Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 49
Found at i:1212075 original size:18 final size:18
Alignment explanation
Indices: 1212052--1212087 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1212042 AACCATAACT
*
1212052 TAAGATTTATACTTTAGG
1 TAAGATTTATACGTTAGG
1212070 TAAGATTTATACGTTAGG
1 TAAGATTTATACGTTAGG
1212088 GTTTAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (18 bp):
TAAGATTTATACGTTAGG
Found at i:1217146 original size:31 final size:31
Alignment explanation
Indices: 1217082--1217151 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1217072 CTTTTAAAAC
*
1217082 TTGCAATAAAGTCCCTCAACTTTTAGTTCGT
1 TTGCAATAAAGTCCCTCAACATTTAGTTCGT
* *
1217113 TTGTAATACAGTCCCAT-AACATTTAG-TCTGT
1 TTGCAATAAAGTCCC-TCAACATTTAGTTC-GT
1217144 TTGCAATA
1 TTGCAATA
1217152 TAGTATCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.06
31 30 0.91
32 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (31 bp):
TTGCAATAAAGTCCCTCAACATTTAGTTCGT
Found at i:1219852 original size:19 final size:17
Alignment explanation
Indices: 1219809--1219852 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1219799 TACATACACA
*
1219809 TAAAATATTTATGTTAT
1 TAAAATATGTATGTTAT
*
1219826 TAATATATGTATGTTCACT
1 TAAAATATGTATGTT-A-T
1219845 TAAAATAT
1 TAAAATAT
1219853 TTTTAAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (17 bp):
TAAAATATGTATGTTAT
Found at i:1233636 original size:6 final size:6
Alignment explanation
Indices: 1233625--1233693 Score: 106
Period size: 6 Copynumber: 11.5 Consensus size: 6
1233615 GACACGTATT
1233625 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1233673 ACC-CG ACCGACCG ACC-CG ACC
1 ACCACG ACC-A-CG ACCACG ACC
1233694 CGAGACGGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.17
6 45 0.75
8 5 0.08
ACGTcount: A:0.30, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1234219 original size:6 final size:6
Alignment explanation
Indices: 1234198--1234335 Score: 230
Period size: 6 Copynumber: 23.5 Consensus size: 6
1234188 TCGGGTCGGC
*
1234198 GGTCG- GGTCG- GGTCGT GGTCGT GGGTCGT GGTCGT GGTCGT GGGCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT -GGTCGT GGTCGT GGTCGT GGTCGT
1234245 GGTCGT GGTCGT GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1234292 GGTCGT GGTC-T GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1234336 AATACGTGTC
Statistics
Matches: 127, Mismatches: 2, Indels: 7
0.93 0.01 0.05
Matches are distributed among these distances:
5 20 0.16
6 101 0.80
7 6 0.05
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1234265 original size:41 final size:41
Alignment explanation
Indices: 1234198--1234335 Score: 226
Period size: 41 Copynumber: 3.4 Consensus size: 41
1234188 TCGGGTCGGC
1234198 GGTCG-GGTCG-GGTCGTGGTCGTGGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTC--GGGTCGTGGTCGTGGTCGT
*
1234239 GGGCGTGGTCGTGGTCGTGGTCGGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGGGTCGTGGTCGTGGTCGT
*
1234280 GGTCGTGGTCGTGGTCGTGGTCTGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGTGGTCGGGTCGTGGTCGTGGTCGT
1234321 GGTCGTGGTCGTGGT
1 GGTCGTGGTCGTGGT
1234336 AATACGTGTC
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
41 77 0.84
42 5 0.05
43 10 0.11
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (41 bp):
GGTCGTGGTCGTGGTCGTGGTCGGGTCGTGGTCGTGGTCGT
Found at i:1236113 original size:24 final size:24
Alignment explanation
Indices: 1236050--1236113 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
1236040 GTGTGGCCTT
1236050 TAGTTGAAAG-AAATAACACTCCA
1 TAGTTGAAAGAAAATAACACTCCA
*
1236073 TAGTTGAAAGAAGATAACACTCTC-
1 TAGTTGAAAGAAAATAACACTC-CA
1236097 TAGTTGAAAGAAAATAA
1 TAGTTGAAAGAAAATAA
1236114 ATCCACCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 10 0.27
24 26 0.70
25 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (24 bp):
TAGTTGAAAGAAAATAACACTCCA
Found at i:1236353 original size:28 final size:28
Alignment explanation
Indices: 1236299--1236370 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
1236289 TTAAAATACC
1236299 TTTTATTTTTATTTTTAACTTATTAAATAAA
1 TTTTATTTTTA---TTAACTTATTAAATAAA
* *
1236330 TTTTGTTTTTATTAACTTATTAAATATA
1 TTTTATTTTTATTAACTTATTAAATAAA
1236358 TTTTATTTTTATT
1 TTTTATTTTTATT
1236371 TTAATGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 28 0.74
31 10 0.26
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTTATTTTTATTAACTTATTAAATAAA
Found at i:1236384 original size:29 final size:28
Alignment explanation
Indices: 1236299--1236723 Score: 122
Period size: 31 Copynumber: 14.6 Consensus size: 28
1236289 TTAAAATACC
* *
1236299 TTTTATTTTTATTTTTAACTTATTAAATAAA
1 TTTTATTTTTA-TTTTAA-TTA-AAAATATA
* *
1236330 TTTTGTTTTTA--TTAACTTATTAAATATA
1 TTTTATTTTTATTTTAA-TTA-AAAATATA
1236358 TTTTATTTTTATTTTAATGTAAAAATATAAA
1 TTTTATTTTTATTTTAAT-TAAAAATAT--A
* * * *
1236389 TTTTATCTTTATCTTCACTTCAAAATATA
1 TTTTATTTTTAT-TTTAATTAAAAATATA
* * *
1236418 TTTTATTCTTATCTTAATTTTTAAAATATA
1 TTTTATTTTTATTTTAA--TTAAAAATATA
** **
1236448 TTTTTAAATGCA--TTAACTTAAAAA-ATA
1 -TTTTATTTTTATTTTAA-TTAAAAATATA
*
1236475 TTTAAATATTTTAATTTTAATATAAAAATAT-
1 TTT---TATTTTTATTTTAAT-TAAAAATATA
* * *
1236506 TTTT-TTTATA-TTCACTTAAAAATATA
1 TTTTATTTTTATTTTAATTAAAAATATA
*
1236532 TTTTATTCTTATTTTAAATTTAAAAATATATA
1 TTTTATTTTTATTTT-AA-TT-AAAA-ATATA
** ** *
1236564 TTTTATAATTATCATAGATTTTAAAAATATC
1 TTTTATTTTTATTTTA-A--TTAAAAATATA
* * * **
1236595 TTTTATTTGTGTCTTAACTTGTCAAATATA
1 TTTTATTTTTATTTTAA-TT-AAAAATATA
* *
1236625 ---T-TTTTTATTTTAATATAAAACACATG
1 TTTTATTTTTATTTTAAT-TAAAA-ATATA
* * * *
1236651 TTTTAATTTTATCTTCACTTAAAAGTATA
1 TTTTATTTTTAT-TTTAATTAAAAATATA
* *
1236680 TTTTGTTCTTATTTTAACTTAAAAA-ATA
1 TTTTATTTTTATTTTAA-TTAAAAATATA
* *
1236708 -TTTATTCTTATCTTAA
1 TTTTATTTTTATTTTAA
1236724 CTTTTCTAAA
Statistics
Matches: 292, Mismatches: 68, Indels: 72
0.68 0.16 0.17
Matches are distributed among these distances:
25 12 0.04
26 24 0.08
27 26 0.09
28 43 0.15
29 47 0.16
30 37 0.13
31 73 0.25
32 27 0.09
33 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTTATTTTTATTTTAATTAAAAATATA
Found at i:1236388 original size:59 final size:57
Alignment explanation
Indices: 1236289--1236569 Score: 196
Period size: 60 Copynumber: 4.8 Consensus size: 57
1236279 ATCTTAAATT
** * ** *
1236289 TTAAAATACCTTTTATTTTTATTTTTAACTTATTAA-ATAAATTTTGTTTTTATTAAC
1 TTAAAATATATTTTATTTTTA-TTTTAATTTAAAAATATAAATTTTATTTTTATTAAC
* * *
1236346 TTATTAAATATATTTTATTTTTATTTTAATGTAAAAATATAAATTTTATCTTTATCTTCAC
1 TTA--AAATATATTTTATTTTTATTTTAATTTAAAAATATAAATTTTAT-TTT-TATTAAC
* * * * ** **
1236407 TTCAAAATATATTTTATTCTTATCTTAATTTTTAAAATAT-ATTTTTAAATGCATTAAC
1 TT-AAAATATATTTTATTTTTATTTTAA-TTTAAAAATATAAATTTTATTTTTATTAAC
* * * * *
1236465 TTAAAAAATATTTAAATATTTTAATTTTAATATAAAAATAT---TTTT-TTTATATTCAC
1 TTAAAATATATTT---TATTTTTATTTTAATTTAAAAATATAAATTTTATTTTTATTAAC
* *
1236521 TTAAAAATATATTTTATTCTTATTTTAAATTTAAAAATATATATTTTAT
1 TT-AAAATATATTTTATTTTTATTTT-AATTTAAAAATATAAATTTTAT
1236570 AATTATCATA
Statistics
Matches: 173, Mismatches: 35, Indels: 30
0.73 0.15 0.13
Matches are distributed among these distances:
54 10 0.06
55 12 0.07
56 8 0.05
57 27 0.16
58 20 0.12
59 37 0.21
60 42 0.24
61 16 0.09
62 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (57 bp):
TTAAAATATATTTTATTTTTATTTTAATTTAAAAATATAAATTTTATTTTTATTAAC
Found at i:1236717 original size:27 final size:29
Alignment explanation
Indices: 1236651--1236726 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1236641 AAAACACATG
* *
1236651 TTTTAATT-TTATCTTCACTTAAAAGTATA
1 TTTT-ATTCTTATCTTAACTTAAAAGAATA
* *
1236680 TTTTGTTCTTATTTTAACTTAAAA-AATA
1 TTTTATTCTTATCTTAACTTAAAAGAATA
1236708 -TTTATTCTTATCTTAACTT
1 TTTTATTCTTATCTTAACTT
1236727 TTCTAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 17 0.43
28 5 0.12
29 18 0.45
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTATTCTTATCTTAACTTAAAAGAATA
Found at i:1236857 original size:29 final size:29
Alignment explanation
Indices: 1236809--1236906 Score: 124
Period size: 29 Copynumber: 3.3 Consensus size: 29
1236799 ATTTTTGAAA
*
1236809 AAAATATATTTTTAAAATTTAAGTTAATAAT
1 AAAATATATTTTT--AATTTAAGTTAAGAAT
***
1236840 AAAATATATTTTTAATTTAAAACAAGAAT
1 AAAATATATTTTTAATTTAAGTTAAGAAT
*
1236869 AAAATATATTTTTAAGTTAAGTTAAGAAT
1 AAAATATATTTTTAATTTAAGTTAAGAAT
*
1236898 AATATATAT
1 AAAATATAT
1236907 ATATATATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 45 0.78
31 13 0.22
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (29 bp):
AAAATATATTTTTAATTTAAGTTAAGAAT
