Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 4 of 59
Found at i:736180 original size:35 final size:35
Alignment explanation
Indices: 736140--736209 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
736130 ATCATTTTAA
* *
736140 ACAACAAATATAACCACAAAATGCCCATGTGCATG
1 ACAACAAATACAACCACAAAATGACCATGTGCATG
* *
736175 ACAACACATACAACCACACAATGACCATGTGCATG
1 ACAACAAATACAACCACAAAATGACCATGTGCATG
736210 TTCAAGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (35 bp):
ACAACAAATACAACCACAAAATGACCATGTGCATG
Found at i:743989 original size:42 final size:45
Alignment explanation
Indices: 743908--743999 Score: 154
Period size: 43 Copynumber: 2.1 Consensus size: 45
743898 CTCTCTCTCT
*
743908 TCTTTTCTTTTTTTTTCTTACTGTCGTATTGTTGTCTTGTCATGN
1 TCTTTTCTTTTTTTTTCTTACTGTCGTATTGTTGTCTTGTCATGC
743953 TCTTTT-TTTTTTTTTC-TACTGTCGTATTGTTG-CTTGTCATGC
1 TCTTTTCTTTTTTTTTCTTACTGTCGTATTGTTGTCTTGTCATGC
743995 TCTTT
1 TCTTT
744000 GACACACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 14 0.30
43 16 0.35
44 10 0.22
45 6 0.13
ACGTcount: A:0.07, C:0.16, G:0.13, T:0.63
Consensus pattern (45 bp):
TCTTTTCTTTTTTTTTCTTACTGTCGTATTGTTGTCTTGTCATGC
Found at i:745221 original size:16 final size:16
Alignment explanation
Indices: 745202--745236 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
745192 TTAAATAAGA
* *
745202 TTTATTTTAATATTAT
1 TTTATCTTAAAATTAT
745218 TTTATCTTAAAATTAT
1 TTTATCTTAAAATTAT
745234 TTT
1 TTT
745237 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATCTTAAAATTAT
Found at i:751026 original size:2 final size:2
Alignment explanation
Indices: 751015--751066 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
751005 GTATCTTCAT
751015 TA TA -A TA TA TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
751057 TA TA TA TA TA
1 TA TA TA TA TA
751067 GTAGTAGACT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:754183 original size:2 final size:2
Alignment explanation
Indices: 754176--754202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
754166 GTGACACTTT
754176 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
754203 GGATTATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:755484 original size:15 final size:15
Alignment explanation
Indices: 755458--755494 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
755448 AAAACAAAAA
755458 AAAAAT-GGAAAAG-
1 AAAAATAGGAAAAGT
755471 AAAGAATAGGAAAAGT
1 AAA-AATAGGAAAAGT
755487 AAAAATAG
1 AAAAATAG
755495 AATGATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 12 0.57
16 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.11
Consensus pattern (15 bp):
AAAAATAGGAAAAGT
Found at i:763535 original size:11 final size:11
Alignment explanation
Indices: 763519--763566 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
763509 GGATTTCCCA
763519 TTTTTTATTCT
1 TTTTTTATTCT
763530 TTTTTTATCTCCT
1 TTTTTTAT-T-CT
*
763543 TTTTTTTTTCT
1 TTTTTTATTCT
*
763554 TATTTTTTTTCT
1 T-TTTTTATTCT
763566 T
1 T
763567 CCAACGTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 11 0.33
12 13 0.39
13 9 0.27
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTATTCT
Found at i:775347 original size:3 final size:3
Alignment explanation
Indices: 775339--775376 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
775329 GTGGGGGAGA
*
775339 GGT GGT GGT GGT GGT GGT GGT GGT GGT GAT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
775377 GGGAGGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.66, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:779663 original size:14 final size:14
Alignment explanation
Indices: 779644--779679 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
779634 TCTTGAAGGT
* *
779644 AAAAAGTTAAAAGA
1 AAAAAGTAAAAAAA
779658 AAAAAGTAAAAAAA
1 AAAAAGTAAAAAAA
779672 AAAAAGTA
1 AAAAAGTA
779680 GGCAATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (14 bp):
AAAAAGTAAAAAAA
Found at i:779955 original size:2 final size:2
Alignment explanation
Indices: 779948--779984 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
779938 ACAGAAAGAA
779948 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
779985 ACAGAACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:787262 original size:3 final size:3
Alignment explanation
Indices: 787254--787285 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
787244 TCCTTTGCTG
*
787254 TCT TCT TCT TCT TCT TCT TCT TCT TCG TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
787286 GTCGTCGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:787290 original size:9 final size:9
Alignment explanation
Indices: 787253--787291 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
787243 ATCCTTTGCT
787253 GTCTTCTTC
1 GTCTTCTTC
*
787262 TTCTTCTTC
1 GTCTTCTTC
*
787271 TTCTTCTTC
1 GTCTTCTTC
*
787280 GTCTTCGTC
1 GTCTTCTTC
787289 GTC
1 GTC
787292 GACGACTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.10, T:0.56
Consensus pattern (9 bp):
GTCTTCTTC
Found at i:793995 original size:2 final size:2
Alignment explanation
Indices: 793988--794050 Score: 67
Period size: 2 Copynumber: 31.5 Consensus size: 2
793978 AAAAGCATGA
* * *
793988 AT AT AT AT AT AT AT AT AT AT AT AT ANT A- AA AG AC AT GA- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT AT AT
794030 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
794051 CAAAGAATAC
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
1 2 0.04
2 49 0.91
3 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.41
Consensus pattern (2 bp):
AT
Found at i:794025 original size:38 final size:36
Alignment explanation
Indices: 793973--794050 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 36
793963 TCTTTATTTG
793973 ATATA-AAAAGCATGAATATATATATATATATATAT
1 ATATATAAAAGCATGAATATATATATATATATATAT
794008 ATATANTAAAAGACATGAATATATATATATATATATAT
1 ATATA-TAAAAG-CATGAATATATATATATATATATAT
794046 ATATA
1 ATATA
794051 CAAAGAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 5 0.12
37 5 0.12
38 30 0.75
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (36 bp):
ATATATAAAAGCATGAATATATATATATATATATAT
Found at i:796254 original size:2 final size:2
Alignment explanation
Indices: 796247--796280 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
796237 TTTTCTTTCT
796247 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
796281 GCCAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:805572 original size:33 final size:32
Alignment explanation
Indices: 805501--805683 Score: 128
Period size: 33 Copynumber: 5.7 Consensus size: 32
805491 AAGTTTTTAA
**
805501 TTTTATTAATAT-TGTATAATTTA-TTTATTT
1 TTTTATTAATATCTGTATTTTTTATTTTATTT
* * *
805531 ATTAATTAATATCATGTATTTTTTGTTTTATTT
1 TTTTATTAATATC-TGTATTTTTTATTTTATTT
* * * *
805564 TTTTATTAACA-CGGTACTGTTTTATTTTTTTT
1 TTTTATTAATATCTGTA-TTTTTTATTTTATTT
* **
805596 TGTTTATTAATATC-GTACTTTTTAATCATACTTT
1 T-TTTATTAATATCTGTA-TTTTTTATTTTA-TTT
805630 TTTTATTAATAT-TGTATTATTTTAATTTT-TTT
1 TTTTATTAATATCTGTATT-TTTT-ATTTTATTT
* *
805662 ATTTATTAATATC-ATATTTTTT
1 TTTTATTAATATCTGTATTTTTT
805684 TATCATTATC
Statistics
Matches: 119, Mismatches: 23, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
30 10 0.08
31 7 0.06
32 42 0.35
33 52 0.44
34 8 0.07
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (32 bp):
TTTTATTAATATCTGTATTTTTTATTTTATTT
Found at i:805667 original size:65 final size:62
Alignment explanation
Indices: 805501--805689 Score: 173
Period size: 65 Copynumber: 2.9 Consensus size: 62
805491 AAGTTTTTAA
* * * * **
805501 TTTTATTAATATTGTATAATTT-ATTTATTTATTAATTAATATCATGTATTTTTTGTTTTATTT
1 TTTTATTAATATTGTATATTTTAATTTTTTTATTTATTAATATC--GTATTTTTTATCATATTT
* ** * * * *
805564 TTTTATTAACACGGTACTGTTTTATTTTTTTTTGTTTATTAATATCGTACTTTTTAATCATACTT
