Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_pilon, whole genome shotgun sequence
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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:968841 original size:20 final size:22
Alignment explanation
Indices: 968805--968846 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
968795 ACCATTCAGA
968805 GGGGAATCGGTACCCCT-TGAG
1 GGGGAATCGGTACCCCTCTGAG
*
968826 GGGGAATCGGT-TCCCTCTGAG
1 GGGGAATCGGTACCCCTCTGAG
968847 CAATCTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.17, C:0.24, G:0.38, T:0.21
Consensus pattern (22 bp):
GGGGAATCGGTACCCCTCTGAG
Found at i:969848 original size:18 final size:18
Alignment explanation
Indices: 969825--969862 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
969815 CATTTAATCT
*
969825 TCTGGTCGTGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
*
969843 TCTGGTGGAGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
969861 TC
1 TC
969863 ATGTTGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.26, G:0.29, T:0.42
Consensus pattern (18 bp):
TCTGGTCGAGCTTGTTCC
Found at i:971472 original size:21 final size:22
Alignment explanation
Indices: 971442--971500 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
971432 AGAACCCCAG
971442 GGGGGTATCGATTCCCCTAC-A
1 GGGGGTATCGATTCCCCTACAA
* * *
971463 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTACAA
*
971485 GGGAGTATCGATTCCC
1 GGGGGTATCGATTCCC
971501 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTACAA
Found at i:975350 original size:22 final size:21
Alignment explanation
Indices: 975308--975347 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
975298 GATTTTATTT
*
975308 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
975329 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
975348 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:977310 original size:19 final size:19
Alignment explanation
Indices: 977286--977327 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
977276 GGTTCCCTCC
977286 GAGCATACTGGAATTCTCG
1 GAGCATACTGGAATTCTCG
977305 GAGCATACTGGAATTCTCG
1 GAGCATACTGGAATTCTCG
977324 GAGC
1 GAGC
977328 CAAACCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCATACTGGAATTCTCG
Found at i:977956 original size:45 final size:45
Alignment explanation
Indices: 977887--978344 Score: 664
Period size: 45 Copynumber: 10.2 Consensus size: 45
977877 TGTTTTTATA
* *
977887 CCATAAATGAAATGCATAACGGTGCAATAAAGGCATGAAAAGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* * * ** *
977932 CCATAAATGAAATGCATAATGGTGCATTAAACGAATGAAAAAATA
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* *
977977 CCATAAATGAAACGCATAACGGTGCATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* *
978022 CCATAAATGAAATGCATAAGGGTGCATTAAAGGCATGAAAAGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
978067 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* *
978112 CCATCAATGAAATTCATAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* *
978157 CCATAAATGAGATGCATAACGGTGCATTAAGGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
** * *
978202 CCATAAATGAAATGCATGTCGATGCATTAAAGGCATGAAACGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* *
978247 CCATAAATGAAATGCATAACGGTGTATTAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
* * ***
978292 CTATAAATGAAATGTATAATTATGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
*
978337 TCATAAAT
1 CCATAAAT
978345 TTAATAATGA
Statistics
Matches: 368, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 368 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
Found at i:980195 original size:45 final size:45
Alignment explanation
Indices: 980144--980317 Score: 285
Period size: 45 Copynumber: 3.9 Consensus size: 45
980134 CCATGTGTGC
* *
980144 CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCGTTAATGG
1 CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGG
* *
980189 CACCTTTTATGTCGATAATGCACCGTTATACATTTTCATTAGTGG
1 CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGG
*
980234 CATCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGG
1 CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGG
* *
980279 CATCTTTTATGCCGATAATGCACCATTATGCATTTTCAT
1 CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCAT
980318 AAACTTAAAC
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 121 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (45 bp):
CACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTAGTGG
Found at i:984133 original size:5 final size:5
Alignment explanation
Indices: 984123--984156 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
984113 AGGAGGCAAC
984123 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
984157 GAACCCAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:986822 original size:17 final size:18
Alignment explanation
Indices: 986800--986833 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
986790 ACATATGCTA
986800 ATATACT-ATGCACGTAT
1 ATATACTAATGCACGTAT
986817 ATATACTAATGCACGTA
1 ATATACTAATGCACGTA
986834 CAAAAAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (18 bp):
ATATACTAATGCACGTAT
Found at i:988197 original size:22 final size:23
Alignment explanation
Indices: 988155--988198 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
988145 TATGCCTTGG
* *
988155 TTTTTATAGAGATAATTCCCTCC
1 TTTTTACAGAGATAATCCCCTCC
988178 TTTTTACAGAGA-AATCCCCTC
1 TTTTTACAGAGATAATCCCCTC
988199 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTTTACAGAGATAATCCCCTCC
Found at i:989030 original size:55 final size:55
Alignment explanation
Indices: 988965--989400 Score: 382
Period size: 55 Copynumber: 7.9 Consensus size: 55
988955 CGAAGGACAT
* * * * * *
988965 GTCCGTTCCCTCTTCTTTGAGGGAGTATAGAACTTGAATAATCTTCGGAAAATGG
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGAAAACGG
* * * *
989020 GTCCGCTCCCTCTTCTTTC-AGGAAGTATA-AGACTTGAAAAATCTTGGGAAAATGG
1 GTCCGCTCCCTCTTCTTTCAAGG-AGTATAGA-ACTCGAACAATCTTCGGAAAACGG
* * * * *
989075 GTCTGCTCCCTCTTTTTTCAGGGAGTATAGGACTCGAACAATCTTCGGAAAACGT
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGAAAACGG
** * * * * *
989130 GTTTGCTCCCTATTCTTTTAAGGAGTATAGGACTCGAACGATCTTC-GACAAACGT
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGA-AAACGG
* * * *
989185 GCCCGTTCCTTCTTCTTTCAAGGAGTATATG-ACAT-GAACAATCTTCGGCAAACGG
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATA-GAAC-TCGAACAATCTTCGGAAAACGG
* * * * * * * * *
989240 GTCCTCTTCTTCTTCCTTCAAGAAGTATA-AGACTCGAATAATTTTCGGTAAACGT
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGA-ACTCGAACAATCTTCGGAAAACGG
* * *
989295 GTCAGCTCCTTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGCAAACGG
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGAAAACGG
* * * * *
989350 GT-CGCTCCTTCTTTTTTCAAGGAGTATAGGACTCAAACAATCTTCGAAAAA
1 GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGAAAA
989401 TGTGTCTGCT
Statistics
Matches: 314, Mismatches: 55, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
54 49 0.16
55 259 0.82
56 6 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (55 bp):
GTCCGCTCCCTCTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCGGAAAACGG
Found at i:989651 original size:37 final size:37
Alignment explanation
Indices: 989609--989770 Score: 204
Period size: 37 Copynumber: 4.4 Consensus size: 37
989599 ATCATGCTCG
** *
989609 GAAGGCTTACT-GATGGCTTGCTTCACTACTCATCCGT
1 GAAGGCTTA-TAGATGATTTGCTTCACTACTCTTCCGT
* *
989646 GAAGGCTTA-AGATTAATTTGCTTCACTACTCCTCCGT
1 GAAGGCTTATAGA-TGATTTGCTTCACTACTCTTCCGT
* * **
989683 TAAGGCTTATAGATGATTTCCTTCACTACTCTTCTAT
1 GAAGGCTTATAGATGATTTGCTTCACTACTCTTCCGT
989720 GAAGGCTTATAGATGATTTGCTTCACTACTCTTCCGT
1 GAAGGCTTATAGATGATTTGCTTCACTACTCTTCCGT
989757 GAAGGCTTA-AGATG
1 GAAGGCTTATAGATG
989771 GCCCGGAAGA
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
36 7 0.06
37 98 0.91
38 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (37 bp):
GAAGGCTTATAGATGATTTGCTTCACTACTCTTCCGT
Found at i:990124 original size:37 final size:36
Alignment explanation
Indices: 990074--990338 Score: 305
Period size: 37 Copynumber: 7.2 Consensus size: 36
990064 TACTGATGGC
* * * * *
990074 TTGCTTCAGTACTCTTCCGTGAAGACTGAAAATTGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTAAGA-TGAT
* *
990111 TTGATTCACTACTCTTCCGTGAAGGCTTATAGATGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTA-AGATGAT
* * * *
990148 TTGCTTCACTACTCTTTCATGAATGTTTATAGATGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTA-AGATGAT
* *
990185 TTACTTCACTGCTCTTACGTGAAGGCTTAAGATGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTAAGATGAT
* *
990221 TTTCTTCATTACTCTTACGTGAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTAAGA-TGAT
*