Found at i:1236906 original size:2 final size:2
Alignment explanation
Indices: 1236899--1236932 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1236889 GTTAAGAATA
1236899 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
1236933 TAAAATAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1236963 original size:10 final size:10
Alignment explanation
Indices: 1236898--1236966 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
1236888 AGTTAAGAAT
1236898 AATATATATA
1 AATATATATA
*
1236908 TATATATATA
1 AATATATATA
*
1236918 TATATATATA
1 AATATATATA
*
1236928 TATAT-TA-A
1 AATATATATA
1236936 AATA-ATAATA
1 AATATAT-ATA
*
1236946 AA-ATATTTA
1 AATATATATA
*
1236955 AATATATTTA
1 AATATATATA
1236965 AA
1 AA
1236967 AAAATATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
8 5 0.10
9 8 0.16
10 38 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATATATATA
Found at i:1237052 original size:29 final size:28
Alignment explanation
Indices: 1236996--1237063 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1236986 GATAAAGATA
*
1236996 AAATATATTTTTAATTTAAAAATAATAT
1 AAATATATTTTTAATGTAAAAATAATAT
*
1237024 ATTATATATTTTTAATAAGT-AAAAT-ATAT
1 A-AATATATTTTTAAT--GTAAAAATAATAT
1237053 AAATATATTTT
1 AAATATATTTT
1237064 CTTGAACCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.29
29 18 0.53
30 5 0.15
31 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AAATATATTTTTAATGTAAAAATAATAT
Found at i:1237094 original size:2 final size:2
Alignment explanation
Indices: 1237089--1237140 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1237079 AAAAAAGATA
1237089 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
1237131 AT AT AT AT AT
1 AT AT AT AT AT
1237141 TTTACTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1237990 original size:21 final size:21
Alignment explanation
Indices: 1237964--1238035 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
1237954 TTTCAGTAAG
* *
1237964 AGTATCCATACTTCTGGGGAA
1 AGTATCGATACTTCTGGGAAA
1237985 AGTATCGATACTTCT-GGAAA
1 AGTATCGATACTTCTGGGAAA
*
1238005 ACGTATCGATACTTCTGGTAAA
1 A-GTATCGATACTTCTGGGAAA
1238027 AGTATCGAT
1 AGTATCGAT
1238036 TCTCAAGGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 5 0.11
21 36 0.78
22 5 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTTCTGGGAAA
Found at i:1239895 original size:30 final size:30
Alignment explanation
Indices: 1239853--1239930 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
1239843 AAGGTGTTAC
*
1239853 AAAAAGTAAAATATATTTAATAAGTTAAGAT
1 AAAAA-TAAAATATATTTAATAAGTTAAAAT
1239884 AAAAATAAAATATATTTAATAAGTTAAAAT
1 AAAAATAAAATATATTTAATAAGTTAAAAT
1239914 AAAAATAAAATATATTT
1 AAAAATAAAATATATTT
1239931 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 41 0.89
31 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAATAAAATATATTTAATAAGTTAAAAT
Found at i:1240212 original size:19 final size:19
Alignment explanation
Indices: 1240179--1240217 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1240169 GCACCTTTTG
1240179 ATTTTAATAATT-AAATTT
1 ATTTTAATAATTAAAATTT
*
1240197 ATTTTAATTTATTAAAATTT
1 ATTTTAA-TAATTAAAATTT
1240217 A
1 A
1240218 GACCAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTAATAATTAAAATTT
Found at i:1240436 original size:2 final size:2
Alignment explanation
Indices: 1240429--1240461 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1240419 AGTTTACTCT
1240429 TA TA 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 TA TA T
1240462 CTTTATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1247960 original size:20 final size:20
Alignment explanation
Indices: 1247935--1247974 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1247925 AGTTTTAGTC
*
1247935 CAAATTGACCCAAGTAAAAT
1 CAAATTGACCCAAATAAAAT
1247955 CAAATTGACCCAAATAAAAT
1 CAAATTGACCCAAATAAAAT
1247975 TCAAGCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (20 bp):
CAAATTGACCCAAATAAAAT
Found at i:1248215 original size:22 final size:22
Alignment explanation
Indices: 1248185--1248237 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1248175 AAAAAATCGA
1248185 GACTTAAACCTCTCATTTTATT
1 GACTTAAACCTCTCATTTTATT
*
1248207 GGCTTAAACCTCTCATTTTATT
1 GACTTAAACCTCTCATTTTATT
1248229 GACTTAAAC
1 GACTTAAAC
1248238 ATTCTCGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.42
Consensus pattern (22 bp):
GACTTAAACCTCTCATTTTATT
Found at i:1253688 original size:29 final size:24
Alignment explanation
Indices: 1253633--1253681 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1253623 AGTAGATAGT
1253633 TTTTTATTTTATTTTATGAATTTG
1 TTTTTATTTTATTTTATGAATTTG
1253657 TTTTTATTTTATTTTATGAATTTG
1 TTTTTATTTTATTTTATGAATTTG
1253681 T
1 T
1253682 ACGGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATTTTATGAATTTG
Found at i:1255953 original size:16 final size:16
Alignment explanation
Indices: 1255932--1255962 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1255922 ATAGTGCTAC
1255932 AGTGTACCGATGCACT
1 AGTGTACCGATGCACT
1255948 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
1255963 AAAAACATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (16 bp):
AGTGTACCGATGCACT
Found at i:1256007 original size:21 final size:21
Alignment explanation
Indices: 1255983--1256022 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1255973 AATATAAATT
* * *
1255983 GTGTATCGGTGCATTGCTATA
1 GTGTACCGATGCACTGCTATA
1256004 GTGTACCGATGCACTGCTA
1 GTGTACCGATGCACTGCTA
1256023 CAGTAACTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTATA
Found at i:1256595 original size:24 final size:23
Alignment explanation
Indices: 1256550--1256614 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
1256540 AGCTCGTATA
*
1256550 AATTGCACCGAAG-GACCGCGTAG
1 AATTGCACCGAAGTG-CCACGTAG
1256573 CAATTGCACCGAAGTGCCACGTAG
1 -AATTGCACCGAAGTGCCACGTAG
* *
1256597 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1256615 TACAAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.43
24 20 0.54
25 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1264033 original size:15 final size:15
Alignment explanation
Indices: 1264013--1264047 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1264003 TCGGAGTCCA
1264013 AGTTGGGATGATCCT
1 AGTTGGGATGATCCT
1264028 AGTTGGGATGATCCT
1 AGTTGGGATGATCCT
1264043 AGTTG
1 AGTTG
1264048 ATCCCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (15 bp):
AGTTGGGATGATCCT
Found at i:1272664 original size:20 final size:20
Alignment explanation
Indices: 1272635--1272677 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1272625 ATTCCACCAC
*
1272635 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1272655 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1272675 ATG
1 ATG
1272678 GGCTCTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1275848 original size:30 final size:28
Alignment explanation
Indices: 1275806--1275886 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
1275796 TATTATTATT
*
1275806 TTTATTTAAGATAAAAAAATTAAATAGTA
1 TTTATATAAGATAAAAAAATTAAATA-TA
* * * *
1275835 TTTATCATGAGATAAAAAAATTTATTATT
1 TTTAT-ATAAGATAAAAAAATTAAATATA
*
1275864 TTTATATAAGATAAAAAGATTAA
1 TTTATATAAGATAAAAAAATTAA
1275887 GCTTTAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
28 15 0.35
29 11 0.26
30 17 0.40
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (28 bp):
TTTATATAAGATAAAAAAATTAAATATA
Found at i:1278551 original size:21 final size:21
Alignment explanation
Indices: 1278457--1278544 Score: 140
Period size: 21 Copynumber: 4.2 Consensus size: 21
1278447 ATTCTGACTA
*
1278457 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
1278478 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
*
1278499 TCGCGTTGCGATTTCCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
1278520 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
1278541 TCGC
1 TCGC
1278545 AATGCGAATA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:1279478 original size:24 final size:24
Alignment explanation
Indices: 1279427--1279480 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1279417 GTATTCGAAA
*
1279427 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1279451 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1279475 TTTGAT
1 TTTGAT
1279481 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1282018 original size:20 final size:19
Alignment explanation
Indices: 1281990--1282044 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1281980 CAATCATCTT
*
1281990 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