1 TTTTATTAATATTGTA-TATTTTA-ATTTTTTTATTTATTAATATCGTA-TTTTTTATCATA-TT
805629 T
62 T
*
805630 TTTTATTAATATTGTATTATTTTAATTTTTTTATTTATTAATATCATATTTTTTTATCAT
1 TTTTATTAATATTGTA-TATTTTAATTTTTTTATTTATTAATATCGTA-TTTTTTATCAT
805690 TATCCCACAG
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
63 13 0.13
64 7 0.07
65 39 0.40
66 39 0.40
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (62 bp):
TTTTATTAATATTGTATATTTTAATTTTTTTATTTATTAATATCGTATTTTTTATCATATTT
Found at i:805685 original size:32 final size:31
Alignment explanation
Indices: 805590--805685 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
805580 CTGTTTTATT
*
805590 TTTTTTTGTTTATTAATATCGTA-CTTTTTAA
1 TTTTTTT-TTTATTAATATCGTATTTTTTTAA
* * *
805621 TCATACTTTTTTTATTAATATTGTATTATTTTAA
1 T--T-TTTTTTTTATTAATATCGTATTTTTTTAA
*
805655 TTTTTTTATTTATTAATATCATATTTTTTTA
1 TTTTTTT-TTTATTAATATCGTATTTTTTTA
805686 TCATTATCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 5 0.10
32 21 0.40
33 15 0.29
34 11 0.21
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTTTTTTTTATTAATATCGTATTTTTTTAA
Found at i:805934 original size:33 final size:32
Alignment explanation
Indices: 805895--806002 Score: 96
Period size: 33 Copynumber: 3.3 Consensus size: 32
805885 AATTTTTTTG
805895 TTTATTAATATCGTACTTTTTTAATCATACTTT
1 TTTATTAATATCGTACTTTTTTAAT-ATACTTT
* * **
805928 TTTATTAATATTGCACCGTTTTAAT-T--TTT
1 TTTATTAATATCGTACTTTTTTAATATACTTT
* *
805957 GTTTATTAATATCATACTTTTTTATTATACATTGTT
1 -TTTATTAATATCGTACTTTTTTAATATAC--T-TT
805993 TTTATTAATA
1 TTTATTAATA
806003 ACATCCAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
29 3 0.05
30 19 0.33
31 2 0.03
33 21 0.36
35 11 0.19
36 2 0.03
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (32 bp):
TTTATTAATATCGTACTTTTTTAATATACTTT
Found at i:806275 original size:42 final size:42
Alignment explanation
Indices: 806211--806296 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
806201 TAACGTGACG
**
806211 TTAAAGCATCAAATATATATAAACTCGGGATTTAAACTTTTA
1 TTAAAGCATCAAATATATATAAACTCAAGATTTAAACTTTTA
* *
806253 TTAATGCATCGAATATATATAAACTCAAGATTTAAACTTTTA
1 TTAAAGCATCAAATATATATAAACTCAAGATTTAAACTTTTA
806295 TT
1 TT
806297 TTTGCTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (42 bp):
TTAAAGCATCAAATATATATAAACTCAAGATTTAAACTTTTA
Found at i:816084 original size:2 final size:2
Alignment explanation
Indices: 816077--816121 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
816067 TGGTTTTATT
* *
816077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
816119 TA T
1 TA T
816122 TGTTTAGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:816197 original size:2 final size:2
Alignment explanation
Indices: 816190--816232 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
816180 GTTTATTTAT
* *
816190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
816232 T
1 T
816233 GTTTTGCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:822275 original size:2 final size:2
Alignment explanation
Indices: 822268--822293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
822258 ATGGTTTTAT
822268 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
822294 AAGATTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:823621 original size:2 final size:2
Alignment explanation
Indices: 823614--823642 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
823604 AGTATGTATG
823614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
823643 TTAGGTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:838182 original size:80 final size:79
Alignment explanation
Indices: 838080--838336 Score: 383
Period size: 80 Copynumber: 3.2 Consensus size: 79
838070 CAAATTTTAT
* * * * **
838080 TATTAATTCATATTATAAATATTTAAAATAAAATAATGACTATACAAAATAGAATAAATTAAGTT
1 TATTAATTCATATTATAAATATTTAAAGTAAAATAATAATTATAGAAAATAGAATAAATTAAAAT
838145 TTATTATTTATGAA
66 TTATTATTTATGAA
*
838159 CTATTAATTCATATTATAAATATTTAAAGTAAAATAAAAATTATAGAAAATAGAATAAATTAAAA
1 -TATTAATTCATATTATAAATATTTAAAGTAAAATAATAATTATAGAAAATAGAATAAATTAAAA
838224 TTTATTA-TTATTGAAA
65 TTTATTATTTA-TG-AA
* * *
838240 TATTAATTCATATTATAAATATTTAAAGTAAAACAATAATTATAGAAAATATAATAAATGAAAAT
1 TATTAATTCATATTATAAATATTTAAAGTAAAATAATAATTATAGAAAATAGAATAAATTAAAAT
838305 TTATTATTTATGAA
66 TTATTATTTATGAA
838319 TATTAATTCATA-TATAAA
1 TATTAATTCATATTATAAA
838337 ATGAATATCA
Statistics
Matches: 163, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
78 6 0.04
79 17 0.10
80 135 0.83
81 5 0.03
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (79 bp):
TATTAATTCATATTATAAATATTTAAAGTAAAATAATAATTATAGAAAATAGAATAAATTAAAAT
TTATTATTTATGAA
Found at i:838340 original size:23 final size:24
Alignment explanation
Indices: 838314--838360 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
838304 TTTATTATTT
*
838314 ATGAATATTAATTCATA-TATAAA
1 ATGAATATCAATTCATATTATAAA
838337 ATGAATATCAATTCATATTATAAA
1 ATGAATATCAATTCATATTATAAA
838361 TATTTAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
ATGAATATCAATTCATATTATAAA
Found at i:838492 original size:100 final size:100
Alignment explanation
Indices: 838241--838542 Score: 297
Period size: 102 Copynumber: 3.0 Consensus size: 100
838231 TTATTGAAAT
* *
838241 ATTAATTCATATTATAAATATTTAAAGTAAAACAATAATTA-TAGAAAATATAATAAATGAAAAT
1 ATTAATTCATATTATAAATATTTAAAATAAAATAATAA-TAGTAGAAAATATAATAAATGAAAAT
838305 TTATTATTTATGAATATTAATTCATATATAAAATGA
65 TTATTATTTATGAATATTAATTCATATATAAAATGA
* * * *
838341 ATATCAATTCATATTATAAATATTTAAAACAAAATAAAAATTGTAGAAAATATAATAAATGACAA
1 AT-T-AATTCATATTATAAATATTTAAAATAAAATAATAATAGTAGAAAATATAATAAATGAAAA
* ** ***
838406 TTTATTATTTATGATAAATATT-TTTGGTA-ATTTTAT-A
64 TTTATTATTTATG---AATATTAATTCATATATAAAATGA
* * * * * * * **
838443 ATTAATTCATAATATAAATATTTAAAATGAAATAATGATAGTACAAAATAGAAAAAAATTAAGTT
1 ATTAATTCATATTATAAATATTTAAAATAAAATAATAATAGTAGAAAATA-TAATAAATGAAAAT
*
838508 TTATTATTTATGAAAAATTAATTCATATTATAAAA
65 TTATTATTTATG-AATATTAATTCATA-TATAAAA
838543 ATGTTTAAAA
Statistics
Matches: 160, Mismatches: 32, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
99 6 0.04
100 46 0.29
101 23 0.14
102 71 0.44
103 4 0.03
104 4 0.03
105 6 0.04
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (100 bp):
ATTAATTCATATTATAAATATTTAAAATAAAATAATAATAGTAGAAAATATAATAAATGAAAATT
TATTATTTATGAATATTAATTCATATATAAAATGA
Found at i:846011 original size:11 final size:11
Alignment explanation
Indices: 845986--846041 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
845976 ATTATCTATA
* *
845986 ATTTTTTTGTC
1 ATTTTTTTATT
845997 ATTTTTTTATT
1 ATTTTTTTATT
**
846008 ATTTAATTATT
1 ATTTTTTTATT
846019 ATTTTTATT-TT
1 ATTTTT-TTATT
846030 A-TTTTTTATT
1 ATTTTTTTATT
846040 AT
1 AT
846042 CATGTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 2 0.06
10 7 0.19
11 25 0.69
12 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:846037 original size:25 final size:25
Alignment explanation
Indices: 846001--846076 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
845991 TTTGTCATTT
*
846001 TTTTATTATTTAATTATTATTTTTA
1 TTTTATTTTTTAATTATTATTTTTA
*
846026 TTTTATTTTTT-ATTATCATGTTTTA
1 TTTTATTTTTTAATTATTAT-TTTTA
846051 TATTT-TTATTTCTAATTATTATTTTT
1 T-TTTATT-TTT-TAATTATTATTTTT
846077 TATACTTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 7 0.16
25 18 0.42
26 6 0.14
27 5 0.12
28 7 0.16
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (25 bp):
TTTTATTTTTTAATTATTATTTTTA
Found at i:846068 original size:28 final size:28
Alignment explanation
Indices: 846026--846080 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
846016 ATTATTTTTA
* *
846026 TTTTATTTTTTATTATCATGTTTTATAT
1 TTTTATTTCTAATTATCATGTTTTATAT
* *
846054 TTTTATTTCTAATTATTATTTTTTATA
1 TTTTATTTCTAATTATCATGTTTTATA
