Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 5 of 126
Found at i:1235306 original size:59 final size:59
Alignment explanation
Indices: 1235110--1235288 Score: 349
Period size: 59 Copynumber: 3.0 Consensus size: 59
1235100 TTTTTTTAAA
*
1235110 AAAAATTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1 AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1235169 AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1 AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1235228 AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1 AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
1235287 AA
1 AA
1235289 GACTATTCGG
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 119 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (59 bp):
AAAAGTTCTAATTTGAAGCGAGCCCACATTTGCCAGATGTGAGCTTGAGGATAACGAAG
Found at i:1235840 original size:23 final size:23
Alignment explanation
Indices: 1235814--1235870 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1235804 CTTCATTGGG
* *
1235814 TCATCCGGACGAGGCATCTCTTC
1 TCATCAGGACGAGGAATCTCTTC
1235837 TCATCAGGACGAGGAATCTCTTC
1 TCATCAGGACGAGGAATCTCTTC
*
1235860 TCATCGGGACG
1 TCATCAGGACG
1235871 TCAATGGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.25
Consensus pattern (23 bp):
TCATCAGGACGAGGAATCTCTTC
Found at i:1238798 original size:36 final size:35
Alignment explanation
Indices: 1238758--1238828 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1238748 GCTGGATCCG
*
1238758 AGTTTATAAGTACTACTAAAAATGCCTTTAATGGTT
1 AGTTTATAA-TACTACTAAAAATACCTTTAATGGTT
** *
1238794 AGTTTATAATTTTACTATAAATACCTTTAATGGTT
1 AGTTTATAATACTACTAAAAATACCTTTAATGGTT
1238829 GGCTTAGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (35 bp):
AGTTTATAATACTACTAAAAATACCTTTAATGGTT
Found at i:1247022 original size:12 final size:12
Alignment explanation
Indices: 1246984--1247026 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1246974 TATACTAAAA
*
1246984 ACATATACATAT
1 ACATACACATAT
* * *
1246996 ATATACATATTT
1 ACATACACATAT
1247008 ACATACACATAT
1 ACATACACATAT
1247020 ACATACA
1 ACATACA
1247027 TACCTGGCCG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.33
Consensus pattern (12 bp):
ACATACACATAT
Found at i:1247141 original size:4 final size:4
Alignment explanation
Indices: 1247132--1247161 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1247122 ACAATCTTTA
1247132 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
1247162 GCTGTGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1249775 original size:20 final size:20
Alignment explanation
Indices: 1249746--1249788 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1249736 AACAAAGGTC
*
1249746 TTATCTTTTTTATCCATAAA
1 TTATCATTTTTATCCATAAA
*
1249766 TTATCATTTTTCTCCATAAA
1 TTATCATTTTTATCCATAAA
1249786 TTA
1 TTA
1249789 CCCAATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATCATTTTTATCCATAAA
Found at i:1249799 original size:21 final size:20
Alignment explanation
Indices: 1249753--1249799 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1249743 GTCTTATCTT
* * *
1249753 TTTTATCCATAAATTATCAT
1 TTTTCTCCATAAATTACCAA
1249773 TTTTCTCCATAAATTACCCAA
1 TTTTCTCCATAAATTA-CCAA
1249794 TTTTCT
1 TTTTCT
1249800 TCAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTCTCCATAAATTACCAA
Found at i:1257290 original size:55 final size:55
Alignment explanation
Indices: 1257226--1257335 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
1257216 GACCTCTTGT
1257226 CACTACAAATGACTCTTTTAGTCAAAGATAAGCCACTACATCTAAATCATCACAA
1 CACTACAAATGACTCTTTTAGTCAAAGATAAGCCACTACATCTAAATCATCACAA
*
1257281 CACTACAAATGACTCTTTTTGTCAAAGATAAGCCACTACATCTAAATCATCACAA
1 CACTACAAATGACTCTTTTAGTCAAAGATAAGCCACTACATCTAAATCATCACAA
1257336 TATTAGAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (55 bp):
CACTACAAATGACTCTTTTAGTCAAAGATAAGCCACTACATCTAAATCATCACAA
Found at i:1258353 original size:17 final size:16
Alignment explanation
Indices: 1258333--1258364 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1258323 ATCACACTTG
1258333 AAAGAGAAACATAAAGT
1 AAAGAGAAAC-TAAAGT
1258350 AAAGAGAAACTAAAG
1 AAAGAGAAACTAAAG
1258365 CATGAAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.06, G:0.19, T:0.09
Consensus pattern (16 bp):
AAAGAGAAACTAAAGT
Found at i:1262806 original size:17 final size:18
Alignment explanation
Indices: 1262786--1262820 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1262776 TTTGAAGATA
*
1262786 TGTAATTTTAAAA-ATTT
1 TGTAATCTTAAAAGATTT
1262803 TGTAATCTTAAAAGATTT
1 TGTAATCTTAAAAGATTT
1262821 GATTTCGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (18 bp):
TGTAATCTTAAAAGATTT
Found at i:1262821 original size:17 final size:17
Alignment explanation
Indices: 1262780--1262821 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1262770 ATAATTTTTG
* *
1262780 AAGATATGTAATTTTAA
1 AAGATTTGTAATCTTAA
1262797 AA-ATTTTGTAATCTTAA
1 AAGA-TTTGTAATCTTAA
1262814 AAGATTTG
1 AAGATTTG
1262822 ATTTCGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (17 bp):
AAGATTTGTAATCTTAA
Found at i:1266981 original size:9 final size:9
Alignment explanation
Indices: 1266969--1267017 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1266959 AAAAATTAGA
1266969 AAAAAATAT
1 AAAAAATAT
* *
1266978 AAAAATTGT
1 AAAAAATAT
*
1266987 AAAAATTAT
1 AAAAAATAT
*
1266996 AAAATATAT
1 AAAAAATAT
*
1267005 AGAAAATAT
1 AAAAAATAT
1267014 AAAA
1 AAAA
1267018 TATAAAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:1266982 original size:19 final size:19
Alignment explanation
Indices: 1266953--1267010 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 19
1266943 TAAAAAAATT
1266953 AATATTAAAAATTAGAAAAA
1 AATA-TAAAAATTAGAAAAA
*
1266973 AATATAAAAATT-GTAAAA
1 AATATAAAAATTAGAAAAA
*
1266991 ATTATAAAATATATAGAAAA
1 AATATAAAA-AT-TAGAAAA
1267011 TATAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.41
19 10 0.31
20 5 0.16
21 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AATATAAAAATTAGAAAAA
Found at i:1266990 original size:18 final size:18
Alignment explanation
Indices: 1266953--1267017 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
1266943 TAAAAAAATT
*
1266953 AATATTAAAAATTAGAAAAA
1 AATA-TAAAAATT-GTAAAA
1266973 AATATAAAAATTGTAAAA
1 AATATAAAAATTGTAAAA
* * *
1266991 ATTAT-AAAATATATAGAA
1 AATATAAAAAT-TGTAAAA
1267009 AATATAAAA
1 AATATAAAA
1267018 TATAAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 5 0.13
18 18 0.47
19 11 0.29
20 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AATATAAAAATTGTAAAA
Found at i:1267018 original size:18 final size:17
Alignment explanation
Indices: 1266970--1267021 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
1266960 AAAATTAGAA
*
1266970 AAAAATATAAAA-ATTGT
1 AAAAATATAAAATA-TAT
1266987 AAAAATTATAAAATATAT
1 AAAAA-TATAAAATATAT
1267005 AGAAAATATAAAATATA
1 A-AAAATATAAAATATA
1267022 AAATTTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AAAAATATAAAATATAT
Found at i:1267041 original size:43 final size:45
Alignment explanation
Indices: 1266971--1267081 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 45
1266961 AAATTAGAAA
* * * *
1266971 AAAATATAAAA-ATTGTAAAA--ATTATAAAATATATAGAAAATAT
1 AAAATATAAAATTTTGTAAAATCATAAAAAAAT-TATACAAAATAT
*
1267014 AAAATATAAAATTTTGTAAAGTCATAAAAAAATTATACAAAATAT
1 AAAATATAAAATTTTGTAAAATCATAAAAAAATTATACAAAATAT
* *
1267059 AAAGAAATATAAATTTCGTAAAA
1 AAA-ATATA-AAATTTTGTAAAA
1267082 AAAGTTTATA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
43 11 0.20
44 7 0.13
45 14 0.25
46 12 0.22
47 11 0.20
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (45 bp):
AAAATATAAAATTTTGTAAAATCATAAAAAAATTATACAAAATAT
Found at i:1275487 original size:51 final size:52
Alignment explanation
Indices: 1275429--1275544 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
1275419 ATTGGTATAA
* ** * *
1275429 TAACAAATTTAGTCCTTAAA-ATTTTACACATTATGTCAAATTGGTATTG-TT