1282010 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
1282029 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1282045 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1282059 original size:33 final size:33
Alignment explanation
Indices: 1282017--1282110 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1282007 GGAAATGACT
1282017 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1282050 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1282083 ATCGCAAAGCCAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1282111 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1282073 original size:19 final size:19
Alignment explanation
Indices: 1281997--1282075 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
1281987 CTTAATGTCT
* **
1281997 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
1282017 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1282036 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1282050 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1282069 ATCGCAA
1 ATCGCAA
1282076 CGAGGGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.49
20 9 0.18
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1282292 original size:14 final size:14
Alignment explanation
Indices: 1282273--1282309 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1282263 CATCAATTAA
1282273 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1282287 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1282301 ACAAATCAA
1 ACAAATCAA
1282310 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1284245 original size:19 final size:20
Alignment explanation
Indices: 1284204--1284258 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1284194 AAAAATGACT
*
1284204 ATCGCAACGCGAGAATGAAA
1 ATCGCAACGCGAGAATAAAA
1284224 ATCGCAACGCGA-AATAAAA
1 ATCGCAACGCGAGAATAAAA
*
1284243 ATCGCAACGAGAGAAT
1 ATCGCAACGCGAGAAT
1284259 CGCAATGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAGAATAAAA
Found at i:1284331 original size:20 final size:20
Alignment explanation
Indices: 1284306--1284368 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1284296 TCGCGTTGCG
1284306 ATTTTGTCGTTGCGATTTTC
1 ATTTTGTCGTTGCGATTTTC
1284326 ATTTTG-CGTTGCGATTTTC
1 ATTTTGTCGTTGCGATTTTC
* *
1284345 ATTCTCTCGTTGCGATTTTC
1 ATTTTGTCGTTGCGATTTTC
1284365 ATTT
1 ATTT
1284369 CAACCAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
ATTTTGTCGTTGCGATTTTC
Found at i:1284572 original size:94 final size:94
Alignment explanation
Indices: 1284460--1284835 Score: 584
Period size: 94 Copynumber: 4.1 Consensus size: 94
1284450 ATGGATTGCA
* * * *
1284460 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAACACGCAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1284524 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1284553 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATGCACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1284618 TTAGTAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1284647 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1284712 TTAGCAGAATTGACAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1284741 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1284801 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1284831 TTACT
1 TTACT
1284836 AAGCAATCTA
Statistics
Matches: 264, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
90 40 0.15
93 22 0.08
94 202 0.77
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1286562 original size:19 final size:19
Alignment explanation
Indices: 1286519--1286606 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
1286509 TTTTGGTTGA
*
1286519 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCG-G
1286539 AATGAAAATCGCAACGCGG
1 AATGAAAATCGCAACGCGG
**
1286558 AATGACTATCGCAA--C-G
1 AATGAAAATCGCAACGCGG
* *
1286574 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGG
1286591 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
1286607 AGAGAATCAC
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 25 0.45
20 17 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGG
Found at i:1286587 original size:33 final size:33
Alignment explanation
Indices: 1286517--1286637 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
1286507 TCTTTTGGTT
1286517 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
* **
1286556 GGAATGACTATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1286589 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1286622 GAAACCAAAATCGCAA
1 GAAATGAAAATCGCAA
1286638 TATTTTCGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
33 54 0.74
35 1 0.01
36 1 0.01
37 3 0.04
39 14 0.19
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1286664 original size:20 final size:20
Alignment explanation
Indices: 1286639--1286677 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1286629 AAATCGCAAT
*
1286639 ATTTTCGTGTTGCGATTTTC
1 ATTTTCATGTTGCGATTTTC
*
1286659 ATTTTCATGTTGTGATTTT
1 ATTTTCATGTTGCGATTTT
1286678 AAGTTTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
ATTTTCATGTTGCGATTTTC
Found at i:1287240 original size:20 final size:20
Alignment explanation
Indices: 1287217--1287311 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
1287207 GCGATAGTCA
1287217 TATTCGCATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
** * *
1287237 TATTCGTGTTGCGATTTTCC
1 TATTCGCATTGCGATTTACG
1287257 TAATTCGCATTGCGATTTACG
1 T-ATTCGCATTGCGATTTACG
* * *
1287278 TAATCGCGTTGGGATTTACG
1 TATTCGCATTGCGATTTACG
1287298 TATTCGCATTGCGA
1 TATTCGCATTGCGA
1287312 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TATTCGCATTGCGATTTACG
Found at i:1287265 original size:41 final size:40
Alignment explanation
Indices: 1287217--1287311 Score: 136
Period size: 41 Copynumber: 2.4 Consensus size: 40
1287207 GCGATAGTCA
* * *
1287217 TATTCGCATTGCGATTTACGTATTCGTGTTGCGATTTTCC
1 TATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACC
* *
1287257 TAATTCGCATTGCGATTTACGTAATCGCGTTGGGATTTACG
1 T-ATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACC
1287298 TATTCGCATTGCGA
1 TATTCGCATTGCGA
1287312 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 14 0.29
41 35 0.71
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (40 bp):
TATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACC
Found at i:1287324 original size:41 final size:41
Alignment explanation
Indices: 1287294--1287375 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1287284 CGTTGGGATT
1287294 TACGT-ATTCGCATTGCGAATTAGGAAAATCGCAACGCGAA
1 TACGTAATTCGCATTGCGAATTAGGAAAATCGCAACGCGAA
* *
1287334 TACGTAAATCGCAATGCGAATTAGGAAAATCGCAACGCGAA
1 TACGTAATTCGCATTGCGAATTAGGAAAATCGCAACGCGAA
1287375 T
1 T
1287376 TTGGGAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 5 0.13
41 34 0.87
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (41 bp):
TACGTAATTCGCATTGCGAATTAGGAAAATCGCAACGCGAA
Found at i:1287332 original size:21 final size:21
Alignment explanation
Indices: 1287308--1287394 Score: 113
Period size: 21 Copynumber: 4.2 Consensus size: 21
1287298 TATTCGCATT
1287308 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1287329 GCGAA-TACGTAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1287349 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1287370 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1287391 GCGA
1 GCGA
1287395 TAGTCAGAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.30
21 39 0.70
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1287407 original size:41 final size:41
Alignment explanation
Indices: 1287301--1287394 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
1287291 ATTTACGTAT
* * *
1287301 TCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATTAGCAAAATCGCAACGCGAATACGGAAA
* **
1287342 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGCAAAATCGCAACGCGAA-TACGGAAA
1287384 TCGCAATGCGA
1 TCGCAATGCGA
1287395 TAGTCAGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 32 0.67
42 16 0.33
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.19
Consensus pattern (41 bp):
TCGCAATGCGAATTAGCAAAATCGCAACGCGAATACGGAAA
Found at i:1292086 original size:48 final size:48
Alignment explanation
Indices: 1292032--1292139 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 48
1292022 CATAATTTAA
* * * **
1292032 ACAACTTTTTTAGAAAATATGTGAAATAGTGGTGCATTATCATATTCT
1 ACAACTTTTTCAGAAAACAGGTGAAATAGTGACGCATTATCATATTCT
* * *
1292080 GCAAC-TTTTCAGAAAACGGGTGAAATAGTGACGCATTATCATCTTCT