846081 CTTTACGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTTATTTCTAATTATCATGTTTTATAT
Found at i:846311 original size:17 final size:16
Alignment explanation
Indices: 846278--846330 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
846268 TATATTCAAA
*
846278 TTATTAT-TATTATTT
1 TTATTATCTATCATTT
846293 TTATTATCATATCATTT
1 TTATTATC-TATCATTT
*
846310 TT-TTATCTATTATTAT
1 TTATTATCTATCATT-T
846326 TTATT
1 TTATT
846331 TATTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 13 0.41
16 8 0.25
17 11 0.34
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATCTATCATTT
Found at i:849829 original size:3 final size:3
Alignment explanation
Indices: 849821--849856 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
849811 TACGGGAGAA
849821 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
849857 TATGATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:851976 original size:2 final size:2
Alignment explanation
Indices: 851969--851997 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
851959 ACAATCTTTA
851969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
851998 ATACCAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:872867 original size:23 final size:22
Alignment explanation
Indices: 872834--872913 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
872824 GCAATGCCTA
*
872834 AGTCACACAATGCCTTACAAACT
1 AGTCACGCAATGCCTTAC-AACT
*
872857 AGTCACGCAATGCCTTACTAACA
1 AGTCACGCAATGCCTTAC-AACT
*
872880 AGTCCATGCAATGCC-TATCAACT
1 AGT-CACGCAATGCCTTA-CAACT
*
872903 AGTCAAGCAAT
1 AGTCACGCAAT
872914 NCACAGTGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
22 7 0.14
23 31 0.63
24 11 0.22
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (22 bp):
AGTCACGCAATGCCTTACAACT
Found at i:873034 original size:177 final size:175
Alignment explanation
Indices: 872735--873089 Score: 683
Period size: 177 Copynumber: 2.0 Consensus size: 175
872725 TGCGTGACTT
872735 AATCACAGTGTGACTAGTTTTTAGTCATTACGTGATTGATTTTAGGCATTACGTGACTAATTGTT
1 AATCACAGTGTGACTAGTTTTTAGTCATTACGTGATTGATTTTAGGCATTACGTGACTAATTGTT
872800 ATACATTGTATGACTGATTTTTAAGCAATGCCTAAGTCACACAATGCCTTACAAACTAGTCACGC
66 ATACATTGTATGACTGATTTTTAAGCAATGCCTAAGTCACACAATGCCTTACAAACTAGTCACGC
872865 AATGCCTTACTAACAAGTCCATGCAATGCCTATCAACTAGTCAAGC
131 AATGCCTTACTAACAAGT-CATGCAATGCCTATCAACTAGTCAAGC
872911 AATNCACAGTGTGACTAGTTTTTAGTCATTACGTGATTGATTTTAGGCATTACGTGACTAATTGT
1 AAT-CACAGTGTGACTAGTTTTTAGTCATTACGTGATTGATTTTAGGCATTACGTGACTAATTGT
872976 TATACATTGTATGACTGATTTTTAAGCAATGCCTAAGTCACACAATGCCTTACAAACTAGTCACG
65 TATACATTGTATGACTGATTTTTAAGCAATGCCTAAGTCACACAATGCCTTACAAACTAGTCACG
*
873041 CAATGCCTTACTAACAAGTCATGCAATGCCTATCAACTAGTCATGC
130 CAATGCCTTACTAACAAGTCATGCAATGCCTATCAACTAGTCAAGC
873087 AAT
1 AAT
873090 ACCTTATTAG
Statistics
Matches: 177, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
176 32 0.18
177 145 0.82
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (175 bp):
AATCACAGTGTGACTAGTTTTTAGTCATTACGTGATTGATTTTAGGCATTACGTGACTAATTGTT
ATACATTGTATGACTGATTTTTAAGCAATGCCTAAGTCACACAATGCCTTACAAACTAGTCACGC
AATGCCTTACTAACAAGTCATGCAATGCCTATCAACTAGTCAAGC
Found at i:873044 original size:23 final size:23
Alignment explanation
Indices: 873011--873126 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
873001 GCAATGCCTA
*
873011 AGTCACACAATGCCTTACAAACT
1 AGTCACGCAATGCCTTACAAACT
* *
873034 AGTCACGCAATGCCTTACTAACA
1 AGTCACGCAATGCCTTACAAACT
*
873057 AGTCATGCAATGCC-TATC-AACT
1 AGTCACGCAATGCCTTA-CAAACT
* * * *
873079 AGTCATGCAATACCTTATTAGAAATT
1 AGTCACGCAATGCC---TTACAAACT
873105 AGTCACGCAATGCCTTATCAAA
1 AGTCACGCAATGCCTTA-CAAA
873127 AACTAATCAT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
22 18 0.24
23 37 0.49
24 3 0.04
26 17 0.23
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACAAACT
Found at i:873144 original size:21 final size:21
Alignment explanation
Indices: 873120--873162 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
873110 CGCAATGCCT
873120 TATCAAAAACTAATCATGCAA
1 TATCAAAAACTAATCATGCAA
* ** *
873141 TATCCAAAGTTAGTCATGCAA
1 TATCAAAAACTAATCATGCAA
873162 T
1 T
873163 GCCTTATTAG
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:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (21 bp):
TATCAAAAACTAATCATGCAA
Found at i:873169 original size:73 final size:73
Alignment explanation
Indices: 873078--873302 Score: 281
Period size: 73 Copynumber: 3.1 Consensus size: 73
873068 GCCTATCAAC
* **
873078 TAGTCATGCAATACCTTATTAGAAATTAGTCACGCAATGCCTTATCAAAAACTAATCATGCAATA
1 TAGTCATGCAATGCCTTATTAGAAATTAGTCACGCAATGCCTTATCAAAAACTAATCACACAATA
*
873143 TCCAAAGT
66 CCCAAAGT
* * * * *
873151 TAGTCATGCAATGCCTTATTAGAAACTAGTCACGCAATGCCTTATAAAAAACTAGTCACACCATG
1 TAGTCATGCAATGCCTTATTAGAAATTAGTCACGCAATGCCTTATCAAAAACTAATCACACAATA
873216 CCCAAAGT
66 CCCAAAGT
* * * ** *
873224 TAATCACGCAATGCCTTATCAGAAATTAGTCATACAATGCCTTATCAAAAA-TCAATCACATAAT
1 TAGTCATGCAATGCCTTATTAGAAATTAGTCACGCAATGCCTTATCAAAAACT-AATCACACAAT
*
873288 ACCTAAAGT
65 ACCCAAAGT
*
873297 CAGTCA
1 TAGTCA
873303 CACAATGCTT
Statistics
Matches: 128, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
72 1 0.01
73 127 0.99
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (73 bp):
TAGTCATGCAATGCCTTATTAGAAATTAGTCACGCAATGCCTTATCAAAAACTAATCACACAATA
CCCAAAGT
Found at i:873275 original size:26 final size:26
Alignment explanation
Indices: 873011--873275 Score: 138
Period size: 26 Copynumber: 11.0 Consensus size: 26
873001 GCAATGCCTA
* *
873011 AGTCACACAATGCCTTA-C--AAACT
1 AGTCACGCAATGCCTTATCAAAAATT
* *
873034 AGTCACGCAATGCCTTA-CTAACA--
1 AGTCACGCAATGCCTTATCAAAAATT
* *
873057 AGTCATGCAATGCC-TATC---AACT
1 AGTCACGCAATGCCTTATCAAAAATT
* * * *
873079 AGTCATGCAATACCTTATTAGAAATT
1 AGTCACGCAATGCCTTATCAAAAATT
*
873105 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAATT
* * * *
873131 AATCATGCAA-----TATCCAAAGTT
1 AGTCACGCAATGCCTTATCAAAAATT
* * * *
873152 AGTCATGCAATGCCTTATTAGAAACT
1 AGTCACGCAATGCCTTATCAAAAATT
* *
873178 AGTCACGCAATGCCTTATAAAAAACT
1 AGTCACGCAATGCCTTATCAAAAATT
* * *
873204 AGTCACACCATGCC----C-AAAGTT
1 AGTCACGCAATGCCTTATCAAAAATT
* *
873225 AATCACGCAATGCCTTATCAGAAATT
1 AGTCACGCAATGCCTTATCAAAAATT
**
873251 AGTCATACAATGCCTTATCAAAAAT
1 AGTCACGCAATGCCTTATCAAAAAT
873276 CAATCACATA
Statistics
Matches: 183, Mismatches: 40, Indels: 35
0.71 0.16 0.14
Matches are distributed among these distances:
20 1 0.01
21 32 0.17
22 15 0.08
23 34 0.19
25 3 0.02
26 98 0.54
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAAAAATT
Found at i:873338 original size:22 final size:22
Alignment explanation
Indices: 873298--873339 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
873288 ACCTAAAGTC
*
873298 AGTCACACAATGCTTAAAAACT
1 AGTCACACAATGCTAAAAAACT
* *
873320 AGTCACATAATTCTAAAAAA
1 AGTCACACAATGCTAAAAAA
873340 TCACCAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (22 bp):
AGTCACACAATGCTAAAAAACT
Found at i:881625 original size:8 final size:8
Alignment explanation
Indices: 881600--881659 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
881590 AGATAAAAAA
881600 AATAATTTT
1 AATAA-TTT
881609 AATTAATTT
1 AA-TAATTT
881618 AATAATTT
1 AATAATTT
*
881626 TATATATTT
1 AATA-ATTT
* *
881635 AATTATAT
1 AATAATTT
881643 AA-AA-TT
1 AATAATTT
881649 AATAATTT
1 AATAATTT
881657 AAT
1 AAT
881660 TATTAATAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 19 0.46
9 13 0.32
10 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATAATTT
Found at i:881980 original size:24 final size:22
Alignment explanation
Indices: 881944--881989 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
881934 AAAAATTTAA
881944 ATTTTATTTATGTAATTTATTT
1 ATTTTATTTATGTAATTTATTT
881966 ATTTATATTTGATGTAATTTATTT
1 ATTT-TATTT-ATGTAATTTATTT
