Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 77 of 427
Found at i:19081177 original size:19 final size:19
Alignment explanation
Indices: 19081153--19081190 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19081143 ATTAATATAT
19081153 CATATTTAATTTTTATTAA
1 CATATTTAATTTTTATTAA
19081172 CATATTTAATTTTTATTAA
1 CATATTTAATTTTTATTAA
19081191 TTTTGAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
CATATTTAATTTTTATTAA
Found at i:19085065 original size:16 final size:18
Alignment explanation
Indices: 19085039--19085074 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19085029 GACATATCTT
19085039 AACAGGAAAA-GATTAAA
1 AACAGGAAAAGGATTAAA
19085056 AACA-GAAAAGGATTAAA
1 AACAGGAAAAGGATTAAA
19085073 AA
1 AA
19085075 ATTACCCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.11
Consensus pattern (18 bp):
AACAGGAAAAGGATTAAA
Found at i:19086876 original size:7 final size:7
Alignment explanation
Indices: 19086864--19086888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19086854 TAGAATACAA
19086864 GAAAATT
1 GAAAATT
19086871 GAAAATT
1 GAAAATT
19086878 GAAAATT
1 GAAAATT
19086885 GAAA
1 GAAA
19086889 TACTTGACAA
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (7 bp):
GAAAATT
Found at i:19103288 original size:24 final size:24
Alignment explanation
Indices: 19103256--19103305 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19103246 AAGATGTAAG
19103256 AATGGAAAGAAATTAGCATAAACA
1 AATGGAAAGAAATTAGCATAAACA
19103280 AATGGAAAGAAATTAGCATAAACA
1 AATGGAAAGAAATTAGCATAAACA
19103304 AA
1 AA
19103306 GTCGTTTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (24 bp):
AATGGAAAGAAATTAGCATAAACA
Found at i:19107150 original size:18 final size:18
Alignment explanation
Indices: 19107127--19107161 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19107117 AGCTTTTCTT
19107127 CCAGAAGTGCTTTTGAAG
1 CCAGAAGTGCTTTTGAAG
19107145 CCAGAAGTGCTTTTGAA
1 CCAGAAGTGCTTTTGAA
19107162 AAGCAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
CCAGAAGTGCTTTTGAAG
Found at i:19114996 original size:27 final size:26
Alignment explanation
Indices: 19114940--19115077 Score: 204
Period size: 27 Copynumber: 5.2 Consensus size: 26
19114930 AGCATGGCTG
* *
19114940 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
19114966 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
19114993 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
19115020 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
19115047 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
19115074 CCAG
1 CCAG
19115078 GATGCTTCCT
Statistics
Matches: 105, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.14
27 88 0.84
28 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.25, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:19116521 original size:24 final size:24
Alignment explanation
Indices: 19116486--19116538 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
19116476 CCAACACTGT
19116486 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCTAAATCC
*
19116510 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCTAAATCC
19116534 TCTCC
1 TCTCC
19116539 TGATAGACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCCCTAATCAGCTCCTAAATCC
Found at i:19135983 original size:22 final size:22
Alignment explanation
Indices: 19135957--19135998 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
19135947 GTTTATTCCC
19135957 TCTTCAAGCTACTAAAGAACCT
1 TCTTCAAGCTACTAAAGAACCT
19135979 TCTTCAAGCTACTAAAGAAC
1 TCTTCAAGCTACTAAAGAAC
19135999 ATTAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (22 bp):
TCTTCAAGCTACTAAAGAACCT
Found at i:19141483 original size:31 final size:31
Alignment explanation
Indices: 19141448--19141517 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
19141438 CTTGTCACTT
*
19141448 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAA
* * * *
19141479 GTAGCCGGAGCTACCATTTTTGACTGATCAA
1 GTAGCCGAAGCTACCACTATTCACTGATCAA
19141510 GTAGCCGA
1 GTAGCCGA
19141518 TGATCAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAA
Found at i:19141539 original size:46 final size:46
Alignment explanation
Indices: 19141472--19141563 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
19141462 CACTATTCAC
* * *
19141472 TGATCAGGTAGCCGGAGCTACCATTTTTGACTGATCAAGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCCGA
* *
19141518 TGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCCGA
19141564 AGCTACCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (46 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAGCCGA
Found at i:19141553 original size:31 final size:31
Alignment explanation
Indices: 19141518--19141576 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
19141508 AAGTAGCCGA
*
19141518 TGATCAGGTAGCTGAAGCTACCACTTTTCAC
1 TGATCAGGTAGCCGAAGCTACCACTTTTCAC
19141549 TGATCAGGTAGCCGAAGCTACCACTTTT
1 TGATCAGGTAGCCGAAGCTACCACTTTT
19141577 TACTTGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (31 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCAC
Found at i:19141646 original size:50 final size:50
Alignment explanation
Indices: 19141556--19141732 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
19141546 CACTGATCAG
* * * *
19141556 GTAGCCGAAGCTACCACTTTTTACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTATCCTTGATCAGATAAGT
* *
19141607 GTAGCCGAAGCTATCTCTTATCACTTTCATTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
* *
19141657 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCTTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
19141707 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
19141733 GTTGCCATGG
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 95 0.81
51 22 0.19
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
Found at i:19149815 original size:27 final size:27
Alignment explanation
Indices: 19149784--19149837 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
19149774 GGTAAGAAGT
* * *
19149784 GTACTATCTACATAGGTTACAAGAGTC
1 GTACTATCTACACAGATCACAAGAGTC
19149811 GTACTATCTACACAGATCACAAGAGTC
1 GTACTATCTACACAGATCACAAGAGTC
19149838 TCAAATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (27 bp):
GTACTATCTACACAGATCACAAGAGTC
Found at i:19162838 original size:13 final size:13
Alignment explanation
Indices: 19162822--19162858 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
19162812 ATAAGGGACA
19162822 CATGGCCGTGTCG
1 CATGGCCGTGTCG
*
19162835 CATGGCCGTGTCT
1 CATGGCCGTGTCG
*
19162848 CATGGCTGTGT
1 CATGGCCGTGT
19162859 GTCACACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.35, T:0.30
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:19163379 original size:2 final size:2
Alignment explanation
Indices: 19163372--19163410 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19163362 TATCTCTATC
19163372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19163411 GCTTAATTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19164126 original size:40 final size:39
Alignment explanation
Indices: 19164072--19164175 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 39
19164062 CACACCAGAA
* * **
19164072 AGAAGCTCATAAGAGCTGATCCGACTGAAATATGC-CAAAC
1 AGAAGCTCATAAGAGCTGATCC-AC-CAAAAACACTCAAAC
* *
19164112 AGAAGCTCATAAGAGCTGGTCCACCAAAAACACTCTAAC
1 AGAAGCTCATAAGAGCTGATCCACCAAAAACACTCAAAC
*
19164151 AGAAACTCATAAGAGCTGATCCACC
1 AGAAGCTCATAAGAGCTGATCCACC
19164176 CGAAACACGC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 5 0.09
39 29 0.53
40 21 0.38
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.16
Consensus pattern (39 bp):
AGAAGCTCATAAGAGCTGATCCACCAAAAACACTCAAAC
Found at i:19176566 original size:19 final size:21