1 ACAACTTTTTCAGAAAACAGGTGAAATAGTGACGCATTATCATATTCT
1292127 ACAAC-TTTTCAGA
1 ACAACTTTTTCAGA
1292140 GGTCATTCAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
47 47 0.92
48 4 0.08
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (48 bp):
ACAACTTTTTCAGAAAACAGGTGAAATAGTGACGCATTATCATATTCT
Found at i:1295996 original size:23 final size:23
Alignment explanation
Indices: 1295963--1296030 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1295953 ATTATTATAT
1295963 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1295986 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
** *
1296009 GGCACTTTGGTGCAATTTTACG
1 GGCACTACGGTGCAATTCTACG
1296031 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1301205 original size:23 final size:23
Alignment explanation
Indices: 1301179--1301238 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1301169 ATGGCACTAT
*
1301179 GGTGCAATTCTACGCGGCACTCC
1 GGTGCAATTCTACGCAGCACTCC
* * *
1301202 GGTGCAATTCTACGTAGTACTTC
1 GGTGCAATTCTACGCAGCACTCC
*
1301225 GGTGCAATTATACG
1 GGTGCAATTCTACG
1301239 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
GGTGCAATTCTACGCAGCACTCC
Found at i:1301290 original size:16 final size:17
Alignment explanation
Indices: 1301269--1301301 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1301259 TGCACAACCT
1301269 CTATAG-ACTCACATAC
1 CTATAGTACTCACATAC
*
1301285 CTATAGTTCTCACATAC
1 CTATAGTACTCACATAC
1301302 GTCCATGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CTATAGTACTCACATAC
Found at i:1302070 original size:21 final size:21
Alignment explanation
Indices: 1302019--1302071 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1302009 AGTAGGGTGC
* *
1302019 TACCTAAAATGTTATTTTTTC
1 TACCTAAAATGTTAATTTTTA
* *
1302040 TACATGAAATGTTAATTTTTA
1 TACCTAAAATGTTAATTTTTA
1302061 TACCTAAAATG
1 TACCTAAAATG
1302072 AATATTTTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTTTA
Found at i:1302174 original size:45 final size:45
Alignment explanation
Indices: 1302080--1302212 Score: 178
Period size: 45 Copynumber: 2.9 Consensus size: 45
1302070 TGAATATTTT
*
1302080 CGATATTAATATTTTCTATAGAAAAAATAACATTTTAGATAGCGAC
1 CGATATTAATATTTTCTATAG-AAAAATAACATTTTAGGTAGCGAC
* *
1302126 CGATATTAATATTTTTTATAGGAAAATAACATTTTAGGTAGC-ATC
1 CGATATTAATATTTTCTATAGAAAAATAACATTTTAGGTAGCGA-C
* *
1302171 CGATATTAATATTTTCGGTAGAAAAAAATAACATTTTAGGTA
1 CGATATTAATATTTTC--TATAGAAAAATAACATTTTAGGTA
1302213 ACACTCCACC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
44 1 0.01
45 35 0.45
46 20 0.26
47 21 0.27
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (45 bp):
CGATATTAATATTTTCTATAGAAAAATAACATTTTAGGTAGCGAC
Found at i:1303442 original size:65 final size:64
Alignment explanation
Indices: 1303330--1303475 Score: 172
Period size: 65 Copynumber: 2.3 Consensus size: 64
1303320 ACACTTTGTA
* * **
1303330 TGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCCAGGAGTG-ATTTGATGCATGGTC
1 TGCATCGGTACA-TAAAATACATTCGATGTTTCAAAAGAACCAGGAGTGCA-TCAATGCATGGT-
1303393 TG
63 TG
* *
1303395 TGCATCGGTACATAAAATACATTCGATGTTTCAATAA-AATCATGAGTGCATCAATGCATGGTTG
1 TGCATCGGTACATAAAATACATTCGATGTTTCAA-AAGAACCAGGAGTGCATCAATGCATGGTTG
*
1303459 TGCATCGGTACACAAAA
1 TGCATCGGTACATAAAA
1303476 CGCATTCAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
64 19 0.27
65 49 0.69
66 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (64 bp):
TGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAACCAGGAGTGCATCAATGCATGGTTG
Found at i:1303843 original size:13 final size:13
Alignment explanation
Indices: 1303825--1303858 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1303815 TAAGATTTTC
*
1303825 TTTGAAAATCATT
1 TTTGAAAATCAAT
1303838 TTTG-AAATCAAT
1 TTTGAAAATCAAT
1303850 TTTGAAAAT
1 TTTGAAAAT
1303859 TAGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:1304187 original size:31 final size:32
Alignment explanation
Indices: 1304151--1304219 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
1304141 AGCATTCAAG
1304151 TTCAAACATCCAAAACATA-AATCCAAAAACA
1 TTCAAACATCCAAAACATACAATCCAAAAACA
*
1304182 TTCAAACATCCAAAATATATCAATCCAAAAACA
1 TTCAAACATCCAAAACATA-CAATCCAAAAACA
1304215 -TCAAA
1 TTCAAA
1304220 ATGTTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 18 0.51
32 5 0.14
33 12 0.34
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (32 bp):
TTCAAACATCCAAAACATACAATCCAAAAACA
Found at i:1305636 original size:13 final size:13
Alignment explanation
Indices: 1305614--1305643 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1305604 GGCAATTTTA
*
1305614 AAAACTATGTTTG
1 AAAACAATGTTTG
1305627 AAAACAATGTTTG
1 AAAACAATGTTTG
1305640 AAAA
1 AAAA
1305644 TTAATATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (13 bp):
AAAACAATGTTTG
Found at i:1306190 original size:44 final size:44
Alignment explanation
Indices: 1306112--1306229 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 44
1306102 CGACGAGTGT
* *
1306112 ATCGATACACTG-CATAGTGTATCGATGCACATTCAAGGAATGC
1 ATCGGTACACTGTCATAGTGTATCGATGCATATTCAAGGAATGC
* * *
1306155 ATTGGTGCACCT-TCATAGTGTATCGATGCATATTCAAGGGATGC
1 ATCGGTACA-CTGTCATAGTGTATCGATGCATATTCAAGGAATGC
*
1306199 ATCGGTACACTGTCATAGTTTATCGATGCAT
1 ATCGGTACACTGTCATAGTGTATCGATGCAT
1306230 TGCGCATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 8 0.12
44 56 0.88
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
ATCGGTACACTGTCATAGTGTATCGATGCATATTCAAGGAATGC
Found at i:1315331 original size:131 final size:130
Alignment explanation
Indices: 1315088--1315357 Score: 416
Period size: 131 Copynumber: 2.1 Consensus size: 130
1315078 CTGCAAACAG
*
1315088 ATAAACAATATACTCAACTCCACAACAATCAAGGGGTTTAAATTCCCTGCTAGAAAAAAATATAT
1 ATAAACAATATACTCAACTCCACAACAATCAAGGGGTTTAAATTCCCTGCTACAAAAAAATATAT
* * *
1315153 CATAAGAGTCGAGGTAGCTTGGCTAAAATATCAAATGACAGGTAACATACATCAAACTTAAAAAA
66 CATAAGAGTCGAGGTAGCTTGGCTAAAATATCAAAGGACAGGCAACATACATCAAACGTAAAAAA
** * *
1315218 ATAAACAATATTGTCAACTCCACAATAATCAAGGGGGTTTAAATTCCCTGCTACAAAAACATATA
1 ATAAACAATATACTCAACTCCACAACAATCAA-GGGGTTTAAATTCCCTGCTACAAAAAAATATA
* * * *
1315283 TCATAAGAGTTGAGGTAGCTTGGCTAAAATATCAAAGGCCATGCAACATACATCAAACGTAAGAA
65 TCATAAGAGTCGAGGTAGCTTGGCTAAAATATCAAAGGACAGGCAACATACATCAAACGTAAAAA
1315348 A
130 A
1315349 ATAAA-AATA
1 ATAAACAATA
1315358 ATTAAATAAG
Statistics
Matches: 127, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
130 33 0.26
131 94 0.74
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (130 bp):
ATAAACAATATACTCAACTCCACAACAATCAAGGGGTTTAAATTCCCTGCTACAAAAAAATATAT
CATAAGAGTCGAGGTAGCTTGGCTAAAATATCAAAGGACAGGCAACATACATCAAACGTAAAAAA
Found at i:1330864 original size:21 final size:21
Alignment explanation
Indices: 1330835--1330874 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1330825 CACCTTAGAC
*
1330835 TCCACCTGAGTGAGCTTGGTA
1 TCCACCTGAGCGAGCTTGGTA
* *
1330856 TCCATCTGAGCGATCTTGG
1 TCCACCTGAGCGAGCTTGG
1330875 AGTTAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (21 bp):
TCCACCTGAGCGAGCTTGGTA
Found at i:1345287 original size:2 final size:2
Alignment explanation
Indices: 1345280--1345320 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1345270 ATCTTAAATC
1345280 AT 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 AT A
1345321 ACTAACCCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1350060 original size:16 final size:16
Alignment explanation
Indices: 1350039--1350072 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1350029 TCAATTACAA
*
1350039 GTCAGGTTCATAACAG
1 GTCAGGTTCAAAACAG
*
1350055 GTCAGGTTGAAAACAG
1 GTCAGGTTCAAAACAG
1350071 GT
1 GT
1350073 TGGGCAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (16 bp):
GTCAGGTTCAAAACAG
Found at i:1351105 original size:9 final size:9
Alignment explanation
Indices: 1351091--1351128 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1351081 CGAAAGATAT
1351091 AAACTTTAA
1 AAACTTTAA
1351100 AAAC-TTAA
1 AAACTTTAA
*
1351108 AGAATTTTAA
1 A-AACTTTAA
1351118 AAACTTTAA
1 AAACTTTAA
1351127 AA
1 AA
1351129 TTTAATAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (9 bp):
AAACTTTAA
Found at i:1352346 original size:29 final size:25
Alignment explanation
Indices: 1352314--1352371 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
1352304 AATGTTAGAT
1352314 AAAAATAATAAATAAATATTAAATAAATC
1 AAAAA-AATAAATAAA-A-T-AATAAATC
1352343 AAAAAAATAAATAAAATAATAAATC
1 AAAAAAATAAATAAAATAATAAATC
1352368 AAAA
1 AAAA
1352372 GAAAAAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.41
26 1 0.03
27 1 0.03
28 10 0.34
29 5 0.17