881990 GTTTGTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 5 0.23
24 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (22 bp):
ATTTTATTTATGTAATTTATTT
Found at i:891027 original size:30 final size:30
Alignment explanation
Indices: 890991--891050 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
890981 AAGCTGGAAG
890991 AGTTCCAATAGCTTTCACCAAAAACAGACA
1 AGTTCCAATAGCTTTCACCAAAAACAGACA
891021 AGTTCCAATAGCTTTCACCAAAAACAGACA
1 AGTTCCAATAGCTTTCACCAAAAACAGACA
891051 GAACAATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (30 bp):
AGTTCCAATAGCTTTCACCAAAAACAGACA
Found at i:908318 original size:35 final size:34
Alignment explanation
Indices: 908233--908330 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
908223 AGTTTTTTTT
* * *
908233 GTTGTGCCGCTGGTTAGAGGGTAGAGAACCTTGG
1 GTTGTGCCGCCGGTTGGAGGGTAGAGAGCCTTGG
*
908267 GTTGTGCCGCCGGTTGGAGAGTAGAGAGCCTTGG
1 GTTGTGCCGCCGGTTGGAGGGTAGAGAGCCTTGG
* *
908301 GTTTGTGCCGCCCGTTGGAGGGTAGGGAGC
1 G-TTGTGCCGCCGGTTGGAGGGTAGAGAGC
908331 ATTTTCTTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
34 31 0.55
35 25 0.45
ACGTcount: A:0.14, C:0.17, G:0.44, T:0.24
Consensus pattern (34 bp):
GTTGTGCCGCCGGTTGGAGGGTAGAGAGCCTTGG
Found at i:911372 original size:18 final size:18
Alignment explanation
Indices: 911351--911385 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
911341 ATCGTATTAT
911351 CGTGTTTAAACGTGTATA
1 CGTGTTTAAACGTGTATA
911369 CGTGTTTAAACGTGTAT
1 CGTGTTTAAACGTGTAT
911386 TCTTGACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (18 bp):
CGTGTTTAAACGTGTATA
Found at i:911665 original size:9 final size:9
Alignment explanation
Indices: 911638--911682 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
911628 ATTTTATTTT
911638 ATCGTGTTA
1 ATCGTGTTA
* *
911647 AACGTATTA
1 ATCGTGTTA
*
911656 ATTGTGTTA
1 ATCGTGTTA
911665 ATCGTGTTA
1 ATCGTGTTA
*
911674 AACGTGTTA
1 ATCGTGTTA
911683 TTAATCGTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (9 bp):
ATCGTGTTA
Found at i:948532 original size:2 final size:2
Alignment explanation
Indices: 948527--948556 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
948517 TATTTTTTGT
*
948527 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
948557 CATGCATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:948565 original size:22 final size:23
Alignment explanation
Indices: 948538--948582 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
948528 ATATATATAT
948538 ATATATATATATATTTA-TACATGC
1 ATATATAT-TA-ATTTACTACATGC
*
948562 ATATCTATTAATTTACTACAT
1 ATATATATTAATTTACTACAT
948583 CTACTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATATTAATTTACTACATGC
Found at i:949061 original size:14 final size:15
Alignment explanation
Indices: 949037--949076 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
949027 TTCTTTTTCT
949037 TTTCTCTCTCTTCAC
1 TTTCTCTCTCTTCAC
949052 TTTC-CTCTC-TCAC
1 TTTCTCTCTCTTCAC
949065 TTTCTCTCTCTT
1 TTTCTCTCTCTT
949077 GCCGCCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
14 10 0.43
15 5 0.22
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTCTCTCTCTTCAC
Found at i:949071 original size:12 final size:12
Alignment explanation
Indices: 949041--949074 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
949031 TTTTCTTTTC
949041 TCTCTCTTCACTT
1 TCTCTC-TCACTT
949054 TCCTCTCTCACTT
1 T-CTCTCTCACTT
949067 TCTCTCTC
1 TCTCTCTC
949075 TTGCCGCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 8 0.40
14 5 0.25
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTCTCACTT
Found at i:949520 original size:8 final size:8
Alignment explanation
Indices: 949502--949553 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 8
949492 TTTCTTGTGT
949502 TTTTAATTA
1 TTTT-ATTA
949511 TTTTATTA
1 TTTTATTA
949519 -TTT-TTA
1 TTTTATTA
949525 TTTT-TTA
1 TTTTATTA
949532 TTTTATTA
1 TTTTATTA
*
949540 TTATATATA
1 TTTTAT-TA
949549 TTTTA
1 TTTTA
949554 GAGGTGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 3 0.08
7 13 0.34
8 12 0.32
9 10 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATTA
Found at i:949528 original size:24 final size:24
Alignment explanation
Indices: 949503--949552 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
949493 TTCTTGTGTT
* *
949503 TTTAATTATT-TTATTATTTTTATT
1 TTTAATT-TTATTATTATATATATT
*
949527 TTTTATTTTATTATTATATATATT
1 TTTAATTTTATTATTATATATATT
949551 TT
1 TT
949553 AGAGGTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTAATTTTATTATTATATATATT
Found at i:950692 original size:17 final size:17
Alignment explanation
Indices: 950670--950704 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
950660 GCGAGCACGT
950670 TAAGCTTTTTGTAATTG
1 TAAGCTTTTTGTAATTG
950687 TAAGCTTTTTGTAATTG
1 TAAGCTTTTTGTAATTG
950704 T
1 T
950705 TCAGGAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TAAGCTTTTTGTAATTG
Found at i:964429 original size:16 final size:15
Alignment explanation
Indices: 964369--964475 Score: 56
Period size: 16 Copynumber: 7.5 Consensus size: 15
964359 TAATATATTC
964369 ATATTTTT-TATTAT
1 ATATTTTTATATTAT
*
964383 -TAATTTTTATATAAT
1 AT-ATTTTTATATTAT
*
964398 ATAATCTCTTA-A--AT
1 AT-AT-TTTTATATTAT
964412 ATATTTTTAATATTAT
1 ATATTTTT-ATATTAT
964428 AT-TTATTT-TATT-T
1 ATATT-TTTATATTAT
*
964441 -T-TATTTAT-TTAT
1 ATATTTTTATATTAT
964453 ATATTTTTTATATTAT
1 ATA-TTTTTATATTAT
964469 ATATTTT
1 ATATTTT
964476 ATTTTAATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 29
0.68 0.05 0.27
Matches are distributed among these distances:
11 5 0.07
12 7 0.10
13 6 0.08
14 15 0.21
15 17 0.23
16 19 0.26
17 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTTTATATTAT
Found at i:964439 original size:14 final size:14
Alignment explanation
Indices: 964422--964478 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 14
964412 ATATTTTTAA
964422 TATTATATTTATTT
1 TATTATATTTATTT
*
964436 TATTTTTATTTA-TT
1 TA-TTATATTTATTT
964450 TA-TATATTT-TTT
1 TATTATATTTATTT
964462 ATATTATA--TATTT
1 -TATTATATTTATTT
964475 TATT
1 TATT
964479 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
12 13 0.36
13 5 0.14
14 10 0.28
15 8 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATATTTATTT
Found at i:964489 original size:14 final size:15
Alignment explanation
Indices: 964416--964496 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 15
964406 TTAAATATAT
964416 TTTTAATATTATATTTA
1 TTTTAATATT-T-TTTA
*
964433 TTTT-ATTTTTATTTA
1 TTTTAATATTT-TTTA
964448 -TTTATATATTTTTTA
1 TTTTA-ATATTTTTTA
* *
964463 TATT-ATATATTTTA
1 TTTTAATATTTTTTA
*
964477 TTTTAAT-TTTTTTC
1 TTTTAATATTTTTTA
964491 TTTTAA
1 TTTTAA
964497 AGGACTATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 26 0.49
15 12 0.23
16 11 0.21
17 4 0.08
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATATTTTTTA
Found at i:973776 original size:17 final size:17
Alignment explanation
Indices: 973733--973782 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
973723 ACCCACCATG
*
973733 AAAA-ACCCAAAAAAAA
1 AAAATACCCAAAAAAGA
**
973749 AAAAT-TTCAAAAAAGA
1 AAAATACCCAAAAAAGA
*
973765 AAAATACCCAAAGAAGA
1 AAAATACCCAAAAAAGA
973782 A
1 A
973783 TTTTACCTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.72, C:0.14, G:0.06, T:0.08
Consensus pattern (17 bp):
AAAATACCCAAAAAAGA
Found at i:978619 original size:23 final size:23
Alignment explanation
Indices: 978593--978641 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
978583 AATAATGTAA
*
978593 TTCTTGTTCCAATCATCCTTGTG
1 TTCTTGTTCCAATCATCCTTATG
* * *
978616 TTCTTGTTTCATTGATCCTTATG
1 TTCTTGTTCCAATCATCCTTATG
978639 TTC
1 TTC
978642 CAAAGATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (23 bp):
TTCTTGTTCCAATCATCCTTATG
Found at i:978757 original size:19 final size:21
Alignment explanation