Alignment explanation
Indices: 19176523--19176566 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
19176513 AAAAAAGGGG
19176523 TAAAATTATCATGGTAAATCA
1 TAAAATTATCATGGTAAATCA
19176544 -AAAATATAT-AT-GTAAAT-A
1 TAAAAT-TATCATGGTAAATCA
19176562 TAAAA
1 TAAAA
19176567 AATAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.05
19 10 0.48
20 7 0.33
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
TAAAATTATCATGGTAAATCA
Found at i:19182145 original size:23 final size:23
Alignment explanation
Indices: 19182089--19182135 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
19182079 TCGCTGAAAC
19182089 CACATGACCAAGAAATCCGACTT
1 CACATGACCAAGAAATCCGACTT
19182112 CACATGACCAAGAAATCCGACTT
1 CACATGACCAAGAAATCCGACTT
19182135 C
1 C
19182136 TTTGAGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (23 bp):
CACATGACCAAGAAATCCGACTT
Found at i:19186094 original size:19 final size:20
Alignment explanation
Indices: 19186052--19186094 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
19186042 TCATGCTTTC
* *
19186052 TATTCACATTTTCATATTCA
1 TATTCAAATTTTCATAATCA
19186072 -ATTCAAATTTTCA-AATCA
1 TATTCAAATTTTCATAATCA
19186090 TATTC
1 TATTC
19186095 CACATTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCAAATTTTCATAATCA
Found at i:19186520 original size:31 final size:32
Alignment explanation
Indices: 19186455--19186523 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
19186445 ATCCATTTTC
*
19186455 TCAATTCAATATCACTTTCAATTCATTTACAAA
1 TCAATTCAATATCACTTT-AATTCATATACAAA
*
19186488 TCAATTCAATTTCACTTT-A-TCAATATACAAA
1 TCAATTCAATATCACTTTAATTC-ATATACAAA
19186519 TCAAT
1 TCAAT
19186524 ATTAATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 14 0.42
33 17 0.52
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (32 bp):
TCAATTCAATATCACTTTAATTCATATACAAA
Found at i:19187274 original size:15 final size:16
Alignment explanation
Indices: 19187245--19187274 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19187235 CTTTCTTTCT
19187245 TTTCTTCTGTTCTCTG
1 TTTCTTCTGTTCTCTG
19187261 TTTCTTCT-TTCTCT
1 TTTCTTCTGTTCTCT
19187275 CTTTTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTCTTCTGTTCTCTG
Found at i:19187574 original size:21 final size:21
Alignment explanation
Indices: 19187539--19187579 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19187529 TATTTATCTC
* *
19187539 ATAAATATTTTTTTAATAATA
1 ATAAATATCTATTTAATAATA
*
19187560 ATAAATATCTATTTACTAAT
1 ATAAATATCTATTTAATAAT
19187580 TAAATAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATATCTATTTAATAATA
Found at i:19188911 original size:2 final size:2
Alignment explanation
Indices: 19188904--19188945 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19188894 GCTTATTCTT
19188904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19188946 CATACATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19189416 original size:44 final size:44
Alignment explanation
Indices: 19189351--19189435 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
19189341 AACATGTGTA
19189351 ACATATATCATGAACTAAGACCACAACTCATGAGTTCAGATGTC
1 ACATATATCATGAACTAAGACCACAACTCATGAGTTCAGATGTC
*
19189395 ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGAT
1 ACATATATCATGAACTAAGACCACAACTCATGAGTTCAGAT
19189436 CACATAGTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (44 bp):
ACATATATCATGAACTAAGACCACAACTCATGAGTTCAGATGTC
Found at i:19189427 original size:20 final size:20
Alignment explanation
Indices: 19189358--19189427 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
19189348 GTAACATATA
*
19189358 TCATGAACTAAGACCACAAC
1 TCATGAACTCAGACCACAAC
** * *
19189378 TCATGAGTTCAGATGTCACATATA
1 TCATGAACTCAGA--CCACA-A-C
19189402 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
19189422 TCATGA
1 TCATGA
19189428 GTTCAGATCA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
20 16 0.43
21 1 0.03
22 8 0.22
23 1 0.03
24 11 0.30
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:19189433 original size:20 final size:20
Alignment explanation
Indices: 19189368--19189439 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
19189358 TCATGAACTA
19189368 AGACCACAACTCATGAGTTC
1 AGACCACAACTCATGAGTTC
* * **
19189388 AGATGTCACATATATCATGAACTC
1 AGA--CCACA-A-CTCATGAGTTC
19189412 AGACCACAACTCATGAGTTC
1 AGACCACAACTCATGAGTTC
*
19189432 AGATCACA
1 AGACCACA
19189440 TAGTCCCTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 18 0.46
21 1 0.03
22 8 0.21
23 1 0.03
24 11 0.28
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (20 bp):
AGACCACAACTCATGAGTTC
Found at i:19190775 original size:25 final size:27
Alignment explanation
Indices: 19190738--19190790 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
19190728 TCAAACATGC
19190738 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
19190764 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
19190790 A
1 A
19190791 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:19192306 original size:32 final size:32
Alignment explanation
Indices: 19192269--19192333 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
19192259 AATGCTTACC
19192269 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
19192301 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
19192333 A
1 A
19192334 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:19197171 original size:12 final size:12
Alignment explanation
Indices: 19197154--19197196 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
19197144 AGTACTACCT
19197154 CGGCCTCGACCA
1 CGGCCTCGACCA
19197166 CGGCCTCGACCA
1 CGGCCTCGACCA
19197178 CGGCCTCGACCA
1 CGGCCTCGACCA
19197190 CGGCCTC
1 CGGCCTC
19197197 TTCCCGAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.14, C:0.51, G:0.26, T:0.09
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:19198821 original size:25 final size:27
Alignment explanation
Indices: 19198784--19198836 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
19198774 TCAAACATGC
19198784 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
19198810 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
19198836 A
1 A
19198837 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:19200352 original size:32 final size:32
Alignment explanation
Indices: 19200315--19200379 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
19200305 AATGCTTACC
19200315 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
*
19200347 ATGCCCATCATCCATTAACTATTAAATTGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
19200379 A
1 A
19200380 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:19202125 original size:22 final size:21
Alignment explanation
Indices: 19202095--19202160 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
19202085 TACAAATTAA
19202095 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
19202117 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
19202138 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
19202157 ATCT
1 ATCT
19202161 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:19202147 original size:19 final size:19
Alignment explanation
Indices: 19202112--19202209 Score: 128
Period size: 19 Copynumber: 5.2 Consensus size: 19
19202102 AGATTACAAG
19202112 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
19202133 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
19202152 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
* *
19202169 ATCATATCTAATATCGCAT
1 ATCATATCTAAGATTGCAT
* *
19202188 ATCATATTTAAGATTTCAT
1 ATCATATCTAAGATTGCAT
19202207 ATC
1 ATC
19202210 CTTAAAGATT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.22
19 45 0.65
20 1 0.01
21 8 0.12
