Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 4 of 318
Found at i:1117506 original size:46 final size:46
Alignment explanation
Indices: 1117331--1117506 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
1117321 TGTAACCCGC
* * *
1117331 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * *
1117377 CCATAAGTGAACTCGGACTCAATTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
1117427 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1117470 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1117507 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 67 0.61
47 31 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:1128170 original size:16 final size:17
Alignment explanation
Indices: 1128138--1128170 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1128128 TTTATAAGTA
*
1128138 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
1128155 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
1128171 GTTTCATCAT
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:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:1128613 original size:92 final size:92
Alignment explanation
Indices: 1128456--1128728 Score: 411
Period size: 92 Copynumber: 3.0 Consensus size: 92
1128446 TTTGACATGA
* * *
1128456 TGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
* *
1128521 CATGGTCTTATTCTTTTCATGTCACGT
66 CATGGTCTTATTCGTTTCATATCACGT
* * *
1128548 TGCCATGGTATCTTTCAACCACGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
1128613 CATGGTCTTATTCGTTTCATATCACGT
66 CATGGTCTTATTCGTTTCATATCACGT
* * * *
1128640 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
** *
1128705 CATGGTCTTACACATTTCATATCA
66 CATGGTCTTATTCGTTTCATATCA
1128729 GAGAGCACAC
Statistics
Matches: 163, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 163 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCGTTTCATATCACGT
Found at i:1128729 original size:46 final size:46
Alignment explanation
Indices: 1128456--1128728 Score: 368
Period size: 46 Copynumber: 5.9 Consensus size: 46
1128446 TTTGACATGA
* * * *
1128456 TGCCATAGTATCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* * *
1128502 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *** *
1128548 TGCCATGGTATCTTTCAACCACGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1128594 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
1128640 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
1128686 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
1128729 GAGAGCACAC
Statistics
Matches: 206, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 202 0.98
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:1136546 original size:29 final size:29
Alignment explanation
Indices: 1136504--1136562 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1136494 ACGCTGCCAA
1136504 AACCAGCATTTTGCTGCTACTCCACTGTC
1 AACCAGCATTTTGCTGCTACTCCACTGTC
1136533 AACCAGCATTTTGCTGCTACTCCACTGTC
1 AACCAGCATTTTGCTGCTACTCCACTGTC
1136562 A
1 A
1136563 TTTTTCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.31
Consensus pattern (29 bp):
AACCAGCATTTTGCTGCTACTCCACTGTC
Found at i:1156223 original size:24 final size:24
Alignment explanation
Indices: 1156182--1156227 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1156172 TGTGATAAAT
*
1156182 TTTTTTCTAATTTAGTACCTGAGC
1 TTTTTTCCAATTTAGTACCTGAGC
* *
1156206 TTTTTTCCATTTTGGTACCTGA
1 TTTTTTCCAATTTAGTACCTGA
1156228 ATTTTACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTTTTCCAATTTAGTACCTGAGC
Found at i:1161943 original size:31 final size:31
Alignment explanation
Indices: 1161905--1161966 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1161895 AAATTAGTCC
*
1161905 TTGAACTATTTGAAAGT-TTTTATTTAAATCA
1 TTGAACTATTCGAAA-TATTTTATTTAAATCA
1161936 TTGAACTATTCGAAATATTTTATTTAAATCA
1 TTGAACTATTCGAAATATTTTATTTAAATCA