Indices: 978717--978767 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
978707 TTCACTTTTA
978717 TTTTAATATATATAATTTAAT
1 TTTTAATATATATAATTTAAT
*
978738 TTTTAATTTA-ATAA-TTAAT
1 TTTTAATATATATAATTTAAT
978757 TATTATAATAT
1 T-TT-TAATAT
978768 CAAAGTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.23
20 6 0.23
21 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAATATATATAATTTAAT
Found at i:983900 original size:2 final size:2
Alignment explanation
Indices: 983893--983931 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
983883 AAAACATGAA
983893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
983932 AACATGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:992883 original size:5 final size:5
Alignment explanation
Indices: 992873--992902 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
992863 TTCTCTTCCC
*
992873 TTTCT TTTCT TTTCT TTTCC TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
992903 CTTCACTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:992896 original size:20 final size:21
Alignment explanation
Indices: 992861--992902 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
992851 AGCTACAAAG
992861 TTTTCTCTTCCCTTTCTTTTC
1 TTTTCTCTTCCCTTTCTTTTC
*
992882 TTTTCT-TTTCCTTTCTTTTC
1 TTTTCTCTTCCCTTTCTTTTC
992902 T
1 T
992903 CTTCACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTCTTCCCTTTCTTTTC
Found at i:993900 original size:55 final size:55
Alignment explanation
Indices: 993840--993950 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
993830 CATGGACTGC
*
993840 AATTTGTTTCTGTGATGAAAACCAAGTCTAATCTGAAAGTAGTTGGGTCGGCTGT
1 AATTTGTTTCTGTGATGAAAACCAAGTCTAATCCGAAAGTAGTTGGGTCGGCTGT
993895 AATTTGTTTCTGTGATGAAAACCAAGTCTAATCCGAAAGTAGTTGGGTCGGCTGT
1 AATTTGTTTCTGTGATGAAAACCAAGTCTAATCCGAAAGTAGTTGGGTCGGCTGT
993950 A
1 A
993951 TGAGTTCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (55 bp):
AATTTGTTTCTGTGATGAAAACCAAGTCTAATCCGAAAGTAGTTGGGTCGGCTGT
Found at i:1005929 original size:21 final size:21
Alignment explanation
Indices: 1005904--1005962 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1005894 AGCCCTCACT
1005904 ATCTGCAACTAAGCCTGTGAC
1 ATCTGCAACTAAGCCTGTGAC
* * *
1005925 TTCTGCAGCAAAGCCTGTGAC
1 ATCTGCAACTAAGCCTGTGAC
1005946 ATCTGCAACTAAGCCTG
1 ATCTGCAACTAAGCCTG
1005963 CAACAAGGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCTGCAACTAAGCCTGTGAC
Found at i:1005974 original size:33 final size:33
Alignment explanation
Indices: 1005927--1005993 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1005917 CCTGTGACTT
* * **
1005927 CTGCAGCAAAGCCTGTGACATCTGCAACTAAGC
1 CTGCAACAAAGCCTGTAACATCCACAACTAAGC
*
1005960 CTGCAACAAGGCCTGTAACATCCACAACTAAGC
1 CTGCAACAAAGCCTGTAACATCCACAACTAAGC
1005993 C
1 C
1005994 CACAGTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (33 bp):
CTGCAACAAAGCCTGTAACATCCACAACTAAGC
Found at i:1016674 original size:85 final size:86
Alignment explanation
Indices: 1016555--1016720 Score: 289
Period size: 85 Copynumber: 1.9 Consensus size: 86
1016545 AGAATTTGAT
*
1016555 AGGAACTGCCTACCTTCTTTGACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACGGTTTATA
1 AGGAACTGCCTACCTTCTTTGACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACAGTTTATA
*
1016620 TTTTGAATCTTTTTTTTGGCC
66 CTTTGAATCTTTTTTTTGGCC
* *
1016641 AGGAACTGCCTACC-TCTTTGACAATGGAAGACATGGAAGAGTTTCAAAAGTTCTACAGTTTATG
1 AGGAACTGCCTACCTTCTTTGACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACAGTTTATA
1016705 CTTTGAATCTTTTTTT
66 CTTTGAATCTTTTTTT
1016721 GCTCAGCCAA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 62 0.82
86 14 0.18
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (86 bp):
AGGAACTGCCTACCTTCTTTGACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACAGTTTATA
CTTTGAATCTTTTTTTTGGCC
Found at i:1035668 original size:18 final size:20
Alignment explanation
Indices: 1035645--1035683 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1035635 AACAATTTTG
1035645 AAATCA-AGA-ATTAAAATA
1 AAATCAGAGATATTAAAATA
*
1035663 AAATCAGATATATTAAAATA
1 AAATCAGAGATATTAAAATA
1035683 A
1 A
1035684 CAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATCAGAGATATTAAAATA
Found at i:1037078 original size:10 final size:10
Alignment explanation
Indices: 1037063--1037112 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1037053 GTGTAGAAAT
1037063 AAAAAAATTA
1 AAAAAAATTA
1037073 AAAAAAATT-
1 AAAAAAATTA
*
1037082 AAAATAA-TA
1 AAAAAAATTA
* *
1037091 ATATAAATTA
1 AAAAAAATTA
1037101 AAAAAAATTA
1 AAAAAAATTA
1037111 AA
1 AA
1037113 GATATGTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
8 1 0.03
9 10 0.31
10 21 0.66
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:1057696 original size:28 final size:27
Alignment explanation
Indices: 1057657--1057713 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
1057647 AAAACAAATA
* *
1057657 ATTTTATTAATTATTTTTTA-TTTTAAT
1 ATTTTATTAATT-TTATATATTTTTAAT
*
1057684 ATTTTTTTAAATTTTATATATTTTTAAT
1 ATTTTATT-AATTTTATATATTTTTAAT
1057712 AT
1 AT
1057714 AATAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTTTATTAATTTTATATATTTTTAAT
Found at i:1057702 original size:17 final size:18
Alignment explanation
Indices: 1057663--1057710 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1057653 AATAATTTTA
*
1057663 TTAAT-TATTTTT-TATT
1 TTAATATATTTTTAAATT
*
1057679 TTAATATTTTTTTAAATT
1 TTAATATATTTTTAAATT
1057697 TT-ATATATTTTTAA
1 TTAATATATTTTTAA
1057711 TATAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.19
17 17 0.63
18 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAATATATTTTTAAATT
Found at i:1058002 original size:10 final size:10
Alignment explanation
Indices: 1057984--1058024 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1057974 TATAATTAAT
1057984 TATATTAAAAA
1 TATA-TAAAAA
1057995 TATATAAAAA
1 TATATAAAAA
1058005 T-T-TAAAAA
1 TATATAAAAA
1058013 TATATAAAAA
1 TATATAAAAA
1058023 TA
1 TA
1058025 ATTAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.25
9 2 0.07
10 15 0.54
11 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TATATAAAAA
Found at i:1058011 original size:18 final size:18
Alignment explanation
Indices: 1057988--1058023 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1057978 ATTAATTATA
1057988 TTAAAAATATATAAAAAT
1 TTAAAAATATATAAAAAT
1058006 TTAAAAATATATAAAAAT
1 TTAAAAATATATAAAAAT
1058024 AATTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAATATATAAAAAT
Found at i:1105631 original size:23 final size:22
Alignment explanation
Indices: 1105605--1105647 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1105595 GAACAGATGT
1105605 TTAATT-AGATACAAATAAAAAAA
1 TTAATTGAG-TAC-AATAAAAAAA
1105628 TTAATTGAGTACAATAAAAA
1 TTAATTGAGTACAATAAAAA
1105648 TATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (22 bp):
TTAATTGAGTACAATAAAAAAA
Found at i:1105646 original size:22 final size:23
Alignment explanation
Indices: 1105605--1105647 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1105595 GAACAGATGT
1105605 TTAATTAGATACAAATAAAAAAA
1 TTAATTAGATACAAATAAAAAAA
1105628 TTAATT-GAGTAC-AATAAAAA
1 TTAATTAGA-TACAAATAAAAA
1105648 TATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (23 bp):
TTAATTAGATACAAATAAAAAAA
Found at i:1106798 original size:33 final size:33
Alignment explanation
Indices: 1106761--1106823 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1106751 ATGTTAAATT
* *
1106761 AACATATCACGTCATCATCAATTATAATATATC
1 AACATACCACATCATCATCAATTATAATATATC
* * *
1106794 AACATACCATATCATGATTAATTATAATAT
1 AACATACCACATCATCATCAATTATAATAT
1106824 GTTAGCATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.35
Consensus pattern (33 bp):
AACATACCACATCATCATCAATTATAATATATC
Found at i:1107936 original size:37 final size:37