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:19202176 original size:36 final size:37
Alignment explanation
Indices: 19202112--19202202 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 37
19202102 AGATTACAAG
*
19202112 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATCGCAT
*
19202152 ATCATATCTAAGATTG-TATCATATCTAATATCGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATCGCAT
*
19202188 ATCATATTTAAGATT
1 ATCATATCTAAGATT
19202203 TCATATCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
36 32 0.67
38 7 0.15
39 1 0.02
40 8 0.17
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATCGCAT
Found at i:19207233 original size:53 final size:53
Alignment explanation
Indices: 19207152--19207302 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
19207142 CTTACACGGT
* *
19207152 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
19207207 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
19207260 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
19207303 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:19214748 original size:53 final size:53
Alignment explanation
Indices: 19214667--19214817 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
19214657 CTTACACGGT
* *
19214667 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
19214722 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
19214775 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
19214818 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:19219279 original size:13 final size:13
Alignment explanation
Indices: 19219258--19219290 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19219248 TCAGACTTTG
19219258 AAAAA-TAATAAA
1 AAAAATTAATAAA
19219270 AAAAATTAATAAA
1 AAAAATTAATAAA
*
19219283 AATAATTA
1 AAAAATTA
19219291 GAGGCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAATAAA
Found at i:19222177 original size:2 final size:2
Alignment explanation
Indices: 19222170--19222216 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
19222160 CTATGGTAGC
*
19222170 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19222212 TA TA T
1 TA TA T
19222217 GTTAAGTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19225179 original size:2 final size:2
Alignment explanation
Indices: 19225172--19225206 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19225162 GAACTAAATT
19225172 TA 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 TA T
19225207 CATTTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19227541 original size:16 final size:16
Alignment explanation
Indices: 19227509--19227542 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19227499 TTCTATTAAT
*
19227509 ATTTTTATGAGATAAC
1 ATTTTTATGAGAAAAC
*
19227525 ATTTTTATGATAAAAC
1 ATTTTTATGAGAAAAC
19227541 AT
1 AT
19227543 GCAAAGGAGA
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:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTTTTATGAGAAAAC
Found at i:19229725 original size:30 final size:29
Alignment explanation
Indices: 19229657--19229726 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
19229647 AAATGGTATC
19229657 TTTAATAAAAT-TTATAAATATAATTTTA
1 TTTAATAAAATATTATAAATATAATTTTA
* * *
19229685 TTTAATAAAATATTATTAATATATTTTTT
1 TTTAATAAAATATTATAAATATAATTTTA
*
19229714 TTGTTATAAAATA
1 TT-TAATAAAATA
19229727 AAAGATTGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 11 0.31
29 16 0.44
30 9 0.25
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTAATAAAATATTATAAATATAATTTTA
Found at i:19231565 original size:3 final size:3
Alignment explanation
Indices: 19231557--19231600 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
19231547 TAAAAGCTCA
*
19231557 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19231601 AATGAAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19231758 original size:7 final size:7
Alignment explanation
Indices: 19231746--19231784 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
19231736 TGTGACACCC
19231746 TTTTTTG
1 TTTTTTG
19231753 TTTTTTG
1 TTTTTTG
19231760 TTTTTTG
1 TTTTTTG
19231767 TTTTTTG
1 TTTTTTG
19231774 TTTTTT-
1 TTTTTTG
19231780 TTTTT
1 TTTTT
19231785 AGCATTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTTTG
Found at i:19231792 original size:21 final size:21
Alignment explanation
Indices: 19231748--19231793 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19231738 TGACACCCTT
* **
19231748 TTTTGTTTTTTGTTTTTTGTT
1 TTTTGTTTTTTGTTTTTAGCA
19231769 TTTTGTTTTTT-TTTTTAGCA
1 TTTTGTTTTTTGTTTTTAGCA
19231789 TTTTG
1 TTTTG
19231794 ACTAGCAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.80
Consensus pattern (21 bp):
TTTTGTTTTTTGTTTTTAGCA
Found at i:19241181 original size:27 final size:28
Alignment explanation
Indices: 19241151--19241205 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
19241141 ATTTATTAAA
*
19241151 GAAATTTTAAAAGTA-ATTTTTTTTTGT
1 GAAATTTTAAAAGTATATATTTTTTTGT
19241178 GAAATTTTAAAAGTATATATTTTTTTGT
1 GAAATTTTAAAAGTATATATTTTTTTGT
19241206 TAAAAGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (28 bp):
GAAATTTTAAAAGTATATATTTTTTTGT
Found at i:19250402 original size:24 final size:24
Alignment explanation
Indices: 19250369--19250420 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
19250359 TTTGTAGGTC
* *
19250369 AAATAAATTATGCTAAAAAATGCT
1 AAATAAATTATACTAAAAAATACT
* *
19250393 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAAAAAATACT
19250417 AAAT
1 AAAT
19250421 CCTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAAAAAATACT
Found at i:19254346 original size:66 final size:67
Alignment explanation
Indices: 19254260--19254385 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 67
19254250 GAAAAAAATT
* * * * *
19254260 AAAAATATTTTTATTGTATTCTATTGTATTTCATATTAATAATATAT-ACTTATTTACAATCTAA
1 AAAAATATTTATATTGTATTCTATTATATTTCACATCAATAATATATCA-ATATTTACAATCTAA
19254324 GAA
65 GAA
*
19254327 AAAAATATTTATATT-TATTCTATTATATTTTACATCAATAATATATCAATATTTACAAT
1 AAAAATATTTATATTGTATTCTATTATATTTCACATCAATAATATATCAATATTTACAAT
19254386 TTACCAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
66 37 0.71
67 15 0.29
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (67 bp):
AAAAATATTTATATTGTATTCTATTATATTTCACATCAATAATATATCAATATTTACAATCTAAG
AA
Found at i:19254378 original size:74 final size:74
Alignment explanation
Indices: 19254222--19254378 Score: 158
Period size: 74 Copynumber: 2.1 Consensus size: 74
19254212 TATATTTTAC
* * *
19254222 ATCAATAATATACTCATTTACAATATAAGAAAAAAATTAAAAATATTTTTATTGTATTCTATTGT
1 ATCAAT-ATATACTCATTTACAATATAAGAAAAAAATT-AAAATATATTTATTCTATTATATTGT
** *
19254287 ATTTCATATTA
64 ACATCATAATA
* * ** *
19254298 AT-AATATATACTTATTTACAATCTAAGAAAAAAA-T-ATTTATATTTATTCTATTATATTTTAC
1 ATCAATATATACTCATTTACAATATAAGAAAAAAATTAAAATATATTTATTCTATTATATTGTAC
19254360 ATCAATAATA
66 ATC-ATAATA
19254370 TATCAATAT
1 -ATCAATAT
19254379 TTACAATTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
71 22 0.33
72 5 0.07
73 3 0.04
74 32 0.48
75 3 0.04
76 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (74 bp):
ATCAATATATACTCATTTACAATATAAGAAAAAAATTAAAATATATTTATTCTATTATATTGTAC
ATCATAATA
Found at i:19257105 original size:17 final size:17
Alignment explanation
Indices: 19257085--19257120 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
19257075 GAAGTTATCA
19257085 TGTTTTATT-TTTGTTTT
1 TGTTTTATTCTTT-TTTT
19257102 TGTTTTATTCTTTTTTT
1 TGTTTTATTCTTTTTTT
19257119 TG
1 TG
19257121 AAATTTCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.06, C:0.03, G:0.11, T:0.81
Consensus pattern (17 bp):
TGTTTTATTCTTTTTTT
Found at i:19266069 original size:23 final size:23
Alignment explanation
Indices: 19266030--19266075 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