1161967 CTTGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (31 bp):
TTGAACTATTCGAAATATTTTATTTAAATCA
Found at i:1180240 original size:23 final size:23
Alignment explanation
Indices: 1180210--1180254 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1180200 ACATAAATTA
*
1180210 ATTTATTAAATTTTTA-CAAGAT
1 ATTTATTAAACTTTTACCAAGAT
*
1180232 ATTTCATTATACTTTTACCAAGA
1 ATTT-ATTAAACTTTTACCAAGA
1180255 AAATTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTATTAAACTTTTACCAAGAT
Found at i:1182386 original size:15 final size:15
Alignment explanation
Indices: 1182366--1182410 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1182356 AAACCAAGAA
*
1182366 GCTGTTGTTGCTGCT
1 GCTGTTGTTGTTGCT
1182381 GCTGTTGTTGTTGCT
1 GCTGTTGTTGTTGCT
*
1182396 GCTGCTGTTGTTGCT
1 GCTGTTGTTGTTGCT
1182411 CTTGTTCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.33, T:0.49
Consensus pattern (15 bp):
GCTGTTGTTGTTGCT
Found at i:1182391 original size:18 final size:18
Alignment explanation
Indices: 1182368--1182408 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1182358 ACCAAGAAGC
1182368 TGTTGTTGCTGCTGCTGT
1 TGTTGTTGCTGCTGCTGT
1182386 TGTTGTTGCTGCTGCTGT
1 TGTTGTTGCTGCTGCTGT
1182404 TGTTG
1 TGTTG
1182409 CTCTTGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.15, G:0.34, T:0.51
Consensus pattern (18 bp):
TGTTGTTGCTGCTGCTGT
Found at i:1189040 original size:19 final size:19
Alignment explanation
Indices: 1189007--1189051 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1188997 AATTCATACA
*
1189007 TAATAATTTATAATTTT-T
1 TAATTATTTATAATTTTAT
1189025 TAATTATTTCATAATTTTAT
1 TAATTATTT-ATAATTTTAT
1189045 T-ATTATT
1 TAATTATT
1189052 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTATTTATAATTTTAT
Found at i:1192562 original size:21 final size:21
Alignment explanation
Indices: 1192536--1192592 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1192526 TTTTTTTTAC
1192536 TTAAATATTTATATAT-ATAT
1 TTAAATATTTATATATAATAT
* *
1192556 TTCAAATATTCATATTTAATAT
1 TT-AAATATTTATATATAATAT
1192578 TTAAATA-TTATATAT
1 TTAAATATTTATATAT
1192593 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.26
21 17 0.55
22 6 0.19
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAATATTTATATATAATAT
Found at i:1193412 original size:18 final size:18
Alignment explanation
Indices: 1193389--1193425 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1193379 AATGGATATT
1193389 ATCACATCATACATGTGA
1 ATCACATCATACATGTGA
1193407 ATCACATCATACATGTGA
1 ATCACATCATACATGTGA
1193425 A
1 A
1193426 GTGGTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
ATCACATCATACATGTGA
Found at i:1203249 original size:16 final size:16
Alignment explanation
Indices: 1203213--1203259 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1203203 CATTTTCAAG
*
1203213 TTTATAATATATATATAT
1 TTTAT-ATAT-TATGTAT
1203231 TTTATATATTATGTAT
1 TTTATATATTATGTAT
*
1203247 TTTATATAATATG
1 TTTATATATTATG
1203260 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 18 0.67
17 4 0.15
18 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TTTATATATTATGTAT
Found at i:1208565 original size:21 final size:21
Alignment explanation
Indices: 1208539--1208603 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1208529 TTGTTGCTTC
1208539 ACCACTATAAATTGGTCCTGA
1 ACCACTATAAATTGGTCCTGA
*
1208560 ACCACTATAAATTTGTCTTCCTGA
1 ACCACTATAAA-TTG--GTCCTGA
* *
1208584 ACCGCTAAAAATTGGTCCTG
1 ACCACTATAAATTGGTCCTG
1208604 GTGGCATTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 16 0.43
22 3 0.08
23 3 0.08
24 15 0.41
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (21 bp):
ACCACTATAAATTGGTCCTGA
Found at i:1208662 original size:45 final size:45
Alignment explanation
Indices: 1208602--1208687 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
1208592 AAATTGGTCC