1 TAACAAATTTAGCCCACAAACA-TTTACACATTATATCAAATTGATATTGATT
* * * *
1275480 TAACAAATTTAACCCACAAACATTTACATATTATATCAATTTGATCTTGATT
1 TAACAAATTTAGCCCACAAACATTTACACATTATATCAAATTGATATTGATT
1275532 TAACAAATTTAGC
1 TAACAAATTTAGC
1275545 TCGTAACATT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
51 38 0.72
52 15 0.28
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (52 bp):
TAACAAATTTAGCCCACAAACATTTACACATTATATCAAATTGATATTGATT
Found at i:1280424 original size:37 final size:37
Alignment explanation
Indices: 1280383--1280498 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
1280373 CACCCAGTGT
1280383 CTCATCGGCAAAGCTGAAGAAAGTTGGTACCTAGTAC
1 CTCATCGGCAAAGCTGAAGAAAGTTGGTACCTAGTAC
* * ** * **
1280420 CTCAT-----TAGTTCGAAGTAATAGTTGACACCGAGTGT
1 CTCATCGGCAAAGCT-GAAG-AA-AGTTGGTACCTAGTAC
*
1280455 CTCATCGGCAAAGCCGAAGAAAGTTGGTACCTAGTAC
1 CTCATCGGCAAAGCTGAAGAAAGTTGGTACCTAGTAC
1280492 CTCATCG
1 CTCATCG
1280499 AATCTATCCG
Statistics
Matches: 56, Mismatches: 15, Indels: 16
0.64 0.17 0.18
Matches are distributed among these distances:
32 3 0.05
33 4 0.07
34 2 0.04
35 16 0.29
37 23 0.41
38 2 0.04
39 4 0.07
40 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (37 bp):
CTCATCGGCAAAGCTGAAGAAAGTTGGTACCTAGTAC
Found at i:1280474 original size:72 final size:72
Alignment explanation
Indices: 1280353--1280496 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
1280343 CCTAATCGAA
*
1280353 TAGTTCGAAGCAATAGTTGACACCCAGTGTCTCATCGGCAAAGCTGAAGAAAGTTGGTACCTAGT
1 TAGTTCGAAGCAATAGTTGACACCCAGTGTCTCATCGGCAAAGCCGAAGAAAGTTGGTACCTAGT
1280418 ACCTCAT
66 ACCTCAT
* *
1280425 TAGTTCGAAGTAATAGTTGACACCGAGTGTCTCATCGGCAAAGCCGAAGAAAGTTGGTACCTAGT
1 TAGTTCGAAGCAATAGTTGACACCCAGTGTCTCATCGGCAAAGCCGAAGAAAGTTGGTACCTAGT
1280490 ACCTCAT
66 ACCTCAT
1280497 CGAATCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (72 bp):
TAGTTCGAAGCAATAGTTGACACCCAGTGTCTCATCGGCAAAGCCGAAGAAAGTTGGTACCTAGT
ACCTCAT
Found at i:1280875 original size:12 final size:12
Alignment explanation
Indices: 1280852--1280890 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1280842 TATAATTCCC
1280852 ACTAATAATAAT
1 ACTAATAATAAT
* *
1280864 AATAATACTAAT
1 ACTAATAATAAT
*
1280876 ACTAATATTAAT
1 ACTAATAATAAT
1280888 ACT
1 ACT
1280891 TACCTCACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (12 bp):
ACTAATAATAAT
Found at i:1281687 original size:16 final size:15
Alignment explanation
Indices: 1281668--1281717 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
1281658 TTTTGTTTAT
*
1281668 TATTTAATATATGTAA
1 TATTTAATA-ATATAA
1281684 TATTTTAATAATATAA
1 TA-TTTAATAATATAA
*
1281700 TA--TAATAAAATAA
1 TATTTAATAATATAA
1281713 TATTT
1 TATTT
1281718 TTTTAACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 12 0.41
15 1 0.03
16 9 0.31
17 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TATTTAATAATATAA
Found at i:1282467 original size:17 final size:17
Alignment explanation
Indices: 1282417--1282474 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1282407 GGGTGAGAAG
*
1282417 TAAAAGTTTAGGGGGAAAA
1 TAAAAGTTT-GAGGG-AAA
*
1282436 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
1282453 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
1282470 GTAAA
1 -TAAA
1282475 TAGGGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 7 0.21
19 1 0.03
20 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:1284120 original size:50 final size:51
Alignment explanation
Indices: 1284008--1284130 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 51
1283998 CAGATACCCG
* ** * *
1284008 GTGGCCTGCACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAGA
1 GTGGCCTTCACATAGTACCACAATTGTAGCCAAAACTACCTTCTTCACAAA
* *
1284059 GTGGCCTTCACATAGTACCACAATTGT-GACCAAAACTATC-TCTTCTCAAA
1 GTGGCCTTCACATAGTACCACAATTGTAG-CCAAAACTACCTTCTTCACAAA
1284109 GTGGCCTTCACATAGTACCACA
1 GTGGCCTTCACATAGTACCACA
1284131 CTTTAGTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
50 31 0.48
51 33 0.52
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.25
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACAATTGTAGCCAAAACTACCTTCTTCACAAA
Found at i:1285048 original size:3 final size:3
Alignment explanation
Indices: 1285027--1285146 Score: 84
Period size: 3 Copynumber: 39.7 Consensus size: 3
1285017 AAGATTAAAT
* * *
1285027 ATA ATA CTA ATA GTA ATA ATA A-A GATA ATA ATA ATA GTA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A
* * * *
1285073 ATA TTA ATA TTA ATAA ATA A-A A-A CATA ATA ATA ATG ATT ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * * *
1285118 ATG ACA ATA ATA ACA ATC ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1285147 CTAAGTTTTG
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
2 4 0.04
3 78 0.87
4 8 0.09
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1285054 original size:24 final size:24
Alignment explanation
Indices: 1285022--1285107 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
1285012 ATGATAAGAT
*
1285022 TAAATATAATACTAATAGTAATAA
1 TAAATATAATAATAATAGTAATAA
*
1285046 TAAAGATAATAATAATAGTAATAA
1 TAAATATAATAATAATAGTAATAA
*
1285070 TAAATATTAATATTAATA--AATAA
1 TAAATA-TAATAATAATAGTAATAA
*
1285093 -AAACATAATAATAAT
1 TAAATATAATAATAAT
1285108 GATTATAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 9 0.16
22 4 0.07
23 5 0.09
24 27 0.49
25 10 0.18
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (24 bp):
TAAATATAATAATAATAGTAATAA
Found at i:1287251 original size:27 final size:28
Alignment explanation
Indices: 1287220--1287285 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
1287210 TATAAAAAAA
1287220 TACCAAAATATTATAT-ATTTTTTTATT
1 TACCAAAATATTATATCATTTTTTTATT
*
1287247 TACCAAAATATTATATCTTTTTTTTATT
1 TACCAAAATATTATATCATTTTTTTATT
1287275 TACCAAAATAT
1 TACCAAAATAT
1287286 ACCAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (28 bp):
TACCAAAATATTATATCATTTTTTTATT
Found at i:1289901 original size:51 final size:51
Alignment explanation
Indices: 1289812--1289912 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
1289802 ACACATTGTG
1289812 TCAAATTGGTATTGTTTAACAAATTTAACCCACAAACATTTACATATTCTA
1 TCAAATTGGTATTGTTTAACAAATTTAACCCACAAACATTTACATATTCTA
* * * **
1289863 TCAATTTGGTCTTGATTTAACAAATTTAACTC-GTAACATTTACATATTCT
1 TCAAATTGGTATTG-TTTAACAAATTTAACCCACAAACATTTACATATTCT
1289913 GTCTAACAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 28 0.64
52 16 0.36
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (51 bp):
TCAAATTGGTATTGTTTAACAAATTTAACCCACAAACATTTACATATTCTA
Found at i:1291046 original size:124 final size:127
Alignment explanation
Indices: 1290860--1291157 Score: 316
Period size: 124 Copynumber: 2.4 Consensus size: 127
1290850 TAAATATAGT
* * * *** *
1290860 AATTTGATTCGGGTTTATATCATGTAATTTTGGGATTTAGTTGTTTTAAATTTGGGTGTTTTCTG
1 AATTTGATTCGGGTTTAGATCATGTAATTTTGGGTTTTAGTTGTTTCAAATTCAAGTATTTTC-G
* * * * * * * *
1290925 -G-TTTGAATGTTTTTATAGTTGAGAGTTTGAGTGTTAGTGTTG-GGTAATTATAAAGGT-AG
65 AGTTTTGAATGTTTTTATAGTTCAAAGTTTGAGTGTGAATGTTGTGGCAAGTATAAAGATAAC
* * * *
1290984 AATTTGATTCGGGTTTAGATAATTTAATTTTGGGTTTTAATTGTTTCAAGTTCAAGTATTTTCGA
1 AATTTGATTCGGGTTTAGATCATGTAATTTTGGGTTTTAGTTGTTTCAAATTCAAGTATTTTCGA
* * * * *
1291049 GTTTTGAGTTTTTTTGTAGTTCAAAGTTTGAGTGTGAATGTTGTTTGCAGGTATAAAGATAAC
66 GTTTTGAATGTTTTTATAGTTCAAAGTTTGAGTGTGAATGTTG-TGGCAAGTATAAAGATAAC
* *
1291112 AACTTGATTCAGGTTTAGATCATGTAATTTTGGGTTTTAGTTGTTT
1 AATTTGATTCGGGTTTAGATCATGTAATTTTGGGTTTTAGTTGTTT
1291158 TAGGATTTTG
Statistics
Matches: 140, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
123 1 0.01
124 53 0.38
125 34 0.24
127 10 0.07
128 42 0.30
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (127 bp):
AATTTGATTCGGGTTTAGATCATGTAATTTTGGGTTTTAGTTGTTTCAAATTCAAGTATTTTCGA
GTTTTGAATGTTTTTATAGTTCAAAGTTTGAGTGTGAATGTTGTGGCAAGTATAAAGATAAC
Found at i:1297332 original size:16 final size:17
Alignment explanation
Indices: 1297313--1297354 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1297303 AATATACTAA