19266020 ACACGCAAAC
*
19266030 AAAAGAAAAAAAGAGAGA-AAGA
1 AAAAGAAAAAAAAAGAGAGAAGA
*
19266052 AAAAGGAAAGAAAAAGAGAGAAGA
1 AAAA-GAAAAAAAAAGAGAGAAGA
19266076 GGAGTTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAAAAGAGAGAAGA
Found at i:19267638 original size:17 final size:17
Alignment explanation
Indices: 19267618--19267676 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
19267608 TTAATAGATA
19267618 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
19267635 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
19267654 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
19267672 ATTGA
1 ATTGA
19267677 GATTATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:19267648 original size:37 final size:37
Alignment explanation
Indices: 19267607--19267677 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
19267597 TTAATGAATC
19267607 ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
1 ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
*
19267644 ATTAATAGATAATTGAAGTGAATGTGATATTGAG
1 ATTAATAGATAATTGAAGTGAATATGATATTGAG
19267678 ATTATGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.37
Consensus pattern (37 bp):
ATTAATAGATAATTGAAGTGAATATGATATTGAGTTG
Found at i:19267784 original size:35 final size:34
Alignment explanation
Indices: 19267728--19267810 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 34
19267718 GATATTGTCG
* *
19267728 GTTTATCCTG-CTAGTATTGGGCGCA-ACTTTCATCA
1 GTTTAT-CTGACTAGTACTGGGCACACA-TTT-ATCA
* * *
19267763 GTTTATCTGACTAGTGCTGGGCACACATTTGTCG
1 GTTTATCTGACTAGTACTGGGCACACATTTATCA
19267797 GTTTATCTGACTAG
1 GTTTATCTGACTAG
19267811 CGCTAGGCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 19 0.46
35 21 0.51
36 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (34 bp):
GTTTATCTGACTAGTACTGGGCACACATTTATCA
Found at i:19267885 original size:75 final size:75
Alignment explanation
Indices: 19267797--19267963 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 75
19267787 ACATTTGTCG
* *
19267797 GTTTA-TCTGACTAGCGCTAG-GCCCAAATATCGTTGGTTTATCCAACTAGAGTTGGGCTCACT-
1 GTTTATTC-GACTAGCGCTAGAGCCCAAATATCGTTGATTTATCCAACTAGAGCTGGGCTCACTG
19267859 ACTTATATCGTCA
65 A-TTAT-TCGTCA
* * * *
19267872 GTTTATTCGACTAGCG-TTGAGCGCAAATATCGTTGATTTATTCAACTAGAGCTGGGCTCCCTGA
1 GTTTATTCGACTAGCGCTAGAGCCCAAATATCGTTGATTTATCCAACTAGAGCTGGGCTCACTGA
*
19267936 TTATTCGTCG
66 TTATTCGTCA
* *
19267946 GTATATCCGACTAGCGCT
1 GTTTATTCGACTAGCGCT
19267964 GGGCGTAACT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
74 21 0.27
75 55 0.70
76 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (75 bp):
GTTTATTCGACTAGCGCTAGAGCCCAAATATCGTTGATTTATCCAACTAGAGCTGGGCTCACTGA
TTATTCGTCA
Found at i:19273439 original size:46 final size:46
Alignment explanation
Indices: 19273083--19273448 Score: 475
Period size: 46 Copynumber: 8.0 Consensus size: 46
19273073 TTATCTTCGA
* * * * *
19273083 CATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
** * **
19273129 CATGTTGCCATTATATCTTTCAACCATGGTTTTATTCATTTCCCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
19273175 CATGTTGCCATGGTATCTTTTAACCATGGTCTTATTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATAT
** * *
19273221 CACATTGCCTTGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* * * *
19273267 CACGCTGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCCTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
*
19273313 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
* **
19273359 CATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
**
19273405 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
19273449 TTCAGAAAGC
Statistics
Matches: 283, Mismatches: 34, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
45 8 0.03
46 271 0.96
47 4 0.01
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATAT
Found at i:19276431 original size:3 final size:3
Alignment explanation
Indices: 19276423--19276447 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19276413 AAAACTTATT
19276423 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
19276448 CACGTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:19276528 original size:11 final size:11
Alignment explanation
Indices: 19276512--19276553 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
19276502 TATACTAAAT
19276512 AATTAATAATA
1 AATTAATAATA
19276523 AATTAATAATA
1 AATTAATAATA
19276534 GAA-TAATAATA
1 -AATTAATAATA
*
19276545 AAATAATAA
1 AATTAATAA
19276554 AATATCTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATTAATAATA
Found at i:19276592 original size:24 final size:24
Alignment explanation
Indices: 19276540--19276589 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
19276530 AATAGAATAA
*
19276540 TAATAAAATAATAAAATATCTCAT
1 TAATAAAATAATAAAATATCTAAT
**
19276564 TAATAAAATAAT-ATTTATCTAAT
1 TAATAAAATAATAAAATATCTAAT
19276587 TAA
1 TAA
19276590 ATAGTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATAAAATAATAAAATATCTAAT
Found at i:19279615 original size:30 final size:30
Alignment explanation
Indices: 19279581--19279642 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
19279571 ACTTATTTTA
* *
19279581 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
19279611 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
19279641 TT
1 TT
19279643 TCTTATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:19280013 original size:36 final size:36
Alignment explanation
Indices: 19279973--19280050 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
19279963 AGATTTTTCT
*
19279973 TAAATATTATCACAAAATAATTTTAAATATTATCAC
1 TAAATATTATCACAAAATAATTCTAAATATTATCAC
* *
19280009 TAAATATTATTACTAAATAATTCTAAATATTATCAC
1 TAAATATTATCACAAAATAATTCTAAATATTATCAC
19280045 TAAATA
1 TAAATA
19280051 ATTCAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (36 bp):
TAAATATTATCACAAAATAATTCTAAATATTATCAC
Found at i:19280014 original size:13 final size:13
Alignment explanation
Indices: 19279996--19280050 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
19279986 AAAATAATTT
19279996 TAAATATTATCAC
1 TAAATATTATCAC
*
19280009 TAAATATTATTAC
1 TAAATATTATCAC
*
19280022 TAAATA--AT-TC
1 TAAATATTATCAC
19280032 TAAATATTATCAC
1 TAAATATTATCAC
19280045 TAAATA
1 TAAATA
19280051 ATTCAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 2 0.06
12 2 0.06
13 25 0.69
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:19280034 original size:23 final size:23
Alignment explanation
Indices: 19280008--19280059 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
19279998 AATATTATCA
*
19280008 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
19280031 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
19280054 CAAAAT
1 CTAAAT
19280060 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:19286140 original size:18 final size:18
Alignment explanation
Indices: 19286113--19286163 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
19286103 GTTTATAGAT
*
19286113 ATCCTTGGACTTACAGCA
1 ATCCTAGGACTTACAGCA
* * *
19286131 ATCCTCGGACTTGCAGCG
1 ATCCTAGGACTTACAGCA
19286149 ATCCTAGGACTTACA
1 ATCCTAGGACTTACA
19286164 TCGCTCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (18 bp):
ATCCTAGGACTTACAGCA
Found at i:19290570 original size:47 final size:47
Alignment explanation
Indices: 19290496--19290590 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
19290486 TGCCCATATA
*
19290496 ACCACTGTCAACTAGGGCCCCAATTATGCTCCATCTTTTGACAGCAT
1 ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
* *
19290543 ACCACTGTCAACTAGGGCCCCAGTTATGCTCAATCTTTTGATAGCAT
1 ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
19290590 A
1 A