*
1208602 TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCACCACTTGG
1 TGGTGGCATTGGGGATGACGAACTCCATCCATTGCCACCACTTGG
*
1208647 TGGTGGCATTGGGGATGACGAACTCCATCCATTGCCGCCAC
1 TGGTGGCATTGGGGATGACGAACTCCATCCATTGCCACCAC
1208688 CATAGCCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (45 bp):
TGGTGGCATTGGGGATGACGAACTCCATCCATTGCCACCACTTGG
Found at i:1210169 original size:35 final size:35
Alignment explanation
Indices: 1210123--1210191 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1210113 TGAAGAACCT
1210123 TCAACAATCTGTAATATACAAATGACATTATTTGC
1 TCAACAATCTGTAATATACAAATGACATTATTTGC
1210158 TCAACAATCTGTAATATACAAATGACATTATTTG
1 TCAACAATCTGTAATATACAAATGACATTATTTG
1210192 TTATGCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (35 bp):
TCAACAATCTGTAATATACAAATGACATTATTTGC
Found at i:1217034 original size:15 final size:15
Alignment explanation
Indices: 1217014--1217050 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1217004 CTGGATCATA
1217014 TTCATCATCATCCTC
1 TTCATCATCATCCTC
* *
1217029 TTCATCTTCCTCCTC
1 TTCATCATCATCCTC
1217044 TTCATCA
1 TTCATCA
1217051 GACTCCGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:1223781 original size:16 final size:16
Alignment explanation
Indices: 1223760--1223802 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1223750 CAACTATAAG
1223760 TCAAAATGATCCAAAC
1 TCAAAATGATCCAAAC
* * *
1223776 TCAAAATTATTCAAAT
1 TCAAAATGATCCAAAC
1223792 TCAATAATGAT
1 TCAA-AATGAT
1223803 TAAAACTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (16 bp):
TCAAAATGATCCAAAC
Found at i:1224089 original size:20 final size:18
Alignment explanation
Indices: 1224064--1224111 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
1224054 AATATAATCA
1224064 TATCATATTTATAAATACAT
1 TATCATATTT-TAAATA-AT
*
1224084 TATCATAATTTAAATAAT
1 TATCATATTTTAAATAAT
1224102 TATCA-ATTTT
1 TATCATATTTT
1224112 TTTATTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 6 0.23
20 9 0.35
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (18 bp):
TATCATATTTTAAATAAT
Found at i:1224105 original size:18 final size:20
Alignment explanation
Indices: 1224064--1224106 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1224054 AATATAATCA
*
1224064 TATCATATTTATAAATACAT
1 TATCATAATTATAAATACAT
1224084 TATCATAATT-TAAATA-AT
1 TATCATAATTATAAATACAT
1224102 TATCA
1 TATCA
1224107 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
TATCATAATTATAAATACAT
Found at i:1230117 original size:3 final size:3
Alignment explanation
Indices: 1230109--1230137 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1230099 CGCAATGAAT
1230109 CGC CGC CGC CGC CGC CGC CGC CGC CGC CG
1 CGC CGC CGC CGC CGC CGC CGC CGC CGC CG
1230138 ACGTTGGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.34, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:1232845 original size:17 final size:17
Alignment explanation
Indices: 1232823--1232857 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1232813 ACGAGAGGAA
1232823 TCAAAATAGGCCTTGGT
1 TCAAAATAGGCCTTGGT
1232840 TCAAAATAGGCCTTGGT
1 TCAAAATAGGCCTTGGT
1232857 T
1 T
1232858 GTGAACTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (17 bp):
TCAAAATAGGCCTTGGT
Found at i:1233558 original size:17 final size:17
Alignment explanation
Indices: 1233529--1233561 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1233519 ATAGGTAAGG
1233529 TTTTATATGAATTTTAA
1 TTTTATATGAATTTTAA
1233546 TTTT-TATGTAATTTTA
1 TTTTATATG-AATTTTA
1233562 TACTTCAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTTATATGAATTTTAA
Found at i:1233741 original size:31 final size:31
Alignment explanation
Indices: 1233695--1233784 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
1233685 ATTTACTTAA
1233695 ATGTATATAATTAAATCAAAAAT-AAAATTTC
1 ATGTATATAATTAAATC-AAAATCAAAATTTC
* *