990258 TTGCTTCACTACTCTTACGTGGAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTAAGA-TGAT
* * *
990295 TTGCTTCACTACTCTTATGTGAAGGATTAAGACTAAT
1 TTGCTTCACTACTCTTACGTGAAGGCTTAAGA-TGAT
990332 TTGCTTC
1 TTGCTTC
990339 GAAGGTCAAA
Statistics
Matches: 199, Mismatches: 27, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
36 36 0.18
37 161 0.81
38 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (36 bp):
TTGCTTCACTACTCTTACGTGAAGGCTTAAGATGAT
Found at i:990242 original size:110 final size:110
Alignment explanation
Indices: 990115--990326 Score: 293
Period size: 110 Copynumber: 1.9 Consensus size: 110
990105 ATTGATTTGA
* * * *
990115 TTCACTACTCTTCCGTGAAGGCTTATAGA-TGATTTGCTTCACTACTCTTTCATGAATGTTTATA
1 TTCACTACTCTTACGTGAAGGCTTA-AGATTGATTTGCTTCACTACTCTTACATGAAGGCTTA-A
* *
990179 GA-TGATTTACTTCACTGCTCTTACGTGAAGGCTTAAGATGATTTTC
64 GATTGATTTACTTCACTACTCTTACGTGAAGGATTAAGATGATTTTC
* * *
990225 TTCATTACTCTTACGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTACGTGGAGGCTTAAGA
1 TTCACTACTCTTACGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTACATGAAGGCTTAAGA
* *
990290 TTGATTTGCTTCACTACTCTTATGTGAAGGATTAAGA
66 TTGATTTACTTCACTACTCTTACGTGAAGGATTAAGA
990327 CTAATTTGCT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
109 6 0.07
110 83 0.93
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (110 bp):
TTCACTACTCTTACGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTACATGAAGGCTTAAGA
TTGATTTACTTCACTACTCTTACGTGAAGGATTAAGATGATTTTC
Found at i:993018 original size:42 final size:41
Alignment explanation
Indices: 992971--993106 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 41
992961 CATCTCTCAT
*
992971 TTTTTTTTCTTTTTTTCTATTT-TTTTACTTTTTCTTCTTTC
1 TTTTTTTTCTTTTTTTCT-TTTCTTTTTCTTTTTCTTCTTTC
* * *
993012 TATTTTTCCTTTTTTTCTTTTTCTTTTTCTTTTT-TTTTCTTC
1 TTTTTTTTCTTTTTTTC-TTTTCTTTTTCTTTTTCTTCT-TTC
* * *
993054 TTTCTTTTTGTTTTCTTCTTTTCTTTTTCTTTTTC-TGTTTC
1 TTT-TTTTTCTTTTTTTCTTTTCTTTTTCTTTTTCTTCTTTC
993095 TTTTTTTTCTTT
1 TTTTTTTTCTTT
993107 AGCTCTTATG
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
40 8 0.10
41 27 0.34
42 34 0.43
43 11 0.14
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.81
Consensus pattern (41 bp):
TTTTTTTTCTTTTTTTCTTTTCTTTTTCTTTTTCTTCTTTC
Found at i:993032 original size:6 final size:6
Alignment explanation
Indices: 992970--993099 Score: 96
Period size: 6 Copynumber: 21.7 Consensus size: 6
992960 GCATCTCTCA
992970 TTTT-T TTTTCT TTTT-T TCTATT-T TTTTACT TTTTCT TCTTTCT ATTTT-T
1 TTTTCT TTTTCT TTTTCT T-T-TTCT TTTT-CT TTTTCT T-TTTCT -TTTTCT
** *
993019 CCTT-T TTTTCT TTTTCT TTTTC- TTTT-T TTTTCT TCTTTCT TTTT-G
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT
*
993064 TTTTCTT CTTTTCT TTTTCT TTTTCT GTTTCT TTTT
1 TTTTC-T -TTTTCT TTTTCT TTTTCT TTTTCT TTTT
993100 TTTCTTTAGC
Statistics
Matches: 103, Mismatches: 8, Indels: 27
0.75 0.06 0.20
Matches are distributed among these distances:
5 25 0.24
6 48 0.47
7 24 0.23
8 6 0.06
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:993083 original size:29 final size:28
Alignment explanation
Indices: 992973--993106 Score: 100
Period size: 26 Copynumber: 4.7 Consensus size: 28
992963 TCTCTCATTT
*
992973 TTTTTTCTTTTTTTCTATTTTTTTACTTTTTC
1 TTTTTTC-TTTTTT-T-TCTTTTT-CTTTTTC
*
993005 TTCTTTCTATTTTTCCTT-TTTTTCTTTTTC
1 TTTTTTCT-TTTTT--TTCTTTTTCTTTTTC
993035 -TTTTTCTTTTTTTTTCTTCTTTC-TTTT-
1 TTTTTTC-TTTTTTTTCTT-TTTCTTTTTC
* *
993062 TGTTTTC-TTCTTTTCTTTTTCTTTTTC
1 TTTTTTCTTTTTTTTCTTTTTCTTTTTC
*
993089 -TGTTTCTTTTTTTTCTTT
1 TTTTTTCTTTTTTTTCTTT
993107 AGCTCTTATG
Statistics
Matches: 86, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
25 4 0.05
26 17 0.20
27 12 0.14
28 11 0.13
29 14 0.16
30 8 0.09
31 6 0.07
32 12 0.14
33 2 0.02
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTTTCTTTTTTTTCTTTTTCTTTTTC
Found at i:995289 original size:20 final size:20
Alignment explanation
Indices: 995264--995301 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
995254 AATAGTATTG
*
995264 TACTGTATGAATAGTACCAA
1 TACTGTATAAATAGTACCAA
*
995284 TACTGTTTAAATAGTACC
1 TACTGTATAAATAGTACC
995302 GTAAACAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (20 bp):
TACTGTATAAATAGTACCAA
Found at i:995320 original size:10 final size:12
Alignment explanation
Indices: 995296--995333 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
995286 CTGTTTAAAT
*
995296 AGTACCGTAAAC
1 AGTACCGTGAAC
995308 AGTA-C-TGAAC
1 AGTACCGTGAAC
995318 AGTACCGTGAAC
1 AGTACCGTGAAC
995330 AGTA
1 AGTA
995334 TGCCGATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (12 bp):
AGTACCGTGAAC
Found at i:995427 original size:21 final size:21
Alignment explanation
Indices: 995401--995441 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
995391 TTAAAATATG
995401 TATCGATGCACTGCTACAGTT
1 TATCGATGCACTGCTACAGTT
* *
995422 TATCGATGCATTGTTACAGT
1 TATCGATGCACTGCTACAGT
995442 AATTTCAGCA
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:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (21 bp):
TATCGATGCACTGCTACAGTT
Found at i:996365 original size:24 final size:22
Alignment explanation
Indices: 996338--996395 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
996328 CCACTATAGG
996338 CACTGAATATTTATCCCAAAGGAC
1 CACTGAATA--TATCCCAAAGGAC
* *
996362 CACTG-ATATGTCCCAAATGAC
1 CACTGAATATATCCCAAAGGAC
996383 CACTG-ATA-ATCCC
1 CACTGAATATATCCC
996396 TCGACTCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
23 3 0.10
24 5 0.16
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
CACTGAATATATCCCAAAGGAC
Found at i:996377 original size:21 final size:21
Alignment explanation
Indices: 996351--996390 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
996341 TGAATATTTA
996351 TCCCAAAGGACCACTGATATG
1 TCCCAAAGGACCACTGATATG
*
996372 TCCCAAATGACCACTGATA
1 TCCCAAAGGACCACTGATA
996391 ATCCCTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (21 bp):
TCCCAAAGGACCACTGATATG
Found at i:998603 original size:24 final size:25
Alignment explanation
Indices: 998558--998607 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
998548 AGTCTTCCTG
*
998558 ATGATGTATAAAAACATTTATGTAC
1 ATGATGTATAAAAACATCTATGTAC
998583 ATGATGTAT-AAAACATCTATGTAC
1 ATGATGTATAAAAACATCTATGTAC
998607 A
1 A
998608 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (25 bp):
ATGATGTATAAAAACATCTATGTAC
Found at i:1000389 original size:23 final size:23
Alignment explanation
Indices: 1000340--1000390 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1000330 AAAAATCAGG
* ** **
1000340 AGCTCGATTGAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGAACTCA
1000363 AGCTCGATTCAAGCTCGAACTCA
1 AGCTCGATTCAAGCTCGAACTCA
1000386 AGCTC
1 AGCTC
1000391 CAATCAGCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGAACTCA
Found at i:1002112 original size:19 final size:18
Alignment explanation
Indices: 1002084--1002121 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1002074 GTTCCTTTTA
1002084 ACACTCATTAATCCAAAG
1 ACACTCATTAATCCAAAG
1002102 ACACATCATTAATCCAAAG
1 ACAC-TCATTAATCCAAAG
1002121 A
1 A
1002122 GATGGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.21
Consensus pattern (18 bp):
ACACTCATTAATCCAAAG
Found at i:1002584 original size:17 final size:17
Alignment explanation
Indices: 1002562--1002594 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1002552 TTAGTGTTCC
1002562 TTCAATT-TGTTCTTGTT
1 TTCAATTATG-TCTTGTT
1002579 TTCAATTATGTCTTGT
1 TTCAATTATGTCTTGT
1002595 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
TTCAATTATGTCTTGTT
Found at i:1002903 original size:14 final size:13
Alignment explanation
Indices: 1002880--1002936 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1002870 AGTTGTGTAT
1002880 AACTTAAACCCTA
1 AACTTAAACCCTA
1002893 AACTATAAACCCTTA
1 AACT-TAAACCC-TA
* *
1002908 ACCCTAAACCCTA
1 AACTTAAACCCTA
* * *
1002921 ACCCTAAACCTTA
1 AACTTAAACCCTA
1002934 AAC
1 AAC
1002937 CCTATCACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 20 0.53
14 14 0.37
15 4 0.11
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTAAACCCTA
Found at i:1002937 original size:14 final size:13
Alignment explanation
Indices: 1002884--1002940 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
1002874 GTGTATAACT
**
1002884 TAAACCCTAAACTA
1 TAAACCCT-AACCC
1002898 TAAACCCTTAACCC
1 TAAACCC-TAACCC
1002912 TAAACCCTAACCC
1 TAAACCCTAACCC
*
1002925 TAAACCTTAAACCC
1 TAAACCCT-AACCC
1002939 TA
1 TA
1002941 TCACATAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 13 0.34
14 24 0.63
15 1 0.03
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAACCCTAACCC
Found at i:1004554 original size:24 final size:24
Alignment explanation
Indices: 1004527--1004602 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1004517 TATATCAAAA
1004527 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