1297313 TTATTTATT-AAACATT
1 TTATTTATTCAAACATT
* *
1297329 TTATTAATTCAAATATT
1 TTATTTATTCAAACATT
1297346 TTAGTTTAT
1 TTA-TTTAT
1297355 AATAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 8 0.38
17 9 0.43
18 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTTATTCAAACATT
Found at i:1301293 original size:21 final size:22
Alignment explanation
Indices: 1301268--1301309 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1301258 ACCACCTTCT
1301268 TCATCA-AA-ATTATTCCAATTA
1 TCATCACAAGATT-TTCCAATTA
1301289 TCATCACAAGATTTTCCAATT
1 TCATCACAAGATTTTCCAATT
1301310 TCTTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (22 bp):
TCATCACAAGATTTTCCAATTA
Found at i:1311407 original size:12 final size:12
Alignment explanation
Indices: 1311390--1311417 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1311380 TATAACTTTT
1311390 ATTTTATTATTA
1 ATTTTATTATTA
1311402 ATTTTATTATTA
1 ATTTTATTATTA
1311414 ATTT
1 ATTT
1311418 AAAAGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTATTATTA
Found at i:1312840 original size:37 final size:39
Alignment explanation
Indices: 1312789--1312861 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 39
1312779 AATTAAGAGG
* **
1312789 ATTATATATAAAATTTTAAT-ATATAAA-AAATATTATT
1 ATTAAATATAAAATTGAAATAATATAAATAAATATTATT
*
1312826 ATTAAATATTAAATTGAAATAATATAAATAAATATT
1 ATTAAATATAAAATTGAAATAATATAAATAAATATT
1312862 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 16 0.53
38 7 0.23
39 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (39 bp):
ATTAAATATAAAATTGAAATAATATAAATAAATATTATT
Found at i:1313262 original size:14 final size:14
Alignment explanation
Indices: 1313220--1313279 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1313210 TTTTAATATT
1313220 ATATTTTATATAAAA
1 ATATTTTATAT-AAA
1313235 ATAATTTTA-A-AAA
1 AT-ATTTTATATAAA
1313248 ATATTTTATATAAA
1 ATATTTTATATAAA
** *
1313262 ATATAATATATCAA
1 ATATTTTATATAAA
1313276 ATAT
1 ATAT
1313280 ACTAAAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.15
13 6 0.15
14 18 0.46
15 3 0.08
16 6 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTTTATATAAA
Found at i:1327166 original size:54 final size:54
Alignment explanation
Indices: 1327104--1327211 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1327094 AGCATTTGGT
* *
1327104 TAACCATATTATTTCATTTTCTGAATCATACAAACTATGGTTGACATTGATAAC
1 TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
*
1327158 TAACCATATTATCTCATTTTCTGAAACATATAAACTATGGTTGACATTGATAAC
1 TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
1327212 AATTCGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (54 bp):
TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATTGATAAC
Found at i:1332206 original size:11 final size:10
Alignment explanation
Indices: 1332178--1332273 Score: 53
Period size: 10 Copynumber: 10.0 Consensus size: 10
1332168 ATTTTTTTAT
1332178 TTTTTAAA-A
1 TTTTTAAATA
*
1332187 TTTTAAAATA
1 TTTTTAAATA
1332197 CTTTTTAAAT-
1 -TTTTTAAATA
**
1332207 TTTTTTTA-A
1 TTTTTAAATA
*
1332216 TTTTAAAATA
1 TTTTTAAATA
1332226 TTTTTAAAATA
1 TTTTT-AAATA
1332237 CTTTTT-AAT-
1 -TTTTTAAATA
*
1332246 TTTTT-TA-A
1 TTTTTAAATA
*
1332254 TTTTAAAATA
1 TTTTTAAATA
*
1332264 TTTTAAAATA
1 TTTTTAAATA
1332274 AATTTTTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
8 10 0.15
9 19 0.28
10 20 0.30
11 13 0.19
12 5 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:1332208 original size:29 final size:28
Alignment explanation
Indices: 1332167--1332233 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
1332157 TAAATTATTT
**
1332167 TATTTTTTTATTTTTTAAAATTTTAAAA
1 TATTTTTAAATTTTTTAAAATTTTAAAA
**
1332195 TACTTTTTAAATTTTTTTTAATTTTAAAA
1 TA-TTTTTAAATTTTTTAAAATTTTAAAA
1332224 TATTTTTAAA
1 TATTTTTAAA
1332234 ATACTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTTTAAATTTTTTAAAATTTTAAAA
Found at i:1332221 original size:17 final size:17
Alignment explanation
Indices: 1332199--1332301 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 17
1332189 TTAAAATACT
* *
1332199 TTTTAAATTTTTTTTAA
1 TTTTAAAATATTTTTAA
1332216 TTTTAAAATATTTTTAAAA
1 TTTTAAAATATTTTT--AA
** *
1332235 TACTTTTTAATTTTTTTAA
1 T--TTTAAAATATTTTTAA
1332254 TTTTAAAATA-TTTTAA
1 TTTTAAAATATTTTTAA
** *
1332270 -AAT-AAATTTTTTTAA
1 TTTTAAAATATTTTTAA
1332285 TTTTTAAAATAATTTTT
1 -TTTTAAAAT-ATTTTT
1332302 TGGTATTTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
14 4 0.06
15 7 0.11
16 6 0.10
17 20 0.32
18 4 0.06
19 11 0.17
21 11 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:1332235 original size:29 final size:29
Alignment explanation
Indices: 1332176--1332248 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1332166 TTATTTTTTT
**
1332176 ATTTTTTAAAATTTTAAAATACTTTTTAA
1 ATTTTTTTTAATTTTAAAATACTTTTTAA
1332205 ATTTTTTTTAATTTTAAAATA-TTTTTAAA
1 ATTTTTTTTAATTTTAAAATACTTTTT-AA
**
1332234 ATACTTTTTAATTTT
1 ATTTTTTTTAATTTT
1332249 TTTAATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTTTTTTAATTTTAAAATACTTTTTAA
Found at i:1332249 original size:38 final size:37
Alignment explanation
Indices: 1332164--1332273 Score: 161
Period size: 38 Copynumber: 2.9 Consensus size: 37
1332154 TAATAAATTA
* *
1332164 TTTT-ATTTTTTTATTTTTTAAA-ATTTTAAAATACT
1 TTTTAATTTTTTTAATTTTAAAATATTTTAAAATACT
1332199 TTTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTT-AA-TTTTTTTAATTTTAAAATA-TTTTAAAATACT
1332239 TTTTAATTTTTTTAATTTTAAAATATTTTAAAATA
1 TTTTAATTTTTTTAATTTTAAAATATTTTAAAATA
1332274 AATTTTTTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
35 4 0.06
37 11 0.16
38 34 0.50
39 3 0.04
40 16 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (37 bp):
TTTTAATTTTTTTAATTTTAAAATATTTTAAAATACT
Found at i:1332279 original size:22 final size:21
Alignment explanation
Indices: 1332252--1332301 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1332242 TAATTTTTTT
1332252 AATTTTAAAATATTTTAAAATA
1 AATTTTAAAAT-TTTTAAAATA
**
1332274 AATTTTTTTAATTTTTAAAATA
1 AA-TTTTAAAATTTTTAAAATA
*
1332296 ATTTTT
1 AATTTT
1332302 TGGTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTAAAATTTTTAAAATA
Found at i:1332282 original size:40 final size:38
Alignment explanation
Indices: 1332164--1332289 Score: 150
Period size: 38 Copynumber: 3.3 Consensus size: 38
1332154 TAATAAATTA
* * *
1332164 TTTT-ATTTTTTTATTTTTTAAA-ATTTTAAAATACTT
1 TTTTAATTTTTTTAATTTTAAAATATTTTAAAATATTT
* *
1332200 TTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATA-CT
1 TTTTAA-TTTTTTTAATTTTAAAATA-TTTTAAAATATTT
1332239 TTTTAATTTTTTTAATTTTAAAATATTTTAAAATAAATTT
1 TTTTAATTTTTTTAATTTTAAAATATTTTAAAAT--ATTT
1332279 TTTTAATTTTT
1 TTTTAATTTTT
1332290 AAAATAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
36 3 0.04
37 10 0.13
38 34 0.44
39 8 0.10
40 22 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (38 bp):
TTTTAATTTTTTTAATTTTAAAATATTTTAAAATATTT
Found at i:1332565 original size:14 final size:14
Alignment explanation
Indices: 1332542--1332578 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1332532 TTACCACTAC
*
1332542 TTTAATATTTAGGG
1 TTTAAGATTTAGGG
1332556 TTTAAGATTTAGGG
1 TTTAAGATTTAGGG
1332570 --TAAGATTTA
1 TTTAAGATTTA
1332579 CAGGTTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.41
14 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTTAAGATTTAGGG
Found at i:1334872 original size:9 final size:9
Alignment explanation
Indices: 1334842--1334907 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
1334832 TTTGGTTAAA
1334842 AATTAACCG
1 AATTAACCG
1334851 AATT-ACCG
1 AATTAACCG
* *
1334859 GATTACCCG
1 AATTAACCG
1334868 AATTAACCG
1 AATTAACCG
*
1334877 AATTACCCG
1 AATTAACCG
1334886 AATTAACCG
1 AATTAACCG
1334895 AATTAACCG
1 AATTAACCG
1334904 AATT
1 AATT
1334908 GAATCACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
8 7 0.14
9 43 0.86
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:1338785 original size:34 final size:33