1233726 ATGTATA-AATCTAAATCACAATCAAAGTTTC
1 ATGTATATAAT-TAAATCAAAATCAAAATTTC
* **
1233757 ATGTGTATAATTGTA-CAAAATCAAAATT
1 ATGTATATAATTAAATCAAAATCAAAATT
1233785 AATATATCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
30 18 0.37
31 28 0.57
32 3 0.06
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (31 bp):
ATGTATATAATTAAATCAAAATCAAAATTTC
Found at i:1234356 original size:31 final size:31
Alignment explanation
Indices: 1234318--1234377 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1234308 GATTACATGA
1234318 ACTAAATTCCCAACTTACACAAAGTACAATG
1 ACTAAATTCCCAACTTACACAAAGTACAATG
*
1234349 ACTAAATTCTCAACTTACACAAAGTACAA
1 ACTAAATTCCCAACTTACACAAAGTACAA
1234378 AGTACACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.23
Consensus pattern (31 bp):
ACTAAATTCCCAACTTACACAAAGTACAATG
Found at i:1239717 original size:44 final size:46
Alignment explanation
Indices: 1239645--1239738 Score: 156
Period size: 44 Copynumber: 2.1 Consensus size: 46
1239635 GACCCAACTA
*
1239645 CTTACATCTCTCCTTCTCCTAGCTTACCTCAAGCCATATTCTCTCCT
1 CTTACATCTCTCC-TCTCCTAGCTTACCTCAAGCCACATTCTCTCCT
1239692 CTTACATCTCT-C-CTCCTAGCTTACCTCAAGCCACATTCTCTCCT
1 CTTACATCTCTCCTCTCCTAGCTTACCTCAAGCCACATTCTCTCCT
1239736 CTT
1 CTT
1239739 TCTTTCTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 34 0.74
46 1 0.02
47 11 0.24
ACGTcount: A:0.17, C:0.41, G:0.04, T:0.37
Consensus pattern (46 bp):
CTTACATCTCTCCTCTCCTAGCTTACCTCAAGCCACATTCTCTCCT
Found at i:1245475 original size:23 final size:23
Alignment explanation
Indices: 1245423--1245468 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1245413 AGATTGCGAC
1245423 AATCAATAGAAATTTTGTTTTGG
1 AATCAATAGAAATTTTGTTTTGG
1245446 AATCAATAGAAATTTTGTTTTGG
1 AATCAATAGAAATTTTGTTTTGG
1245469 GTTCAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (23 bp):
AATCAATAGAAATTTTGTTTTGG
Found at i:1245552 original size:50 final size:51
Alignment explanation
Indices: 1245493--1245600 Score: 209
Period size: 50 Copynumber: 2.1 Consensus size: 51
1245483 ACTAATCAAT
1245493 CTAATTTTATTTTGAAAATATTAGTTTTTTT-TATAAAGATCAACGGCATA
1 CTAATTTTATTTTGAAAATATTAGTTTTTTTGTATAAAGATCAACGGCATA
1245543 CTAATTTTATTTTGAAAATATTAGTTTTTTTGTATAAAGATCAACGGCATA
1 CTAATTTTATTTTGAAAATATTAGTTTTTTTGTATAAAGATCAACGGCATA
1245594 CTAATTT
1 CTAATTT
1245601 ATTCTTAGCG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 31 0.54
51 26 0.46
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (51 bp):
CTAATTTTATTTTGAAAATATTAGTTTTTTTGTATAAAGATCAACGGCATA
Found at i:1247870 original size:46 final size:45
Alignment explanation
Indices: 1247810--1248075 Score: 330
Period size: 46 Copynumber: 6.0 Consensus size: 45
1247800 TTTGACATGA
* * * * * *
1247810 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** **
1247856 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
1247902 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
1247948 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
1247994 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
1248032 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
1248076 AGAGCACACT
Statistics
Matches: 195, Mismatches: 15, Indels: 20
0.85 0.07 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 147 0.75
47 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:1248039 original size:38 final size:38
Alignment explanation
Indices: 1247988--1248063 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1247978 ACATTTTATA
1247988 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1248026 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1248064 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:1250224 original size:11 final size:11
Alignment explanation
Indices: 1250208--1250259 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1250198 TATACTAAAT
1250208 AAATAATAATA