1004551 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
1004575 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
1004599 ATCA
1 ATCA
1004603 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:1004603 original size:24 final size:24
Alignment explanation
Indices: 1004544--1004659 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1004534 CATAAATCAG
* *
1004544 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
*
1004568 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1004592 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1004616 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1004640 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1004660 TCAAATTGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 2 0.02
24 76 0.93
25 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1005800 original size:108 final size:108
Alignment explanation
Indices: 1005611--1005844 Score: 432
Period size: 108 Copynumber: 2.2 Consensus size: 108
1005601 TAGACCATAA
1005611 GGGTATTTTGGTCATTTTGGTTTTTAGTTTTATTCCAATCATAACAGAGCTCAAGGATATCCCAT
1 GGGTATTTTGGTCATTTTGGTTTTTAGTTTTATTCCAATCATAACAGAGCTCAAGGATATCCCAT
*
1005676 TATTCCTAAGCTTGGTGAAATTTTTGGGTCATTTCCATTACAG
66 CATTCCTAAGCTTGGTGAAATTTTTGGGTCATTTCCATTACAG
*
1005719 GGGTATTTTGGTCATTTTGGTTTTTAGTTTTATTCCAATCATAACAGAGCTCAAGGATATCTCAT
1 GGGTATTTTGGTCATTTTGGTTTTTAGTTTTATTCCAATCATAACAGAGCTCAAGGATATCCCAT
* *
1005784 CATTCCTGAGCTTGGTGATATTTTTGGGTCATTTCCATTACAG
66 CATTCCTAAGCTTGGTGAAATTTTTGGGTCATTTCCATTACAG
1005827 GGGTATTTTGGTCATTTT
1 GGGTATTTTGGTCATTTT
1005845 ACAGATCCAC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 122 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (108 bp):
GGGTATTTTGGTCATTTTGGTTTTTAGTTTTATTCCAATCATAACAGAGCTCAAGGATATCCCAT
CATTCCTAAGCTTGGTGAAATTTTTGGGTCATTTCCATTACAG
Found at i:1006389 original size:17 final size:18
Alignment explanation
Indices: 1006357--1006403 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1006347 AACTAACATT
*
1006357 TCTTATGCACATCAATATA
1 TCTTAT-CAGATCAATATA
1006376 T-TTATCAGATCAATATA
1 TCTTATCAGATCAATATA
*
1006393 TCTTTTCAGAT
1 TCTTATCAGAT
1006404 TTATTAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 12 0.48
19 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTTATCAGATCAATATA
Found at i:1007259 original size:13 final size:13
Alignment explanation
Indices: 1007241--1007282 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1007231 TAACAGTCAA
1007241 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1007254 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
1007267 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1007280 CGG
1 CGG
1007283 TCGGGTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.45, T:0.14
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1010333 original size:18 final size:18
Alignment explanation
Indices: 1010288--1010333 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1010278 TAATATTTTA
1010288 TATATCTTAAATTAAATT
1 TATATCTTAAATTAAATT
* * * *
1010306 CACATATTAAATTAATTT
1 TATATCTTAAATTAAATT
1010324 TATATCTTAA
1 TATATCTTAA
1010334 CTACAAAAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATCTTAAATTAAATT
Found at i:1010478 original size:30 final size:30
Alignment explanation
Indices: 1010381--1010485 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
1010371 ATATTATCAA
* * *
1010381 AATAATATATATATATATAAATTAAGATAAG
1 AATAAAATATATTTTTA-AAATTAAGATAAG
* * * *
1010412 AATAAATTATATTTTTTTAATTTAAGGTAA-
1 AATAAAATATA-TTTTTAAAATTAAGATAAG
* *
1010442 ATTAAAATATATTTTTAAAATTAAAATAAG
1 AATAAAATATATTTTTAAAATTAAGATAAG
1010472 AATAAAATATATTT
1 AATAAAATATATTT
1010486 AATAAGTTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
29 14 0.24
30 22 0.38
31 19 0.33
32 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (30 bp):
AATAAAATATATTTTTAAAATTAAGATAAG
Found at i:1010496 original size:25 final size:26
Alignment explanation
Indices: 1010468--1010540 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 26
1010458 AAAATTAAAA
1010468 TAAGAATAAAATATATTTAATAA-GT
1 TAAGAATAAAATATATTTAATAATGT
* **
1010493 TAAG-ATAAAAAATATTTTTTAATGT
1 TAAGAATAAAATATATTTAATAATGT
*
1010518 TAAGATGTAAAAT-TAATTTAATA
1 TAAGA-ATAAAATAT-ATTTAATA
1010541 TGTGAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
24 15 0.41
25 10 0.27
26 1 0.03
27 11 0.30
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAGAATAAAATATATTTAATAATGT
Found at i:1010551 original size:18 final size:18
Alignment explanation
Indices: 1010510--1010559 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1010500 AAAAATATTT
1010510 TTTAATGTTAAGATGTAAA
1 TTTAAT-TTAAGATGTAAA
* * *
1010529 ATTAATTTAATATGTGAA
1 TTTAATTTAAGATGTAAA
*
1010547 TTTAAATTAAGAT
1 TTTAATTTAAGAT
1010560 ATATAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
TTTAATTTAAGATGTAAA
Found at i:1011085 original size:21 final size:21
Alignment explanation
Indices: 1011059--1011109 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1011049 GGTCACTGAT
*
1011059 ATAATTTATCCTTT-ATTTTAA
1 ATAATTTAT-CTTTAAATTTAA
1011080 ATAATTTATCTTTAAATTTAA
1 ATAATTTATCTTTAAATTTAA
*
1011101 TTAATTTAT
1 ATAATTTAT
1011110 AATTATACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATTTATCTTTAAATTTAA
Found at i:1011372 original size:16 final size:15
Alignment explanation
Indices: 1011348--1011378 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1011338 GCAATGAAGC
1011348 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
1011363 AAAAAGAAAAAAAAGA
1 AAAAA-AAAAAAAAGA
1011379 GGAGTGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:1013486 original size:5 final size:6
Alignment explanation
Indices: 1013461--1013485 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1013451 ACCCTACATT
1013461 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
1013486 TTCCTTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:1013623 original size:14 final size:15
Alignment explanation
Indices: 1013597--1013625 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1013587 ATAATTTGAT
1013597 TAACTTGTTTATTAA
1 TAACTTGTTTATTAA
1013612 TAACTT-TTTATTAA
1 TAACTTGTTTATTAA
1013626 AATCTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
TAACTTGTTTATTAA
Found at i:1015540 original size:4 final size:4
Alignment explanation
Indices: 1015533--1015558 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1015523 ATATATATAT
1015533 AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AG
1015559 GAAAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1020950 original size:29 final size:30
Alignment explanation
Indices: 1020917--1020973 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1020907 TGCCCTGTTT
1020917 TTCCAGTTTAGTGCCTAACGTTT-ATTTCG
1 TTCCAGTTTAGTGCCTAACGTTTCATTTCG
*
1020946 TTCCAGTTTGGTGCCTAACGTTTCATTT
1 TTCCAGTTTAGTGCCTAACGTTTCATTT
1020974 TATTACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (30 bp):
TTCCAGTTTAGTGCCTAACGTTTCATTTCG
Found at i:1023001 original size:17 final size:17
Alignment explanation
Indices: 1022979--1023012 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1022969 TTTTTTTTTC
1022979 AACTTTTAAATCATTTA
1 AACTTTTAAATCATTTA
*
1022996 AACTTTTAAATTATTTA
1 AACTTTTAAATCATTTA
1023013 TGTTTCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
AACTTTTAAATCATTTA
Found at i:1023101 original size:20 final size:21
Alignment explanation
Indices: 1023076--1023123 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1023066 ATGTTTTGAT
1023076 AAATATATAGTAT-AGGTATA
1 AAATATATAGTATAAGGTATA
* *
1023096 AAATATATTGTATAAAGTTATA
1 AAATATATAGTAT-AAGGTATA
1023118 AAATAT
1 AAATAT
1023124 TTTTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
22 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATATATAGTATAAGGTATA
Found at i:1026834 original size:21 final size:22
Alignment explanation
Indices: 1026793--1026843 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
1026783 AATATTTACT
* *
1026793 ATCCCTTTTTTCAAAAAGATCG
1 ATCCCTTTTTGCAAAAAGATCA
*
1026815 ATCCCTTTTTGC-AAAGGATCA
1 ATCCCTTTTTGCAAAAAGATCA
1026836 ATCCCTTT
1 ATCCCTTT
1026844 AGGTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (22 bp):
ATCCCTTTTTGCAAAAAGATCA
Found at i:1029151 original size:21 final size:21
Alignment explanation
Indices: 1029125--1029220 Score: 111
Period size: 21 Copynumber: 4.6 Consensus size: 21
1029115 ATATGTTTGG
* **
1029125 GATCGATCCCTTTACCAAATT
1 GATCGATCCCTTCACCAAAAA
1029146 GATCGATCCCTTCACCAAAAA
1 GATCGATCCCTTCACCAAAAA
*
1029167 GATTGATCCCTTCACCAAAAA
1 GATCGATCCCTTCACCAAAAA
* * ** *
1029188 GATTGATCCCTTGATGAAAAG
1 GATCGATCCCTTCACCAAAAA
1029209 GATCGATCCCTT
1 GATCGATCCCTT