Alignment explanation
Indices: 1338747--1338870 Score: 121
Period size: 34 Copynumber: 3.7 Consensus size: 33
1338737 ATTTAAGGAA
1338747 TAAATTAAGGTTTAAGGTTTTTTAAAAAATTAAT
1 TAAATTAAGGTTT-AGGTTTTTTAAAAAATTAAT
* *
1338781 TAAATT-AGGTTTTTGGGTTTTGGGTT--TAAATTAAT
1 TAAATTAAGG--TTTAGGTTTT---TTAAAAAATTAAT
*
1338816 TAAATTAAGGTTTAGGGTTTTTAAGAAAATTAAT
1 TAAATTAAGGTTTAGGTTTTTTAA-AAAATTAAT
*
1338850 TAAATTATGGTTTA-GTTTTTT
1 TAAATTAAGGTTTAGGTTTTTT
1338871 CTTAAATAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
31 2 0.03
33 9 0.12
34 41 0.55
35 17 0.23
36 3 0.04
37 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (33 bp):
TAAATTAAGGTTTAGGTTTTTTAAAAAATTAAT
Found at i:1339082 original size:126 final size:122
Alignment explanation
Indices: 1338933--1339330 Score: 465
Period size: 126 Copynumber: 3.2 Consensus size: 122
1338923 TAAGGATTTT
* ** *
1338933 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTAAGAAGATGATTCTGAAAAGATAATGCCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGA-GATTCTGAAAA-ATGGTGTCAAAA
* * *
1338998 ACACTTCAAACAGGATGCACTGTCAGCAAAATTATTAAAAAAAGCTACCACGTGGATGCTC
64 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCT-CCACGTGGACGCTC
* * *
1339059 TTTTTCTACAGTAGTTCCTGAAAAAATAATTCTGAA-AAGACAGTTCTGAGCAAATGGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATT-TTAAGAAGAGA-TTCTGA-AAAATGGTGTCAAA
* * * *
1339123 AACTCTTCAAGCAGGATGCACTATCAGCAAAAATACTGAAAAAAGCTCCTACGTGGACACTC
63 AACACTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCTCC-ACGTGGACGCTC
* * * *
1339185 TTTTTCTATAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGA-GATTCTGAA-AAATGGTGTCAAAA
** * * *
1339250 ATGCTTTAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCACGTAGACGCTC
64 ACACTTCAAGCAGGATGCACTGTCAGCAAAATT-ATGAAAAAAGCT-CCACGTGGACGCTC
1339311 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
1339331 TTTGGCCTTA
Statistics
Matches: 231, Mismatches: 32, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
125 5 0.02
126 218 0.94
127 8 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (122 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGAGATTCTGAAAAATGGTGTCAAAAAC
ACTTCAAGCAGGATGCACTGTCAGCAAAATTATGAAAAAAGCTCCACGTGGACGCTC
Found at i:1341936 original size:25 final size:25
Alignment explanation
Indices: 1341908--1341955 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1341898 ACTTCTATTT
*
1341908 TATTAAAA-ATATAAAAATAATTTAC
1 TATTAAAATAT-TAAAAACAATTTAC
1341933 TATTAAAATATTAAAAACAATTT
1 TATTAAAATATTAAAAACAATTT
1341956 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAATATTAAAAACAATTTAC
Found at i:1341960 original size:24 final size:24
Alignment explanation
Indices: 1341905--1341960 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
1341895 AGAACTTCTA
*
1341905 TTTTATTAAAAATATAAAAATAAT
1 TTTTATTAAAAATATAAAAACAAT
*
1341929 TTACTATT-AAAATATTAAAAACAAT
1 TT-TTATTAAAAATA-TAAAAACAAT
1341954 TTTTATT
1 TTTTATT
1341961 TTATTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTATTAAAAATATAAAAACAAT
Found at i:1342432 original size:18 final size:18
Alignment explanation
Indices: 1342390--1342432 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1342380 GGCTGAGAAA
* *
1342390 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
1342408 AGAATACATATAAGGGCT
1 AGGATACATATAAGGGCT
1342426 AGGATAC
1 AGGATAC
1342433 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:1348982 original size:28 final size:29
Alignment explanation
Indices: 1348944--1349018 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1348934 AAGTTTTTGT
*
1348944 TAATTTATTTAAAATTTTAATTAG-CTCC
1 TAATTTTTTTAAAATTTTAATTAGACTCC
1348972 TAATTTTTTTAAAAATTTTAATTAGACCTCC
1 TAATTTTTTT-AAAATTTTAATTAGA-CTCC
* *
1349003 AAATTTTTTGAAAATT
1 TAATTTTTTTAAAATT
1349019 CTCACTAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 9 0.22
29 14 0.34
30 6 0.15
31 12 0.29
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (29 bp):
TAATTTTTTTAAAATTTTAATTAGACTCC
Found at i:1349011 original size:31 final size:31
Alignment explanation
Indices: 1348945--1349088 Score: 106
Period size: 31 Copynumber: 4.7 Consensus size: 31
1348935 AGTTTTTGTT
1348945 AATTTATTT-AAAATTTTAATT--AG-CTCCTA
1 AATTT-TTTAAAAATTTTAATTAGAGCCTCC-A
*
1348974 ATTTTTTTAAAAATTTTAATTAGA-CCTCCA
1 AATTTTTTAAAAATTTTAATTAGAGCCTCCA
* * * * *
1349004 AATTTTTTGAAAATTCTCACTA-AGCTTTCCA
1 AATTTTTTAAAAATTTTAATTAGAGC-CTCCA
* * *
1349035 AA-ATTTTAGAAGATTTTAATTAGATCCTCCA
1 AATTTTTTA-AAAATTTTAATTAGAGCCTCCA
1349066 TAA-TTTTTAAAAATTTTAATTAG
1 -AATTTTTTAAAAATTTTAATTAG
1349089 GTCTTCCAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
28 3 0.03
29 17 0.19
30 23 0.26
31 37 0.42
32 9 0.10
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (31 bp):
AATTTTTTAAAAATTTTAATTAGAGCCTCCA
Found at i:1366744 original size:25 final size:25
Alignment explanation
Indices: 1366715--1366763 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1366705 TGACAGAACT
1366715 GAGAGAATAGGATTTGAATACAAAA
1 GAGAGAATAGGATTTGAATACAAAA
1366740 GAGAGAATAGGATTTGAATACAAA
1 GAGAGAATAGGATTTGAATACAAA
1366764 TTCAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (25 bp):
GAGAGAATAGGATTTGAATACAAAA
Found at i:1367855 original size:13 final size:13
Alignment explanation
Indices: 1367839--1367863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1367829 CAAGTATTCA
1367839 ACCCAACCCAATT
1 ACCCAACCCAATT
1367852 ACCCAACCCAAT
1 ACCCAACCCAAT
1367864 CCAATCATAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:1367904 original size:6 final size:6
Alignment explanation
Indices: 1367896--1367967 Score: 117
Period size: 6 Copynumber: 11.7 Consensus size: 6
1367886 ATTTAATAAA
*
1367896 TAAAAA TAAAATC CTAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC
1 TAAAAC TAAAA-C -TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC
1367946 TAAAAC TAAAAC TAAAAC TAAA
1 TAAAAC TAAAAC TAAAAC TAAA
1367968 GTCTAAAAGT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
6 57 0.90
7 1 0.02
8 5 0.08
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAC
Found at i:1368021 original size:9 final size:9
Alignment explanation
Indices: 1368007--1368046 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1367997 GTTGTGATTC
1368007 AATTCGGGT
1 AATTCGGGT
*
1368016 AATTCGGTT
1 AATTCGGGT
1368025 AATTCGGGT
1 AATTCGGGT
*
1368034 AATTCGGTT
1 AATTCGGGT
1368043 AATT
1 AATT
1368047 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:1368030 original size:18 final size:18
Alignment explanation
Indices: 1368007--1368046 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1367997 GTTGTGATTC
1368007 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
1368025 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
1368043 AATT
1 AATT
1368047 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:1368433 original size:6 final size:6
Alignment explanation
Indices: 1368424--1368465 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1368414 TATATTTTAT
1368424 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
1368466 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:1368513 original size:18 final size:17
Alignment explanation
Indices: 1368474--1368510 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1368464 TAAAAAATAA
1368474 ATTTATTATGTTTTTAT
1 ATTTATTATGTTTTTAT
*
1368491 ATTTATT-TATTTTTAT
1 ATTTATTATGTTTTTAT
1368507 ATTT
1 ATTT
1368511 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTATTATGTTTTTAT
Found at i:1368587 original size:23 final size:22
Alignment explanation
Indices: 1368547--1368595 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1368537 GTTAGTAATA
*
1368547 TTTTTTAAAATTTATTATTATAT
1 TTTTTTAAAATATATTA-TATAT
*
1368570 TTTTTTGAAAATAT-TTATGTAT
1 TTTTTT-AAAATATATTATATAT
1368592 TTTT
1 TTTT
1368596 ATATATTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTTAAAATATATTATATAT
Found at i:1377905 original size:17 final size:18
Alignment explanation
Indices: 1377883--1377918 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1377873 ATTTACAAAA
1377883 AGGGAAAAAG-AATTCCC
1 AGGGAAAAAGAAATTCCC
1377900 AGGGAAAAAGAAATTCCC
1 AGGGAAAAAGAAATTCCC
1377918 A
1 A
1377919 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.11
Consensus pattern (18 bp):
AGGGAAAAAGAAATTCCC
Found at i:1380073 original size:3 final size:3
Alignment explanation
Indices: 1380015--1380064 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1380005 TAATCTAGTC
* *
1380015 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TCT- TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
1380060 GTA TT
1 TTA TT
1380065 GGTATTATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1380453 original size:18 final size:18
Alignment explanation
Indices: 1380432--1380466 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1380422 TACACCTATA
*
1380432 TATATATGTACACATTTT
1 TATATATATACACATTTT
*
1380450 TATATATATACATATTT
1 TATATATATACACATTT
1380467 CTTTCTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATATATACACATTTT
Found at i:1380553 original size:24 final size:24
Alignment explanation
Indices: 1380496--1380555 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
1380486 AAAATATACT
*
1380496 TTATATATA-ATTTGTAATTTATG
1 TTATATACATATTTGTAATTTATG
* *
1380519 TATACACACATATTT-TAATTTATAG
1 T-TATATACATATTTGTAATTTAT-G
1380544 TTATATACATAT
1 TTATATACATAT
1380556 ATATCTCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.03
24 22 0.76
25 6 0.21
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (24 bp):
TTATATACATATTTGTAATTTATG
Found at i:1382735 original size:10 final size:10
Alignment explanation
Indices: 1382719--1382776 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1382709 CAACTCCGAC
1382719 CAGCTCAATT
1 CAGCTCAATT
* *
1382729 GAGCTCATTT
1 CAGCTCAATT
1382739 CAGCTCAA-T
1 CAGCTCAATT
1382748 CGAGCTCAATT
1 C-AGCTCAATT
*
1382759 TAGCTACAATT
1 CAGCT-CAATT
1382770 CAGCTCA
1 CAGCTCA
1382777 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:1382742 original size:20 final size:20
Alignment explanation
Indices: 1382719--1382779 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
1382709 CAACTCCGAC
1382719 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
1382739 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
1382760 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
1382780 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:1398965 original size:13 final size:13
Alignment explanation
Indices: 1398916--1398965 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
1398906 ACACTCAAAA
*
1398916 TTTTCAAAA-TAC
1 TTTTCAAAAGCAC
*
1398928 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
1398941 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
1398954 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1398966 ATTAAGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 13 0.43
13 13 0.43
14 4 0.13
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1407525 original size:31 final size:31
Alignment explanation
Indices: 1407476--1407550 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1407466 CAAATTTTGG
** *
1407476 GAAATTTTCTTTATGCCCTTCAAAA-TATTT
1 GAAATTTTAATTAAGCCCTTCAAAATTATTT
* *
1407506 GAAAATTTTAATTAAGCCCTTTAAAATTTTTT
1 G-AAATTTTAATTAAGCCCTTCAAAATTATTT
1407538 GAAATTTTAATTA
1 GAAATTTTAATTA
1407551 GACCCTCCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 32 0.84
32 5 0.13
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (31 bp):
GAAATTTTAATTAAGCCCTTCAAAATTATTT
Found at i:1411154 original size:561 final size:561
Alignment explanation
Indices: 1410092--1411213 Score: 2235
Period size: 561 Copynumber: 2.0 Consensus size: 561
1410082 TGTCATATTA
*
1410092 GCTTTTTTTCCAAATCAAGAAATCACATATTCTTAAAGTAAACTTGAAATTTGATAAGATTTGTT
1 GCTTTTTCTCCAAATCAAGAAATCACATATTCTTAAAGTAAACTTGAAATTTGATAAGATTTGTT
1410157 TGATTAAAGTGGCTAATTATGGACCCTCAAGTATATAATTCATTGAATTGGGTGTATTTTTTAAT
66 TGATTAAAGTGGCTAATTATGGACCCTCAAGTATATAATTCATTGAATTGGGTGTATTTTTTAAT
1410222 TTGTTTAAGATATAATTTAATTTAATTTTTGACACATTACCTACTTAATCATTTATTTGATAAGA
131 TTGTTTAAGATATAATTTAATTTAATTTTTGACACATTACCTACTTAATCATTTATTTGATAAGA
1410287 ATGACAAAACTAATAATAAAGATGATTGCTTGTTAATGAGTGAAAAGAGATAAGAACAAATTCCA
196 ATGACAAAACTAATAATAAAGATGATTGCTTGTTAATGAGTGAAAAGAGATAAGAACAAATTCCA
1410352 TGGCATAAGCATTGAGTCCCACTTACCAAAGCAAAGCATATTTGCTTATGTGAAATCTATGCCCT
261 TGGCATAAGCATTGAGTCCCACTTACCAAAGCAAAGCATATTTGCTTATGTGAAATCTATGCCCT
1410417 AGATTAAAAAAAAAAAAAGTTGCCTTTTAAATTTTAGCTCGATTGGCATGGGTATTATTGTTAAT
326 AGATTAAAAAAAAAAAAAGTTGCCTTTTAAATTTTAGCTCGATTGGCATGGGTATTATTGTTAAT
1410482 GCAAGAGGACGTGAGTTTGAATGTGTTGAAGCGCATTATTCTCTTATTTATGGTTTAGAAAGGGG
391 GCAAGAGGACGTGAGTTTGAATGTGTTGAAGCGCATTATTCTCTTATTTATGGTTTAGAAAGGGG
1410547 TTATGGGTAGTTCTAGAGCAGATCAAAACCTATAATGAGATTGTTAAAAATATTATTTTTAAATT
456 TTATGGGTAGTTCTAGAGCAGATCAAAACCTATAATGAGATTGTTAAAAATATTATTTTTAAATT
1410612 TTTGTTAAAATATGTCACAAGTCCTTATACTTTTCAAAAAT
521 TTTGTTAAAATATGTCACAAGTCCTTATACTTTTCAAAAAT
1410653 GCTTTTTCTCCAAATCAAGAAATCACATATTCTTAAAGTAAACTTGAAATTTGATAAGATTTGTT
1 GCTTTTTCTCCAAATCAAGAAATCACATATTCTTAAAGTAAACTTGAAATTTGATAAGATTTGTT
1410718 TGATTAAAGTGGCTAATTATGGACCCTCAAGTATATAATTCATTGAATTGGGTGTATTTTTTAAT
66 TGATTAAAGTGGCTAATTATGGACCCTCAAGTATATAATTCATTGAATTGGGTGTATTTTTTAAT
1410783 TTGTTTAAGATATAATTTAATTTAATTTTTGACACATTACCTACTTAATCATTTATTTGATAAGA
131 TTGTTTAAGATATAATTTAATTTAATTTTTGACACATTACCTACTTAATCATTTATTTGATAAGA
1410848 ATGACAAAACTAATAATAAAGATGATTGCTTGTTAATGAGTGAAAAGAGATAAGAACAAATTCCA
196 ATGACAAAACTAATAATAAAGATGATTGCTTGTTAATGAGTGAAAAGAGATAAGAACAAATTCCA
1410913 TGGCATAAGCATTGAGTCCCACTTACCAAAGCAAAGCATATTTGCTTATGTGAAATCTATGCCCT
261 TGGCATAAGCATTGAGTCCCACTTACCAAAGCAAAGCATATTTGCTTATGTGAAATCTATGCCCT
1410978 AGATTAAAAAAAAAAAAAGTTGCCTTTTAAATTTTAGCTCGATTGGCATGGGTATTATTGTTAAT
326 AGATTAAAAAAAAAAAAAGTTGCCTTTTAAATTTTAGCTCGATTGGCATGGGTATTATTGTTAAT
1411043 GCAAGAGGACGTGAGTTTGAATGTGTTGAAGCGCATTATTCTCTTATTTATGGTTTAGAAAGGGG
391 GCAAGAGGACGTGAGTTTGAATGTGTTGAAGCGCATTATTCTCTTATTTATGGTTTAGAAAGGGG
1411108 TTATGGGTAGTTCTAGAGCAGATCAAAACCTATAATGAGATTGTTAAAAATATTATTTTTAAATT
456 TTATGGGTAGTTCTAGAGCAGATCAAAACCTATAATGAGATTGTTAAAAATATTATTTTTAAATT
1411173 TTTGTTAAAATATGTCACAAGTCCTTATACTTTTCAAAAAT
521 TTTGTTAAAATATGTCACAAGTCCTTATACTTTTCAAAAAT
1411214 TTAGAATTTA
Statistics
Matches: 560, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
561 560 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (561 bp):
GCTTTTTCTCCAAATCAAGAAATCACATATTCTTAAAGTAAACTTGAAATTTGATAAGATTTGTT
TGATTAAAGTGGCTAATTATGGACCCTCAAGTATATAATTCATTGAATTGGGTGTATTTTTTAAT
TTGTTTAAGATATAATTTAATTTAATTTTTGACACATTACCTACTTAATCATTTATTTGATAAGA
ATGACAAAACTAATAATAAAGATGATTGCTTGTTAATGAGTGAAAAGAGATAAGAACAAATTCCA
TGGCATAAGCATTGAGTCCCACTTACCAAAGCAAAGCATATTTGCTTATGTGAAATCTATGCCCT
AGATTAAAAAAAAAAAAAGTTGCCTTTTAAATTTTAGCTCGATTGGCATGGGTATTATTGTTAAT
GCAAGAGGACGTGAGTTTGAATGTGTTGAAGCGCATTATTCTCTTATTTATGGTTTAGAAAGGGG
TTATGGGTAGTTCTAGAGCAGATCAAAACCTATAATGAGATTGTTAAAAATATTATTTTTAAATT
TTTGTTAAAATATGTCACAAGTCCTTATACTTTTCAAAAAT
Found at i:1413512 original size:29 final size:30
Alignment explanation
Indices: 1413478--1413536 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
1413468 TTTCTTTATG
*
1413478 ATTTTATACTTTTT-AATTTTTAAAAATAA
1 ATTTTATAATTTTTAAATTTTTAAAAATAA
1413507 ATTTTATAATTTTTAAAAATTTTTAAAAAT
1 ATTTTATAATTTTT--AAATTTTTAAAAAT
1413537 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.50
32 13 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTTATAATTTTTAAATTTTTAAAAATAA
Found at i:1413529 original size:10 final size:10
Alignment explanation
Indices: 1413492--1413552 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
1413482 TATACTTTTT
1413492 AATTTTTAAA
1 AATTTTTAAA
*
1413502 AATAAATTTT-AT
1 AAT---TTTTAAA