Alignment explanation
Indices: 1107865--1107936 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1107855 TCCTGTAACA
** * **
1107865 TGTGGCATAGGTCAATAATATGACTACATTTAACCCT
1 TGTGGCATAGGTCAATAATAAAACCACAAGTAACCCT
1107902 TGTGGCATAGGTCAATAATAAAACCACAAGTAACC
1 TGTGGCATAGGTCAATAATAAAACCACAAGTAACC
1107937 ACAGTAGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (37 bp):
TGTGGCATAGGTCAATAATAAAACCACAAGTAACCCT
Found at i:1121714 original size:14 final size:14
Alignment explanation
Indices: 1121684--1121732 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
1121674 ATTTTTTTTT
1121684 TTTTTAGTTTAA--A
1 TTTTTAG-TTAATTA
1121697 TTTTT-GTTAATTA
1 TTTTTAGTTAATTA
1121710 TTTTTAGTTAATTA
1 TTTTTAGTTAATTA
*
1121724 -ATTTAGTTA
1 TTTTTAGTTA
1121733 TTTGATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.12
12 1 0.03
13 19 0.59
14 8 0.25
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (14 bp):
TTTTTAGTTAATTA
Found at i:1129212 original size:18 final size:18
Alignment explanation
Indices: 1129189--1129224 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1129179 ATACAGATTG
1129189 AATATAAGATTT-TGCAGA
1 AATATAAG-TTTCTGCAGA
1129207 AATATAAGTTTCTGCAGA
1 AATATAAGTTTCTGCAGA
1129225 CAATCCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (18 bp):
AATATAAGTTTCTGCAGA
Found at i:1133841 original size:125 final size:125
Alignment explanation
Indices: 1133619--1133870 Score: 423
Period size: 125 Copynumber: 2.0 Consensus size: 125
1133609 ATTAGTTAGG
* *
1133619 GAGAGGAATTGAATTGGGCAATAAGCAGGTTTAACCGTCCATGTCCTCCCAAATTGGTTGGCTAT
1 GAGAGGAATTGAATTGGGCAACAAGCAGGTTTAACCGTCCATGTCCTCCCAAATTGGTTCGCTAT
* *
1133684 AGGCCTAATCATTATAGCTGAAGACTATTCGTTTGCGCCAGCTGAAAATTTCATCCATGA
66 AGGCCTAATCATTATAGCTGAAGACTACTCGTTTGCCCCAGCTGAAAATTTCATCCATGA
* * *
1133744 GAGAGGAATTGAATTGGGCACCAAGCAGGTTTAACCTTCCATGTCCTCCCAAATTGGTTCGCTCT
1 GAGAGGAATTGAATTGGGCAACAAGCAGGTTTAACCGTCCATGTCCTCCCAAATTGGTTCGCTAT
* *
1133809 AGGCCTAATCATTATAGCTGAAGACTACTCGTTTGCCCCAGTTGGAAATTTCATCCATGA
66 AGGCCTAATCATTATAGCTGAAGACTACTCGTTTGCCCCAGCTGAAAATTTCATCCATGA
1133869 GA
1 GA
1133871 ACTATACATA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (125 bp):
GAGAGGAATTGAATTGGGCAACAAGCAGGTTTAACCGTCCATGTCCTCCCAAATTGGTTCGCTAT
AGGCCTAATCATTATAGCTGAAGACTACTCGTTTGCCCCAGCTGAAAATTTCATCCATGA
Found at i:1137493 original size:3 final size:3
Alignment explanation
Indices: 1137485--1137547 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
1137475 TACGTATACC
* * *
1137485 CAT CAT CAT CAT GCA- CAC CAT C-C CAT CAT CAT CAT ACA- CAC CAT
1 CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT CAT -CAT CAT CAT
1137529 CA- CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CA
1137548 GCTCATACGC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 7 0.14
3 39 0.78
4 4 0.08
ACGTcount: A:0.35, C:0.40, G:0.02, T:0.24
Consensus pattern (3 bp):
CAT
Found at i:1137545 original size:26 final size:23
Alignment explanation
Indices: 1137483--1137542 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
1137473 TATACGTATA
*
1137483 CCCATCATCATCATGCACACCAT
1 CCCATCATCATCATACACACCAT
1137506 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
1137529 CACATCATCATCAT
1 CCCATCATCATCAT
1137543 CATCAGCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.23
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:1139582 original size:2 final size:2
Alignment explanation
Indices: 1139575--1139601 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1139565 TACCGTATTG
1139575 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1139602 CAAATAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1140027 original size:2 final size:2
Alignment explanation
Indices: 1140020--1140088 Score: 75
Period size: 2 Copynumber: 34.5 Consensus size: 2
1140010 NNNNNATGTG
* * * *
1140020 TA TA TA TA TA TA TA TA TA TA CA CA TA TG TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1140062 TA CA TA CA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1140089 TTACATACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1140098 original size:28 final size:28
Alignment explanation
Indices: 1140018--1140099 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
1140008 NNNNNNNATG
* *
1140018 TGTATATATATATATATATATACACATA
1 TGTATATATATATATATACATACATATA
*
1140046 TGTGTATATATATATATACATACATATA
1 TGTATATATATATATATACATACATATA
*
1140074 TGTATATATATATATTTACATACATA
1 TGTATATATATATATATACATACATA
1140100 GATATGTGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (28 bp):
TGTATATATATATATATACATACATATA
Found at i:1141799 original size:18 final size:18
Alignment explanation
Indices: 1141776--1141811 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1141766 ATACAGATTG
1141776 AATATAAGATTT-TGCAGA
1 AATATAA-ATTTCTGCAGA
1141794 AATATAAATTTCTGCAGA
1 AATATAAATTTCTGCAGA
1141812 CAATCCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (18 bp):
AATATAAATTTCTGCAGA
Found at i:1141928 original size:17 final size:18
Alignment explanation
Indices: 1141882--1141928 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
1141872 TCACAAGCTG
1141882 TTGTTAAAATACCTTGAC
1 TTGTTAAAATACCTTGAC
* *
1141900 TCATGTTCAAATACCTTTA-
1 T--TGTTAAAATACCTTGAC
1141919 TTGTTAAAAT
1 TTGTTAAAAT
1141929 GGAGTTACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 1 0.04
20 14 0.58
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (18 bp):
TTGTTAAAATACCTTGAC
Found at i:1143542 original size:11 final size:11
Alignment explanation
Indices: 1143526--1143551 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1143516 CTATTTAGAA
1143526 TTATGGATCAG
1 TTATGGATCAG
1143537 TTATGGATCAG
1 TTATGGATCAG
1143548 TTAT
1 TTAT
1143552 CTATTGAGTT
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:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (11 bp):
TTATGGATCAG
Found at i:1147137 original size:11 final size:11
Alignment explanation
Indices: 1147121--1147146 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1147111 AACTCAATAG
1147121 ATAACTGATCC
1 ATAACTGATCC
1147132 ATAACTGATCC
1 ATAACTGATCC
1147143 ATAA
1 ATAA
1147147 TTCTAAATAG
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:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (11 bp):
ATAACTGATCC
Found at i:1148746 original size:11 final size:11
Alignment explanation
Indices: 1148730--1148755 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1148720 CTATTTAGAA
1148730 TTATGGATCAG
1 TTATGGATCAG
1148741 TTATGGATCAG
1 TTATGGATCAG
1148752 TTAT
1 TTAT
1148756 CTATTGAGTT
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:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (11 bp):
TTATGGATCAG
Found at i:1153484 original size:21 final size:21
Alignment explanation
Indices: 1153455--1153496 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1153445 AGAGTTGAGA
*
1153455 CTTGAGATTTTGCCACTTATT
1 CTTGAGATTTTGCAACTTATT
*
1153476 CTTGTGATTTTGCAACTTATT
1 CTTGAGATTTTGCAACTTATT
1153497 AAGTAGGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (21 bp):
CTTGAGATTTTGCAACTTATT
Found at i:1156682 original size:108 final size:108
Alignment explanation
Indices: 1156557--1156765 Score: 357
Period size: 108 Copynumber: 1.9 Consensus size: 108
1156547 AGTTAAGGCA
**
1156557 AAAACAACAAAAATTAGAGTTGACAAAAGGAGTCAGAACTCTGAAGGGCTTTCCTTGGCAGTCTT
1 AAAACAACAAAAATTAGAGTTGACAAAACCAGTCAGAACTCTGAAGGGCTTTCCTTGGCAGTCTT
1156622 CTGCCTTAATGTCACC-TTCGAAATAACTAGAAAATGGTTGGCC
66 CTGCCTTAATGTCACCATT-GAAATAACTAGAAAATGGTTGGCC
* *
1156665 AAAACAACAAATATTAGAGTTGACAAAACCAGTCTGAACTCTGAAGGGCTTTCCTTGGCAGTCTT
1 AAAACAACAAAAATTAGAGTTGACAAAACCAGTCAGAACTCTGAAGGGCTTTCCTTGGCAGTCTT
*
1156730 CTGCCTTGATGTCACCATTGAAATAACTAGAAAATG
