAGTG
35911 GCTACACTTA
Statistics
Matches: 151, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
45 42 0.28
46 69 0.46
49 1 0.01
52 39 0.26
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (47 bp):
TCTGATCAAGAGACAAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:35803 original size:45 final size:46
Alignment explanation
Indices: 35761--35910 Score: 248
Period size: 46 Copynumber: 3.3 Consensus size: 46
35751 TGACAAGTGG
* *
35761 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA-
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
35806 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
** *
35852 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
35898 AAAGTGATAAGTG
1 AAAGTGATAAGTG
35911 GCTACACTTA
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 43 0.43
46 56 0.57
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
Found at i:35918 original size:37 final size:37
Alignment explanation
Indices: 35874--36019 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
35864 GATAGCTTTA
*
35874 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
35911 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
35948 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
35985 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
36020 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:37803 original size:72 final size:72
Alignment explanation
Indices: 37711--37855 Score: 195
Period size: 72 Copynumber: 2.0 Consensus size: 72
37701 CCGAAAAAGC
* * *
37711 ATCATTAATTCACAAGTTGAAGACAGACAAAAGTGA-ATGGTAATTAATTAATATA-AAAGGGGG
1 ATCATTAATTCACAAGTTGAAGAAAGAC-AAAGT-ATACGGTAATTAATTAATATAGAAAGGAGG
*
37774 TTAAGGCGA
64 TTAAGACGA
* * *
37783 ATCATTAATTCATAGGTTGAAGAAAGACAAAGTATACGGTATTTAATTAATATAGAAAGGAGGTT
1 ATCATTAATTCACAAGTTGAAGAAAGACAAAGTATACGGTAATTAATTAATATAGAAAGGAGGTT
37848 AAGACGA
66 AAGACGA
37855 A
1 A
37856 GATGAAGATT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
70 1 0.02
71 22 0.34
72 41 0.64
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (72 bp):
ATCATTAATTCACAAGTTGAAGAAAGACAAAGTATACGGTAATTAATTAATATAGAAAGGAGGTT
AAGACGA
Found at i:44307 original size:3 final size:3
Alignment explanation
Indices: 44299--44338 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
44289 TTTTGCACAC
44299 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44339 AGCAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:50534 original size:11 final size:12
Alignment explanation
Indices: 50509--50537 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
50499 ATATTTCTAG
50509 AAAAAGAAGGAA
1 AAAAAGAAGGAA
50521 AAAAAGAAGGAA
1 AAAAAGAAGGAA
50533 AAAAA
1 AAAAA
50538 TAAAGTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGGAA
Found at i:53759 original size:94 final size:94
Alignment explanation
Indices: 53607--53795 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
53597 CCATATCATA
53607 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
1 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
*
53672 TAAAGTTTCAACTCTCTTCTTTTTTATGC
66 TAAAGTTTCAACTCTCTTCCTTTTTATGC
*
53701 TTTCATATCCCTTGTTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
1 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
*
53766 TAAAGTTTCAGCTCTCTTCCTTTTTATGC
66 TAAAGTTTCAACTCTCTTCCTTTTTATGC
53795 T
1 T
53796 CTCCACTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (94 bp):
TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
TAAAGTTTCAACTCTCTTCCTTTTTATGC
Found at i:59883 original size:3 final size:3
Alignment explanation
Indices: 59877--59903 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
59867 AATATTCTTC
59877 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
59904 CCAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62943 original size:37 final size:37
Alignment explanation
Indices: 62853--62933 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
62843 TATACATTTG
* *
62853 AAAATGTTAGAAGTTAGATC-TTTGGGAGAAATTTTT
1 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
62889 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
1 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
*
62926 AAAGTGTT
1 AAAATGTT
62934 GTTTATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 18 0.44
37 23 0.56
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (37 bp):
AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
Found at i:63924 original size:17 final size:16
Alignment explanation
Indices: 63900--63940 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
63890 ATAATAATAA
63900 TATAATTTTAT-TATTT
1 TATAATTTTATATA-TT
63916 TAGTAA-TTTATATATT
1 TA-TAATTTTATATATT
63932 TATAATTTT
1 TATAATTTT
63941 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:63970 original size:29 final size:29
Alignment explanation
Indices: 63937--64002 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
63927 ATATTTATAA
*
63937 TTTTTAA-AAAATTAAATTAAAATTTTATT
1 TTTTTAAGAAAA-TAAAATAAAATTTTATT
* *
63966 TTTTTAAGAGAATAAAATATAATTTTATT
1 TTTTTAAGAAAATAAAATAAAATTTTATT
63995 TTTATTAA
1 TTT-TTAA
64003 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTTAAGAAAATAAAATAAAATTTTATT
Found at i:68419 original size:15 final size:17
Alignment explanation
Indices: 68389--68421 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
68379 AAAATAAAAA
68389 AATTATATATATACATG
1 AATTATATATATACATG
68406 AATT-TATA-ATACATG
1 AATTATATATATACATG
68421 A
1 A
68422 TCCTCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AATTATATATATACATG