1413514 AATTTTTAAA
1 AATTTTTAAA
1413524 AATTTTTAAA
1 AATTTTTAAA
*
1413534 AA-TTTAAAA
1 AATTTTTAAA
1413543 AATTATTTAA
1 AATT-TTTAA
1413553 TTACTGACGT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 12 0.29
10 17 0.41
11 4 0.10
12 4 0.10
13 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:1417235 original size:19 final size:19
Alignment explanation
Indices: 1417208--1417248 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1417198 TTTTTGAGGG
1417208 ATTAAATTATTATTTCATA
1 ATTAAATTATTATTTCATA
* *
1417227 ATTATATTATTATTTTATA
1 ATTAAATTATTATTTCATA
1417246 ATT
1 ATT
1417249 TTTCTGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTAAATTATTATTTCATA
Found at i:1417765 original size:39 final size:39
Alignment explanation
Indices: 1417711--1417798 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
1417701 TGAAGAATGG
* **
1417711 GTGGACGAGAACCTTCCGGCAAGAACGAA-TGGCTAGCTA
1 GTGGATGAGAACCTTCCAACAAGAAC-AAGTGGCTAGCTA
*
1417750 GTGGATGAGAACCTTCCAACAAGAGCAAGTGGCTAGCTA
1 GTGGATGAGAACCTTCCAACAAGAACAAGTGGCTAGCTA
1417789 GT-GATGAGAA
1 GTGGATGAGAA
1417799 TGGTTGATCC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 10 0.23
39 34 0.77
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (39 bp):
GTGGATGAGAACCTTCCAACAAGAACAAGTGGCTAGCTA
Found at i:1422815 original size:16 final size:16
Alignment explanation
Indices: 1422781--1422821 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1422771 ATTCTACTCA
*
1422781 TAACACTATTATCTGT
1 TAACACTATTATCTAT
1422797 TAACAGCTATTAT-TAT
1 TAACA-CTATTATCTAT
1422813 TAACA-TATT
1 TAACACTATT
1422822 TACCACAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
16 12 0.52
17 7 0.30
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (16 bp):
TAACACTATTATCTAT
Found at i:1428595 original size:89 final size:89
Alignment explanation
Indices: 1428444--1428621 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
1428434 ACTTCTTATC
1428444 GCCACCAAAAACAGGCATAGAAATCAAATTTGTCTCGAAATCCAATCCCACTACCACAGTCCTAC
1 GCCACCAAAAACAGGCATAGAAATCAAATTTGTCTCGAAATCCAATCCCACTACCACAGTCCTAC
1428509 CAGTATTATCAACAGCATAAAAAT
66 CAGTATTATCAACAGCATAAAAAT
*
1428533 GCCACCAAAAACAGGCATAGCAATCAAATTTGTCTCGAAATCCAATCCCACTACCACAGTCCTAC
1 GCCACCAAAAACAGGCATAGAAATCAAATTTGTCTCGAAATCCAATCCCACTACCACAGTCCTAC
1428598 CAGTATTATCAACAGCATAAAAAT
66 CAGTATTATCAACAGCATAAAAAT
1428622 TCCCTTTATA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (89 bp):
GCCACCAAAAACAGGCATAGAAATCAAATTTGTCTCGAAATCCAATCCCACTACCACAGTCCTAC
CAGTATTATCAACAGCATAAAAAT
Found at i:1430298 original size:31 final size:31
Alignment explanation
Indices: 1430262--1430327 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1430252 TTACAATCCG
*
1430262 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
*
1430293 GTCACTGAACTATTTAAAAGTTTTTATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
1430324 GTCA
1 GTCA
1430328 ATAGGCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (31 bp):
GTCACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:1431157 original size:18 final size:19
Alignment explanation
Indices: 1431122--1431158 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1431112 TAAGGTAGAA
1431122 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
1431141 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
1431159 ACTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:1431208 original size:21 final size:21
Alignment explanation
Indices: 1431184--1431225 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1431174 CTAAAGAAAT
1431184 ATTA-ACTAATGTTAATAATAA
1 ATTAGACTAA-GTTAATAATAA
* *
1431205 ATTAGATTAAGTTATTAATAA
1 ATTAGACTAAGTTAATAATAA
1431226 TAATATGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTAGACTAAGTTAATAATAA
Found at i:1438456 original size:79 final size:79
Alignment explanation
Indices: 1438362--1438519 Score: 280
Period size: 79 Copynumber: 2.0 Consensus size: 79
1438352 TTGGTTTTTT
* *
1438362 TTATAAACAGTAGTCCATTCACCAACTATTTCTTTTAGATGCTTTTTACCTCTATCCATGAGGCC
1 TTATAAACAGTAGTCCATTCACCAACTATTTCTTTTAGAGGCTTTTTACCTCTATCCATAAGGCC
1438427 TGCTCAAATAATCA
66 TGCTCAAATAATCA
* *
1438441 TTATGAACAGTAGTCCATTCATCAACTATTTCTTTTAGAGGCTTTTTACCTCTATCCATAAGGCC
1 TTATAAACAGTAGTCCATTCACCAACTATTTCTTTTAGAGGCTTTTTACCTCTATCCATAAGGCC
1438506 TGCTCAAATAATCA
66 TGCTCAAATAATCA
1438520 ACAATTATTA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (79 bp):
TTATAAACAGTAGTCCATTCACCAACTATTTCTTTTAGAGGCTTTTTACCTCTATCCATAAGGCC
TGCTCAAATAATCA
Found at i:1445117 original size:31 final size:31
Alignment explanation
Indices: 1445082--1445147 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1445072 TTACAATCCG
*
1445082 GTCACTGAACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
*
1445113 GTCACTGAACTATTTAAAAGTTTTTATTTAA
1 GTCACTGAACTATTTAAAAGTTTTCATTTAA
1445144 GTCA
1 GTCA
1445148 ATAGGCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (31 bp):
GTCACTGAACTATTTAAAAGTTTTCATTTAA
Found at i:1450937 original size:21 final size:21
Alignment explanation
Indices: 1450911--1450951 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1450901 AGACGAGCAA
* *
1450911 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1450932 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1450952 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:1459137 original size:19 final size:19
Alignment explanation
Indices: 1459113--1459175 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1459103 TCTAATTAAG
1459113 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
1459132 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
1459151 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
1459170 TAATAA
1 TAATAA
1459176 ACTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:1459239 original size:18 final size:17
Alignment explanation
Indices: 1459210--1459244 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1459200 GTAATGTTTC
*
1459210 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
1459227 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
1459245 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:1459741 original size:26 final size:27
Alignment explanation
Indices: 1459688--1459747 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1459678 TTTTTTTGGT
* ***
1459688 ATATTTTGATAAATAAAAATATTTATA
1 ATATTTTAATAAATAAAAATAAAGATA
1459715 ATATTTTAATAAATAAAAA-AAAGATA
1 ATATTTTAATAAATAAAAATAAAGATA
*
1459741 ACATTTT
1 ATATTTT
1459748 GATTATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (27 bp):
ATATTTTAATAAATAAAAATAAAGATA
Found at i:1461997 original size:19 final size:19
Alignment explanation
Indices: 1461973--1462035 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1461963 TCTAATTAAG
1461973 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
1461992 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
1462011 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
1462030 TAATAA
1 TAATAA
1462036 ACTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:1462099 original size:18 final size:17
Alignment explanation
Indices: 1462070--1462104 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1462060 GTAATGTTTC
*
1462070 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
1462087 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
1462105 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:1462590 original size:26 final size:27
Alignment explanation
Indices: 1462537--1462596 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1462527 TTTTTTGGGT
* ***
1462537 ATATTTTGATAAATAAAAATATTTATA
1 ATATTTTAATAAATAAAAATAAAGATA
1462564 ATATTTTAATAAATAAAAA-AAAGATA
1 ATATTTTAATAAATAAAAATAAAGATA
*
1462590 ACATTTT
1 ATATTTT
1462597 GATTATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (27 bp):
ATATTTTAATAAATAAAAATAAAGATA
Found at i:1477703 original size:13 final size:14
Alignment explanation