1029221 TCATGTAACA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
GATCGATCCCTTCACCAAAAA
Found at i:1030274 original size:20 final size:19
Alignment explanation
Indices: 1030249--1030295 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1030239 AATTAGTTTA
1030249 ATATTTAAATAG-TATTATGT
1 ATATTTAAATAGTTATT-T-T
*
1030269 ATATTTAGATAGTTATTTT
1 ATATTTAAATAGTTATTTT
1030288 ATATTTAA
1 ATATTTAA
1030296 TGTGTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (19 bp):
ATATTTAAATAGTTATTTT
Found at i:1031177 original size:2 final size:2
Alignment explanation
Indices: 1031170--1031204 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1031160 TCTAACCATA
1031170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1031205 TCTTTTCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1036952 original size:21 final size:21
Alignment explanation
Indices: 1036926--1036978 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1036916 AAGGTGCTGC
1036926 AAATTGAGTTATAACTATTAT
1 AAATTGAGTTATAACTATTAT
1036947 AAATTGAGTTATAACTATTAT
1 AAATTGAGTTATAACTATTAT
1036968 AAATTGAGTTA
1 AAATTGAGTTA
1036979 CGACTGTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (21 bp):
AAATTGAGTTATAACTATTAT
Found at i:1036992 original size:21 final size:21
Alignment explanation
Indices: 1036923--1037019 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 21
1036913 ATTAAGGTGC
*
1036923 TGCAAATTGAGTTATAACTAT
1 TGCAAATTGAGTTATAACTGT
** *
1036944 TATAAATTGAGTTATAACTAT
1 TGCAAATTGAGTTATAACTGT
** **
1036965 TATAAATTGAGTTACGACTGT
1 TGCAAATTGAGTTATAACTGT
* *
1036986 TGCAAATTGA-TTATAAGTGA
1 TGCAAATTGAGTTATAACTGT
*
1037006 TGCAAATCGAGTTA
1 TGCAAATTGAGTTA
1037020 CGACTGCTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
20 15 0.24
21 48 0.76
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
TGCAAATTGAGTTATAACTGT
Found at i:1039002 original size:24 final size:24
Alignment explanation
Indices: 1038975--1039023 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1038965 TTTTAAATTC
1038975 AACTT-ATCGATGACTTTTTATGAT
1 AACTTAAT-GATGACTTTTTATGAT
*
1038999 AACTTAATTATGACTTTTTATGAT
1 AACTTAATGATGACTTTTTATGAT
1039023 A
1 A
1039024 CCTTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (24 bp):
AACTTAATGATGACTTTTTATGAT
Found at i:1044773 original size:23 final size:23
Alignment explanation
Indices: 1044711--1044817 Score: 103
Period size: 23 Copynumber: 4.6 Consensus size: 23
1044701 GAAGTGTCAT
* * *
1044711 GTAGAATTTGTTCCAAAGGATCGC
1 GTAGAATTTGTCCCGAAGGA-CAC
1044735 GTAGAATTTGTCCCGAAGGACAAC
1 GTAGAATTTGTCCCGAAGGAC-AC
*
1044759 GTAGAA-TTGTTCCGAAGGACCAC
1 GTAGAATTTGTCCCGAAGGA-CAC
*
1044782 ATAG-ATTTGTCCCGAAGGACCAC
1 GTAGAATTTGTCCCGAAGGA-CAC
*
1044805 ATAG-ATTTGTCCC
1 GTAGAATTTGTCCC
1044818 ATAGGACCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
22 1 0.01
23 47 0.64
24 26 0.35
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
GTAGAATTTGTCCCGAAGGACAC
Found at i:1044832 original size:23 final size:23
Alignment explanation
Indices: 1044740--1044825 Score: 120
Period size: 23 Copynumber: 3.7 Consensus size: 23
1044730 ATCGCGTAGA
* *
1044740 ATTTGTCCCGAAGGACAACGTAG
1 ATTTGTCCCGAAGGACCACATAG
* *
1044763 AATTGTTCCGAAGGACCACATAG
1 ATTTGTCCCGAAGGACCACATAG
1044786 ATTTGTCCCGAAGGACCACATAG
1 ATTTGTCCCGAAGGACCACATAG
1044809 ATTTGTCCC-ATAGGACC
1 ATTTGTCCCGA-AGGACC
1044826 GTGTAGAACC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 1 0.02
23 55 0.98
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.23
Consensus pattern (23 bp):
ATTTGTCCCGAAGGACCACATAG
Found at i:1045735 original size:19 final size:19
Alignment explanation
Indices: 1045690--1045735 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1045680 AAACCATTTT
1045690 TATGAACAGTATTATACGG
1 TATGAACAGTATTATACGG
* **
1045709 TATAAACAGTATTATATTG
1 TATGAACAGTATTATACGG
1045728 TATGAACA
1 TATGAACA
1045736 ATACTGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (19 bp):
TATGAACAGTATTATACGG
Found at i:1046664 original size:32 final size:32
Alignment explanation
Indices: 1046594--1046747 Score: 190
Period size: 32 Copynumber: 4.9 Consensus size: 32
1046584 GAAGGACCTA
* *
1046594 TCCATATGTTCC-TAAGAACATAGGTAA--CTG
1 TCCATATGTCCCGAAAG-ACATAGGTAATTCTG
*
1046624 TCCATATGTCCCGAAAGACATAGGCAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
* *
1046656 TTCATATGTCCCGAAAGACATATGTAATAT-TG
1 TCCATATGTCCCGAAAGACATAGGTAAT-TCTG
* * *
1046688 TCCATATATCCTGAAAGACATAGGTAATACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTG
1046720 TCCATATGTCCCGAAAGACATAGGTAAT
1 TCCATATGTCCCGAAAGACATAGGTAAT
1046748 CCCTCGACTC
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
30 20 0.19
31 3 0.03
32 82 0.77
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATTCTG
Found at i:1054102 original size:23 final size:23
Alignment explanation
Indices: 1054059--1054103 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1054049 TACTTAATAA
*
1054059 TTTACATAAATGCATATAGTATG
1 TTTACATAAATGCATAGAGTATG
*
1054082 TTTACA-AAATGGATAAGAGTAT
1 TTTACATAAATGCAT-AGAGTAT
1054104 AACAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (23 bp):
TTTACATAAATGCATAGAGTATG
Found at i:1054548 original size:24 final size:24
Alignment explanation
Indices: 1054521--1054620 Score: 89
Period size: 23 Copynumber: 4.2 Consensus size: 24
1054511 AAAGTGCCAC
*
1054521 GTAGAATTTTTCCCGAAGGACCGT
1 GTAGAATTTATCCCGAAGGACCGT
* **
1054545 GTAGACTTTATCCCGAAGGACCAC
1 GTAGAATTTATCCCGAAGGACCGT
* *
1054569 GTAGAA-TTGTCCCGAAGAACC--
1 GTAGAATTTATCCCGAAGGACCGT
** *
1054590 ACACATATTTATCCCGAAGGACCGT
1 GTAGA-ATTTATCCCGAAGGACCGT
1054615 GTAGAA
1 GTAGAA
1054621 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 26 0.46
24 26 0.46
25 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (24 bp):
GTAGAATTTATCCCGAAGGACCGT
Found at i:1054997 original size:37 final size:37
Alignment explanation
Indices: 1054947--1055021 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1054937 CAAGCCGTCC
1054947 TCATATCTAATATAAAACAAATGAGTTACACTCACCT
1 TCATATCTAATATAAAACAAATGAGTTACACTCACCT
*
1054984 TCATATCTAATATAAAACAAATGAGTTGCACTCACCT
1 TCATATCTAATATAAAACAAATGAGTTACACTCACCT
1055021 T
1 T
1055022 TGCCTCACGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (37 bp):
TCATATCTAATATAAAACAAATGAGTTACACTCACCT
Found at i:1057265 original size:13 final size:13
Alignment explanation
Indices: 1057222--1057277 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
1057212 GACGAACCGA
1057222 TCAACTCACT-AG
1 TCAACTCACTGAG
* *
1057234 TTAACTCGCTGAG
1 TCAACTCACTGAG
* *
1057247 TTAACTCACTAAG
1 TCAACTCACTGAG
*
1057260 TCAACTCATTGAG
1 TCAACTCACTGAG
1057273 TCAAC
1 TCAAC
1057278 CCGAATAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
12 8 0.22
13 28 0.78
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (13 bp):
TCAACTCACTGAG
Found at i:1057376 original size:19 final size:20
Alignment explanation
Indices: 1057340--1057377 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1057330 TTTGACCAGA
*
1057340 GTTGACCATTGACTTTGACT
1 GTTGACCATTGACATTGACT
*
1057360 GTTGA-CATTGTCATTGAC
1 GTTGACCATTGACATTGAC
1057378 CAAAAAGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
GTTGACCATTGACATTGACT
Found at i:1058012 original size:16 final size:16
Alignment explanation
Indices: 1057991--1058030 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1057981 TACTATGTGA
1057991 ATTGTTTTATTGAGAT
1 ATTGTTTTATTGAGAT
1058007 ATTGTTTTATTGAGAT
1 ATTGTTTTATTGAGAT
1058023 ATTGTTTT
1 ATTGTTTT
1058031 GGGTAGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (16 bp):
ATTGTTTTATTGAGAT
Found at i:1061266 original size:2 final size:2
Alignment explanation
Indices: 1061259--1061290 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1061249 CTAGAACAGA
1061259 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
1061291 GGAAACCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1065716 original size:16 final size:15
Alignment explanation
Indices: 1065695--1065727 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1065685 AAAAAATTAT
1065695 TTAATTTAATTTTGAA
1 TTAATTTAATTTT-AA
1065711 TTAATTTAATTTTAA
1 TTAATTTAATTTTAA
1065726 TT
1 TT
1065728 TTTGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTAATTTAATTTTAA
Found at i:1068377 original size:2 final size:2
Alignment explanation
Indices: 1068370--1068439 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1068360 ATTAAGGCAA
1068370 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
1068412 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
1068440 TTAAAAACAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1080010 original size:123 final size:123
Alignment explanation
Indices: 1079788--1080010 Score: 277
Period size: 123 Copynumber: 1.8 Consensus size: 123