66 CTGCCTTAATGTCACCATTGAAATAACTAGAAAATG
1156766 ATTAGCCATA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 93 0.98
109 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (108 bp):
AAAACAACAAAAATTAGAGTTGACAAAACCAGTCAGAACTCTGAAGGGCTTTCCTTGGCAGTCTT
CTGCCTTAATGTCACCATTGAAATAACTAGAAAATGGTTGGCC
Found at i:1157195 original size:94 final size:94
Alignment explanation
Indices: 1157016--1157196 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 94
1157006 CCGAGGTAAG
* *
1157016 GCAACTGTATTTCAGACAGATCCTAAACAGCAGAAAGAGAACTTGAGCTGGTCATGGTTGGTGAA
1 GCAACTGTATTGCAGACAAATCCTAAACAGCAGAAAGAGAACTTGAGCTGGTCATGGTTGGTGAA
* *
1157081 CAACTCAAGTGGCTGCTAAAAAATGATGA
66 CAACTCAAGTGACTGATAAAAAATGATGA
* * *
1157110 GCAACTGTATTGCAGACAAATTCTAACCAGCAGAAAGAGAACTTGAGCTGGTCATGGTTGGTGAG
1 GCAACTGTATTGCAGACAAATCCTAAACAGCAGAAAGAGAACTTGAGCTGGTCATGGTTGGTGAA
* *
1157175 GAACTCATA-TGATTGATAAAAA
66 CAACTCA-AGTGACTGATAAAAA
1157197 GAGTGCATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 76 0.99
95 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (94 bp):
GCAACTGTATTGCAGACAAATCCTAAACAGCAGAAAGAGAACTTGAGCTGGTCATGGTTGGTGAA
CAACTCAAGTGACTGATAAAAAATGATGA
Found at i:1160170 original size:51 final size:51
Alignment explanation
Indices: 1160104--1160216 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
1160094 CAAATCAAAG
* *
1160104 CAACCAATCAAGAAACATCACTAATTATCAAACAAGGCACAAAATCTGAAC
1 CAACCAATCAAGAAACATCACTAATGATCAAAAAAGGCACAAAATCTGAAC
* * *
1160155 TAACCAATCAAGAAACATCACTAATGATCAAAAAAGGCACGAAATTTGAAC
1 CAACCAATCAAGAAACATCACTAATGATCAAAAAAGGCACAAAATCTGAAC
*
1160206 CAACCATTCAA
1 CAACCAATCAA
1160217 CTAATGATCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (51 bp):
CAACCAATCAAGAAACATCACTAATGATCAAAAAAGGCACAAAATCTGAAC
Found at i:1162445 original size:16 final size:18
Alignment explanation
Indices: 1162412--1162454 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
1162402 TCTTAAAAAT
1162412 AAATATTTATAATCTTAA
1 AAATATTTATAATCTTAA
*
1162430 AAATATTT-T-ATTTTAA
1 AAATATTTATAATCTTAA
*
1162446 AAAAATTTA
1 AAATATTTA
1162455 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 13 0.59
17 1 0.05
18 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATTTATAATCTTAA
Found at i:1164213 original size:18 final size:18
Alignment explanation
Indices: 1164187--1164230 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1164177 AATTATTTTC
*
1164187 CATTTTTTCCTATT-TTCT
1 CATTCTTTCCT-TTCTTCT
*
1164205 CCTTCTTTCCTTTCTTCT
1 CATTCTTTCCTTTCTTCT
1164223 CATTCTTT
1 CATTCTTT
1164231 TCTCACTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.64
Consensus pattern (18 bp):
CATTCTTTCCTTTCTTCT
Found at i:1165249 original size:25 final size:24
Alignment explanation
Indices: 1165221--1165272 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1165211 AGTTATTGAA
1165221 AAACCAAGACAATTGTGTCCGTTAG
1 AAACC-AGACAATTGTGTCCGTTAG
* **
1165246 AAA-CGGACAATTGTGTTTGTTAG
1 AAACCAGACAATTGTGTCCGTTAG
1165269 AAAC
1 AAAC
1165273 AAACATCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 19 0.83
24 1 0.04
25 3 0.13
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (24 bp):
AAACCAGACAATTGTGTCCGTTAG
Found at i:1165254 original size:23 final size:23
Alignment explanation
Indices: 1165228--1165272 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1165218 GAAAAACCAA
1165228 GACAATTGTGTCCGTTAGAAACG
1 GACAATTGTGTCCGTTAGAAACG
**
1165251 GACAATTGTGTTTGTTAGAAAC
1 GACAATTGTGTCCGTTAGAAAC
1165273 AAACATCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (23 bp):
GACAATTGTGTCCGTTAGAAACG
Found at i:1176789 original size:93 final size:92
Alignment explanation
Indices: 1176669--1176953 Score: 480
Period size: 93 Copynumber: 3.1 Consensus size: 92
1176659 AAGCCTCATT
*
1176669 AGTCTCTGATGCAGGGTCCAAGCCATTGCTGATCTGCAATGCGGTGTTGGGAGGATTCACATCAG
1 AGTCTCTGATGCAGGGTCCAAGTCATTGCTGATCTGCAATGCGGTGTTGGGAGG-TTCACATCAG
* *
1176734 AGCATGCAAGTGCAAGAGTCCAACCACA
65 AGCATGCAAGTGCAAGAGTCCCACCAGA
* *
1176762 AGTCTCTGATGCAGGGTCCAAGTCATTGCCGATCTGCAATGCGGTGTTGGGACGGTTTACATCAG
1 AGTCTCTGATGCAGGGTCCAAGTCATTGCTGATCTGCAATGCGGTGTTGGGA-GGTTCACATCAG
*
1176827 AGCATGCAAGTGCAAGAGTCCCGCCAGA
65 AGCATGCAAGTGCAAGAGTCCCACCAGA
1176855 AGTCTCTGATGCAGGGTCCAAGTCATTGCTGATCTGCAATGCGGTGTTGGGAGGGTTCACATCAG
1 AGTCTCTGATGCAGGGTCCAAGTCATTGCTGATCTGCAATGCGGTGTTGGGA-GGTTCACATCAG
*
1176920 AGCATGCGAGTGCAAGAGTCCCACCAGA
65 AGCATGCAAGTGCAAGAGTCCCACCAGA
1176948 AGTCTC
1 AGTCTC
1176954 AGCAGCTGGT
Statistics
Matches: 180, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
93 178 0.99
94 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (92 bp):
AGTCTCTGATGCAGGGTCCAAGTCATTGCTGATCTGCAATGCGGTGTTGGGAGGTTCACATCAGA
GCATGCAAGTGCAAGAGTCCCACCAGA
Found at i:1196943 original size:25 final size:27
Alignment explanation
Indices: 1196888--1196956 Score: 115
Period size: 25 Copynumber: 2.6 Consensus size: 27
1196878 CGAATTATGC
1196888 TCCCAAATCCATCATTTAAACACACAG
1 TCCCAAATCCATCATTTAAACACACAG
*
1196915 TCCCAAACCCATCATTT-AA-ACACAG
1 TCCCAAATCCATCATTTAAACACACAG
1196940 TCCCAAATCCATCATTT
1 TCCCAAATCCATCATTT
1196957 TGGTCATTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 22 0.55
26 2 0.05
27 16 0.40
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.25
Consensus pattern (27 bp):
TCCCAAATCCATCATTTAAACACACAG
Found at i:1200662 original size:2 final size:2
Alignment explanation
Indices: 1200655--1200696 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1200645 ATGGGTTAAA
*
1200655 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1200697 TAAATAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1215228 original size:2 final size:2
Alignment explanation
Indices: 1215221--1215260 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1215211 TCTCATCACC
* *
1215221 CT CT CT CT CT CT CT GT CT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1215261 TTTCCTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1219404 original size:58 final size:57
Alignment explanation
Indices: 1219325--1219445 Score: 224
Period size: 58 Copynumber: 2.1 Consensus size: 57
1219315 TTTTGATATG
1219325 TAAAATTTTTATATTTTTTAAGTGGCTAATACAAAATCAACAATCAAAATTTTTAAT
1 TAAAATTTTTATATTTTTTAAGTGGCTAATACAAAATCAACAATCAAAATTTTTAAT
1219382 TNAAAATTTTTATATTTTTTAAGTGGCTAATACAAAATCAACAATCAAAATTTTTAAT
1 T-AAAATTTTTATATTTTTTAAGTGGCTAATACAAAATCAACAATCAAAATTTTTAAT
*
1219440 TCAAAT
1 TAAAAT
1219446 AAATCAACTA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 5 0.08
58 57 0.92
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.41
Consensus pattern (57 bp):
TAAAATTTTTATATTTTTTAAGTGGCTAATACAAAATCAACAATCAAAATTTTTAAT
Found at i:1219956 original size:26 final size:26
Alignment explanation
Indices: 1219922--1219972 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1219912 AAAATAAATA
1219922 ATTTATTAA-TTATTA-ATTATTTTTAT
1 ATTTATTAACTT-TTATA-TATTTTTAT
*
1219948 ATTTTTTAACTTTTATATATTTTTA
1 ATTTATTAACTTTTATATATTTTTA
1219973 ATATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTATTAACTTTTATATATTTTTAT
Found at i:1219963 original size:16 final size:17
Alignment explanation
Indices: 1219942--1219973 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1219932 TATTAATTAT
1219942 TTTTATAT-TTTTTAAC
1 TTTTATATATTTTTAAC
1219958 TTTTATATATTTTTAA
1 TTTTATATATTTTTAA
1219974 TATAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATATATTTTTAAC
Found at i:1223330 original size:15 final size:15
Alignment explanation
Indices: 1223310--1223339 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1223300 AGTGCCTATG
1223310 TCATAGCTGTGCCTA
1 TCATAGCTGTGCCTA
1223325 TCATAGCTGTGCCTA
1 TCATAGCTGTGCCTA
1223340 ATCAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