Found at i:70569 original size:31 final size:31
Alignment explanation
Indices: 70509--70604 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
70499 ACTTAGCAAC
* *
70509 TCAGTGACTTAAATTAAAAA-ATGCAAATAGT
1 TCAGTGACTTAAA-TAAAAACTTTCAAATAGT
* ** **
70540 TTAGTGTTTTAAATAAAAACTTTTGAATAGT
1 TCAGTGACTTAAATAAAAACTTTCAAATAGT
*
70571 TCAGTGACTTAAATGAAAACTTTCAAATAGT
1 TCAGTGACTTAAATAAAAACTTTCAAATAGT
70602 TCA
1 TCA
70605 ATGATCATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
30 6 0.12
31 45 0.88
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TCAGTGACTTAAATAAAAACTTTCAAATAGT
Found at i:72113 original size:18 final size:18
Alignment explanation
Indices: 72090--72131 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
72080 TTTCTTTTTT
72090 AGTTGCAAAACAAGTTTC
1 AGTTGCAAAACAAGTTTC
72108 AGTTGCAAAACAAGTTTC
1 AGTTGCAAAACAAGTTTC
72126 AGTTGC
1 AGTTGC
72132 CACTTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (18 bp):
AGTTGCAAAACAAGTTTC
Found at i:91195 original size:28 final size:28
Alignment explanation
Indices: 91155--91220 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
91145 AATAAAGATA
*
91155 AAATTATATTTTAATACC-TTAAAATAAT
1 AAATTATAATTTAAT-CCTTTAAAATAAT
* *
91183 AAATTTTAATTTAATCCTTTAAAATTAT
1 AAATTATAATTTAATCCTTTAAAATAAT
91211 AAATATATAA
1 AAAT-TATAA
91221 ATAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.06
28 26 0.81
29 4 0.12
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATTATAATTTAATCCTTTAAAATAAT
Found at i:92710 original size:31 final size:31
Alignment explanation
Indices: 92675--92745 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
92665 ATTGATGCAA
92675 TATACATATAAAAAATTAA-TTTTACTTCAAT
1 TATACATATAAAAAATTAATTTTTA-TTCAAT
*** *
92706 TATACATATAAATTTTTAATTTTTATTTAAT
1 TATACATATAAAAAATTAATTTTTATTCAAT
92737 TATACATAT
1 TATACATAT
92746 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (31 bp):
TATACATATAAAAAATTAATTTTTATTCAAT
Found at i:97574 original size:20 final size:20
Alignment explanation
Indices: 97536--97575 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
97526 AAATATTTTA
*
97536 TTAACTAATAATTATAATTT
1 TTAACTAATAATTACAATTT
97556 TTAACTAAATAATT-CAATTT
1 TTAACT-AATAATTACAATTT
97576 AAAGGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAACTAATAATTACAATTT
Found at i:104109 original size:15 final size:15
Alignment explanation
Indices: 104090--104132 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
104080 TTGTTTATCA
104090 ATTTCATGTTTACTGG
1 ATTTCATGTTTA-TGG
* *
104106 -TTTCGTGTTCATGG
1 ATTTCATGTTTATGG
104120 ATTTCATGTTTAT
1 ATTTCATGTTTAT
104133 CAGTTTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (15 bp):
ATTTCATGTTTATGG
Found at i:108421 original size:111 final size:111
Alignment explanation
Indices: 108227--108557 Score: 574
Period size: 111 Copynumber: 3.0 Consensus size: 111
108217 TTCGTTTTAC
* *
108227 TTACTGTGAAGCTTCATAAAAATTAAAATTTCTAACTTCCGTCTCATGAAAAAAAATTCTCTCCT
1 TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCTCCT
*
108292 TATTTGCAA-TTTAACCCGACTTGACTCCCAAATGAATCGAATCTAG
66 TATTT-AAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATCTAG
* *
108338 TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCTGTCTCATGAAAAAAAATTATCTCCT
1 TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCTCCT
*
108403 TATTTAAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATGTAG
66 TATTTAAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATCTAG
*
108449 TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCTCTT
1 TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCTCCT
*
108514 TATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATCT
66 TATTTAAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATCT
108558 GAATGCACCT
Statistics
Matches: 208, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
110 2 0.01
111 206 0.99
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (111 bp):
TTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCTCCT
TATTTAAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATCTAG
Found at i:111001 original size:13 final size:13
Alignment explanation
Indices: 110983--111008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110973 CAAAAATAAC
110983 ATATATAATAAGA
1 ATATATAATAAGA
110996 ATATATAATAAGA
1 ATATATAATAAGA
111009 TTATTGTTTA
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATATATAATAAGA
Found at i:113523 original size:24 final size:24
Alignment explanation
Indices: 113491--113538 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
113481 TCACTTACAG
113491 ATGACTTTCATGACATGAAAGAAT
1 ATGACTTTCATGACATGAAAGAAT
113515 ATGACTTTCATGACATGAAAGAAT
1 ATGACTTTCATGACATGAAAGAAT
113539 GACGCCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (24 bp):
ATGACTTTCATGACATGAAAGAAT
Found at i:115468 original size:24 final size:24
Alignment explanation
Indices: 115436--115485 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
115426 TCTAATTTAA
115436 GATAATTTAGAATCAATAAAATTT
1 GATAATTTAGAATCAATAAAATTT
115460 GATAATTTAGAATCAATAAAATTT
1 GATAATTTAGAATCAATAAAATTT
115484 GA
1 GA
115486 GGTTTTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (24 bp):
GATAATTTAGAATCAATAAAATTT
Found at i:119102 original size:87 final size:87
Alignment explanation
Indices: 119000--119303 Score: 428
Period size: 87 Copynumber: 3.5 Consensus size: 87
118990 GATCTTTTAT
* * ** * *
119000 TTTAACCCGCTCCACTGTAGTCGATGGAGGCAAGGCTTTGTTTTTGATCAGCTTCACTGTTAACG
1 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACG
*
119065 CAGGAAGGCAAGATCTGCAATC
66 CAGGAAGGCAAGATCTGCTATC
* *
119087 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAACG
1 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACG
* *
119152 CAGGAATGCAAGATTTGCTATC
66 CAGGAAGGCAAGATCTGCTATC
* ** * * *
119174 TTCAACCAGCTCCACTATAATCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTATTAACA
1 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACG
*
119239 CAAGAAGGCAAGATCTGCTATC
66 CAGGAAGGCAAGATCTGCTATC
* *
119261 TTAAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
119304 AGTCCATTAA
Statistics
Matches: 190, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 190 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
TTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACG
CAGGAAGGCAAGATCTGCTATC
Found at i:119233 original size:42 final size:41
Alignment explanation
Indices: 119108--119233 Score: 94
Period size: 42 Copynumber: 3.0 Consensus size: 41
119098 CCACTGCAAC
* * *
119108 CGATGGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAA
1 CGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACT-ATAA
* * * * * *
119150 CGCA-GGAATGCAA-GATTTGCTATCTTCAACCAGCTCCACTATAA
1 CG-ATGG-AGGCAAGGCTTTG-T-T-TTCGATCTGCTTCACTATAA
119194 TCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTAT
1 -CGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTAT
119234 TAACACAAGA
Statistics
Matches: 61, Mismatches: 15, Indels: 16
0.66 0.16 0.17
Matches are distributed among these distances:
42 23 0.38
43 8 0.13
44 11 0.18
45 19 0.31
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (41 bp):
CGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTATAA
Found at i:119820 original size:13 final size:13
Alignment explanation
Indices: 119797--119838 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
119787 ATTTTTACTC
119797 TTTCATTTTTCTTT
1 TTTCA-TTTTCTTT
*
119811 TTTCATTTTCGTT
1 TTTCATTTTCTTT
*
119824 TTTCA-TCTCTTT
1 TTTCATTTTCTTT
119836 TTT
1 TTT
119839 TGTTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:120218 original size:6 final size:6
Alignment explanation
Indices: 120207--120256 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
120197 CCTTGACCTC
* * * *
120207 TCCTTT TCCTTT TCCTTT TTCTTT TTCTTT TCTCTTT TCATTT TCATTT
1 TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TC-CTTT TCCTTT TCCTTT
120256 T
1 T
120257 GACTTTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (6 bp):
TCCTTT
Found at i:120309 original size:34 final size:34
Alignment explanation
Indices: 120229--120314 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
120219 TCCTTTTTCT
* *
120229 TTTTCTTTTCTCTTTTCATTTTCATTTTGACTTTGA
1 TTTTCTTTTTTCTTTT--TCTTCATTTTGACTTTGA
** *
120265 TTTTGATTTTTCTTTTTCTTCTTTTTGACTTTGA
1 TTTTCTTTTTTCTTTTTCTTCATTTTGACTTTGA
120299 TTTTCTTTTTT-TTTTT
1 TTTTCTTTTTTCTTTTT
120315 GAATTGGATC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 5 0.12
34 25 0.58
36 13 0.30
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.73
Consensus pattern (34 bp):
TTTTCTTTTTTCTTTTTCTTCATTTTGACTTTGA
Found at i:126421 original size:17 final size:19
Alignment explanation
Indices: 126391--126425 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
126381 GCGCAAATAC
126391 ATATGAATATTATATAAAT
1 ATATGAATATTATATAAAT
126410 ATAT-AATA-TATATAAA
1 ATATGAATATTATATAAA
126426 ATGTGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
ATATGAATATTATATAAAT
Found at i:142533 original size:19 final size:19
Alignment explanation
Indices: 142496--142533 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
142486 AAAAATAACA
*
142496 TTTTTTATATTTAATATAT
1 TTTTTTATATTTAAAATAT
142515 TTTTTTA-ATTTCAAAATAT
1 TTTTTTATATTT-AAAATAT
142534 ATAGTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTATATTTAAAATAT
Found at i:146029 original size:18 final size:17
Alignment explanation
Indices: 145990--146039 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
145980 TCAAAAAATA
145990 TATTTTTATACTAA-ATT
1 TATTTTTATAC-AATATT
*
146007 TATTTTTATGCAATATT
1 TATTTTTATACAATATT
146024 TGATTTTTATACAATA
1 T-ATTTTTATACAATA
146040 AAATATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 14 0.48
18 13 0.45
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (17 bp):
TATTTTTATACAATATT
Found at i:148653 original size:31 final size:32
Alignment explanation
Indices: 148607--148666 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
148597 TTTATATTTA
*
148607 TATTTATAG-TGTTTTTAAATTTTAAAATGTG
1 TATTTAGAGTTGTTTTTAAATTTTAAAATGTG
* *
148638 TATTTAGAGTTTTTTTTTAATTTTAAAAT
1 TATTTAGAGTTGTTTTTAAATTTTAAAAT
148667 TTCATATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (32 bp):
TATTTAGAGTTGTTTTTAAATTTTAAAATGTG
Found at i:152096 original size:26 final size:26
Alignment explanation
Indices: 152067--152118 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
152057 AAGTGGTTTG
152067 AGTTAAACAATACTAGTTTGAAATCT
1 AGTTAAACAATACTAGTTTGAAATCT
152093 AGTTAAACAATACTAGTTTGAAATCT
1 AGTTAAACAATACTAGTTTGAAATCT
152119 TGAAGGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (26 bp):
AGTTAAACAATACTAGTTTGAAATCT
Found at i:152110 original size:14 final size:14
Alignment explanation
Indices: 152067--152110 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
152057 AAGTGGTTTG
152067 AGTTAAACAATACT
1 AGTTAAACAATACT
**
152081 AGTTTGA-AAT-CT
1 AGTTAAACAATACT
152093 AGTTAAACAATACT
1 AGTTAAACAATACT
152107 AGTT
1 AGTT
152111 TGAAATCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 7 0.29