1079778 ATGCAGTTTT
* * * *
1079788 CAAGAATGGATTTCAACTTTACAACAAAGGACATCCAATTTAAAGCTCAACTTCATAGCAAAGAA
1 CAAGAATGGATTTCAACTTCACAACAAAGGACATCCAATTCAAAGCTCAACTTCACAACAAAGAA
* *
1079853 GCCATCCACAATTTCAACTTTACAGCGAAAGATATTAATATCAAAGTGATTCAATTTA
66 GCCATCCACAATTTCAACTTCACAACGAAAGATATTAATATCAAAGTGATTCAATTTA
* ** * * *
1079911 CAAGATTGGATTTCAACTTCACAATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGA
1 CAAGAATGGATTTCAACTTCACAACAAAGGACATCCAATTCAAAGCTCAACTTCACAACAAAGAA
* ** * *
1079976 GCCA-CCTACGATTTTGACTTCACAATGAAGGATAT
66 GCCATCC-ACAATTTCAACTTCACAACGAAAGATAT
1080011 CGTACCCAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
122 2 0.02
123 80 0.98
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (123 bp):
CAAGAATGGATTTCAACTTCACAACAAAGGACATCCAATTCAAAGCTCAACTTCACAACAAAGAA
GCCATCCACAATTTCAACTTCACAACGAAAGATATTAATATCAAAGTGATTCAATTTA
Found at i:1081112 original size:17 final size:18
Alignment explanation
Indices: 1081090--1081131 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1081080 CTTTAGATTA
1081090 TTTATTTAATTATTAT-T
1 TTTATTTAATTATTATCT
*
1081107 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1081125 TTTATTT
1 TTTATTT
1081132 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1081177 original size:3 final size:3
Alignment explanation
Indices: 1081171--1081235 Score: 59
Period size: 3 Copynumber: 22.3 Consensus size: 3
1081161 TCTTTACTAC
*
1081171 TAT TATT TAT TAT T-T TAT TA- TAT T-T CTCT T-T TATT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TA-T TAT TAT TAT
1081215 TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1081236 TCATTTCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
2 9 0.17
3 38 0.70
4 7 0.13
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1081191 original size:15 final size:16
Alignment explanation
Indices: 1081171--1081235 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 16
1081161 TCTTTACTAC
1081171 TATTAT-TTATTATTT
1 TATTATATTATTATTT
*
1081186 TATTATATT-TCTCTTT
1 TATTATATTAT-TATTT
1081202 TATT-TATTATTA--T
1 TATTATATTATTATTT
1081215 TATTATTATTATTATTT
1 TATTA-TATTATTATTT
1081232 TATT
1 TATT
1081236 TCATTTCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 5 0.12
15 20 0.49
16 11 0.27
17 5 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATATTATTATTT
Found at i:1081236 original size:5 final size:5
Alignment explanation
Indices: 1081180--1081284 Score: 66
Period size: 5 Copynumber: 19.4 Consensus size: 5
1081170 CTATTATTTA
* *
1081180 TTATT TTATT ATATT TCTCTT TTATTT ATTATT ATTATT ATTATT ATTATT
1 TTATT TTATT TTATT T-TATT TTA-TT -TTATT -TTATT -TTATT -TTATT
* * * * * *
1081231 TTATT TCATT TCATT TCATT TCATT TCATT TTGTT TTATTT TTATTT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTA-TT TTATT
1081283 TT
1 TT
1081285 CCCATTTCCT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
5 48 0.55
6 37 0.42
7 3 0.03
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (5 bp):
TTATT
Found at i:1081331 original size:32 final size:31
Alignment explanation
Indices: 1081264--1081346 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
1081254 TTTCATTTTG
**
1081264 TTTTATTTTTATTTTTATTTTCCCATTTCCTT
1 TTTTA-TTTTATTTTTATTTTCCCATTTAATT
* * *
1081296 TTTTATTTTATTTTTGTTTTCTCTTTTAATAT
1 TTTTATTTTATTTTTATTTTCCCATTTAAT-T
* *
1081328 TTTTATATT-TTATTATTTT
1 TTTTATTTTATTTTTATTTT
1081347 TCTTTTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 28 0.67
32 14 0.33
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (31 bp):
TTTTATTTTATTTTTATTTTCCCATTTAATT
Found at i:1081484 original size:24 final size:23
Alignment explanation
Indices: 1081443--1081494 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1081433 TTCTTTGATT
*
1081443 TATTT-TTTTAATTTTAATTTAA
1 TATTTCTTTTAATTTTAATATAA
*
1081465 TATTTCTTTTATTTTATAATATAA
1 TATTTCTTTTAATTT-TAATATAA
*
1081489 TTTTTC
1 TATTTC
1081495 AACTTTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 12 0.48
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTCTTTTAATTTTAATATAA
Found at i:1082119 original size:20 final size:20
Alignment explanation
Indices: 1082091--1082132 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1082081 ACTATGCATC
1082091 ACTTACAACACATATTCATT
1 ACTTACAACACATATTCATT
*
1082111 ACTTGCAACACATATTCATT
1 ACTTACAACACATATTCATT
1082131 AC
1 AC
1082133 ACATGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33
Consensus pattern (20 bp):
ACTTACAACACATATTCATT
Found at i:1090688 original size:40 final size:40
Alignment explanation
Indices: 1090633--1090719 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
1090623 TCGCACGTTG
1090633 AGTTAACTCGAATTGGATTGAGTTAACTCATATTGAACCT
1 AGTTAACTCGAATTGGATTGAGTTAACTCATATTGAACCT
1090673 AGTTAACTCGAATTGGATTGAGTTAACTCATATTGAACCT
1 AGTTAACTCGAATTGGATTGAGTTAACTCATATTGAACCT
1090713 AGTTAAC
1 AGTTAAC
1090720 CTGAACTGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (40 bp):
AGTTAACTCGAATTGGATTGAGTTAACTCATATTGAACCT
Found at i:1090707 original size:20 final size:20
Alignment explanation
Indices: 1090630--1090701 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1090620 CTATCGCACG
1090630 TTGAGTTAACTCGAATTGGA
1 TTGAGTTAACTCGAATTGGA
*
1090650 TTGAGTTAACTC-ATATTGAA
1 TTGAGTTAACTCGA-ATTGGA
*
1090670 CCT-AGTTAACTCGAATTGGA
1 -TTGAGTTAACTCGAATTGGA
1090690 TTGAGTTAACTC
1 TTGAGTTAACTC
1090702 ATATTGAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGAGTTAACTCGAATTGGA
Found at i:1090716 original size:20 final size:20
Alignment explanation
Indices: 1090653--1090719 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1090643 AATTGGATTG
1090653 AGTTAACTCATATTGAACCT
1 AGTTAACTCATATTGAACCT
* *
1090673 AGTTAACTCGA-ATTGGA-TT
1 AGTTAACTC-ATATTGAACCT
1090692 GAGTTAACTCATATTGAACCT
1 -AGTTAACTCATATTGAACCT
1090713 AGTTAAC
1 AGTTAAC
1090720 CTGAACTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (20 bp):
AGTTAACTCATATTGAACCT
Found at i:1092176 original size:187 final size:190
Alignment explanation
Indices: 1091861--1092238 Score: 710
Period size: 187 Copynumber: 2.0 Consensus size: 190
1091851 AAAGACCAAT
1091861 TTATTGGGAATACTGTATGTATATGAAATTTTTGAAATGAAAAAAATGCCCTTAGACCTCAAAAT
1 TTATTGGGAATACTGTATGTATATGAAATTTTTGAAATGAAAAAAATGCCCTTAGACCTCAAAAT
1091926 GGCTGAAATACCCTCAAGCTCTTAATTGAATAAAAATAACATTGAGTTTTAAATGACCTAAATTA
66 GGCTGAAATACCCTCAAGCTCTTAATTGAATAAAAATAACATTGAGTTTTAAATGACCTAAATTA
1091991 TCACA-CCCAATTTAGGGGCTTAATTTTATAGTAATG-ATTTAATTCATA-TTGAAAGAA
131 TCACACCCCAATTTAGGGGCTTAATTTTATAGTAATGAATTTAATTCATATTTGAAAGAA
1092048 TTATTGGGAATACTGTATGTATATGAAATTTTTGAAATGAAAAAAATGCCCTTAGACCTCAAAAT
1 TTATTGGGAATACTGTATGTATATGAAATTTTTGAAATGAAAAAAATGCCCTTAGACCTCAAAAT
1092113 GGCTGAAATACCCTCAAGCTCTTAATTGAAT-AAAATAACATTGAGTTTTAAAATGACCTAAATT
66 GGCTGAAATACCCTCAAGCTCTTAATTGAATAAAAATAACATTGAGTTTT-AAATGACCTAAATT
1092177 ATCACACCCCAATTTAGGGGCTTAATTTTATAGTAATGAATTTAATTCATATTTTGAAAGAA
130 ATCACACCCCAATTTAGGGGCTTAATTTTATAGTAATGAATTTAATTCATA-TTTGAAAGAA
1092239 ATTGTGGATT
Statistics
Matches: 186, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
186 18 0.10
187 116 0.62
188 31 0.17
189 12 0.06
191 9 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (190 bp):
TTATTGGGAATACTGTATGTATATGAAATTTTTGAAATGAAAAAAATGCCCTTAGACCTCAAAAT
GGCTGAAATACCCTCAAGCTCTTAATTGAATAAAAATAACATTGAGTTTTAAATGACCTAAATTA
TCACACCCCAATTTAGGGGCTTAATTTTATAGTAATGAATTTAATTCATATTTGAAAGAA
Found at i:1094976 original size:31 final size:31
Alignment explanation
Indices: 1094938--1095073 Score: 157
Period size: 31 Copynumber: 4.4 Consensus size: 31
1094928 CTAATTTGAC
* * *
1094938 TCTTGGGTAGGCTCTGCGGCCCTGGGATTTT
1 TCTTGGGTAGGCCCTGCGGCCCTGAGATCTT
* *
1094969 TCTTGGGTAGGCCCCGTGGCCCTGAGAT-TAT
1 TCTTGGGTAGGCCCTGCGGCCCTGAGATCT-T
* * *
1095000 TCTTGGGTAAGCCCTGCAGCCCTAAGATCTT
1 TCTTGGGTAGGCCCTGCGGCCCTGAGATCTT
* * *
1095031 TCTTGGCTAGGCCCTGTGGCCCTGAGAACTT
1 TCTTGGGTAGGCCCTGCGGCCCTGAGATCTT
1095062 TCTTGGGTAGGC
1 TCTTGGGTAGGC
1095074 TTTCAGGCCC
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
30 1 0.01
31 85 0.98
32 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.31, T:0.31
Consensus pattern (31 bp):
TCTTGGGTAGGCCCTGCGGCCCTGAGATCTT
Found at i:1098971 original size:14 final size:15
Alignment explanation
Indices: 1098952--1098988 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1098942 TTCCCACCTC
1098952 ATTCTTTTTC-TTCT
1 ATTCTTTTTCTTTCT
*
1098966 ATTCTTGTTCTTTCT
1 ATTCTTTTTCTTTCT
1098981 ATT-TTTTT
1 ATTCTTTTT
1098989 TTGGAGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (15 bp):
ATTCTTTTTCTTTCT
Found at i:1105612 original size:36 final size:35
Alignment explanation
Indices: 1105524--1105630 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 35
1105514 ATTGTTGATA