1 AAATAATAATA
*
1250219 AAATAAT-ATT
1 AAATAATAATA
* *
1250229 AAATATCTCATA
1 AAATA-ATAATA
*
1250241 AAATATTAATA
1 AAATAATAATA
1250252 AAATAATA
1 AAATAATA
1250260 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1251912 original size:93 final size:89
Alignment explanation
Indices: 1251746--1251986 Score: 233
Period size: 93 Copynumber: 2.7 Consensus size: 89
1251736 TGAAAACCCC
*
1251746 TCAAATTTTTAAAAAAAAAGCAATTAAGTCCCTATATTTTTTTATACTCAATTGGGTACTTGAAC
1 TCAAATTTTTAAAAAAAAAGCAATTAAGTCCCCATATTTTTTTATACTCAATTGGGTACTTGAAC
1251811 TTTCAAAATGAATCAAAAAGGCCT
66 TTTCAAAATGAATCAAAAAGGCCT
* * * * ** **
1251835 TCAAACTTTTTAAAAAAAAAGCAATTAAGCTCTGCCCCTTTTTTTTTGTATTTGATTTTGTACTT
1 TCAAA-TTTTTAAAAAAAAAGCAATTAAG-TC--CCCATATTTTTTTATACTCAATTGGGTACTT
* * ** *
1251900 GAACTTTTAAAATGTATCAAAAATACCC
62 GAACTTTCAAAATGAATCAAAAAGGCCT
* ** * *
1251928 TCAAA--TTT-AAAAAAAA-CAATTAA-ACCCC-TATTTTTTTGCACTCAATTAGATACTTGAAC
1 TCAAATTTTTAAAAAAAAAGCAATTAAGTCCCCATATTTTTTTATACTCAATTGGGTACTTGAAC
1251987 CGTTAAAATG
Statistics
Matches: 125, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
83 23 0.18
84 3 0.02
86 1 0.01
88 7 0.06
89 13 0.10
90 26 0.21
91 2 0.02
93 50 0.40
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (89 bp):
TCAAATTTTTAAAAAAAAAGCAATTAAGTCCCCATATTTTTTTATACTCAATTGGGTACTTGAAC
TTTCAAAATGAATCAAAAAGGCCT
Found at i:1255137 original size:156 final size:153
Alignment explanation
Indices: 1254824--1255129 Score: 388
Period size: 156 Copynumber: 2.0 Consensus size: 153
1254814 GGTTAAAGCA
* * * * *
1254824 GGAGGTTGAGGAGGTTGTATGCTTGCAGAAACAGTTGAGGAGGCAAATAAGCTTGCAAATACACC
1 GGAGGTTGAGGAGGTCGAATGCTTGCAGAAACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* ** *
1254889 ACTGCTGCTGCTATTGCTAGCACCACTGCTAACCAGGCTGATGCTACGGTTACAACTTCCATTTA
66 ACTGCTGCTGCTA-T-CTA-CACCACTGCTAACCAAGCTGACACTACGGCTACAACTTCCATTTA
1254954 AGCCAGCCGATGGTGGAGCTGGTGCC
128 AGCCAGCCGATGGTGGAGCTGGTGCC
* *
1254980 GGAGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGAGGTAAATAAGCTCGAAAATACACC
1 GGAGGTTGAGGAGGTCGAATGCTTGCAGAAACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
* *
1255045 GCTGCTGCTGCTA-C-A-ACCACTGCTAATCAAGCTGACACTA-GTGCTACAACTTCCATTTAAG
66 ACTGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACTACG-GCTACAACTTCCATTTAAG
* * *
1255106 CTAGCTGGA-GGTGGAGCCGGTGCC
130 CCAGC-CGATGGTGGAGCTGGTGCC
1255130 AGTGCCGGTG
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
149 1 0.01
150 57 0.43
151 2 0.02
152 1 0.01
153 1 0.01
156 70 0.53
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (153 bp):
GGAGGTTGAGGAGGTCGAATGCTTGCAGAAACAGTCGAGGAGGCAAATAAGCTCGAAAATACACC
ACTGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACTACGGCTACAACTTCCATTTAAGC
CAGCCGATGGTGGAGCTGGTGCC
Found at i:1256724 original size:2 final size:2
Alignment explanation
Indices: 1256719--1256760 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1256709 GGATAAGTTA
* *
1256719 AT AT AT AT AG AT AG 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
1256761 TAACAAGGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1257978 original size:24 final size:23
Alignment explanation
Indices: 1257951--1257996 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1257941 ATTATAAGAG
1257951 TTAAAATATAATTTTATGATTTTA
1 TTAAAATATAATTTTAT-ATTTTA
**
1257975 TTAACTTATAATTTTATATTTT
1 TTAAAATATAATTTTATATTTT
1257997 TAAAGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAAAATATAATTTTATATTTTA
Found at i:1258027 original size:29 final size:28
Alignment explanation
Indices: 1257973--1258036 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1257963 TTTATGATTT
* *
1257973 TATTAACTTATAATTTTATATTTTTAAA
1 TATTAAATTAAAATTTTATATTTTTAAA
*
1258001 GTATTAAATTAAAATTTTATCA-TTTTAGA
1 -TATTAAATTAAAATTTTAT-ATTTTTAAA
1258030 TATTAAA
1 TATTAAA