13 6 0.25
14 11 0.46
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (14 bp):
AGTTAAACAATACT
Found at i:156283 original size:18 final size:16
Alignment explanation
Indices: 156244--156293 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
156234 GTAATGAGCG
*
156244 TAAAAATATAATTAATA
1 TAAAAATAT-ATTAAAA
156261 TAAAAATATATTAAAA
1 TAAAAATATATTAAAA
*
156277 TGAAAAACTCTATTAAA
1 T-AAAAA-TATATTAAA
156294 CTTGTGAGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAAATATATTAAAA
Found at i:174231 original size:23 final size:24
Alignment explanation
Indices: 174187--174231 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
174177 AAATACAATG
** *
174187 AAAAATGTTAATTTATTTTTGAAA
1 AAAAATGTTAATCCATTGTTGAAA
174211 AAAAATGTTAATCCA-TGTTGA
1 AAAAATGTTAATCCATTGTTGA
174232 GTGTAATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (24 bp):
AAAAATGTTAATCCATTGTTGAAA
Found at i:179318 original size:27 final size:26
Alignment explanation
Indices: 179275--179325 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
179265 CACATCCCTC
179275 ATTTTAAAAAAATTATATTATATATT
1 ATTTTAAAAAAATTATATTATATATT
179301 ATTTTAATTAAAAA-TATATTATATA
1 ATTTTAA--AAAAATTATATTATATA
179326 ACATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.30
27 11 0.48
28 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTTAAAAAAATTATATTATATATT
Found at i:179777 original size:16 final size:16
Alignment explanation
Indices: 179743--179775 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
179733 TAGCAATGAC
179743 ATTTAAAATTTTTAAA
1 ATTTAAAATTTTTAAA
179759 ATTTATAAATTTTTAAA
1 ATTTA-AAATTTTTAAA
179776 TTAGTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTAAAATTTTTAAA
Found at i:179828 original size:8 final size:9
Alignment explanation
Indices: 179801--179848 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
179791 TTACACTTTT
*
179801 AATTTTAAA
1 AATTATAAA
*
179810 AATCATAAA
1 AATTATAAA
179819 AATTATAAA
1 AATTATAAA
179828 AATTATAAA
1 AATTATAAA
179837 AATTATAAA
1 AATTATAAA
179846 AAT
1 AAT
179849 ATTTAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:185761 original size:31 final size:31
Alignment explanation
Indices: 185693--185763 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
185683 TTTACCCTTT
* *
185693 ATTTT-AATTTGGTACTTGTGTTTTGTTTTA
1 ATTTTCAATTTGGTACATGAGTTTTGTTTTA
* * *
185723 ATATTCAATTTGGTACATGAGTTTTTTTTTC
1 ATTTTCAATTTGGTACATGAGTTTTGTTTTA
*
185754 TTTTTCAATT
1 ATTTTCAATT
185764 AAGTGTTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.61
Consensus pattern (31 bp):
ATTTTCAATTTGGTACATGAGTTTTGTTTTA
Found at i:187267 original size:14 final size:14
Alignment explanation
Indices: 187248--187280 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
187238 TTATAGGTGT
187248 AAAGGTGAAGTTAA
1 AAAGGTGAAGTTAA
187262 AAAGGTGAAGTTAA
1 AAAGGTGAAGTTAA
187276 AAAGG
1 AAAGG
187281 GGAAATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.18
Consensus pattern (14 bp):
AAAGGTGAAGTTAA
Found at i:187842 original size:13 final size:13
Alignment explanation
Indices: 187824--187848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187814 ATTTACCATT
187824 TTTTAAAAAATAA
1 TTTTAAAAAATAA
187837 TTTTAAAAAATA
1 TTTTAAAAAATA
187849 CAGTACTTTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:195759 original size:27 final size:27
Alignment explanation
Indices: 195721--195773 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
195711 TGGGTATTGC
195721 CGTGGCTGTTGCTGAGCAGGTGGTGGT
1 CGTGGCTGTTGCTGAGCAGGTGGTGGT
195748 CGTGGCTGTTGCTGAGCAGGTGGTGG
1 CGTGGCTGTTGCTGAGCAGGTGGTGG
195774 GTATTGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.08, C:0.15, G:0.49, T:0.28
Consensus pattern (27 bp):
CGTGGCTGTTGCTGAGCAGGTGGTGGT
Found at i:195791 original size:33 final size:33
Alignment explanation
Indices: 195640--195791 Score: 156
Period size: 33 Copynumber: 4.8 Consensus size: 33
195630 TTGTTGTGAT
* *
195640 GGTGGTGGGTACTGCGGAGGCTGCTG-TAGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGCT-GAGCA
* * * *
195673 GGTAGTGGGTACTGCGGAGGCTGCTGTTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGCTGAGCA
* *
195706 GGTGGTGGGTATTGCCGTGGCTGTTGCTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGCTGAGCA
195739 GGTGGT-GG---T-C-GTGGCTGTTGCTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGCTGAGCA
* *
195766 GGTGGTGGGTATTGCGGTGGTTGTTG
1 GGTGGTGGGTACTGCGGTGGCTGTTG
195792 TGGCGGGAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
27 23 0.22
28 3 0.03
29 1 0.01
31 1 0.01
32 3 0.03
33 72 0.69
34 1 0.01
ACGTcount: A:0.11, C:0.13, G:0.48, T:0.28
Consensus pattern (33 bp):
GGTGGTGGGTACTGCGGTGGCTGTTGCTGAGCA
Found at i:195794 original size:24 final size:24
Alignment explanation
Indices: 195767--195815 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
195757 TGCTGAGCAG
* * *
195767 GTGGTGGGTATTGCGGTGGTTGTT
1 GTGGCGGGAATTGAGGTGGTTGTT
*
195791 GTGGCGGGAATTGAGGTTGTTGTT
1 GTGGCGGGAATTGAGGTGGTTGTT
195815 G
1 G
195816 GCCTTGTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.04, G:0.49, T:0.39
Consensus pattern (24 bp):
GTGGCGGGAATTGAGGTGGTTGTT
Found at i:207365 original size:13 final size:13
Alignment explanation
Indices: 207347--207371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207337 CGAAAATCGA
207347 AAAAAGGAAGAGC
1 AAAAAGGAAGAGC
207360 AAAAAGGAAGAG
1 AAAAAGGAAGAG
207372 TAGAATTATG
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:0.64, C:0.04, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAGAGC
Found at i:214433 original size:21 final size:21
Alignment explanation
Indices: 214394--214434 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
214384 ATCCAATTTT
*
214394 TTATTTTAGTCTATATTGTAC
1 TTATTTTAATCTATATTGTAC
214415 TTATTCTTAATCTAT-TTGTA
1 TTATT-TTAATCTATATTGTA
214435 TTGTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (21 bp):
TTATTTTAATCTATATTGTAC
Found at i:214909 original size:22 final size:21
Alignment explanation
Indices: 214884--214924 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
214874 ATTGAAAATT
*
214884 AAAATAATTAAAAATTAGAATC
1 AAAAT-ATTAAAAAATAGAATC
*
214906 AAAATTTTAAAAAATAGAA
1 AAAATATTAAAAAATAGAA
214925 GTTAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAATATTAAAAAATAGAATC
Found at i:219718 original size:20 final size:20
Alignment explanation
Indices: 219685--219724 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
219675 AAATTAAGAT
219685 ATACAAAAACATATAAATAC
1 ATACAAAAACATATAAATAC
* * *
219705 ATACATAAATATATATATAC
1 ATACAAAAACATATAAATAC
219725 TTATGAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (20 bp):
ATACAAAAACATATAAATAC
Found at i:219754 original size:36 final size:35
Alignment explanation
Indices: 219713--219794 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 35
219703 ACATACATAA
*
219713 ATATATATATACTTATGAAAATAAAAATAT-GTATATGT
1 ATATATATATA--TAT-AAAA-AAAAATATAGTATACGT
*
219751 ATATAAATATATATAAAAAAAAATATGAGTATACGT
1 ATATATATATATATAAAAAAAAATAT-AGTATACGT
219787 ATATATAT
1 ATATATAT
219795 TAAACAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
34 8 0.21
35 4 0.10
36 17 0.44
38 10 0.26
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (35 bp):
ATATATATATATATAAAAAAAAATATAGTATACGT
Found at i:219867 original size:22 final size:23
Alignment explanation
Indices: 219841--219889 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
219831 TACAAGCACT
*
219841 TATA-TGATAATA-ATAAGATATA
1 TATATTGAAAATACATAAG-TATA
219863 TATATTTGAAAATACATAAGTATA
1 TATA-TTGAAAATACATAAGTATA
219887 TAT
1 TAT
219890 GAATAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
TATATTGAAAATACATAAGTATA
Found at i:219934 original size:3 final size:3
Alignment explanation
Indices: 219923--219987 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
219913 CAATAATACC
* * *
219923 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
219968 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
219988 AGTTAACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.98
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:221687 original size:43 final size:43
Alignment explanation
Indices: 221627--221742 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 43
221617 TTTTAATCCA
* * * *
221627 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAAC-TCAGGGAGATAAGATCACTGGCTTCAATCTG
* *
221670 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCACTGGCTTCAATCTG
221714 CTCCACTGTAACCTCAGGGAGATAAGATC
1 CTCCACTGTAA-CTCAGGGAGATAAGATC
221743 TGAAATTCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 24 0.38
44 39 0.62
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (43 bp):
CTCCACTGTAACTCAGGGAGATAAGATCACTGGCTTCAATCTG
Found at i:221782 original size:46 final size:45
Alignment explanation
Indices: 221659--222002 Score: 261
Period size: 46 Copynumber: 7.8 Consensus size: 45
221649 TAGGATAGTG
* * * *
221659 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CT
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** * *
221702 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
221749 TCTTTGGTCTGTTCCACCGTAATCTCAGGGAGATAAGATCTGAAAT
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* * *
221795 TCTTTGGTCTGTTCCACCGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * *
221838 --TGTGATCT-TCTCTACTGTAA-CTTCAGAGAGATAAGATC-----
1 TCTTTGATCTGT-TCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * * * *
221876 -CTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* *
221918 ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
221965 TCTTTGGTCTGTTCCACTGTAATCTTAGGGAGATAAGA
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGA
222003 CCTGTATTAT
Statistics
Matches: 244, Mismatches: 39, Indels: 32
0.77 0.12 0.10
Matches are distributed among these distances:
39 25 0.10
40 3 0.01
41 28 0.11
44 70 0.29
45 1 0.00
46 114 0.47
47 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:230839 original size:23 final size:23
Alignment explanation
Indices: 230813--230857 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
230803 CAAACCTGTG
*
230813 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
230836 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
230858 TTGAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:232590 original size:30 final size:31
Alignment explanation
Indices: 232535--232596 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
232525 TAGTAATTAT
*
232535 AAAATTACATTTTATCCCCTAAAAATAATAA
1 AAAATTACATTTAATCCCCTAAAAATAATAA
** *
232566 AAAATTA-ATTTAATCCTTTAAAAATTATAA
1 AAAATTACATTTAATCCCCTAAAAATAATAA
232596 A
1 A
232597 GATATAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATTACATTTAATCCCCTAAAAATAATAA
Found at i:233793 original size:26 final size:24
Alignment explanation
Indices: 233763--233812 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
233753 AAATAAAAAA
*
233763 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
233789 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
233813 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:234966 original size:22 final size:23