*
1105524 ATGCTCAAATTAGGTTATTCC-TCTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCAT-TAGTATT-GAAAT
1105560 ATGCT-AAATTAGGTTATCCCATTAGTATTGCAAAT
1 ATGCTCAAATTAGGTTATCCCATTAGTATTG-AAAT
*
1105595 ATGCTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCATTAGTATT-GAAAT
1105631 GGCGATTTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
34 1 0.02
35 30 0.46
36 33 0.51
37 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (35 bp):
ATGCTCAAATTAGGTTATCCCATTAGTATTGAAAT
Found at i:1109726 original size:36 final size:35
Alignment explanation
Indices: 1109638--1109745 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 35
1109628 AATGTTGATA
*
1109638 ATGCTCAAATTAGGTTATTCCACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATT-GAAAT
1109674 ATGCT-AAATTAGGTTATCCCACTAGTATTGCAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTG-AAAT
1109709 ATGCTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATT-GAAAT
1109745 A
1 A
1109746 AAGATTTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
34 1 0.01
35 32 0.47
36 34 0.50
37 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (35 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTGAAAT
Found at i:1111344 original size:12 final size:12
Alignment explanation
Indices: 1111329--1111373 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
1111319 CGGTTTTTTT
*
1111329 ACCGGATAAAAA
1 ACCGGTTAAAAA
1111341 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
1111355 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1111367 ACCGGTT
1 ACCGGTT
1111374 TTATCCGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1111355 original size:14 final size:13
Alignment explanation
Indices: 1111335--1111374 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
1111325 TTTTACCGGA
1111335 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1111348 TGAAAAAACCGG-T
1 T-AAAAAACCGGTT
1111361 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1111374 T
1 T
1111375 TATCCGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1113278 original size:21 final size:21
Alignment explanation
Indices: 1113254--1113293 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1113244 TTTATTTTAT
1113254 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1113275 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1113294 ACTTGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1113861 original size:15 final size:15
Alignment explanation
Indices: 1113811--1113864 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 15
1113801 ATCTGGAATA
1113811 TTAAAA-CGG-TTTT
1 TTAAAACCGGTTTTT
*
1113824 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1113839 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1113856 TTAAAACCG
1 TTAAAACCG
1113865 AAACCGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.15
14 3 0.09
15 12 0.36
17 13 0.39
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1113873 original size:21 final size:18
Alignment explanation
Indices: 1113828--1113861 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1113818 GGTTTTTTAT
1113828 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1113845 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1113862 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1113981 original size:15 final size:17
Alignment explanation
Indices: 1113955--1113986 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1113945 TTCTATGGGA
1113955 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1113971 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1113987 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1122858 original size:22 final size:22
Alignment explanation
Indices: 1122816--1122858 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1122806 AGTTAAATCA
**
1122816 AATTTTAATTTTATTTCTAATT
1 AATTTTAATTTTATTAATAATT
1122838 AATTTTAATTTT-TATAATAAT
1 AATTTTAATTTTAT-TAATAAT
1122859 AAAATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTTAATTTTATTAATAATT
Found at i:1122873 original size:29 final size:30
Alignment explanation
Indices: 1122833--1122896 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1122823 ATTTTATTTC
* *
1122833 TAATTAATTTTAATTTTTATAATAAT-AAAA
1 TAATTAATTTT-ATATTTAGAATAATGAAAA
*
1122863 TAATTAA-TTTATATTTAGAATAGTGAAAA
1 TAATTAATTTTATATTTAGAATAATGAAAA
1122892 TAATT
1 TAATT
1122897 TTAAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 12 0.40
30 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TAATTAATTTTATATTTAGAATAATGAAAA
Found at i:1125877 original size:51 final size:54
Alignment explanation
Indices: 1125822--1125935 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 54
1125812 CTTAATATTG
* *
1125822 TTTATATATTAAC-TTAAAAAATAAT-TTTTTTTCTTAACTT-GTT-AAATATAT
1 TTTATATATTAACATTAAAAAA-AATATTTTATTCTTAACTTAATTAAAATATAT
* *
1125873 TTTATA-CTT-ACATTCAAAAAAATATTTTATTCTTAACTTAATTAAAAATATAT
1 TTTATATATTAACATTAAAAAAAATATTTTATTCTTAACTTAATT-AAAATATAT
1125926 TTTAT-TATTA
1 TTTATATATTA
1125936 TATTGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
49 5 0.10
50 23 0.45
51 8 0.16
53 15 0.29
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (54 bp):
TTTATATATTAACATTAAAAAAAATATTTTATTCTTAACTTAATTAAAATATAT
Found at i:1125919 original size:25 final size:24
Alignment explanation
Indices: 1125830--1125919 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 24
1125820 TGTTTATATA
*
1125830 TTAACTTAA-AAAATAATTTTTTTTC
1 TTAACTTAATAAAAT-A-TTTTATTC
** *
1125855 TTAACTTGTTAAATATATTTTATAC
1 TTAACTTAATAAA-ATATTTTATTC
*
1125880 TT-ACATTCAAAAAAATATTTTATTC
1 TTAAC-TT-AATAAAATATTTTATTC
1125905 TTAACTTAATTAAAA
1 TTAACTTAA-TAAAA
1125920 ATATATTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
24 4 0.08
25 35 0.70
26 9 0.18
27 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (24 bp):
TTAACTTAATAAAATATTTTATTC
Found at i:1125927 original size:28 final size:30
Alignment explanation
Indices: 1125870--1125937 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
1125860 TTGTTAAATA
1125870 TATTTTATACTTACATTCAAAAAAATATTT
1 TATTTTATACTTACATTCAAAAAAATATTT
*
1125900 TATTCTTA-ACTTA-ATT-AAAAATATATTT
1 TATT-TTATACTTACATTCAAAAAAATATTT
1125928 TATTATTATA
1 TATT-TTATA
1125938 TTGATTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 18 0.53
29 4 0.12
30 9 0.26
31 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTTATACTTACATTCAAAAAAATATTT
Found at i:1125993 original size:63 final size:63
Alignment explanation
Indices: 1125914--1126089 Score: 300
Period size: 63 Copynumber: 2.8 Consensus size: 63
1125904 CTTAACTTAA
1125914 TTAAAAATATATTTTATTATTATATTGATTTTGCAAAATATATTTTATTCTCATTTAAAACTT
1 TTAAAAATATATTTTATTATTATATTGATTTTGCAAAATATATTTTATTCTCATTTAAAACTT
1125977 TTAAAAATATATTTTATTATTATATTGATTTTGCAAAATATATTTTATTCTCATTTAAAACTT
1 TTAAAAATATATTTTATTATTATATTGATTTTGCAAAATATATTTTATTCTCATTTAAAACTT
* *
1126040 TTAAAAATATATTTTATTATTATTTTAACTTTTG-AAAGTATATATTTTAT
1 TTAAAAATATATTTTATTATTATATTGA-TTTTGCAAA--ATATATTTTAT
1126090 CTTACTTTAT
Statistics
Matches: 108, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
63 92 0.85
64 5 0.05
65 11 0.10
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (63 bp):
TTAAAAATATATTTTATTATTATATTGATTTTGCAAAATATATTTTATTCTCATTTAAAACTT
Found at i:1126233 original size:26 final size:26
Alignment explanation
Indices: 1126198--1126281 Score: 71
Period size: 31 Copynumber: 3.0 Consensus size: 26
1126188 AAATACTTTA
1126198 TTCATATCTTAACTTAAAAATATATAT
1 TTCAT-TCTTAACTTAAAAATATATAT
*
1126225 TTTATTCTTATTTTAACTTTAAAAA-ATATAT
1 TTCATTC-----TTAAC-TTAAAAATATATAT
* *
1126256 TTCATTCTTAACTTATATATATATAT
1 TTCATTCTTAACTTAAAAATATATAT
1126282 ATAATCTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
25 5 0.11
26 13 0.28
27 4 0.09
31 17 0.37
32 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (26 bp):
TTCATTCTTAACTTAAAAATATATAT
Found at i:1126234 original size:59 final size:56
Alignment explanation
Indices: 1126162--1126303 Score: 178
Period size: 57 Copynumber: 2.5 Consensus size: 56
1126152 CAACTTTAAA
*
1126162 ATATTTTAATCTTATTTTAATTTAAAAAATACTTTATTCATATCTTAACTTAAAAATAT
1 ATATTTTAATCTTATTTTAATTTAAAAAATA-TAT-TTCAT-TCTTAACTTAAAAATAT
* * *
1126221 ATATTTTATTCTTATTTTAACTTTAAAAAATATATTTCATTCTTAACTTATATATAT
1 ATATTTTAATCTTATTTTAA-TTTAAAAAATATATTTCATTCTTAACTTAAAAATAT
* *
1126278 ATA-TATAATCTTAATCTTAATTTAAA
1 ATATTTTAATCTT-ATTTTAATTTAAA
1126304 CATATTTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
56 13 0.18
57 24 0.32
58 5 0.07
59 21 0.28
60 11 0.15
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (56 bp):
ATATTTTAATCTTATTTTAATTTAAAAAATATATTTCATTCTTAACTTAAAAATAT
Found at i:1126263 original size:31 final size:31
Alignment explanation
Indices: 1125888--1126265 Score: 209