1258037 ATCCTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTAAATTAAAATTTTATATTTTTAAA
Found at i:1263241 original size:31 final size:31
Alignment explanation
Indices: 1263203--1263264 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1263193 CAGGTTGCCT
1263203 GAGTTTGGTTACATTCATGCCGATTCATGTA
1 GAGTTTGGTTACATTCATGCCGATTCATGTA
1263234 GAGTTTGGTTACATTCATGCCGATTCATGTA
1 GAGTTTGGTTACATTCATGCCGATTCATGTA
1263265 CTTACTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (31 bp):
GAGTTTGGTTACATTCATGCCGATTCATGTA
Found at i:1263642 original size:54 final size:56
Alignment explanation
Indices: 1263577--1263686 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
1263567 TAGTGAACTG
1263577 AAGATCGATAAAAATTGACCATT-GG-ACACACACATAAATACATGCATGCATACA
1 AAGATCGATAAAAATTGACCATTGGGCACACACACATAAATACATGCATGCATACA
* *
1263631 AAGATCGATAAAAGTTGACCATTGGGCACACACACATAAATGCATGCATGCATACA
1 AAGATCGATAAAAATTGACCATTGGGCACACACACATAAATACATGCATGCATACA
1263687 TATATATACC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 22 0.42
55 2 0.04
56 28 0.54
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (56 bp):
AAGATCGATAAAAATTGACCATTGGGCACACACACATAAATACATGCATGCATACA
Found at i:1264937 original size:14 final size:14
Alignment explanation
Indices: 1264918--1264946 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1264908 GAATTAATTT
1264918 AGAAAATCTGTTCA
1 AGAAAATCTGTTCA
1264932 AGAAAATCTGTTCA
1 AGAAAATCTGTTCA
1264946 A
1 A
1264947 TCGTGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AGAAAATCTGTTCA
Found at i:1266263 original size:22 final size:22
Alignment explanation
Indices: 1266238--1266292 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1266228 TTAATTTTAA
*
1266238 TATTATGTA-TACTATTATATTT
1 TATTATCTATTACTATTATA-TT
*
1266260 TATTA-CTATTATTATTATATT
1 TATTATCTATTACTATTATATT
*
1266281 TATTATTTATTA
1 TATTATCTATTA
1266293 GCATTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATCTATTACTATTATATT
Found at i:1266298 original size:22 final size:22
Alignment explanation
Indices: 1266251--1266346 Score: 63
Period size: 22 Copynumber: 4.2 Consensus size: 22
1266241 TATGTATACT
* **
1266251 ATTATATTTTATTA-CTATTATT
1 ATTATA-TTTATTATTTATTAGC
1266273 ATTATATTTATTATTTATTAGC
1 ATTATATTTATTATTTATTAGC
**
1266295 ATTAGTA-TTATT-TTTACTTAAT
1 ATTA-TATTTATTATTTA-TTAGC
*
1266317 ACTTATATGTATATATTTATATAGC
1 A-TTATATTTAT-TATTTAT-TAGC
1266342 ATTAT
1 ATTAT
1266347 TAATAGTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
21 11 0.19
22 26 0.45
23 8 0.14
24 6 0.10
25 7 0.12
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTATATTTATTATTTATTAGC
Found at i:1266477 original size:23 final size:23
Alignment explanation
Indices: 1266451--1266514 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 23
1266441 ATGAACATAC
*
1266451 TTTTAATATTATTATGTATTTAT
1 TTTTAATATTATTATGTATATAT
1266474 TTTTAATATATATATATGTATATAT
1 TTTTAATAT-TAT-TATGTATATAT
1266499 TTATGTAATATTATTA
1 TT-T-TAATATTATTA
1266515 ATAGTTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 9 0.25
24 3 0.08
25 14 0.39
26 4 0.11
27 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTTAATATTATTATGTATATAT
Found at i:1266819 original size:24 final size:24
Alignment explanation
Indices: 1266785--1266843 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1266775 TTCTAATATG
1266785 TATATATTATGTA-A-ATATTTTAA
1 TATATATTATGTATACAT-TTTTAA
*
1266808 TACTATATTATGTATACATTTTTTA
1 TA-TATATTATGTATACATTTTTAA
1266833 TATATATTATG
1 TATATATTATG
1266844 AACATATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 2 0.06
24 20 0.62
25 8 0.25
26 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (24 bp):
TATATATTATGTATACATTTTTAA
Found at i:1267090 original size:22 final size:21
Alignment explanation
Indices: 1267044--1267087 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1267034 CCTAGTATAT