19290591 ACCTTTGTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (47 bp):
ACCACTGTCAACTAGGGCCCCAATTATGCTCAATCTTTTGACAGCAT
Found at i:19299000 original size:4 final size:4
Alignment explanation
Indices: 19298991--19299044 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
19298981 CTTATTACTA
* * **
19298991 TTAT TTAT TTAT TTAT CTAT TTAT TTAT TTAC TTGC TTAT TT-T TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
19299038 ATAT TTA
1 TTAT TTA
19299045 AAAACAAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:19302371 original size:30 final size:30
Alignment explanation
Indices: 19302297--19302372 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
19302287 TGGTTAACAC
* *
19302297 ATCCCTTTTCATAAATCGGTAACCAAAGTT
1 ATCCCTTTTCATAATTCGATAACCAAAGTT
* *
19302327 ATCCCTTTTCATAATTCGATAGCCGAAGGTT
1 ATCCCTTTTCATAATTCGATAACC-AAAGTT
19302358 -TCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
19302373 TGATGGTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAACCAAAGTT
Found at i:19302392 original size:30 final size:30
Alignment explanation
Indices: 19302358--19302433 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
19302348 GCCGAAGGTT
19302358 TCCCTTTTCATAATTTGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCATCACCA
* *
19302388 TCCC-TTTCATAAATCGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCATCACCA
19302417 TCCCTTTTTCATAATTT
1 TCCC-TTTTCATAATTT
19302434 ATAGCCGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.68
30 4 0.10
31 9 0.22
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.41
Consensus pattern (30 bp):
TCCCTTTTCATAATTTGATGGTCATCACCA
Found at i:19302544 original size:30 final size:30
Alignment explanation
Indices: 19302358--19302582 Score: 129
Period size: 30 Copynumber: 7.5 Consensus size: 30
19302348 GCCGAAGGTT
*
19302358 TCCCTTTTCATAATTTGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCGTCACCA
* * *
19302388 TCCC-TTTCATAAATCGATGGTCATCACCA
1 TCCCTTTTCATAATTTGATGGTCGTCACCA
* * * *
19302417 TCCCTTTTTCATAATTT-ATAGCCG-AAGCTA
1 TCCC-TTTTCATAATTTGATGGTCGTCA-CCA
* ***
19302447 TCCCTTTTCAATAGA-TTGATAGTCGAGGCCA
1 TCCCTTTTC-ATA-ATTTGATGGTCGTCACCA
* * ** ** * *
19302478 TTCCTTTTTATTGTACGATAGTCG-AAGCCA
1 TCCCTTTTCATAATTTGATGGTCGTCA-CCA
*
19302508 TTCCTTTTCATAATTTGATGGTCGTCACCA
1 TCCCTTTTCATAATTTGATGGTCGTCACCA
* **
19302538 TCCCTTTTCATTATTCAATGGTCGTCACCAA
1 TCCCTTTTCATAATTTGATGGTCGTCACC-A
*
19302569 T-CATTTTCATAATT
1 TCCCTTTTCATAATT
19302583 GATAACCGAA
Statistics
Matches: 150, Mismatches: 34, Indels: 22
0.73 0.17 0.11
Matches are distributed among these distances:
29 33 0.22
30 89 0.59
31 28 0.19
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (30 bp):
TCCCTTTTCATAATTTGATGGTCGTCACCA
Found at i:19302607 original size:29 final size:30
Alignment explanation
Indices: 19302570--19302637 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
19302560 CGTCACCAAT
*
19302570 CATTTTCATA-ATTGATAACCGAAG-CTATC
1 CATTTTCATAGATCGATAACCGAAGTC-ATC
* *
19302599 CTTTTTCATAGATCGATAGCCGAAGTCATC
1 CATTTTCATAGATCGATAACCGAAGTCATC
19302629 CATTTTCAT
1 CATTTTCAT
19302638 TCATCGATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.27
30 23 0.70
31 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (30 bp):
CATTTTCATAGATCGATAACCGAAGTCATC
Found at i:19302644 original size:30 final size:30
Alignment explanation
Indices: 19302570--19302645 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
19302560 CGTCACCAAT
*
19302570 CATTTTCA-TAATTGATAACCGAAGCTATC
1 CATTTTCATTAATCGATAACCGAAGCTATC
* *
19302599 CTTTTTCA-TAGATCGATAGCCGAAG-TCATC
1 CATTTTCATTA-ATCGATAACCGAAGCT-ATC
*
19302629 CATTTTCATTCATCGAT
1 CATTTTCATTAATCGAT
19302646 GCTCGCCGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 10 0.26
30 28 0.72
31 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (30 bp):
CATTTTCATTAATCGATAACCGAAGCTATC
Found at i:19304964 original size:13 final size:15
Alignment explanation
Indices: 19304939--19304975 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
19304929 ATTGACAACA
19304939 TAATAATTAAAT-ATT
1 TAATAA-TAAATAATT
19304954 TAA-AATAAATAATT
1 TAATAATAAATAATT
19304968 TAATAATA
1 TAATAATA
19304976 TTTTCTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAAATAATT
Found at i:19304975 original size:24 final size:24
Alignment explanation
Indices: 19304908--19304978 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
19304898 TTTGAGTATA
*
19304908 TAAACATAAAAAATTAATAATATT
1 TAAACATAAATAATTAATAATATT
*
19304932 GACAACAT-AATAATT-A-AATATT
1 TA-AACATAAATAATTAATAATATT
19304954 TAAA-ATAAATAATTTAATAATATT
1 TAAACATAAATAA-TTAATAATATT
19304978 T
1 T
19304979 TCTTATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.05
21 7 0.18
22 9 0.23
23 2 0.05
24 14 0.36
25 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (24 bp):
TAAACATAAATAATTAATAATATT
Found at i:19310367 original size:11 final size:11
Alignment explanation
Indices: 19310353--19310377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19310343 TTTTAAAAAA
19310353 ATTATTAAATT
1 ATTATTAAATT
19310364 ATTATTAAATT
1 ATTATTAAATT
19310375 ATT
1 ATT
19310378 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:19316563 original size:18 final size:18
Alignment explanation
Indices: 19316542--19316734 Score: 224
Period size: 18 Copynumber: 10.7 Consensus size: 18
19316532 GAGTCCACAC
* * *
19316542 TGTGCTCTAAGTTAGCAT
1 TGTGCTCCAAGTTTGCAA
*
19316560 TGTGCTCCAAGTTAGCAA
1 TGTGCTCCAAGTTTGCAA
* *
19316578 TGTGCTCTAAGTTTGCAT
1 TGTGCTCCAAGTTTGCAA
19316596 TGTGCTCCAAGTTTGCAA
1 TGTGCTCCAAGTTTGCAA
* ** *
19316614 TCTGCTGTAAGTTCGCAA
1 TGTGCTCCAAGTTTGCAA
* *
19316632 TATGCTCCAAGTTTGCAT
1 TGTGCTCCAAGTTTGCAA
*
19316650 TGTGCTCCAAGTTTGCCA
1 TGTGCTCCAAGTTTGCAA
19316668 TGTGCTCCAAGTTTGCAA
1 TGTGCTCCAAGTTTGCAA
* *
19316686 TGTGCTCCAAGTTCGCAT
1 TGTGCTCCAAGTTTGCAA
* * *
19316704 TTTGTTCCAAGTTTGCAC
1 TGTGCTCCAAGTTTGCAA
19316722 TGTGCTCCAAGTT
1 TGTGCTCCAAGTT
19316735 CAAATCATGC
Statistics
Matches: 147, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 147 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (18 bp):
TGTGCTCCAAGTTTGCAA
Found at i:19323081 original size:27 final size:29
Alignment explanation
Indices: 19323045--19323115 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
19323035 AAATTAATTT
19323045 ATAATAAAATTATAATTTAA-CTTCT-AA
1 ATAATAAAATTATAATTTAATCTTCTAAA
* * *
19323072 AT-ATGAAAATAATTATTTAATCTTTTAAA
1 ATAAT-AAAATTATAATTTAATCTTCTAAA
19323101 ATAATAAAATTATAA
1 ATAATAAAATTATAA
19323116 AATAATACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 15 0.43
28 4 0.11
29 12 0.34
30 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
ATAATAAAATTATAATTTAATCTTCTAAA
Found at i:19323144 original size:23 final size:22
Alignment explanation
Indices: 19323094--19323144 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
19323084 TTATTTAATC
19323094 TTTTAA-AATAATAAAATTATA
1 TTTTAATAATAATAAAATTATA
***
19323115 AAATAATACATAATAAAATTATA
1 TTTTAATA-ATAATAAAATTATA
19323138 TTTTAAT
1 TTTTAAT
19323145 CTTTTAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
21 3 0.14
22 1 0.05
23 18 0.82
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAATAATAATAAAATTATA
Found at i:19323955 original size:24 final size:23
Alignment explanation
Indices: 19323919--19323985 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 23
19323909 AGTATCCAAC
*
19323919 TTAAT-AATAAAAATTACAAATAAT
1 TTAATAAAT-AAAA-TAAAAATAAT
*
19323943 TTAATAAATAAAA-ATAAA-AAT
1 TTAATAAATAAAATAAAAATAAT
19323964 TTAA-AAATAAAAATAAAAATAA
1 TTAATAAAT-AAAATAAAAATAA
19323986 AAAAACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 4 0.11
21 11 0.30
22 8 0.22