Alignment explanation
Indices: 234941--234986 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
234931 CAACCAAACG
234941 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
234963 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
234986 A
1 A
234987 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:234992 original size:23 final size:23
Alignment explanation
Indices: 234948--234992 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
234938 ACGAATTCAA
*
234948 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
234971 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
234993 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:236638 original size:47 final size:47
Alignment explanation
Indices: 236569--236664 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
236559 CTTATACCGT
236569 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
1 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
236616 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
1 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
236663 TT
1 TT
236665 CNNNNNNNNN
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:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (47 bp):
TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
Found at i:238785 original size:44 final size:46
Alignment explanation
Indices: 238719--238854 Score: 154
Period size: 44 Copynumber: 3.0 Consensus size: 46
238709 GAGAGATAAG
* * * * * *
238719 ATCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 ATCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
*
238763 ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAT
1 ATCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * *
238809 -TCTTTG-TCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGTAT
1 ATCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
238853 AT
1 AT
238855 GAACCTAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
44 68 0.87
45 8 0.10
46 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (46 bp):
ATCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:251357 original size:20 final size:20
Alignment explanation
Indices: 251324--251363 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
251314 AAATTAAGAT
251324 ATACAAAAACATATAAATAC
1 ATACAAAAACATATAAATAC
* * *
251344 ATACATAAATATATATATAC
1 ATACAAAAACATATAAATAC
251364 TTATGAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (20 bp):
ATACAAAAACATATAAATAC
Found at i:251504 original size:22 final size:23
Alignment explanation
Indices: 251478--251526 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
251468 TACAAGCACT
*
251478 TATA-TGATAATA-ATAAGATATA
1 TATATTGAAAATACATAAG-TATA
251500 TATATTTGAAAATACATAAGTATA
1 TATA-TTGAAAATACATAAGTATA
251524 TAT
1 TAT
251527 GAATAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
TATATTGAAAATACATAAGTATA
Found at i:251571 original size:3 final size:3
Alignment explanation
Indices: 251560--251615 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
251550 CAATAATACC
* * *
251560 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
251605 AAT AAT AAT AA
1 AAT AAT AAT AA
251616 AGTTAACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:255713 original size:35 final size:35
Alignment explanation
Indices: 255674--255747 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
255664 CGTAAATAAC
*
255674 CATGCATTTCCATGTGTTTTAGCTTTTGTATTTGG
1 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
255709 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
1 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
255744 CATG
1 CATG
255748 TATCTTGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (35 bp):
CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
Found at i:258920 original size:4 final size:4
Alignment explanation
Indices: 258913--258967 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
258903 TACATACATA
* * * * * *
258913 TATG TATG TATG TATC TATG CATG TATA TATA TAGG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
258961 TATG TAT
1 TATG TAT
258968 ATGTGCTGAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:258939 original size:20 final size:20
Alignment explanation
Indices: 258914--258967 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
258904 ACATACATAT
258914 ATGTATGTATGTATCTATGC
1 ATGTATGTATGTATCTATGC
* * **
258934 ATGTATATATATAGGTATGC
1 ATGTATGTATGTATCTATGC
258954 ATGTATGTATGTAT
1 ATGTATGTATGTAT
258968 ATGTGCTGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (20 bp):
ATGTATGTATGTATCTATGC
Found at i:258951 original size:28 final size:28
Alignment explanation
Indices: 258910--258969 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
258900 ATATACATAC
* * *
258910 ATATATGTATGTATGTATCTATGCATGT
1 ATATATATAGGTATGCATCTATGCATGT
* *
258938 ATATATATAGGTATGCATGTATGTATGT
1 ATATATATAGGTATGCATCTATGCATGT
258966 ATAT
1 ATAT
258970 GTGCTGATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (28 bp):
ATATATATAGGTATGCATCTATGCATGT
Found at i:260847 original size:31 final size:30
Alignment explanation
Indices: 260789--260850 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
260779 GGATTGTACC
*
260789 TAAATTAATTTCAAATTAAATATTTAAGTT
1 TAAATTAATTTCAAATTAAATACTTAAGTT
*
260819 TAAATTTAATGTTC-AATTTAATACTTAAGTT
1 TAAA-TTAAT-TTCAAATTAAATACTTAAGTT
260850 T
1 T
260851 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 21 0.75
32 3 0.11
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