1267044 ATACTATGTATATATTTTTAA
1 ATACTATGTATATATTTTTAA
*
1267065 ATACTATATTATATATATTTTAA
1 ATACTAT-GTATATAT-TTTTAA
1267088 TACCGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
ATACTATGTATATATTTTTAA
Found at i:1267096 original size:22 final size:22
Alignment explanation
Indices: 1267052--1267096 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1267042 ATATACTATG
*
1267052 TATATATTTTTAAATACTATAT
1 TATATATTTTTAAATACCATAT
*
1267074 TATATATATTTT-AATACCGTAT
1 TATATAT-TTTTAAATACCATAT
1267096 T
1 T
1267097 TTGTACATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATATTTTTAAATACCATAT
Found at i:1267204 original size:19 final size:18
Alignment explanation
Indices: 1267180--1267222 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1267170 ACGTGTATAT
1267180 ATATATA-TATATACTTTTC
1 ATATATAGTAT-TA-TTTTC
*
1267199 ATATATAGTATTATTTTT
1 ATATATAGTATTATTTTC
1267217 ATATAT
1 ATATAT
1267223 CATTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATATAGTATTATTTTC
Found at i:1268307 original size:14 final size:15
Alignment explanation
Indices: 1268284--1268329 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1268274 TTTTGAGCAA
1268284 TTTAAT-TTTTTTCT
1 TTTAATGTTTTTTCT
*
1268298 TTT-ATGTTTTTTTT
1 TTTAATGTTTTTTCT
*
1268312 TTTAAATTTTTTTTCT
1 TTT-AATGTTTTTTCT
1268328 TT
1 TT
1268330 ATTTTCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.08
14 13 0.50
16 11 0.42
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTAATGTTTTTTCT
Found at i:1268330 original size:15 final size:16
Alignment explanation
Indices: 1268289--1268330 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1268279 AGCAATTTAA
*
1268289 TTTTTTTCTTT-TATG
1 TTTTTTTCTTTAAATG
*
1268304 TTTTTTTTTTTAAAT-
1 TTTTTTTCTTTAAATG
1268319 TTTTTTTCTTTA
1 TTTTTTTCTTTA
1268331 TTTTCCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTAAATG
Found at i:1271164 original size:2 final size:2
Alignment explanation
Indices: 1271159--1271195 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1271149 CCGTGTGTTT
1271159 TA 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 TA T
1271196 TGAACCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1278936 original size:2 final size:2
Alignment explanation
Indices: 1278925--1278957 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1278915 AAAATGACTA
*
1278925 AT AT AA 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 A
1278958 AAACCTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1286022 original size:43 final size:43
Alignment explanation
Indices: 1285975--1286063 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
1285965 TAATTTTTTA
1285975 AAAAAAAATCTATAACAAAGATAATTTAGTAAAATGTGCTTCT
1 AAAAAAAATCTATAACAAAGATAATTTAGTAAAATGTGCTTCT
1286018 AAAAAAAATCTATAACAAAGATAATTTAGTAAAATGTGCTTCT
1 AAAAAAAATCTATAACAAAGATAATTTAGTAAAATGTGCTTCT
1286061 AAA
1 AAA
1286064 TAATCTTACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (43 bp):
AAAAAAAATCTATAACAAAGATAATTTAGTAAAATGTGCTTCT
Found at i:1291429 original size:22 final size:24
Alignment explanation
Indices: 1291404--1291449 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1291394 TAGTTTTTAA
*
1291404 TCGTA-AAA-ATTGATAATTTTTT
1 TCGTATAAAGATTAATAATTTTTT
*
1291426 TCGTATAAAGATTAATTATTTTTT
1 TCGTATAAAGATTAATAATTTTTT
1291450 AATGAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 12 0.60
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (24 bp):
TCGTATAAAGATTAATAATTTTTT
Found at i:1295796 original size:47 final size:47
Alignment explanation
Indices: 1295732--1295842 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
1295722 GACATTGAGT
*
1295732 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
1295779 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