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAAAATAAATAAAATAATAAATC
Found at i:1353352 original size:18 final size:19
Alignment explanation
Indices: 1353329--1353367 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1353319 TAATTTTACA
1353329 CTTAA-GGAACCGATTCCC
1 CTTAAGGGAACCGATTCCC
*
1353347 CTTAAGGGGTACCGATTCCC
1 CTTAA-GGGAACCGATTCCC
1353367 C
1 C
1353368 CACGCTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (19 bp):
CTTAAGGGAACCGATTCCC
Found at i:1356799 original size:23 final size:22
Alignment explanation
Indices: 1356756--1356799 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1356746 AAACACAATA
* *
1356756 ATTTGAAAATTATAAATTTTTT
1 ATTTGAAAATTAGAAAATTTTT
*
1356778 ATTTCGAAATTTAGAAAATTTT
1 ATTT-GAAAATTAGAAAATTTT
1356800 GAAAAAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTTGAAAATTAGAAAATTTTT
Found at i:1357200 original size:21 final size:21
Alignment explanation
Indices: 1357174--1357230 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
1357164 TTCCCTGTGG
1357174 GGGGAATCGGTTCCCTTCAAA
1 GGGGAATCGGTTCCCTTCAAA
* *
1357195 GGGGAATCAGTTCCC-TCAAG
1 GGGGAATCGGTTCCCTTCAAA
* *
1357215 GGGGGATCGATTCCCT
1 GGGGAATCGGTTCCCT
1357231 CTGCACTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTTCAAA
Found at i:1362105 original size:20 final size:19
Alignment explanation
Indices: 1362063--1362101 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1362053 GTTTGTTTTC
1362063 ATTTTTAATTTTGAAACAT
1 ATTTTTAATTTTGAAACAT
1362082 ATTTTTATATTTT-AAACAT
1 ATTTTTA-ATTTTGAAACAT
1362101 A
1 A
1362102 ATTTATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTTAATTTTGAAACAT
Found at i:1369438 original size:20 final size:19
Alignment explanation
Indices: 1369413--1369498 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 19
1369403 TTTTGGTGCA
1369413 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCC-T
* *
1369433 GAGGGAATTGATTCCCCCTTT
1 GAGGGAATCGATACCCCC--T
*
1369454 GAAGGGGAA-CTGATTCCCCCT
1 G-A-GGGAATC-GATACCCCCT
1369475 -AGGGGAATCGATACCCCCT
1 GA-GGGAATCGATACCCCCT
1369494 GAGGG
1 GAGGG
1369499 TTCTGGTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
19 19 0.35
20 18 0.33
21 3 0.05
22 1 0.02
23 14 0.25
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (19 bp):
GAGGGAATCGATACCCCCT
Found at i:1369491 original size:19 final size:20
Alignment explanation
Indices: 1369415--1369498 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
1369405 TTGGTGCAGA
1369415 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCC-TGAG
* *
1369435 GGGAATTGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC--TG-AG
*
1369458 GGGAA-CTGATTCCCCCT-AG
1 GGGAATC-GATACCCCCTGAG
1369477 GGGAATCGATACCCCCTGAG
1 GGGAATCGATACCCCCTGAG
1369497 GG
1 GG
1369499 TTCTGGTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
19 16 0.30
20 19 0.36
21 3 0.06
22 1 0.02
23 14 0.26
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (20 bp):
GGGAATCGATACCCCCTGAG
Found at i:1371918 original size:13 final size:13
Alignment explanation
Indices: 1371900--1371924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1371890 AATAAATTTT
1371900 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1371913 AAGATTTTCTAA
1 AAGATTTTCTAA
1371925 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:1373686 original size:14 final size:14
Alignment explanation
Indices: 1373669--1373719 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
1373659 GAAAAACAAG
1373669 TAAATAAATAAAAT
1 TAAATAAATAAAAT
1373683 TAAATAAATAATAAT
1 TAAATAAATAA-AAT
*
1373698 ATAAA-AAATAATAT
1 -TAAATAAATAAAAT
1373712 TAATATAA
1 TAA-ATAA
1373720 TATATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 14 0.44
15 11 0.34
16 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATAAATAAAAT
Found at i:1373697 original size:3 final size:3
Alignment explanation
Indices: 1373689--1373744 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
1373679 AAATTAAATA
*
1373689 AAT AAT AAT -AT AA- AA- AAT AAT ATT AAT -AT AAT ATAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT
1373732 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1373745 CAATAATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 32 0.70
4 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1373724 original size:7 final size:7
Alignment explanation
Indices: 1373685--1373741 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
1373675 AATAAAATTA
*
1373685 AATAAAT
1 AATATAT
1373692 AATAATAT
1 AAT-ATAT
* *
1373700 AAAAAAT
1 AATATAT
1373707 AATAT-T
1 AATATAT
1373713 -A-ATAT
1 AATATAT
1373718 AATATAT
1 AATATAT
1373725 AATATAT
1 AATATAT
1373732 AATA-AT
1 AATATAT
1373738 AATA
1 AATA
1373742 ATACAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 8 0.20
7 24 0.59
8 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AATATAT
Found at i:1373733 original size:25 final size:26
Alignment explanation
Indices: 1373685--1373751 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
1373675 AATAAAATTA
1373685 AATAA-ATAATAATATAAAAAATAAT
1 AATAATATAATAATATAAAAAATAAT
*
1373710 ATTAATATAAT-ATATAATATATAATAAT
1 AATAATATAATAATATAA-A-A-AATAAT
*
1373738 AATAATACAATAAT
1 AATAATATAATAAT
1373752 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 10 0.29
26 6 0.18
27 1 0.03
28 15 0.44
29 2 0.06
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
AATAATATAATAATATAAAAAATAAT
Found at i:1373742 original size:23 final size:24
Alignment explanation
Indices: 1373689--1373744 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1373679 AAATTAAATA
*
1373689 AATAATAATATAAAAAATAATATT
1 AATAATAATATAAAAAATAATAAT
* *
1373713 AAT-ATAATATATAATAT-ATAAT
1 AATAATAATATAAAAAATAATAAT
1373735 AATAATAATA
1 AATAATAATA
1373745 CAATAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 18 0.64
24 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAATAATATAAAAAATAATAAT
Found at i:1373889 original size:36 final size:36
Alignment explanation
Indices: 1373794--1374136 Score: 257
Period size: 38 Copynumber: 9.0 Consensus size: 36
1373784 TAAAAATAAT
* * * *
1373794 TATTTTCAAAACCATAAAATATAATATATTTTCAAAA
1 TATTTTAAAAACTATATATTAT-ATATATTTTCAAAA
1373831 TATTTT-AAAACTATATATTATAT-T-TTTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTCAAAA
1373864 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
1 TATTTTAAAAACTATATATTATATATA--TTTTCAAAA
* * *
1373902 TGTTTTAAAAACTATATTATATATATATATATAT-ATATA
1 TATTTTAAAAACTATA-TAT-TATATATAT-TTTCA-AAA
* ** * * **
1373941 TATATTCAAAATGTTTTAAAAACTATATATTATATATATATTCAAA
1 TAT-TTTAAAA---ACT--ATA-TAT-TA-TATATAT-TTTCAAAA
* *
1373987 -ATGTTTTAAAAACTCTATATTATATATATTTTCATAAT
1 TA--TTTTAAAAACTATATATTATATATATTTTCA-AAA
*
1374025 TTTTTTAAAAACTATATATTATATACATATTTTCAAAA
1 TATTTTAAAAACTATATATTATAT--ATATTTTCAAAA
*
1374063 TGTTTTAAAAACTATATATTATATA-AGTTTTCAAAAA
1 TATTTTAAAAACTATATATTATATATA-TTTTC-AAAA
1374100 TATTTTAAAAACTATATATTATATATATATTTCAAAA
1 TATTTTAAAAACTATATATTATATATAT-TTTCAAAA
1374137 ATCATTTGCA
Statistics
Matches: 251, Mismatches: 28, Indels: 54
0.75 0.08 0.16
Matches are distributed among these distances:
33 15 0.06
34 18 0.07
35 4 0.02
36 18 0.07
37 62 0.25
38 65 0.26
39 20 0.08
40 17 0.07
41 1 0.00
43 2 0.01
45 9 0.04
46 19 0.08
47 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (36 bp):
TATTTTAAAAACTATATATTATATATATTTTCAAAA
Found at i:1373900 original size:38 final size:38
Alignment explanation
Indices: 1373794--1374136 Score: 300
Period size: 37 Copynumber: 9.0 Consensus size: 38
1373784 TAAAAATAAT
* * * * *
1373794 TATTTTCAAAACCATAAAATATA-ATATATTTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
1373831 TATTTT-AAAAC--TATA-TAT-TATATTTTTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
1373864 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
*
1373902 TGTTTTAAAAACTATATTATATATATATATATATATATAT-ATATTCAA
1 TATTTTAAAAACTATA-TAT-TATATATAT-T-T-T-T-TCA-A---AA
* *
1373950 AATGTTTTAAAAACTATATATTATATATA--TATTCAAAA
1 TA--TTTTAAAAACTATATATTATATATATTTTTTCAAAA
* * *
1373988 TGTTTTAAAAACTCTATATTATATATA--TTTTCATAAT
1 TATTTTAAAAACTATATATTATATATATTTTTTCA-AAA
* * *
1374025 TTTTTTAAAAACTATATATTATATACATATTTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
* *
1374063 TGTTTTAAAAACTATATATTATATA-A-GTTTTCAAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTC-AAAA
*
1374100 TATTTTAAAAACTATATATTATATATA-TATTTCAAAA
1 TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
1374137 ATCATTTGCA
Statistics
Matches: 261, Mismatches: 20, Indels: 50