TAAATTAATTTCAAATTAAATACTTAAGTT
Found at i:266884 original size:11 final size:11
Alignment explanation
Indices: 266868--266892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
266858 TATAGATTTC
266868 ATTAATAAAAA
1 ATTAATAAAAA
266879 ATTAATAAAAA
1 ATTAATAAAAA
266890 ATT
1 ATT
266893 TCTGCACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAATAAAAA
Found at i:274982 original size:18 final size:18
Alignment explanation
Indices: 274959--275001 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
274949 TCAATTTTAA
*
274959 AAATTATAAAATATTATT
1 AAATTATAAAATATAATT
274977 AAATTATAAAATATAATT
1 AAATTATAAAATATAATT
274995 AAATTAT
1 AAATTAT
275002 TCAAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTATAAAATATAATT
Found at i:281662 original size:21 final size:22
Alignment explanation
Indices: 281630--281670 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
281620 AATACTACAA
*
281630 TTTTAGGTGAGATAGTAAGGGT
1 TTTTAGGTGAGAAAGTAAGGGT
281652 TTTTAGG-GAGAAAGTAAGG
1 TTTTAGGTGAGAAAGTAAGG
281671 ATCTTCACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.37, T:0.32
Consensus pattern (22 bp):
TTTTAGGTGAGAAAGTAAGGGT
Found at i:283816 original size:23 final size:23
Alignment explanation
Indices: 283790--283837 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
283780 AAATACACTA
283790 AATTATTTT-TATATTG-AATATAT
1 AATT-TTTTGTATA-TGCAATATAT
283813 AATTTTTTGTATATGCAATATAT
1 AATTTTTTGTATATGCAATATAT
283836 AA
1 AA
283838 ACATAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (23 bp):
AATTTTTTGTATATGCAATATAT
Found at i:285001 original size:13 final size:13
Alignment explanation
Indices: 284983--285007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284973 GTTTTTTCTT
284983 AATTTGATACTTA
1 AATTTGATACTTA
284996 AATTTGATACTT
1 AATTTGATACTT
285008 TTTTTTTAAT
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTGATACTTA
Found at i:285514 original size:31 final size:31
Alignment explanation
Indices: 285456--285566 Score: 118
Period size: 31 Copynumber: 3.5 Consensus size: 31
285446 GACCCTCTAA
* * *
285456 AAATTTAAGTATCAACTTAAGAAAAAATGTC
1 AAATTTAAGTACCAAATTAAGAAAAAATATC
* *
285487 AAGTTT-AGATACCAAATTAAGAGAAAATATC
1 AAATTTAAG-TACCAAATTAAGAAAAAATATC
*
285518 AAATTTAAGTACCAAATTAA-AAAATATATATT
1 AAATTTAAGTACCAAATTAAGAAAA-A-ATATC
*
285550 AAATTTAAATACCAAAT
1 AAATTTAAGTACCAAAT
285567 ATTATATTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
30 5 0.07
31 40 0.60
32 22 0.33
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (31 bp):
AAATTTAAGTACCAAATTAAGAAAAAATATC
Found at i:288182 original size:21 final size:21
Alignment explanation
Indices: 288149--288188 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
288139 TTTTAGGCAA
* *
288149 TTTTTTTATATTCTTTTTTAC
1 TTTTTTTACATTCTCTTTTAC
*
288170 TTTTTTTCCATTCTCTTTT
1 TTTTTTTACATTCTCTTTT
288189 GCTTCCCCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTACATTCTCTTTTAC
Found at i:289142 original size:3 final size:3
Alignment explanation
Indices: 289134--289158 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
289124 TCAACATCAA
289134 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
289159 TAAAATGGAT
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:295170 original size:16 final size:17
Alignment explanation
Indices: 295149--295182 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
295139 AATTAGAGAA
295149 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
295165 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
295182 T
1 T
295183 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:299151 original size:11 final size:11
Alignment explanation
Indices: 299124--299190 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
299114 AAATATTATA
*
299124 ATTAATTTAAAT
1 ATTAA-TTAATT
299136 A-TAATTAATT
1 ATTAATTAATT
299146 ATTAATTAATT
1 ATTAATTAATT
*
299157 A-TAA-CAATT
1 ATTAATTAATT
*
299166 ATAAATCTATATT
1 ATTAAT-TA-ATT
*
299179 ATTATTTAATT
1 ATTAATTAATT
299190 A
1 A
299191 GTGTCATAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.11
10 11 0.25
11 17 0.39
12 4 0.09
13 7 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:299158 original size:36 final size:37
Alignment explanation
Indices: 299118--299190 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
299108 ATAAAAAAAT
*
299118 ATTATAATTAATT-TAAATATA-ATTAATTA-TTAATTA
1 ATTATAA-CAATTATAAATATATATT-ATTATTTAATTA
*
299154 ATTATAACAATTATAAATCTATATTATTATTTAATTA
1 ATTATAACAATTATAAATATATATTATTATTTAATTA
299191 GTGTCATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.12
36 18 0.56
37 10 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTATAACAATTATAAATATATATTATTATTTAATTA
Found at i:305138 original size:7 final size:7
Alignment explanation
Indices: 305126--305197 Score: 72
Period size: 7 Copynumber: 10.3 Consensus size: 7
305116 CTAAAACTAC
305126 CACTTAT
1 CACTTAT
305133 CACTTAT
1 CACTTAT
305140 CACTTAT
1 CACTTAT
305147 CACTTAT
1 CACTTAT
*
305154 CACTTGT
1 CACTTAT
* *
305161 CGCTTGT
1 CACTTAT
* *
305168 CGCTTGT
1 CACTTAT
* *
305175 CGCTTGT
1 CACTTAT
305182 CACTTAT
1 CACTTAT
*
305189 CACTGAT
1 CACTTAT
305196 CA
1 CA
305198 GATAAGTGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.19, C:0.29, G:0.11, T:0.40
Consensus pattern (7 bp):
CACTTAT
Found at i:305152 original size:21 final size:21
Alignment explanation
Indices: 305126--305197 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
305116 CTAAAACTAC
*
305126 CACTTATCACTTATCACTTAT
1 CACTTATCACTTGTCACTTAT
* *