23 2 0.05
24 9 0.24
25 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAATAAATAAAATAAAAATAAT
Found at i:19323961 original size:5 final size:6
Alignment explanation
Indices: 19323948--19323988 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
19323938 ATAATTTAAT
19323948 AAATAA AAATAA AAATTTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
19323989 AACATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:19323973 original size:20 final size:21
Alignment explanation
Indices: 19323940--19323983 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
19323930 AATTACAAAT
19323940 AATTTAATAAATAAAAATAAA
1 AATTTAATAAATAAAAATAAA
19323961 AATTTAA-AAATAAAAATAAA
1 AATTTAATAAATAAAAATAAA
19323981 AAT
1 AAT
19323984 AAAAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTTAATAAATAAAAATAAA
Found at i:19323989 original size:20 final size:20
Alignment explanation
Indices: 19323948--19323990 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
19323938 ATAATTTAAT
**
19323948 AAATAAAAATAAAAATTTAA
1 AAATAAAAATAAAAATAAAA
19323968 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
19323988 AAA
1 AAA
19323991 CATATAATTT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:19324016 original size:9 final size:9
Alignment explanation
Indices: 19324003--19324053 Score: 68
Period size: 9 Copynumber: 5.7 Consensus size: 9
19323993 TATAATTTTA
19324003 TTAATTCGAG
1 TTAATTCG-G
19324013 -TAATTCGG
1 TTAATTCGG
**
19324021 TTAATTCAA
1 TTAATTCGG
19324030 TTAATTCGG
1 TTAATTCGG
19324039 TTAATTCGG
1 TTAATTCGG
19324048 TTAATT
1 TTAATT
19324054 TTATACTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
8 1 0.03
9 35 0.97
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (9 bp):
TTAATTCGG
Found at i:19324033 original size:27 final size:27
Alignment explanation
Indices: 19324002--19324053 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
19323992 ATATAATTTT
19324002 ATTAATTCGAG-TAATTCGGTTAATTCA
1 ATTAATTCG-GTTAATTCGGTTAATTCA
19324029 ATTAATTCGGTTAATTCGGTTAATT
1 ATTAATTCGGTTAATTCGGTTAATT
19324054 TTATACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (27 bp):
ATTAATTCGGTTAATTCGGTTAATTCA
Found at i:19336022 original size:16 final size:15
Alignment explanation
Indices: 19335997--19336030 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
19335987 ATAACATAAA
19335997 ATTTTAATAATATAT
1 ATTTTAATAATATAT
19336012 ATTTTATATAATATAT
1 ATTTTA-ATAATATAT
19336028 ATT
1 ATT
19336031 ACATACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTAATAATATAT
Found at i:19344527 original size:3 final size:3
Alignment explanation
Indices: 19344519--19344569 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19344509 TATTTATGTT
19344519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19344567 TTA
1 TTA
19344570 AGTAATGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19346768 original size:46 final size:44
Alignment explanation
Indices: 19346664--19346771 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
19346654 TGTCTTTGAC
** * * *
19346664 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
19346708 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
19346754 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
19346772 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:19352483 original size:43 final size:45
Alignment explanation
Indices: 19352436--19352542 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 45
19352426 TGTCTTTGAC
* * *
19352436 ATGGACTTACATGAATTC-TTCCTGTCTCCAATG-CATA-TATAAT
1 ATGGACTTACATG-ACTCAATCCTGTCTCCAAAGCCATATTATAAT
* *
19352479 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGACTCAATCCTGTCTCCAAAGCCATA-TTATAAT
*
19352525 ATGGACTTACATGGCTCA
1 ATGGACTTACATGACTCA
19352543 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
42 2 0.04
43 26 0.47
44 4 0.07
46 23 0.42
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGACTCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:19352534 original size:46 final size:43
Alignment explanation
Indices: 19352455--19352542 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 43
19352445 CATGAATTCT
*
19352455 TCCTGTCTCCAATGCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCATATATAATATGGACTTACATGGCTCAA
*
19352498 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAG-CATA--TATAATATGGACTTACATGGCTCA
19352543 TTTCTGTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 13 0.32
44 4 0.10
46 23 0.57
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (43 bp):
TCCTGTCTCCAAAGCATATATAATATGGACTTACATGGCTCAA
Found at i:19353912 original size:44 final size:44
Alignment explanation
Indices: 19353812--19353903 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
19353802 TGTTCAGGGA
*
19353812 TACTTCGACCTT-GAGTCGATGAGGCACCATAAGTGTCGTATTGT
1 TACTTCGA-CTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
* **
19353856 TACTTCGACTTCGAGTCGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
19353900 TACT
1 TACT
19353904 GTTGCTTCGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 3 0.07
44 40 0.93
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACTGT
Found at i:19354142 original size:18 final size:18
Alignment explanation
Indices: 19354087--19354144 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
19354077 ATTACTGGAC
19354087 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* * *
19354105 TG-AT---TGTTTGATAC
1 TGAATAACTGATTGTTAT
19354119 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
19354137 TGAATAAC
1 TGAATAAC
19354145 AATAAACAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
17 2 0.07
18 17 0.57
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:19361340 original size:38 final size:38
Alignment explanation
Indices: 19361289--19361365 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
19361279 TTTGGTTTAC
19361289 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
1 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
19361327 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
1 ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
19361365 A
1 A
19361366 GAGACTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (38 bp):
ATAGAAAAGGGGGAATCTACCGGAAACAAACATTAATG
Found at i:19364604 original size:47 final size:47
Alignment explanation
Indices: 19364535--19364629 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
19364525 AACAGATAGT
*
19364535 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGATATCAGCAA
1 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
*
19364582 AGCTAGATCTAGAAATTTAGTGTTTGTATATAGTCCGAGATCAGCAA
1 AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
19364629 A
1 A
19364630 CGTTTTAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (47 bp):
AGCTAGATCTAGAAATTTAGTGTTTGTATATACTCCGAGATCAGCAA
Found at i:19365948 original size:24 final size:25
Alignment explanation
Indices: 19365921--19365970 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
19365911 TATCTATATC
19365921 TAATCATA-TAATAAATTA-TTAATA
1 TAAT-ATATTAATAAATTATTTAATA
*
19365945 TAATTTATTAATAAATTATTTAATA
1 TAATATATTAATAAATTATTTAATA
19365970 T
1 T
19365971 TTAGATCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 14 0.61
25 7 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATATATTAATAAATTATTTAATA
Found at i:19365958 original size:11 final size:11
Alignment explanation
Indices: 19365929--19365969 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
19365919 TCTAATCATA
19365929 TAATAAATTAT
1 TAATAAATTAT
19365940 TAATATAATTTAT
1 TAATA-AA-TTAT
19365953 TAATAAATTATT
1 TAATAAATTA-T
19365965 TAATA
1 TAATA
19365970 TTTAGATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.30