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.08
34 8 0.03
36 43 0.16
37 68 0.26
38 63 0.24
39 9 0.03
40 9 0.03
41 3 0.01
42 3 0.01
43 1 0.00
44 3 0.01
45 2 0.01
48 10 0.04
49 3 0.01
50 14 0.05
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (38 bp):
TATTTTAAAAACTATATATTATATATATTTTTTCAAAA
Found at i:1373926 original size:2 final size:2
Alignment explanation
Indices: 1373914--1373945 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1373904 TTTTAAAAAC
1373914 TA TA T- 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 TA TA T
1373946 TCAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1373949 original size:50 final size:48
Alignment explanation
Indices: 1373876--1373981 Score: 169
Period size: 50 Copynumber: 2.2 Consensus size: 48
1373866 TTTTAAAAAC
* *
1373876 TATATAT-TATATATATTTTTTCAAAATGTTTTAAAAACTATATTATATA
1 TATATATATATATATATATATTCAAAATGTTTTAAAAACTATA-TAT-TA
1373925 TATATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTA
1 TATATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTA
1373973 TATATATAT
1 TATATATAT
1373982 TCAAAATGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
48 11 0.20
49 10 0.19
50 33 0.61
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (48 bp):
TATATATATATATATATATATTCAAAATGTTTTAAAAACTATATATTA
Found at i:1374057 original size:28 final size:28
Alignment explanation
Indices: 1374009--1374062 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1373999 CTCTATATTA
* * *
1374009 TATATATTTTCATAATTTTTTTAAAAAC
1 TATATATTATCATAATATTTTCAAAAAC
1374037 TATATATTAT-ATACATATTTTCAAAA
1 TATATATTATCATA-ATATTTTCAAAA
1374063 TGTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (28 bp):
TATATATTATCATAATATTTTCAAAAAC
Found at i:1374155 original size:75 final size:74
Alignment explanation
Indices: 1373927--1374136 Score: 309
Period size: 75 Copynumber: 2.8 Consensus size: 74
1373917 ATTATATATA
* *
1373927 TATATATATATATATATATTC-AAAATGTTTTAAAAACTATATATTATATATATA-TTCAAAATG
1 TATATAT-TATATATATTTTCAAAAATATTTTAAAAACTATATATTATATATATATTTCAAAATG
1373990 TTTTAAAAAC
65 TTTTAAAAAC
* * * * *
1374000 TCTATATTATATATATTTTCATAATTTTTTTAAAAACTATATATTATATACATATTTTCAAAATG
1 TATATATTATATATATTTTCAAAAATATTTTAAAAACTATATATTATATATATA-TTTCAAAATG
1374065 TTTTAAAAAC
65 TTTTAAAAAC
1374075 TATATATTATATA-AGTTTTCAAAAATATTTTAAAAACTATATATTATATATATATTTCAAAA
1 TATATATTATATATA-TTTTCAAAAATATTTTAAAAACTATATATTATATATATATTTCAAAA
1374137 ATCATTTGCA
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
72 12 0.10
73 35 0.29
74 9 0.07
75 66 0.54
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (74 bp):
TATATATTATATATATTTTCAAAAATATTTTAAAAACTATATATTATATATATATTTCAAAATGT
TTTAAAAAC
Found at i:1374167 original size:4 final size:4
Alignment explanation
Indices: 1374153--1374184 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
1374143 TGCAAACTAT
1374153 ATAA TATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATA
1374185 CGGACGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:1374176 original size:75 final size:74
Alignment explanation
Indices: 1373949--1374176 Score: 246
Period size: 75 Copynumber: 3.1 Consensus size: 74
1373939 TATATATTCA
* * * *
1373949 AAATGTTTTAAAAACTATATATTATATATATA-TTCAAAATGTTTTAAAAACTCTATATTATATA
1 AAATATTTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAACTATATAATATAAA
**
1374013 TATTTTCAT
66 TATTTAAAT
* * *
1374022 AATTTTTTTAAAAACTATATATTATATACATATTTTCAAAATGTTTTAAAAACTATATATTATAT
1 AAATATTTTAAAAACTATATATTATATATATA-TTTCAAAATGTTTTAAAAACTATATA--ATAT
* *
1374087 AAGT-TTTCAA-
63 AAATATTTAAAT
** **
1374097 AAATATTTTAAAAACTATATATTATATATATATTTCAAAAATCATTTGCAAACTATATAATATAA
1 AAATATTTTAAAAACTATATATTATATATATATTTC-AAAATGTTTTAAAAACTATATAATATAA
**
1374162 ATAAATAAAT
65 ATATTTAAAT
1374172 AAATA
1 AAATA
1374177 AATAAATACG
Statistics
Matches: 128, Mismatches: 20, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
73 36 0.28
74 7 0.05
75 76 0.59
76 4 0.03
77 5 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (74 bp):
AAATATTTTAAAAACTATATATTATATATATATTTCAAAATGTTTTAAAAACTATATAATATAAA
TATTTAAAT
Found at i:1374988 original size:31 final size:31
Alignment explanation
Indices: 1374951--1375021 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
1374941 AACGTTACAA
* *
1374951 ACAAACGTTACCATTTTAAGTATCTAATGTT
1 ACAAACGTTACCATTTTAAATATCTAATATT
*
1374982 ATAAACGTTACCATTTTAAATATCTAATATT
1 ACAAACGTTACCATTTTAAATATCTAATATT
1375013 ACAAACGTT
1 ACAAACGTT
1375022 GTTTAATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (31 bp):
ACAAACGTTACCATTTTAAATATCTAATATT
Found at i:1375829 original size:10 final size:10
Alignment explanation
Indices: 1375814--1375887 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
1375804 ATTTAATAAT
1375814 TAAACGAACA
1 TAAACGAACA
1375824 TAAACGAAC-
1 TAAACGAACA
1375833 ---ACGAACA
1 TAAACGAACA
*
1375840 TAAATGAACA
1 TAAACGAACA
*
1375850 CAAAC-ATA-A
1 TAAACGA-ACA
1375859 TTGAACACGAACA
1 -T-AA-ACGAACA
1375872 TAAACGAACA
1 TAAACGAACA
1375882 TAAACG
1 TAAACG
1375888 TTGGAGATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
6 6 0.12
9 2 0.04
10 32 0.64
11 4 0.08
12 4 0.08
13 2 0.04
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:1375838 original size:16 final size:16
Alignment explanation
Indices: 1375817--1375881 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
1375807 TAATAATTAA
1375817 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1375833 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
* **
1375849 ACAAACATAATTGAAC
1 ACGAACATAAACGAAC
1375865 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1375881 A
1 A
1375882 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1376979 original size:14 final size:14
Alignment explanation
Indices: 1376960--1376991 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1376950 GATTGGGATA
1376960 AACATAAATGAACG
1 AACATAAATGAACG
1376974 AACATAAATGAACG
1 AACATAAATGAACG
1376988 AACA
1 AACA
1376992 AAAACGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:1377093 original size:40 final size:40
Alignment explanation
Indices: 1377043--1377144 Score: 195
Period size: 40 Copynumber: 2.5 Consensus size: 40
1377033 ATGAGACCTA
*
1377043 TGTTCGTGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1377083 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1377123 TGTTCATGTTCGTTCATTTAAT
1 TGTTCATGTTCGTTCATTTAAT
1377145 AAATAAACGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (40 bp):
TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
Found at i:1377357 original size:14 final size:14
Alignment explanation
Indices: 1377338--1377365 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1377328 AACTATACCC
1377338 TTATTCTCAAATAG
1 TTATTCTCAAATAG
1377352 TTATTCTCAAATAG
1 TTATTCTCAAATAG
1377366 GTGCTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTATTCTCAAATAG
Found at i:1377668 original size:48 final size:48
Alignment explanation
Indices: 1377616--1377711 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
1377606 AATCATACAT
1377616 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
1 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
*
1377664 TAAGATATGCGAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
1 TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
1377712 GATAAGAGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (48 bp):
TAAGATATGCAAACGTATACTAAGTATTTAAATTTGAAAATTAAGAGA
Found at i:1379345 original size:31 final size:32
Alignment explanation
Indices: 1379304--1379364 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
1379294 TAGGATAAAC
1379304 TACACATTTAATACCTAAACTATCAATTTTAA
1 TACACATTTAATACCTAAACTATCAATTTTAA
*
1379336 TACAC-TTTAATACCTAAACTTTCAATTTT
1 TACACATTTAATACCTAAACTATCAATTTT
1379365 TTAAAGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (32 bp):
TACACATTTAATACCTAAACTATCAATTTTAA
Found at i:1382486 original size:16 final size:16
Alignment explanation
Indices: 1382465--1382498 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1382455 CCATTACACG
* *
1382465 TTCAAATTATTTTAAA
1 TTCAAATCAATTTAAA
1382481 TTCAAATCAATTTAAA
1 TTCAAATCAATTTAAA
1382497 TT
1 TT
1382499 GGATTATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCAAATCAATTTAAA
Found at i:1385217 original size:21 final size:21
Alignment explanation
Indices: 1385193--1385250 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1385183 TAATTTAATT
1385193 CAATATAAATTTTTAAATTTA
1 CAATATAAATTTTTAAATTTA
* *