305147 CACTTATCACTTGTCGCTTGT
1 CACTTATCACTTGTCACTTAT
* * *
305168 CGCTTGTCGCTTGTCACTTAT
1 CACTTATCACTTGTCACTTAT
*
305189 CACTGATCA
1 CACTTATCA
305198 GATAAGTGTA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.11, T:0.40
Consensus pattern (21 bp):
CACTTATCACTTGTCACTTAT
Found at i:305817 original size:21 final size:21
Alignment explanation
Indices: 305793--305834 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
305783 CTTTTTATTC
*
305793 AATTAACTATCGAAACTTTAA
1 AATTAACTAACGAAACTTTAA
**
305814 AATTTCCTAACGAAACTTTAA
1 AATTAACTAACGAAACTTTAA
305835 TACTAACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (21 bp):
AATTAACTAACGAAACTTTAA
Found at i:315936 original size:53 final size:53
Alignment explanation
Indices: 315855--316005 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
315845 CTTACACGGT
* *
315855 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
315910 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
315963 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
316006 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:346127 original size:31 final size:30
Alignment explanation
Indices: 346092--346149 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
346082 TTATAAGTTG
346092 TTATATTTTTTAAAAATTAAAAATTTAATTT
1 TTATATTTTTT-AAAATTAAAAATTTAATTT
* *
346123 TTATATTTTTTAAATTTTAAAATTTAA
1 TTATATTTTTTAAAATTAAAAATTTAA
346150 GTTGAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATATTTTTTAAAATTAAAAATTTAATTT
Found at i:355349 original size:31 final size:31
Alignment explanation
Indices: 355305--355366 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
355295 TTTCTTAATT
**
355305 AATTTGAAAAAATACGAA-TTAGACATAAAAA
1 AATTTGAAAAAATAAAAAGTTAGA-ATAAAAA
355336 AATTT-AAAGAAATAAAAAGTTAGAATAAAAA
1 AATTTGAAA-AAATAAAAAGTTAGAATAAAAA
355367 TAAGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.11
31 19 0.70
32 5 0.19
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (31 bp):
AATTTGAAAAAATAAAAAGTTAGAATAAAAA
Found at i:356456 original size:21 final size:22
Alignment explanation
Indices: 356431--356478 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
356421 TTTAATTAGG
356431 AAATATATT-TTTAA-ATTATAA
1 AAATATATTATTTAATATT-TAA
356452 AAATATATTATTTAATATTTAA
1 AAATATATTATTTAATATTTAA
356474 AAATA
1 AAATA
356479 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.36
22 13 0.52
23 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATATTATTTAATATTTAA
Found at i:362050 original size:26 final size:24
Alignment explanation
Indices: 362020--362069 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
362010 AAATAAAAAA
*
362020 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
362046 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
362070 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:363310 original size:5 final size:5
Alignment explanation
Indices: 363300--363347 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
363290 CAATTAAACA
* * *
363300 TATAG TATAG TATAG TATAG TATAA TATAA TATAA TATAG TACTAG TA
1 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TA-TAG TA
363348 ATTGTATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (5 bp):
TATAG
Found at i:363389 original size:15 final size:17
Alignment explanation
Indices: 363362--363396 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
363352 TATGTAACCA
363362 AAAATTATAATTA-ATT
1 AAAATTATAATTATATT
363378 AAAATT-TAATTATATT
1 AAAATTATAATTATATT
363394 AAA
1 AAA
363397 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTATAATTATATT
Found at i:363389 original size:21 final size:20
Alignment explanation
Indices: 363364--363403 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
363354 TGTAACCAAA
*
363364 AATTATAATTAATTAAAATTT
1 AATTAT-ATTAAATAAAATTT
363385 AATTATATTAAATAAAATT
1 AATTATATTAAATAAAATT
363404 ATTAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTATATTAAATAAAATTT
Found at i:371884 original size:17 final size:17
Alignment explanation
Indices: 371862--371895 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
371852 ATCCACTAAT
*
371862 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
371879 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
371896 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:376522 original size:17 final size:17
Alignment explanation
Indices: 376500--376533 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
376490 ATCCACTAAT
*
376500 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
376517 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
376534 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:381504 original size:21 final size:22
Alignment explanation
Indices: 381472--381522 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
381462 TTTTAAACGA
381472 CTTAAA-TTTTACTCAAA-C-T
1 CTTAAATTTTTACTCAAATCTT
381491 CTTAATATTTTTACTCAAATCTT
1 CTTAA-ATTTTTACTCAAATCTT
381514 CTTAAATTT
1 CTTAAATTT
381523 CGAAAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.18
20 1 0.04
21 11 0.39
22 5 0.18
23 6 0.21
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTAAATTTTTACTCAAATCTT
Found at i:384338 original size:15 final size:15
Alignment explanation
Indices: 384320--384354 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
384310 TTTTTAGAGT
384320 GTTTTTTTTTATTTG-
1 GTTTTTTTTT-TTTGA
384335 GTTTTTTTTTTTTGA
1 GTTTTTTTTTTTTGA
384350 GTTTT
1 GTTTT
384355 ATTGGTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (15 bp):
GTTTTTTTTTTTTGA
Done.