12 10 0.37
13 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATAAATTAT
Found at i:19367013 original size:21 final size:21
Alignment explanation
Indices: 19366961--19367033 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
19366951 TATTTTAAAT
*
19366961 AAAAATAAAATATTACAATTAA
1 AAAAATAAAA-ATTAAAATTAA
*
19366983 AAAAATTAAAAATTAAAATTCA
1 AAAAA-TAAAAATTAAAATTAA
*
19367005 AAAAATAAAAA-TAAATTTTAA
1 AAAAATAAAAATTAAA-ATTAA
*
19367026 AAATATAA
1 AAAAATAA
19367034 TTTTTTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.09
21 16 0.36
22 19 0.43
23 5 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTAAAATTAA
Found at i:19371128 original size:13 final size:13
Alignment explanation
Indices: 19371107--19371170 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
19371097 TTTTAAATCA
19371107 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
19371120 ACTTCTCAAAATT
1 ACTTTTCAAAAGT
* * * *
19371133 ATTTTTCCACAGC
1 ACTTTTCAAAAGT
*
19371146 ACTTTTTAAAAGT
1 ACTTTTCAAAAGT
*
19371159 ACTTCTCAAAAG
1 ACTTTTCAAAAG
19371171 CAATGCTAAA
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:19377728 original size:41 final size:41
Alignment explanation
Indices: 19377676--19377758 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
19377666 TCACTATATT
19377676 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
1 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
*
19377717 AAAGTATGTATGAATTGATGCACTTTTGCAAAATCATTGCA
1 AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
19377758 A
1 A
19377759 GTGCAAATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (41 bp):
AAAGTACGTATGAATTGATGCACTTTTGCAAAATCATTGCA
Found at i:19379291 original size:25 final size:24
Alignment explanation
Indices: 19379262--19379309 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
19379252 TAAATAAAAA
19379262 ATTT-AAAATATAATAAATCAAATAC
1 ATTTAAAAATATAA-AAA-CAAATAC
19379287 ATTTAAAAATATAAAAACAAATA
1 ATTTAAAAATATAAAAACAAATA
19379310 TTAAAACAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 7 0.32
26 9 0.41
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAATATAAAAACAAATAC
Found at i:19379407 original size:28 final size:29
Alignment explanation
Indices: 19379376--19379434 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
19379366 TTGAAAATAT
** *
19379376 AATAAAAAGTAGTTAT-ATTAAAATTAAA
1 AATAAAAAGTAAATATAATTAAAAATAAA
*
19379404 AATAAAATGTAAATATAATTAAAAATAAA
1 AATAAAAAGTAAATATAATTAAAAATAAA
19379433 AA
1 AA
19379435 ATATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (29 bp):
AATAAAAAGTAAATATAATTAAAAATAAA
Found at i:19379442 original size:23 final size:23
Alignment explanation
Indices: 19379397--19379443 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
19379387 GTTATATTAA
**
19379397 AATTAAAAATAAAATGTAAATAT
1 AATTAAAAATAAAAAATAAATAT
*
19379420 AATTAAAAATAAAAAATATATAT
1 AATTAAAAATAAAAAATAAATAT
19379443 A
1 A
19379444 TTTAGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTAAAAATAAAAAATAAATAT
Found at i:19380425 original size:21 final size:22
Alignment explanation
Indices: 19380399--19380457 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
19380389 GTTTTAAGAA
*
19380399 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
19380420 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
19380442 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
19380458 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:19380472 original size:26 final size:24
Alignment explanation
Indices: 19380428--19380477 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
19380418 ATTTGTTTTA
*
19380428 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
19380452 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
19380478 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:19381525 original size:42 final size:42
Alignment explanation
Indices: 19381478--19381684 Score: 207
Period size: 42 Copynumber: 4.9 Consensus size: 42
19381468 TTTGATTTAG
* * *
19381478 TCGATGATGCACTTACGTACCAGTATAATTGCTTCGGTATAT
1 TCGATGATGCACTTGCGTGCTAGTATAATTGCTTCGGTATAT
** * * * * *
19381520 TCGATGATGCACTTTTGTTCTAGTATGATTGTTTCTGTTTAT
1 TCGATGATGCACTTGCGTGCTAGTATAATTGCTTCGGTATAT
* *
19381562 CCGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATAT
1 TCGATGATGCACT-TGCGTGCTAGTATAATTGCTTCGGTATAT
** * * * * *
19381605 TCGATGATGCACTTTTGTTCTAGTATGATTGTTTCTGTTTAT
1 TCGATGATGCACTTGCGTGCTAGTATAATTGCTTCGGTATAT
* *
19381647 CCGATGATGCACTATGCGTGCTAATATAATTGCTTCGG
1 TCGATGATGCACT-TGCGTGCTAGTATAATTGCTTCGG
19381685 CTTGTTCAGT
Statistics
Matches: 129, Mismatches: 34, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
42 79 0.61
43 50 0.39
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (42 bp):
TCGATGATGCACTTGCGTGCTAGTATAATTGCTTCGGTATAT
Found at i:19381621 original size:85 final size:85
Alignment explanation
Indices: 19381479--19381752 Score: 369
Period size: 85 Copynumber: 3.2 Consensus size: 85
19381469 TTGATTTAGT
* * * *
19381479 CGATGATGCACT-TACGTACCAGTATAATTGCTTCGGTATATTCGATGATGCACTTTTGTTCTAG
1 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATATTCGATGATGCACTTTTGTTCTAG
19381543 TATGATTGTTTCTGTTTATC
66 TATGATTGTTTCTGTTTATC
19381563 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATATTCGATGATGCACTTTTGTTCTAG
1 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATATTCGATGATGCACTTTTGTTCTAG
19381628 TATGATTGTTTCTGTTTATC
66 TATGATTGTTTCTGTTTATC
* *
19381648 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGCT-TGTTC-AGTGATGCAC-TATGTATA
1 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGG-TATATTCGA-TGATGCACTTTTGT-T-
* * * **
19381710 CCAGTATACATT-CTTCAATTTATC
62 CTAGTAT-GATTGTTTCTGTTTATC
19381734 CGATGATGCACTATGCGTG
1 CGATGATGCACTATGCGTG
19381753 TCAGTATACT
Statistics
Matches: 173, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
84 17 0.10
85 118 0.68
86 35 0.20
87 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (85 bp):
CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATATTCGATGATGCACTTTTGTTCTAG
TATGATTGTTTCTGTTTATC
Found at i:19381758 original size:43 final size:43
Alignment explanation
Indices: 19381479--19381784 Score: 230
Period size: 43 Copynumber: 7.2 Consensus size: 43
19381469 TTGATTTAGT
* * * * *
19381479 CGATGATGCACT-TACGTACCAGTATAATTGCTTCGGTATATT
1 CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGGTTTATC
** * * * *
19381521 CGATGATGCACT-TTTGTTCTAGTATGATTGTTTCTGTTTATC
1 CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGGTTTATC
* * *
19381563 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGTATATT
1 CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGGTTTATC
** * * * *
19381606 CGATGATGCACT-TTTGTTCTAGTATGATTGTTTCTGTTTATC
1 CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGGTTTATC
*
19381648 CGATGATGCACTATGCGTGCTAATATAATTGCTTCGGCTTGT-TC
1 CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGG-TT-TATC
* ** * * **
19381692 AG-TGATGCACTATGTATACCAGTATACATT-CTTCAATTTATC
1 CGATGATGCACTATGCGTGCTAGTATA-ATTGCTTCGGTTTATC
* * * *
19381734 CGATGATGCACTATGCGTG-TCAGTATACTTTCTTCTGTTTATT
1 CGATGATGCACTATGCGTGCT-AGTATAATTGCTTCGGTTTATC
*
19381777 AGATGATG
1 CGATGATG
19381785 TAATGTGGTG
Statistics
Matches: 203, Mismatches: 52, Indels: 17
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.00
42 85 0.42
43 108 0.53
44 8 0.04
45 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (43 bp):
CGATGATGCACTATGCGTGCTAGTATAATTGCTTCGGTTTATC
Found at i:19382297 original size:29 final size:30
Alignment explanation
Indices: 19382232--19382296 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
19382222 AATAGTCCAT