1385214 CAATGAT-AATTTTTTATTTTA
1 CAAT-ATAAATTTTTAAATTTA
* *
1385235 TAA-ATAAATATTTAAA
1 CAATATAAATTTTTAAA
1385251 AAGTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.07
20 7 0.24
21 18 0.62
22 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
CAATATAAATTTTTAAATTTA
Found at i:1387149 original size:28 final size:27
Alignment explanation
Indices: 1387109--1387162 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
1387099 TGCAACTTAT
*
1387109 TTGGTTAGGAAAAATACGAGAAAAAAAA
1 TTGGTCAGGAAAAATACGA-AAAAAAAA
1387137 TTGGTCAGGAAAAATACGAAAAAAAA
1 TTGGTCAGGAAAAATACGAAAAAAAA
1387163 TAAGTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (27 bp):
TTGGTCAGGAAAAATACGAAAAAAAAA
Found at i:1389570 original size:19 final size:19
Alignment explanation
Indices: 1389546--1389586 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1389536 ATTTTTCCTC
1389546 GGATCAAATAACTAGTTGA
1 GGATCAAATAACTAGTTGA
1389565 GGATCAAATAACTAGTTGA
1 GGATCAAATAACTAGTTGA
1389584 GGA
1 GGA
1389587 AAGAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (19 bp):
GGATCAAATAACTAGTTGA
Found at i:1392611 original size:21 final size:21
Alignment explanation
Indices: 1392578--1392622 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1392568 TAATTTTTTA
*
1392578 AAAAATAAAAGTTTATATACT
1 AAAAATAAAAGTTTAGATACT
* * *
1392599 AAAACTAATAGTTTAGGTACT
1 AAAAATAAAAGTTTAGATACT
1392620 AAA
1 AAA
1392623 TGTATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAAATAAAAGTTTAGATACT
Found at i:1393049 original size:24 final size:24
Alignment explanation
Indices: 1393020--1393071 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1393010 TGGATTTTAG
* * *
1393020 ATTTTTTTTTAAATTTTGAATATAT
1 ATTTTTTATT-AATTTAGAATAAAT
1393045 ATTTTTTATTAATTTAGAATAAAT
1 ATTTTTTATTAATTTAGAATAAAT
1393069 ATT
1 ATT
1393072 CAACCATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTTTTATTAATTTAGAATAAAT
Found at i:1395322 original size:9 final size:9
Alignment explanation
Indices: 1395305--1395349 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1395295 TTTGACCAAT
1395305 TTTGAACCGG
1 TTTG-ACCGG
1395315 TTTGACCGG
1 TTTGACCGG
1395324 TTTGACCGG
1 TTTGACCGG
*
1395333 TCTGAACCGG
1 TTTG-ACCGG
*
1395343 GTTGACC
1 TTTGACC
1395350 CGACCCGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 20 0.65
10 11 0.35
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (9 bp):
TTTGACCGG
Found at i:1395341 original size:19 final size:18
Alignment explanation
Indices: 1395305--1395349 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1395295 TTTGACCAAT
*
1395305 TTTGAACCGGTTTGACCGG
1 TTTG-ACCGGTCTGACCGG
1395324 TTTGACCGGTCTGAACCGG
1 TTTGACCGGTCTG-ACCGG
*
1395343 GTTGACC
1 TTTGACC
1395350 CGACCCGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (18 bp):
TTTGACCGGTCTGACCGG
Found at i:1395364 original size:14 final size:14
Alignment explanation
Indices: 1395345--1395372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1395335 TGAACCGGGT
1395345 TGACCCGACCCGAC
1 TGACCCGACCCGAC
1395359 TGACCCGACCCGAC
1 TGACCCGACCCGAC
1395373 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:1395368 original size:19 final size:20
Alignment explanation
Indices: 1395346--1395394 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
1395336 GAACCGGGTT
1395346 GACCCGACCCGAC-TGACCC
1 GACCCGACCCGACTTGACCC
1395365 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC--TTGACCC
1395387 GACCCGAC
1 GACCCGAC
1395395 TGTTGACCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
22 14 0.52
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.08
Consensus pattern (20 bp):
GACCCGACCCGACTTGACCC
Found at i:1395387 original size:17 final size:17
Alignment explanation
Indices: 1395343--1395402 Score: 84
Period size: 17 Copynumber: 3.4 Consensus size: 17
1395333 TCTGAACCGG
1395343 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
1395360 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
1395379 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
1395396 GTTGACC
1 GTTGACC
1395403 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 22 0.59
19 15 0.41
ACGTcount: A:0.18, C:0.43, G:0.23, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:1395408 original size:7 final size:7
Alignment explanation
Indices: 1395396--1395422 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1395386 CGACCCGACT
1395396 GTTGACC
1 GTTGACC
1395403 GTTGACC
1 GTTGACC
1395410 GTTGACC
1 GTTGACC
1395417 GTTGAC
1 GTTGAC
1395423 TTCCTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
GTTGACC
Found at i:1396333 original size:31 final size:32
Alignment explanation
Indices: 1396289--1396361 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
1396279 TGTGACTCTT
* *
1396289 AGGTAGGCTCTGCGGCCCTGAGAT-TATTCTC
1 AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
* * *
1396320 GGGTAGGCCCTGCGGCCCTAAGATGTGTTCTT
1 AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
1396352 AGGTAGGCCC
1 AGGTAGGCCC
1396362 CACGGCCCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (32 bp):
AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
Found at i:1402651 original size:14 final size:14
Alignment explanation
Indices: 1402632--1402678 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 14
1402622 TGAACCGGGT
1402632 TGACCCGACCCGAC
1 TGACCCGACCCGAC
1402646 TGACCCGACCCGAC
1 TGACCCGACCCGAC
1402660 TGTTGACCCGACCCGAC
1 ---TGACCCGACCCGAC
1402677 TG
1 TG
1402679 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 16 0.53
17 14 0.47
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:1402668 original size:17 final size:17
Alignment explanation
Indices: 1402630--1402684 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
1402620 TCTGAACCGG
1402630 GTTGACCCGACCCGAC-
1 GTTGACCCGACCCGACT
1402646 --TGACCCGACCCGACT
1 GTTGACCCGACCCGACT
1402661 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
1402678 GTTGACC
1 GTTGACC
1402685 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.39
17 22 0.61
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:1402690 original size:7 final size:7
Alignment explanation
Indices: 1402678--1402711 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1402668 CGACCCGACT
1402678 GTTGACC
1 GTTGACC
1402685 GTTGACC
1 GTTGACC
1402692 GTTGACC
1 GTTGACC
1402699 GTTGACC
1 GTTGACC
1402706 GTTGAC
1 GTTGAC
1402712 TTCCTTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GTTGACC
Found at i:1403628 original size:31 final size:32
Alignment explanation
Indices: 1403584--1403656 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
1403574 TGTGACTCTT
* *
1403584 AGGTAGGCTCTGCGGCCCTGAGAT-TATTCTC
1 AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
* * *
1403615 GGGTAGGCCCTGCGGCCCTAAGATGTGTTCTT
1 AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
1403647 AGGTAGGCCC
1 AGGTAGGCCC
1403657 CACGACCCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (32 bp):
AGGTAGGCCCTGCGGCCCTAAGATGTATTCTC
Found at i:1404295 original size:17 final size:17
Alignment explanation
Indices: 1404273--1404308 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1404263 CATATTTTAT
1404273 TAAAT-ATATATAAATTA
1 TAAATAATATA-AAATTA
1404290 TAAATAATATAAAATTA
1 TAAATAATATAAAATTA
1404307 TA
1 TA
1404309 TTAAGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATATAAAATTA
Found at i:1404838 original size:36 final size:37
Alignment explanation
Indices: 1404766--1404839 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 37
1404756 GTTGGAAAAT
*
1404766 ATTTATATATTTTCTTTAAAAAAATTAAATTAATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATAATAAA
*
1404803 ATTTATATAATTTT-TTT-ACAAAATTAAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATTAAAATA-ATAAA
1404839 A
1 A
1404840 AGATTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 1 0.03
36 16 0.48
37 11 0.33
38 5 0.15
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATAATAAA
Found at i:1411860 original size:21 final size:19
Alignment explanation
Indices: 1411836--1411875 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1411826 ATTTTAAATT
1411836 TTTATTTAAATGTATAAAAGA
1 TTTA-TTAAAT-TATAAAAGA
*
1411857 TTTATTGAATTATAAAAGA
1 TTTATTAAATTATAAAAGA
1411876 ACTATAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTATTAAATTATAAAAGA
Found at i:1411885 original size:19 final size:20
Alignment explanation
Indices: 1411848--1411890 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1411838 TATTTAAATG
** *
1411848 TATAAAAGATTTATTGAAT-