Period size: 31 Copynumber: 12.7 Consensus size: 31
1125878 ACTTACATTC
**
1125888 AAAAAA-ATATTTTATTCTTAACTTAA--TT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
* * * *
1125916 -AAAAATATATTTTATTATTATATTGATTTT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
** * *
1125946 GCAAAATATATTTTATTCTCATTTAAAACTTT
1 AAAAAATATATTTTATTCTTATTT-TAACTTT
* * * * *
1125978 TAAAAATATATTTTATTATTATATTGATTTT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
** * *
1126009 GCAAAATATATTTTATTCTCATTTAAAACTTT
1 AAAAAATATATTTTATTCTTATTT-TAACTTT
* *
1126041 TAAAAATATATTTTATTATTATTTTAACTTT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
** * *
1126072 TGAAAGTATA---TATT-TTATCTT-ACTTT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
** * * * * *
1126098 ATTAAATATATTATACTATTACTTTAA-ATT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
** * * *
1126128 ATTAAATATATTTCATT-TGTATCTCAACTTT
1 AAAAAATATATTTTATTCT-TATTTTAACTTT
*
1126159 ---AAA-ATATTTTAATCTTATTTTAA-TTT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
* * *
1126185 -AAAAA-ATACTTTATTCATATCTTAAC-TT
1 AAAAAATATATTTTATTCTTATTTTAACTTT
1126213 AAAAATATATATTTTATTCTTATTTTAACTTT
1 AAAAA-ATATATTTTATTCTTATTTTAACTTT
*
1126245 AAAAAATATATTTCATTCTTA
1 AAAAAATATATTTTATTCTTA
1126266 ACTTATATAT
Statistics
Matches: 267, Mismatches: 62, Indels: 39
0.73 0.17 0.11
Matches are distributed among these distances:
26 14 0.05
27 25 0.09
28 45 0.17
29 8 0.03
30 29 0.11
31 92 0.34
32 54 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (31 bp):
AAAAAATATATTTTATTCTTATTTTAACTTT
Found at i:1126368 original size:17 final size:17
Alignment explanation
Indices: 1126346--1126398 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1126336 ATAAAAATAA
1126346 AATATATTTAATAAATT
1 AATATATTTAATAAATT
**
1126363 AATATA-AAAAT-AA--
1 AATATATTTAATAAATT
*
1126376 AATATATTTAATAAGTT
1 AATATATTTAATAAATT
1126393 AATATA
1 AATATA
1126399 AGAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 6 0.22
14 3 0.11
15 3 0.11
16 3 0.11
17 12 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATATTTAATAAATT
Found at i:1126372 original size:30 final size:30
Alignment explanation
Indices: 1126316--1126412 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
1126306 TATTTTTAAC
*
1126316 ATATATTTAATAAAGTTAAAATAAAAATAAA
1 ATATATTTAATAAA-TTAATATAAAAATAAA
1126347 ATATATTTAATAAATTAATATAAAAATAAA
1 ATATATTTAATAAATTAATATAAAAATAAA
* *
1126377 ATATATTTAATAAGTTAATATAAGAATAAA
1 ATATATTTAATAAATTAATATAAAAATAAA
1126407 ATATAT
1 ATATAT
1126413 ATTTTGAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
30 49 0.78
31 14 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
ATATATTTAATAAATTAATATAAAAATAAA
Found at i:1129760 original size:19 final size:19
Alignment explanation
Indices: 1129719--1129759 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1129709 TTCTGCACAC
*
1129719 AAAGTTTCGAAACTCTGGA
1 AAAGTTTCGAAACTCTCGA
*
1129738 AAAGTTTCTAAACTCTTCGA
1 AAAGTTTCGAAACTC-TCGA
1129758 AA
1 AA
1129760 GAATCGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
AAAGTTTCGAAACTCTCGA
Found at i:1131408 original size:21 final size:23
Alignment explanation
Indices: 1131384--1131430 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1131374 GAAATAAGGA
1131384 AAATATCAAA-TTTAAAA-AAAT
1 AAATATCAAATTTTAAAAGAAAT
* *
1131405 AAATGTTAAATTTTAAAAGAAAT
1 AAATATCAAATTTTAAAAGAAAT
1131428 AAA
1 AAA
1131431 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAATATCAAATTTTAAAAGAAAT
Found at i:1132481 original size:14 final size:13
Alignment explanation
Indices: 1132463--1132511 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
1132453 GAAGATAATA
1132463 ATAATAAATAAAT
1 ATAATAAATAAAT
1132476 ACTAAT-AATATAAT
1 A-TAATAAATA-AAT
1132490 ATAATAAATAATAT
1 ATAATAAATAA-AT
1132504 ATATATAA
1 ATA-ATAA
1132512 TATAGTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.32
14 17 0.55
15 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:1132495 original size:23 final size:22
Alignment explanation
Indices: 1132457--1132515 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1132447 AAAACTGAAG
*
1132457 ATAATAATAATA-AATAAATACT
1 ATAAT-ATAATATAATAAATAAT
1132479 AATAATATAATATAATAAATAAT
1 -ATAATATAATATAATAAATAAT
1132502 ATATATATAATATA
1 ATA-ATATAATATA
1132516 GTTTATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 9 0.27
23 24 0.73
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATATAATATAATAAATAAT
Found at i:1132523 original size:30 final size:28
Alignment explanation
Indices: 1132457--1132588 Score: 98
Period size: 28 Copynumber: 4.7 Consensus size: 28
1132447 AAAACTGAAG
1132457 ATAATAATAATAAATAA-ATACTA-ATAAT
1 ATAAT-ATAATAAATAATATA-TATATAAT
1132485 ATAATATAATAAATAATATATATATAAT
1 ATAATATAATAAATAATATATATATAAT
* **
1132513 ATAGTTTATAATAAACCATAT-T-TATAAT
1 ATA--ATATAATAAATAATATATATATAAT
* * *
1132541 ATAAATATAACACTATAATAT-T-TATATT
1 AT-AATATAATA-AATAATATATATATAAT
1132569 ATAATAT-ATAATATAATATA
1 ATAATATAATAA-ATAATATA
1132589 CAAAATATAA
Statistics
Matches: 85, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
26 9 0.11
27 24 0.28
28 37 0.44
29 2 0.02
30 13 0.15
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
ATAATATAATAAATAATATATATATAAT
Found at i:1135364 original size:45 final size:45
Alignment explanation
Indices: 1135307--1135626 Score: 367
Period size: 45 Copynumber: 7.1 Consensus size: 45
1135297 TATGCACTTT
* * * *
1135307 ACTATAGCATACTTTTATGTTGATAATGCACCCATATGCATTTCA
1 ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* *
1135352 ACTATAGTATACTTTTCTGCTGAAAATGTACCCATATACATTTCA
1 ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* * *
1135397 AC-ATTAGTATA-TTCTTCTATTGAAAATGTACGCATATACATTTCA
1 ACTA-TAGTATACTT-TTCTGTTGATAATGTACCCATATACATTTCA
* * * *
1135442 ACTATAGTATATTTTTCAGTTGATAATGCACCCATATGCATTTCA
1 ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* * * * * *
1135487 ATTATAACT-TACTTTTCTGTTGATAATGCACCTATATGCTTTTCA
1 ACTAT-AGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* * *
1135532 ACTATAGTATACTTTTCTATTGATAATGTACCTATATACATTTAA
1 ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* * *
1135577 ACTATAATATATTTTTCTGTTGATAATGTACCCATATATATTTCA
1 ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
1135622 ACTAT
1 ACTAT
1135627 GACATCATTT
Statistics
Matches: 235, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
44 5 0.02
45 225 0.96
46 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.42
Consensus pattern (45 bp):
ACTATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCA
Found at i:1135550 original size:135 final size:135
Alignment explanation
Indices: 1135307--1135663 Score: 413
Period size: 135 Copynumber: 2.6 Consensus size: 135
1135297 TATGCACTTT
* * *
1135307 ACTATAGCATACTTTT-ATGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTG
1 ACTATAGTATATTTTTCA-GTTGATAATGCACCCATATGCATTTCAACTATACTATACTTTTCTG
*
1135371 CTGAAAATGTACCCATATACATTTCAACATTAGTATATTCTTCTATTGAAAATGTACGC-ATATA
65 CTGAAAATGCACCCATATACATTTCAACATTAGTATATTCTTCTATTGAAAATGTAC-CTATATA
*
1135435 CATTTCA
129 CATTTAA
*
1135442 ACTATAGTATATTTTTCAGTTGATAATGCACCCATATGCATTTCAATTATAACT-TACTTTTCTG
1 ACTATAGTATATTTTTCAGTTGATAATGCACCCATATGCATTTCAACTAT-ACTATACTTTTCTG
* * * * * *
1135506 TTGATAATGCACCTATATGCTTTTCAAC-TATAGTATACTT-TTCTATTGATAATGTACCTATAT
65 CTGAAAATGCACCCATATACATTTCAACAT-TAGTATA-TTCTTCTATTGAAAATGTACCTATAT
1135569 ACATTTAA
128 ACATTTAA
* * * ** *
1135577 ACTATAATATATTTTTCTGTTGATAATGTACCCATATATATTTCAACTATGAC-AT-CATTTCAT
1 ACTATAGTATATTTTTCAGTTGATAATGCACCCATATGCATTTCAACTAT-ACTATACTTTTC-T
* * *
1135640 TCCGAAAATGCACCCATATGCATT
64 GCTGAAAATGCACCCATATACATT
1135664 ATTATTTTAC
Statistics
Matches: 189, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
134 7 0.04
135 177 0.94
136 5 0.03
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (135 bp):
ACTATAGTATATTTTTCAGTTGATAATGCACCCATATGCATTTCAACTATACTATACTTTTCTGC
TGAAAATGCACCCATATACATTTCAACATTAGTATATTCTTCTATTGAAAATGTACCTATATACA
TTTAA
Found at i:1136108 original size:22 final size:22
Alignment explanation
Indices: 1136082--1136123 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1136072 GTATCGATAT
1136082 CCCTACCATGGTATCAATACTA
1 CCCTACCATGGTATCAATACTA
**
1136104 CCCTACTTTGGTATCAATAC
1 CCCTACCATGGTATCAATAC
1136124 CCCCTTCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (22 bp):
CCCTACCATGGTATCAATACTA
Found at i:1140039 original size:24 final size:24
Alignment explanation
Indices: 1140007--1140054 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1139997 GGAAATTATT
1140007 TAACCGTAGGAATACCATTTAATC
1 TAACCGTAGGAATACCATTTAATC
*
1140031 TAACCGTAGGAATATCATTTAATC
1 TAACCGTAGGAATACCATTTAATC
1140055 GACCCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (24 bp):