*
19382232 ATTTTTATAATTTTTAAAAGATTAAATAAA
1 ATTTTTATAATTTTAAAAAGATTAAATAAA
* *
19382262 ATTTTTATCATTTTAAAAAG-TTAAAATATA
1 ATTTTTATAATTTTAAAAAGATT-AAATAAA
19382292 ATTTT
1 ATTTT
19382297 AGTATTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTTTTATAATTTTAAAAAGATTAAATAAA
Found at i:19402852 original size:18 final size:17
Alignment explanation
Indices: 19402821--19402865 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
19402811 TAGCATTACC
**
19402821 AAAAATAAAAAATAAAA
1 AAAAATAATGAATAAAA
19402838 AAAAATCAATGAATAAAA
1 AAAAAT-AATGAATAAAA
*
19402856 TAAAATAATG
1 AAAAATAATG
19402866 TAAAGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAATAATGAATAAAA
Found at i:19403738 original size:5 final size:5
Alignment explanation
Indices: 19403728--19403759 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
19403718 GAAAATTAAG
19403728 ATAAA ATAAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA A
19403760 AATTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:19403738 original size:16 final size:16
Alignment explanation
Indices: 19403719--19403759 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
19403709 GAAGAGAGAG
*
19403719 AAAATTAAGATAAAAT
1 AAAATTAAAATAAAAT
*
19403735 AAAAATAAAATAAAAT
1 AAAATTAAAATAAAAT
19403751 AAAA-TAAAA
1 AAAATTAAAA
19403760 AATTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATTAAAATAAAAT
Found at i:19414359 original size:13 final size:14
Alignment explanation
Indices: 19414343--19414371 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19414333 ATCAACCATT
19414343 AAAAATCTAG-AAA
1 AAAAATCTAGTAAA
19414356 AAAAATCTAGTAAA
1 AAAAATCTAGTAAA
19414370 AA
1 AA
19414372 CTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAATCTAGTAAA
Found at i:19414739 original size:30 final size:30
Alignment explanation
Indices: 19414703--19414764 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
19414693 ACTTAATTTA
19414703 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
19414733 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
19414763 TT
1 TT
19414765 ACTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:19432476 original size:3 final size:3
Alignment explanation
Indices: 19432463--19432495 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19432453 AGGAAAAATC
19432463 TTA TT- TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19432496 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:19432503 original size:12 final size:11
Alignment explanation
Indices: 19432463--19432510 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
19432453 AGGAAAAATC
19432463 TTATTTTATTA
1 TTATTTTATTA
19432474 TTATTATTATTA
1 TTATT-TTATTA
*
19432486 TTATTTTATTT
1 TTATTTTATTA
19432497 TTAATTTTA-TA
1 TT-ATTTTATTA
19432508 TTA
1 TTA
19432511 AATTAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 1 0.03
11 15 0.45
12 17 0.52
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:19434426 original size:53 final size:53
Alignment explanation
Indices: 19434312--19434431 Score: 141
Period size: 53 Copynumber: 2.3 Consensus size: 53
19434302 CCTAGCTCAT
* * * * *
19434312 AAGGAGCATGCAGAATGAGACATATCACAAATCTCACAAAAACCCATGCTTTT
1 AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
** * * *
19434365 AAATAGCACGCAGAGTGAAACTTATCACAAAACTCACAAAAGCCCATACTTTC
1 AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
*
19434418 GAGGAGCACGCAGA
1 AAGGAGCACGCAGA
19434432 CTGAGGCTCA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (53 bp):
AAGGAGCACGCAGAATGAAACATATCACAAAACTCACAAAAACCCATACTTTC
Found at i:19435209 original size:25 final size:25
Alignment explanation
Indices: 19435175--19435225 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
19435165 TTTGAACTAG
19435175 ACTTCAACTCTGTTATTGCAACCAT
1 ACTTCAACTCTGTTATTGCAACCAT
19435200 ACTTCAACTCTGTTATTGCAACCAT
1 ACTTCAACTCTGTTATTGCAACCAT
19435225 A
1 A
19435226 GTTGTAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (25 bp):
ACTTCAACTCTGTTATTGCAACCAT
Found at i:19438271 original size:28 final size:28
Alignment explanation
Indices: 19438209--19438272 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
19438199 ATATTTATAT
**
19438209 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTTAATAATTAGA
*
19438237 TACATTATTTTAATATTT-A-AATTAGA
1 TATATTATTTTAATATTTAATAATTAGA
19438263 GTGATATTAT
1 -T-ATATTAT
19438273 ATATTTAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 23 0.77
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (28 bp):
TATATTATTTTAATATTTAATAATTAGA
Found at i:19448002 original size:43 final size:43
Alignment explanation
Indices: 19447941--19448030 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
19447931 CCTTGCTCGA
** *
19447941 ATCACCGGCATTAAGCCTGCTAGGCTCGAAGACCCGAATACAC
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGACCCGAATACAC
*
19447984 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGACCCGAATACAC
19448027 ATCA
1 ATCA
19448031 TCGAGTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.13
Consensus pattern (43 bp):
ATCACCGGCACAAAGCCTGCTAGGCACGAAGACCCGAATACAC
Found at i:19449667 original size:38 final size:38
Alignment explanation
Indices: 19449571--19449736 Score: 145
Period size: 38 Copynumber: 4.3 Consensus size: 38
19449561 TAAGGTATAA
* * * * * *
19449571 AACCCGAACATAACACCAGCACGAAACCTACGGGACTTT
1 AACCCGGATATAATACCAGCACTAAGCCTGCGGGA-TTT
* * *
19449610 AAACTCAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 -AACCCGGATATAATACCAGCACTAAGCCTGCGGGATTT
* * * *
19449649 AATCTGGATATAATACCAGCACGAAGCCTACGGGATTT
1 AACCCGGATATAATACCAGCACTAAGCCTGCGGGATTT
* *
19449687 AACCCGGATATAATTCCAGCA-TATAGCCTGCGGGTCTTT
1 AACCCGGATATAATACCAGCACTA-AGCCTGCGGG-ATTT
19449726 AAGCCCGGATA
1 AA-CCCGGATA
19449737 CACATCAAAT
Statistics
Matches: 101, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
37 1 0.01
38 58 0.57
39 8 0.08
40 34 0.34
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
AACCCGGATATAATACCAGCACTAAGCCTGCGGGATTT
Found at i:19449736 original size:78 final size:78
Alignment explanation
Indices: 19449571--19449736 Score: 185
Period size: 78 Copynumber: 2.1 Consensus size: 78
19449561 TAAGGTATAA
* * * *
19449571 AACCCGAACATAACACCAGCACGAAACCTACGGGACTTTAAACTCAGATATAATACCAGCACTAG
1 AACCCGGATATAACACCAGCACGAAACCTACGGGACTTTAAACCCAGATATAATACCAGCACTAA
19449636 GCCTGCGGGATTT
66 GCCTGCGGGATTT
* * * * * *
19449649 AATCTGGATATAATACCAGCACGAAGCCTACGGGA-TTT-AACCCGGATATAATTCCAGCA-TAT
1 AACCCGGATATAACACCAGCACGAAACCTACGGGACTTTAAACCCAGATATAATACCAGCACTA-
*
19449711 AGCCTGCGGGTCTTT
65 AGCCTGCGGG-ATTT
19449726 AAGCCCGGATA
1 AA-CCCGGATA
19449737 CACATCAAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
75 2 0.03
76 27 0.38
77 8 0.11
78 35 0.49
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (78 bp):
AACCCGGATATAACACCAGCACGAAACCTACGGGACTTTAAACCCAGATATAATACCAGCACTAA
GCCTGCGGGATTT
Found at i:19452932 original size:17 final size:18
Alignment explanation
Indices: 19452901--19452935 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
19452891 ATGAACTGTA
19452901 AGCTCACCAAAATGTGCG
1 AGCTCACCAAAATGTGCG
19452919 AGCTCACC-AAATGTGCG
1 AGCTCACCAAAATGTGCG
19452936 CACTTACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (18 bp):
AGCTCACCAAAATGTGCG
Found at i:19455153 original size:13 final size:13
Alignment explanation
Indices: 19455135--19455159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19455125 AACATGGATT
19455135 CAAACAAACTATG
1 CAAACAAACTATG
19455148 CAAACAAACTAT
1 CAAACAAACTAT
19455160 TTAATCAAAG
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:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
CAAACAAACTATG
Done.