Indices: 1477678--1477704 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1477668 CAGAAAATTA
1477678 ATTGAATTTTTTTG
1 ATTGAATTTTTTTG
1477692 ATTGAATTTTTTT
1 ATTGAATTTTTTT
1477705 ATCTTTATCA
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:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (14 bp):
ATTGAATTTTTTTG
Found at i:1479181 original size:16 final size:15
Alignment explanation
Indices: 1479162--1479195 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
1479152 AATTGGTTAA
1479162 TTTTAGTTTTTAAACT
1 TTTTAGTTTTTAAA-T
1479178 TTTTAGTTTTTAAAT
1 TTTTAGTTTTTAAAT
1479193 TTT
1 TTT
1479196 AAATTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTAGTTTTTAAAT
Found at i:1481265 original size:28 final size:28
Alignment explanation
Indices: 1481204--1481264 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
1481194 CTTTTTTTAA
*
1481204 AAAATAAAGGTGAAATTTAATTAAAAATT
1 AAAATAAAGGTAAAATTT-ATTAAAAATT
1481233 AAAATAAAGAGTAAAATTT-TTAAAAATAT
1 AAAATAAAG-GTAAAATTTATTAAAAAT-T
1481262 AAA
1 AAA
1481265 TTTAATTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 8 0.28
29 13 0.45
30 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAATAAAGGTAAAATTTATTAAAAATT
Found at i:1483127 original size:33 final size:34
Alignment explanation
Indices: 1483090--1483157 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1483080 ATAAGTTTAA
* *
1483090 TTATTATTTAATA-TAAAATAATTTAAATATATT
1 TTATTATTTAATATTAAAATAAGTTAAAAATATT
* *
1483123 TTATTATTTATTATTAATATAAGTTAAAAATATT
1 TTATTATTTAATATTAAAATAAGTTAAAAATATT
1483157 T
1 T
1483158 AAATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
TTATTATTTAATATTAAAATAAGTTAAAAATATT
Found at i:1483407 original size:21 final size:21
Alignment explanation
Indices: 1483369--1483421 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1483359 CGCTATTTCT
** *
1483369 AATCTCACTGCTACAGTATCC
1 AATCTCACCACTACAGTAACC
* *
1483390 AATCTCACCACTATAGTAACT
1 AATCTCACCACTACAGTAACC
1483411 AATCTCACCAC
1 AATCTCACCAC
1483422 CACCACTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (21 bp):
AATCTCACCACTACAGTAACC
Found at i:1485585 original size:13 final size:13
Alignment explanation
Indices: 1485567--1485594 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1485557 TACTTCTCTC
1485567 ACCTCTTATACAG
1 ACCTCTTATACAG
1485580 ACCTCTTATACAG
1 ACCTCTTATACAG
1485593 AC
1 AC
1485595 AAGTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.29
Consensus pattern (13 bp):
ACCTCTTATACAG
Found at i:1488590 original size:17 final size:18
Alignment explanation
Indices: 1488551--1488590 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1488541 TATTCGAAAT
1488551 TATTAATTTTTTAATCTA
1 TATTAATTTTTTAATCTA
1488569 T-TTAATATTTTT-AT-TA
1 TATTAAT-TTTTTAATCTA
1488585 TATTAA
1 TATTAA
1488591 ATTAAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.15
17 11 0.55
18 6 0.30
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAATTTTTTAATCTA
Found at i:1494106 original size:20 final size:17
Alignment explanation
Indices: 1494077--1494118 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
1494067 TAATTACAAC
1494077 CAATATAATCAAATAGTTA
1 CAATATAATCAAA-A-TTA
1494096 CAATCATAATCAAAATTA
1 CAAT-ATAATCAAAATTA
1494114 CAATA
1 CAATA
1494119 CGCGATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.32
19 5 0.23
20 9 0.41
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (17 bp):
CAATATAATCAAAATTA
Found at i:1501766 original size:31 final size:31
Alignment explanation
Indices: 1501714--1501773 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1501704 AAAAAACTCA
** *
1501714 TTTTAGCTCTTCGTTTAGTTTTTTTTATCTT
1 TTTTAGCTCTTAATTTAGTTTTATTTATCTT
1501745 TTTTAGCTCTTAAATTT-GTTTTATTTATC
1 TTTTAGCTCTT-AATTTAGTTTTATTTATC
1501774 AAATTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.65
Consensus pattern (31 bp):
TTTTAGCTCTTAATTTAGTTTTATTTATCTT
Found at i:1501889 original size:7 final size:8
Alignment explanation
Indices: 1501872--1501928 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
1501862 ATTATTTTTT
1501872 AAAATTAA
1 AAAATTAA
1501880 AAAATTAA
1 AAAATTAA
1501888 AAATATTAA
1 AAA-ATTAA
1501897 AAATATTTAA
1 AAA-A-TTAA
**
1501907 AGTATTAA
1 AAAATTAA
*
1501915 AAAACTATA
1 AAAATTA-A
1501924 AAAAT
1 AAAAT
1501929 ATCTTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 19 0.47
9 16 0.40
10 5 0.12
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (8 bp):
AAAATTAA
Found at i:1501912 original size:18 final size:17
Alignment explanation
Indices: 1501875--1501940 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 17
1501865 ATTTTTTAAA
1501875 ATTAAAAAATTAAAAAT
1 ATTAAAAAATTAAAAAT
* *
1501892 ATTAAAAATATTTAAAGT
1 ATTAAAAA-ATTAAAAAT
1501910 ATTAAAAAACTATAAAAAT
1 ATTAAAAAA-T-TAAAAAT
*
1501929 ATCTTAAAAATT
1 AT-TAAAAAATT
1501941 TTTTTGTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.22
18 17 0.43
19 8 0.20
20 6 0.15
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTAAAAAATTAAAAAT
Found at i:1501939 original size:11 final size:9
Alignment explanation
Indices: 1501875--1501930 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
1501865 ATTTTTTAAA
1501875 ATTAAAAA-
1 ATTAAAAAT
1501883 ATTAAAAAT
1 ATTAAAAAT
1501892 ATTAAAAAT
1 ATTAAAAAT
* *
1501901 ATTTAAAGT
1 ATTAAAAAT
1501910 ATTAAAAA-
1 ATTAAAAAT
1501918 ACTATAAAAAT
1 A-T-TAAAAAT
1501929 AT
1 AT
1501931 CTTAAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 9 0.22
9 23 0.57
10 7 0.17
11 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:1505041 original size:3 final size:3
Alignment explanation
Indices: 1505033--1505072 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1505023 TATTCTTACT
1505033 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1505073 CACAACGTAA
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:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1505997 original size:17 final size:17
Alignment explanation
Indices: 1505971--1506004 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1505961 ATTTCCTAAG
*
1505971 TATGTAATATATTTTAT
1 TATGTAATATAATTTAT
*
1505988 TATGTTATATAATTTAT
1 TATGTAATATAATTTAT
1506005 AACACATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATGTAATATAATTTAT
Found at i:1509886 original size:25 final size:24
Alignment explanation
Indices: 1509858--1509905 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1509848 ATCTAGGCAA
*
1509858 TATAATGGGAAGCTCACAAAGAGCC
1 TATAAAGGGAAGCTC-CAAAGAGCC
1509883 TATAAAGGGAAGCTCCAAAGAGC
1 TATAAAGGGAAGCTCCAAAGAGC
1509906 AATTAATGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.15
Consensus pattern (24 bp):
TATAAAGGGAAGCTCCAAAGAGCC
Found at i:1509920 original size:24 final size:25
Alignment explanation
Indices: 1509854--1509932 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 25
1509844 ACTTATCTAG
1509854 GCAATATAATGGGAAGCTCACAAAGA
1 GCAATATAATGGGAAGCTC-CAAAGA
* *
1509880 GC-CTATAAAGGGAAGCTCCAAAGA
1 GCAATATAATGGGAAGCTCCAAAGA
* * *
1509904 GCAAT-TAATGGGTAGCTTCGAAGA
1 GCAATATAATGGGAAGCTCCAAAGA
1509928 GCAAT
1 GCAAT
1509933 TAACAGGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
24 28 0.62
25 15 0.33
26 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (25 bp):
GCAATATAATGGGAAGCTCCAAAGA
Found at i:1510014 original size:26 final size:25
Alignment explanation
Indices: 1509981--1510029 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1509971 AAGCGAGCAC
1509981 TAATGGGAAGCTCACAAAGAGCCTT
1 TAATGGGAAGCTCACAAAGAGCCTT
**
1510006 TAATCGGGAAGCTCATGAAGAGCC
1 TAAT-GGGAAGCTCACAAAGAGCC
1510030 ATATAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
TAATGGGAAGCTCACAAAGAGCCTT
Found at i:1511538 original size:37 final size:37
Alignment explanation
Indices: 1511488--1511592 Score: 201
Period size: 37 Copynumber: 2.8 Consensus size: 37
1511478 TAGAAATGAT
*
1511488 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAACATAA
1511525 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAACATAA
1511562 CAGTGGTAGCTTCGGCTACATTTCAGTGGTA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTA
1511593 GCTTCGGCTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (37 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAACATAA
Found at i:1511588 original size:23 final size:23
Alignment explanation
Indices: 1511556--1511612 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1511546 TTCAGTGGTA
*
1511556 ACATAACAGTGGTAGCTTCGGCT
1 ACATATCAGTGGTAGCTTCGGCT
*
1511579 ACATTTCAGTGGTAGCTTCGGCT
1 ACATATCAGTGGTAGCTTCGGCT
1511602 ACATATCAGTG
1 ACATATCAGTG
1511613 TTGCACTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ACATATCAGTGGTAGCTTCGGCT
Found at i:1513360 original size:20 final size:21
Alignment explanation
Indices: 1513318--1513361 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1513308 AGCCCATGAA
*
1513318 TTCCATGATATTTCATAATTT
1 TTCCATGATATTTCATAACTT
1513339 TTCCATGA-A-TTCAATAACTT
1 TTCCATGATATTTC-ATAACTT
1513359 TTC
1 TTC
1513362 AATTTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (21 bp):
TTCCATGATATTTCATAACTT
Found at i:1518490 original size:17 final size:17
Alignment explanation
Indices: 1518470--1518509 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1518460 AAGTATATTA
* *
1518470 AAAATATATGTATTTAT
1 AAAATATACGTATATAT
1518487 AAAATATACGTATATAT
1 AAAATATACGTATATAT
*
1518504 ATAATA
1 AAAATA
1518510 AAAATAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (17 bp):
AAAATATACGTATATAT
Found at i:1521475 original size:31 final size:31
Alignment explanation
Indices: 1521430--1521508 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
1521420 TCAAAAAAAA
1521430 TTTAGAAAATTAAAAAAAGCATGTTAAAAATA-T
1 TTTA-AAAA-TAAAAAAAGCAT-TTAAAAATATT
* *
1521463 TTTAAAAATAAAAAAAGTATTTTAAAATATT
1 TTTAAAAATAAAAAAAGCATTTAAAAATATT
1521494 TTTAAAAATAAAAAA
1 TTTAAAAATAAAAAA
1521509 TACATATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 8 0.19
31 27 0.63
32 4 0.09
33 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (31 bp):
TTTAAAAATAAAAAAAGCATTTAAAAATATT
Found at i:1521525 original size:32 final size:31
Alignment explanation
Indices: 1521456--1521517 Score: 65
Period size: 30 Copynumber: 2.0 Consensus size: 31
1521446 AAGCATGTTA
* *
1521456 AAAATATTTTAAAAATA-AAAAAA-GTATTTT
1 AAAATATTTTTAAAA-ATAAAAAAAATATTTT
1521486 AAAATATTTTTAAAAATAAAAAATACATATTT
1 AAAATATTTTTAAAAATAAAAAA-A-ATATTT
1521518 ATTATATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.04
30 20 0.77
33 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAATATTTTTAAAAATAAAAAAAATATTTT
Found at i:1521585 original size:18 final size:18
Alignment explanation
Indices: 1521562--1521597 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1521552 AAGTGGTGCC
1521562 CGAGGCCCGGCCCGTTTT
1 CGAGGCCCGGCCCGTTTT
* *
1521580 CGAGGCCTGGCCTGTTTT
1 CGAGGCCCGGCCCGTTTT
1521598 TTAATCGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.33, G:0.33, T:0.28
Consensus pattern (18 bp):
CGAGGCCCGGCCCGTTTT
Found at i:1523199 original size:5 final size:5
Alignment explanation
Indices: 1523189--1523476 Score: 576
Period size: 5 Copynumber: 57.6 Consensus size: 5
1523179 TTGTTCTAGG
1523189 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1523239 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1523289 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1523339 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1523389 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1523439 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
1523477 ACTTATTTAT
Statistics
Matches: 283, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 283 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1525407 original size:3 final size:3
Alignment explanation
Indices: 1525399--1525436 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1525389 TATCAGTTCA
1525399 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1525437 CATTTGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1525588 original size:6 final size:6
Alignment explanation
Indices: 1525577--1525604 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1525567 ACAATGATAT
1525577 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
1525605 GATTGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:1526062 original size:13 final size:14
Alignment explanation
Indices: 1526040--1526068 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1526030 ATAACTATTT
1526040 TTAT-ATTTTTAAA
1 TTATAATTTTTAAA
1526053 TTATAATTTTTAAA
1 TTATAATTTTTAAA
1526067 TT
1 TT
1526069 TTATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATAATTTTTAAA
Found at i:1526638 original size:19 final size:18
Alignment explanation
Indices: 1526614--1526649 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1526604 AACTTTTATG
1526614 ATTTTTTAAAATAATTTTC
1 ATTTTTTAAAA-AATTTTC
*
1526633 ATTTTTTTAAAAATTTT
1 ATTTTTTAAAAAATTTT
1526650 ATGAAGTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTAAAAAATTTTC
Found at i:1526758 original size:3 final size:3
Alignment explanation
Indices: 1526750--1526774 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1526740 CCATTTGACT
1526750 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1526775 TTAGGGTCAA
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:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1528190 original size:3 final size:3
Alignment explanation
Indices: 1528182--1528209 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1528172 GGTAATGAAT
1528182 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1528210 GAAGTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1531318 original size:17 final size:16
Alignment explanation
Indices: 1531298--1531350 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
1531288 TCTAAAAGAC
1531298 CTTATTTTTTGTCTAAA
1 CTTATTTTTT-TCTAAA
1531315 CTTA--TTTTTC-AAA
1 CTTATTTTTTTCTAAA
*
1531328 CTTATATTTTTTCTAAT
1 CTTAT-TTTTTTCTAAA
1531345 CTTATT
1 CTTATT
1531351 CACTTTTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 7 0.23
14 2 0.06
15 4 0.13
16 7 0.23
17 11 0.35
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60
Consensus pattern (16 bp):
CTTATTTTTTTCTAAA
Found at i:1531874 original size:23 final size:22
Alignment explanation
Indices: 1531848--1531896 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1531838 TAAAAATGTA
1531848 AAATATTAGCTTTATT-AAACAAT
1 AAATATTA--TTTATTAAAACAAT
* *
1531871 AAATGTTATTTTTTAAAACAAT
1 AAATATTATTTATTAAAACAAT
1531893 AAAT
1 AAAT
1531897 GTTAATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (22 bp):
AAATATTATTTATTAAAACAAT
Found at i:1532835 original size:13 final size:14
Alignment explanation
Indices: 1532813--1532841 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1532803 ATAACTATTT
1532813 TTAT-ATTTTTAAA
1 TTATAATTTTTAAA
1532826 TTATAATTTTTAAA
1 TTATAATTTTTAAA
1532840 TT
1 TT
1532842 TTATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATAATTTTTAAA
Found at i:1532923 original size:69 final size:70
Alignment explanation
Indices: 1532791--1532934 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 70
1532781 AAAATGCAAC
* * * * * *
1532791 TATTTTAATTTTATAACTATTTTTATATTTTTAAATTATAATTTTTAAATTTTATAATATTTTAT
1 TATTTTAATATTAAAAATATTTATATATTTTTAAATTAAAATTTTTAAATTTTATAAGATTTTAT
1532856 AACATA
66 AA-ATA
* * *
1532862 TATTTTAATATTAAAAATA-TTATATATTTTT-TATTAAAATTTCTT-AATTTTATAGGGTTTTA
1 TATTTTAATATTAAAAATATTTATATATTTTTAAATTAAAATTT-TTAAATTTTATAAGATTTTA
1532924 TAAATA
65 TAAATA
1532930 TATTT
1 TATTT
1532935 GATTGAATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
68 8 0.13
69 26 0.41
70 13 0.21
71 16 0.25
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (70 bp):
TATTTTAATATTAAAAATATTTATATATTTTTAAATTAAAATTTTTAAATTTTATAAGATTTTAT
AAATA
Done.