TAACCGTAGGAATACCATTTAATC
Found at i:1141324 original size:16 final size:16
Alignment explanation
Indices: 1141303--1141341 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1141293 CATCTCCTCT
*
1141303 GAACTCTGGAGCTCCC
1 GAACTCTAGAGCTCCC
1141319 GAACTCTAGAGCTCCC
1 GAACTCTAGAGCTCCC
*
1141335 AAACTCT
1 GAACTCT
1141342 TCAACCCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.21
Consensus pattern (16 bp):
GAACTCTAGAGCTCCC
Found at i:1142298 original size:45 final size:45
Alignment explanation
Indices: 1142249--1142558 Score: 451
Period size: 45 Copynumber: 6.9 Consensus size: 45
1142239 ACTATAGCGC
* * * *
1142249 ACTTTTCTATTGAGAATGCACCCATATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
* * *
1142294 ACTTTTCTGCTGAAAATGTACCCAAATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
* * *
1142339 ACTCTTCTGTTGAAAATGTACCCATATACATTTCAACTATAGTAC
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
* * * * *
1142384 ACTTTTATGTTGATAATGCACCCATATCCATTTCAACGATAACT-T
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT-AGTAT
*
1142429 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
*
1142474 ACTTTTCTGTTGATAATGTACCCATATACATTTCAATTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
1142519 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT
1142559 GGCATCATTT
Statistics
Matches: 238, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
44 2 0.01
45 234 0.98
46 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
Found at i:1142579 original size:45 final size:45
Alignment explanation
Indices: 1142249--1142595 Score: 446
Period size: 45 Copynumber: 7.7 Consensus size: 45
1142239 ACTATAGCGC
* * *
1142249 ACTTTTCTATTGAGAATGCACCCATATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * * *
1142294 ACTTTTCTGCTGAAAATGTACCCAAATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * * *
1142339 ACTCTTCTGTTGAAAATGTACCCATATACATTTCAACTATAGTAC
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * * *
1142384 ACTTTTATGTTGATAATGCACCCATATCCATTTCAACGATAACT-T
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTAT-AGTAT
1142429 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* *
1142474 ACTTTTCTGTTGATAATGTACCCATATACATTTCAATTATAGTAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* * *
1142519 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCAT
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
* ** *
1142564 -CATTTCATGCCGATAATGCACCCATATGCATT
1 ACTTTTC-TGTTGATAATGCACCCATATACATT
1142596 ATTACTTTCA
Statistics
Matches: 267, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
44 7 0.03
45 258 0.97
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTAT
Found at i:1148460 original size:3 final size:3
Alignment explanation
Indices: 1148452--1148480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1148442 AAGGTTAGAA
1148452 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1148481 AGTAAAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1148525 original size:10 final size:10
Alignment explanation
Indices: 1148512--1148543 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1148502 AAGAAAATAA
*
1148512 AAAATAAAAT
1 AAAATGAAAT
1148522 AAAATGAAAT
1 AAAATGAAAT
1148532 AAAATGAAAT
1 AAAATGAAAT
1148542 AA
1 AA
1148544 GGAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (10 bp):
AAAATGAAAT
Found at i:1149011 original size:7 final size:7
Alignment explanation
Indices: 1148999--1149023 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1148989 TATCATTTCC
1148999 CTCATTT
1 CTCATTT
1149006 CTCATTT
1 CTCATTT
1149013 CTCATTT
1 CTCATTT
1149020 CTCA
1 CTCA
1149024 CATTCTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (7 bp):
CTCATTT
Found at i:1149288 original size:18 final size:19
Alignment explanation
Indices: 1149253--1149290 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1149243 CTTTACCGAT
1149253 GGTGACTCTTCAGCTCTCC
1 GGTGACTCTTCAGCTCTCC
1149272 GGTGAC-CTTC-GCTTCTCC
1 GGTGACTCTTCAGC-TCTCC
1149290 G
1 G
1149291 ACGACACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 10 0.56
19 6 0.33
ACGTcount: A:0.08, C:0.37, G:0.24, T:0.32
Consensus pattern (19 bp):
GGTGACTCTTCAGCTCTCC
Found at i:1149701 original size:23 final size:23
Alignment explanation
Indices: 1149674--1149717 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1149664 AAAAACCAAA
1149674 AATAATAGAAATA-AATAAATACT
1 AATAATA-AAATATAATAAATACT
*
1149697 AATAATATAATATAATAAATA
1 AATAATAAAATATAATAAATA
1149718 ATATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AATAATAAAATATAATAAATACT
Found at i:1149713 original size:19 final size:18
Alignment explanation
Indices: 1149683--1149865 Score: 103
Period size: 17 Copynumber: 10.6 Consensus size: 18
1149673 AAATAATAGA
1149683 AATA-AATA-AATACTAAT
1 AATATAATATAATA-TAAT
1149700 AATATAATATAATA-AAT
1 AATATAATATAATATAAT
*
1149717 AATAT-ATATAATATAGT
1 AATATAATATAATATAAT
1149734 -ATATAATATACCATATAAT
1 AATATAATATA--ATATAAT
** *
1149753 -ATAGCATAT-TTATAAT
1 AATATAATATAATATAAT
*
1149769 -ATA-AATATAACACT-AT
1 AATATAATATAATA-TAAT
*
1149785 AATAT-ATATATTATAA-
1 AATATAATATAATATAAT
1149801 AATATAATATATAATATAAT
1 AATAT-A-ATATAATATAAT
1149821 -ATATAATAT-ATACTATAT
1 AATATAATATAATA-TA-AT
*
1149839 GATAT-ATA-ATATATAAT
1 AATATAATATA-ATATAAT
1149856 -ATATAATATA
1 AATATAATATA
1149866 TAAAATATAT
Statistics
Matches: 133, Mismatches: 11, Indels: 43
0.71 0.06 0.23
Matches are distributed among these distances:
15 4 0.03
16 37 0.28
17 41 0.31
18 13 0.10
19 38 0.29
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (18 bp):
AATATAATATAATATAAT
Found at i:1149727 original size:21 final size:21
Alignment explanation
Indices: 1149675--1149883 Score: 151
Period size: 19 Copynumber: 10.5 Consensus size: 21
1149665 AAAACCAAAA
* *
1149675 ATAATAGAAATAA-ATAA-AT
1 ATAATATATATAATATAATAT
*
1149694 ACTAATA-ATATAATATAATAA
1 A-TAATATATATAATATAATAT
*
1149715 ATAATATATATAATATAGTAT
1 ATAATATATATAATATAATAT
**
1149736 AT-A-ATATACCATATAATAT
1 ATAATATATATAATATAATAT
** *
1149755 AGCATATTTATAATATAA-AT
1 ATAATATATATAATATAATAT
* *
1149775 ATAACA-CTATAATAT-ATAT
1 ATAATATATATAATATAATAT
1149794 AT--TATA-A-AATATAATAT
1 ATAATATATATAATATAATAT
1149811 ATAATATA-AT-ATATAATAT
1 ATAATATATATAATATAATAT
*
1149830 ATACTATATGAT-ATATAATAT
1 ATAATATAT-ATAATATAATAT
*
1149851 ATAATATATAATATATAAAATAT
1 ATAATATAT-ATA-ATATAATAT
*
1149874 ATACTATATA
1 ATAATATATA
1149884 CTATCCCGGA
Statistics
Matches: 152, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.03
17 8 0.05
18 1 0.01
19 53 0.35
20 21 0.14
21 47 0.31
22 1 0.01
23 16 0.11
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAATATATATAATATAATAT
Found at i:1149887 original size:7 final size:7
Alignment explanation
Indices: 1149683--1149874 Score: 139
Period size: 7 Copynumber: 27.1 Consensus size: 7
1149673 AAATAATAGA
*
1149683 AATAAAT
1 AATATAT
1149690 AA-ATACT
1 AATATA-T
1149697 AATAATAT
1 AAT-ATAT
1149705 AATATAAT
1 AATAT-AT
1149713 AA-ATA-
1 AATATAT
1149718 ATATATAT
1 A-ATATAT
1149726 AATATAGT
1 AATATA-T
1149734 ATATAATAT
1 A-AT-ATAT
**
1149743 ACCATAT
1 AATATAT
*
1149750 AATATAG
1 AATATAT
*
1149757 CATAT-T
1 AATATAT
*
1149763 TATAATAT
1 AAT-ATAT
1149771 AA-ATAT
1 AATATAT
*
1149777 AACACTAT
1 AATA-TAT
1149785 AATATAT
1 AATATAT
1149792 -ATATTAT
1 AATA-TAT
*
1149799 AAAATAT
1 AATATAT
1149806 AATATAT
1 AATATAT
1149813 -A-ATAT
1 AATATAT
1149818 AATATAT
1 AATATAT
1149825 AATATAT
1 AATATAT
*
1149832 ACTATAT
1 AATATAT
*
1149839 GATATAT
1 AATATAT
1149846 AATATAT
1 AATATAT
1149853 AATATAT
1 AATATAT
1149860 AATATAT
1 AATATAT
*
1149867 AAAATAT
1 AATATAT
1149874 A
1 A
1149875 TACTATATAC
Statistics
Matches: 149, Mismatches: 18, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
5 5 0.03
6 17 0.11
7 96 0.64
8 21 0.14
9 7 0.05
10 3 0.02
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (7 bp):
AATATAT
Found at i:1151543 original size:33 final size:28
Alignment explanation
Indices: 1151473--1151538 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
1151463 CCGAACCCGG
1151473 CCCGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
* * *
1151501 CTCGACCCGAATATCACACTTATAAAAC
1 CCCGACCCGAATATCACACTTAAAAAAA
*
1151529 CCCAACCCGA
1 CCCGACCCGA
1151539 CCCGACCGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.36, G:0.08, T:0.15
Consensus pattern (28 bp):
CCCGACCCGAATATCACACTTAAAAAAA
Found at i:1160625 original size:3 final size:3
Alignment explanation
Indices: 1160619--1160656 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1160609 CTTTTTTTTA
*
1160619 TAT TAT TAT TAT TAT TAT TGT TAT TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T
1160657 TTGTTTACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Done.