TCATAGCTGTGCCTA
Found at i:1228172 original size:2 final size:2
Alignment explanation
Indices: 1228167--1228195 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1228157 TAGATAATTA
1228167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1228196 CATAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1230948 original size:109 final size:108
Alignment explanation
Indices: 1230825--1231040 Score: 407
Period size: 109 Copynumber: 2.0 Consensus size: 108
1230815 ATAATTTTTG
1230825 TAATGTTAACACAAAGTAGAAAGTAAATATGTTTATATTTAAAGTACAAATATACATATACACAC
1 TAATGTTAACACAAAGTAGAAAGTAAATATGTTTATATTTAAAGTACAAATATACATATACACAC
1230890 ACACACACACACA-TCATATATATATATATATATAATTTATATA
66 ACACACACACACACTCATATATATATATATATATAA-TTATATA
1230933 TNAATGTTAACACAAAGTAGAAAGTAAATATGTTTATATTTAAAGTACAAATATACATATACACA
1 T-AATGTTAACACAAAGTAGAAAGTAAATATGTTTATATTTAAAGTACAAATATACATATACACA
1230998 CACACACACACACACTCATATATATATATATATATAATTATAT
65 CACACACACACACACTCATATATATATATATATATAATTATAT
1231041 TCTTTATAAA
Statistics
Matches: 106, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
108 1 0.01
109 83 0.78
110 22 0.21
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (108 bp):
TAATGTTAACACAAAGTAGAAAGTAAATATGTTTATATTTAAAGTACAAATATACATATACACAC
ACACACACACACACTCATATATATATATATATATAATTATATA
Found at i:1239842 original size:17 final size:18
Alignment explanation
Indices: 1239815--1239850 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1239805 TAACCATGAT
*
1239815 TTGATGTTTATTTAGAAA
1 TTGATGTTTATTTAAAAA
1239833 TTGA-GTTTATTTAAAAA
1 TTGATGTTTATTTAAAAA
1239850 T
1 T
1239851 GATAATGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (18 bp):
TTGATGTTTATTTAAAAA
Found at i:1241112 original size:2 final size:2
Alignment explanation
Indices: 1241105--1241133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1241095 TTTACGCATG
1241105 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1241134 GTCTTTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1259628 original size:2 final size:2
Alignment explanation
Indices: 1259621--1259666 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1259611 CAGTACAATN
1259621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1259663 AT AT
1 AT AT
1259667 TGTATTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1261000 original size:7 final size:7
Alignment explanation
Indices: 1260990--1261019 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1260980 TCGAATCCTA
1260990 ATCATGT
1 ATCATGT
1260997 ATCATGT
1 ATCATGT
1261004 ATCATGT
1 ATCATGT
1261011 ATCATGT
1 ATCATGT
1261018 AT
1 AT
1261020 GTAATTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (7 bp):
ATCATGT
Found at i:1271062 original size:39 final size:39
Alignment explanation
Indices: 1271008--1271088 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
1270998 GTACGACGGT
* *
1271008 GGAGGAGGAGGAGAGGCTGACGGTTGAGGTGGCGGCGGG
1 GGAGGAGGAGGAGAGGCTGACGGTGGAGGAGGCGGCGGG
* *
1271047 GGAGGAGGAGGAGAGGCTGCCTGTGGAGGAGGCGGCGGG
1 GGAGGAGGAGGAGAGGCTGACGGTGGAGGAGGCGGCGGG
1271086 GGA
1 GGA
1271089 AGAGAAACGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.11, G:0.62, T:0.09
Consensus pattern (39 bp):
GGAGGAGGAGGAGAGGCTGACGGTGGAGGAGGCGGCGGG
Found at i:1274105 original size:31 final size:30
Alignment explanation
Indices: 1274067--1274133 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1274057 ATCATTAATC
* *
1274067 ATAAAATTTTATTTAATTTAAAATAAAAAT
1 ATAAAAATTTATTTAATATAAAATAAAAAT
*
1274097 ATAAAAATTTATTTGATATAAAATAAAAAT
1 ATAAAAATTTATTTAATATAAAATAAAAAT
1274127 ATAAAAA
1 ATAAAAA
1274134 CTTAATTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
ATAAAAATTTATTTAATATAAAATAAAAAT
Found at i:1290874 original size:2 final size:2
Alignment explanation
Indices: 1290867--1290899 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1290857 TGGCAGACTA
*
1290867 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1290900 CATAAAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1292172 original size:160 final size:163
Alignment explanation
Indices: 1291841--1292317 Score: 468
Period size: 160 Copynumber: 3.0 Consensus size: 163
1291831 TCATCTTACT
** * ** ** * * * *
1291841 AGTTGATATGATTACGTGATAGAATCGTAATCCGGATCAAAATTTTTTTAA-AAATTGATACTCT
1 AGTTGATATGATTATATGACAGAATCAAAATCCAAATCGAAACTTTCTTAAGAAATTGATACCCT
* * * * * * *
1291905 AAATAT-GGTAAATGA-AAAAAAATATGATAGAC-ATTGATCTATGGAGTTATGCATTAAGTTTG
66 AAACATCGATCAATGAGAAAAAAATGTGCTAGACAATTGATCTATGCAGCTATGCATTAAGTTTG
** * ** * *
1291967 GTTCTGTTTTTGGTAATGGAAAATTTCCTAATG
131 GTTCTACTTTCGACAATGGGAAATTCCCTAATG
* *
1292000 AGTTGATATGATTATATGACAGAATCAAAATCCAAATCGAAACTTT-TTTAGAAAATT-ATATCC
1 AGTTGATATGATTATATGACAGAATCAAAATCCAAATCGAAACTTTCTTAAG-AAATTGATACCC
* * * * * *
1292063 TAAACATCGATTAATGAG-AAGAAATGTGGTTGAC-GTTGATCTATGCAGCTATGCAGTAAGTTT
65 TAAACATCGATCAATGAGAAAAAAATGTGCTAGACAATTGATCTATGCAGCTATGCATTAAGTTT
*
1292126 GATTCTACTTTCGACAATGGGAAATTCCCTAACT-
130 GGTTCTACTTTCGACAATGGGAAATTCCCTAA-TG
* * *
1292160 AGTTGATATGATTCTGTGACAGAATCGAAATCCAAATCGAAACTTTCTTAAGAAATTGATACCCT
1 AGTTGATATGATTATATGACAGAATCAAAATCCAAATCGAAACTTTCTTAAGAAATTGATACCCT
* * * * * *
1292225 AAACATTGATCAATGGGAAAAAAATGTGCTAGTCAATTGATTTGTGCAGCTATGCATTAAGCTTG
66 AAACATCGATCAATGAGAAAAAAATGTGCTAGACAATTGATCTATGCAGCTATGCATTAAGTTTG
*
1292290 GTTCTACTTTCAACAATGGGAAAATTCC
131 GTTCTACTTTCGACAATGGG-AAATTCC
1292318 TTTACCTTAA
Statistics
Matches: 258, Mismatches: 50, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
158 3 0.01
159 47 0.18
160 121 0.47
161 25 0.10
162 12 0.05
163 43 0.17
164 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (163 bp):
AGTTGATATGATTATATGACAGAATCAAAATCCAAATCGAAACTTTCTTAAGAAATTGATACCCT
AAACATCGATCAATGAGAAAAAAATGTGCTAGACAATTGATCTATGCAGCTATGCATTAAGTTTG
GTTCTACTTTCGACAATGGGAAATTCCCTAATG
Found at i:1293464 original size:3 final size:3
Alignment explanation
Indices: 1293458--1293485 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1293448 AAAGCATTGG
1293458 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1293486 ATTAAAGACA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1295545 original size:22 final size:23
Alignment explanation
Indices: 1295512--1295562 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1295502 AAGTTTTAAA
*
1295512 ATAATTTA-AAATAATTATTTTT
1 ATAAATTATAAATAATTATTTTT
*
1295534 A-AAATTATAAATATTTATTTTT
1 ATAAATTATAAATAATTATTTTT
1295556 ATAAATT
1 ATAAATT
1295563 CTCGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAAATTATAAATAATTATTTTT
Found at i:1296584 original size:2 final size:2
Alignment explanation
Indices: 1296579--1296621 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
1296569 ATACNAAAAA
1296579 AT AT AT AT AT AT GA- AT AT AT AT AT AT AT A- AT -T AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1296619 AT A
1 AT A
1296622 AAACGCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1296622 original size:14 final size:15
Alignment explanation
Indices: 1296579--1296622 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
1296569 ATACNAAAAA
1296579 ATATATATATATGAAT
1 ATATATATATAT-AAT
1296595 ATATATATATATAAT
1 ATATATATATATAAT
1296610 -TATATATATATAA
1 ATATATATATATAA
1296623 AACGCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.46
15 3 0.11
16 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:1320349 original size:7 final size:7
Alignment explanation
Indices: 1320337--1320362 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1320327 AATTTTTAAG
1320337 TTAAAGA
1 TTAAAGA
1320344 TTAAAGA
1 TTAAAGA
1320351 TTAAAGA
1 TTAAAGA
1320358 TTAAA
1 TTAAA
1320363 TCAACTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (7 bp):
TTAAAGA
Done.