1 TATAAAAGAACTATAGAATA
1411867 TATAAAAGAACTATAGAATA
1 TATAAAAGAACTATAGAATA
1411887 TATA
1 TATA
1411891 TTACATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (20 bp):
TATAAAAGAACTATAGAATA
Found at i:1413338 original size:23 final size:20
Alignment explanation
Indices: 1413294--1413334 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1413284 CTTATGTTCG
1413294 AGTTCATCATACATAAATAT
1 AGTTCATCATACATAAATAT
1413314 AGTTCATCATACATAAATAT
1 AGTTCATCATACATAAATAT
1413334 A
1 A
1413335 ATAGATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
AGTTCATCATACATAAATAT
Found at i:1413839 original size:16 final size:16
Alignment explanation
Indices: 1413803--1413841 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1413793 ATTATCAATA
*
1413803 AAAATATTAAAAAACTT
1 AAAAT-TTAAAAAAATT
1413820 -AAATTTAAAAAAATT
1 AAAATTTAAAAAAATT
1413835 AAAATTT
1 AAAATTT
1413842 TTAGAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTTAAAAAAATT
Found at i:1414200 original size:21 final size:21
Alignment explanation
Indices: 1414174--1414933 Score: 404
Period size: 21 Copynumber: 36.6 Consensus size: 21
1414164 GTTTCCAGAT
*
1414174 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414195 TCGCAA--CGAACTTAGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414216 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414237 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414258 TCGCAACGCG-ACTATCG-C-A
1 TCGCAACGCGAACT-TCGACTA
* *
1414277 ACG-AACTTG-GAA--T--A-AA
1 TCGCAAC--GCGAACTTCGACTA
1414293 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414314 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414335 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414356 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414377 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414398 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
1414419 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414440 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
1414461 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* * * *
1414482 TCGCAA--CAAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414503 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* * * *
1414524 TCGCAA--AGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
1414545 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414566 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414587 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414608 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414629 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414650 TCGCAA--CGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
1414671 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* * * *
1414692 TCGCAA--CAAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
1414713 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* * *
1414734 TCGCAA--CGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
* * *
1414755 TCGCAACGCGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACT--A
*
1414778 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1414799 TCGCAA--CGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
* *
1414818 TCGCAA--CGAA-TTTGTAATAAA
1 TCGCAACGCGAACTTCG-ACT--A
1414839 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
** *
1414860 TCGCAA--ATAAGTTTCCAGA-T-
1 TCGCAACGCGAA-CTT-C-GACTA
1414880 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1414901 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1414922 TCGCAATGCGAA
1 TCGCAACGCGAA
1414934 TATGTAAATC
Statistics
Matches: 584, Mismatches: 77, Indels: 156
0.71 0.09 0.19
Matches are distributed among these distances:
15 1 0.00
16 6 0.01
17 4 0.01
18 7 0.01
19 157 0.27
20 13 0.02
21 237 0.41
22 7 0.01
23 149 0.26
24 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1414224 original size:42 final size:42
Alignment explanation
Indices: 1414174--1414918 Score: 1100
Period size: 42 Copynumber: 17.9 Consensus size: 42
1414164 GTTTCCAGAT
* *
1414174 TCGCAACGCGAACATCGACTATCGCAACGAACTTAGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414216 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414258 TCGCAA--CG-----CGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414293 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414335 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414377 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
*
1414419 TCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
* * *
1414461 TCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
* *
1414503 TCGCAACGCGAACTTCGACTATCGCAAAGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
*
1414545 TCGCAACGCGAACATCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414587 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414629 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
* * *
1414671 TCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
*
1414713 TCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
* * * *
1414755 TCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGACT--A
1 TCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTGGAATAAA
* * *
1414799 TCGCAA--CGAACTTGGACTATCGCAACGAATTTGTAATAAA
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
** * *** * *
1414839 TCGCAACGCGAACTTCGACTATCGCAAATAAGTTTCCA-GAT
1 TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
1414880 TCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGA
1 TCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGA
1414919 CTATCGCAAT
Statistics
Matches: 644, Mismatches: 42, Indels: 33
0.90 0.06 0.05
Matches are distributed among these distances:
35 33 0.05
37 2 0.00
38 9 0.01
40 16 0.02
41 28 0.04
42 528 0.82
43 4 0.01
44 14 0.02
46 10 0.02
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
TCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAA
Found at i:1421407 original size:52 final size:53
Alignment explanation
Indices: 1421327--1421433 Score: 153
Period size: 52 Copynumber: 2.0 Consensus size: 53
1421317 CACAAGATGG
* *
1421327 GGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
* * *
1421381 GGCACAT-AAATAGGAGACTAGTCTAGAGTTAGGGAATTGCAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
1421433 G
1 G
1421434 AATATTATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 41 0.85
54 7 0.15
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
Found at i:1422745 original size:23 final size:22
Alignment explanation
Indices: 1422727--1422780 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
1422717 TCAATTATTT
*
1422727 TTATTAACAAAATTTAATTCTCA
1 TTATTAA-AAAATTTAATTATCA
1422750 TTATTAAAAAATTATAATCTA-CA
1 TTATTAAAAAATT-TAAT-TATCA
1422773 TATATTAA
1 T-TATTAA
1422781 CTTTTATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.22
23 14 0.52
24 7 0.26
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTAAAAAATTTAATTATCA
Found at i:1423203 original size:20 final size:20
Alignment explanation
Indices: 1423180--1423314 Score: 180
Period size: 20 Copynumber: 6.7 Consensus size: 20
1423170 GATTCTGACT
*
1423180 ATCGCATTGCGATTACGTAA
1 ATCGCAATGCGATTACGTAA
* ** *
1423200 ATCGCAACGCGAATTTGGAAA
1 ATCGCAATGCG-ATTACGTAA
1423221 ATCGCAATGCGATTACGTAA
1 ATCGCAATGCGATTACGTAA
* *
1423241 ATCGCAAAGCGAATACGTAA
1 ATCGCAATGCGATTACGTAA
*
1423261 ATCGCAATACGATTACGTAA
1 ATCGCAATGCGATTACGTAA
*
1423281 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGATTACGTAA
1423301 ATCGCAATGCGATT
1 ATCGCAATGCGATT
1423315 TATATAGCGC
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
20 81 0.84
21 16 0.16
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATTACGTAA
Found at i:1423205 original size:40 final size:40
Alignment explanation
Indices: 1423161--1423314 Score: 172
Period size: 40 Copynumber: 3.8 Consensus size: 40
1423151 GTTTCCAGAT
* *
1423161 TCGCAACGCG-ATTCTGACTATCGCATTGCGATTACGTAAA
1 TCGCAACGCGAATTCTGA-AATCGCAATGCGATTACGTAAA
1423201 TCGCAACGCGAATT-TGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAACGCGAATTCT-G-AAATCGCAATGCGATTACGTAAA
* * *
1423242 TCGCAAAGCGAATAC-GTAAATCGCAATACGATTACGTAAA
1 TCGCAACGCGAATTCTG-AAATCGCAATGCGATTACGTAAA
* *
1423282 TCGCAATGCGAATAC-GTAAATCGCAATGCGATT
1 TCGCAACGCGAATTCTG-AAATCGCAATGCGATT
1423315 TATATAGCGC
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
40 65 0.64
41 36 0.35
42 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
TCGCAACGCGAATTCTGAAATCGCAATGCGATTACGTAAA
Done.