1295826 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
1295843 CTTATCCAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:1310870 original size:14 final size:14
Alignment explanation
Indices: 1310851--1310890 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
1310841 TTAGATTTGA
1310851 TTTTTATATTTAAT
1 TTTTTATATTTAAT
*
1310865 TTTTTAAAATTTAAT
1 TTTTT-ATATTTAAT
1310880 TTTTTATATTT
1 TTTTTATATTT
1310891 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTATATTTAAT
Found at i:1310892 original size:9 final size:8
Alignment explanation
Indices: 1310859--1310925 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
1310849 GATTTTTATA
1310859 TTTAATTT
1 TTTAATTT
**
1310867 TTTAA-AA
1 TTTAATTT
1310874 TTTAATTT
1 TTTAATTT
1310882 TTTATATTTTT
1 TTTA-A--TTT
1310893 TTTAATTT
1 TTTAATTT
*
1310901 GTTAA--T
1 TTTAATTT
1310907 TTTAATTT
1 TTTAATTT
1310915 TTTATATTT
1 TTTA-ATTT
1310924 TT
1 TT
1310926 CGAATTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
6 5 0.11
7 5 0.11
8 21 0.46
9 7 0.15
10 1 0.02
11 7 0.15
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTAATTT
Found at i:1310916 original size:33 final size:34
Alignment explanation
Indices: 1310859--1310925 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
1310849 GATTTTTATA
*
1310859 TTTAATTTTTTAAAATTTAATTTTTTATATTTTT
1 TTTAATTTGTTAAAATTTAATTTTTTATATTTTT
*
1310893 TTTAATTTGTT-AATTTTAATTTTTTATATTTTT
1 TTTAATTTGTTAAAATTTAATTTTTTATATTTTT
1310926 CGAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (34 bp):
TTTAATTTGTTAAAATTTAATTTTTTATATTTTT
Found at i:1310923 original size:15 final size:15
Alignment explanation
Indices: 1310851--1310924 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 15
1310841 TTAGATTTGA
1310851 TTTTTATA-TTTAAT
1 TTTTTATATTTTAAT
* *
1310865 TTTTTAAAATTTAAT
1 TTTTTATATTTTAAT
1310880 TTTTTATATTTTTTTTAAT
1 TTTTTATA----TTTTAAT
*
1310899 TTGTTA-ATTTTAAT
1 TTTTTATATTTTAAT
1310913 TTTTTATATTTT
1 TTTTTATATTTT
1310925 TCGAATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.39
15 18 0.37
18 1 0.02
19 11 0.22
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (15 bp):
TTTTTATATTTTAAT
Found at i:1310940 original size:32 final size:33
Alignment explanation
Indices: 1310866--1310944 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
1310856 ATATTTAATT
**
1310866 TTTTAAAA-TTTAATTTTTTATATTTTTTTTAA
1 TTTTAAAATTTTAATTTTTTATATTTTTTCGAA
*
1310898 TTTGT-TAATTTTAATTTTTTATA-TTTTTCGAA
1 TTT-TAAAATTTTAATTTTTTATATTTTTTCGAA
1310930 TTTTAAAATTTTAAT
1 TTTTAAAATTTTAAT
1310945 GCTGACTCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.03
32 24 0.60
33 15 0.38
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (33 bp):
TTTTAAAATTTTAATTTTTTATATTTTTTCGAA
Found at i:1311031 original size:30 final size:30
Alignment explanation
Indices: 1310995--1311055 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1310985 TCAATTATTA
1310995 ATTTAGTAATATACGTGCAGTTATAGATAT
1 ATTTAGTAATATACGTGCAGTTATAGATAT
1311025 ATTTAGTAATATACGTGCAGTTATAGATAT
1 ATTTAGTAATATACGTGCAGTTATAGATAT
1311055 A
1 A
1311056 CTCTATATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
ATTTAGTAATATACGTGCAGTTATAGATAT
Found at i:1311785 original size:16 final size:17
Alignment explanation
Indices: 1311761--1311793 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1311751 TATCTTTGTC
*
1311761 TTTATTTATTTATTTTA
1 TTTATTTATTAATTTTA
1311778 TTTA-TTATTAATTTTA
1 TTTATTTATTAATTTTA
1311794 AAATACTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATTAATTTTA
Found at i:1311875 original size:12 final size:12
Alignment explanation
Indices: 1311858--1311900 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1311848 TAAATAAATA
1311858 TTTTAAATTATT
1 TTTTAAATTATT
*
1311870 TTTTAAA-AATT
1 TTTTAAATTATT
**
1311881 TTAAAAATTATT
1 TTTTAAATTATT
1311893 TTTTAAAT
1 TTTTAAAT
1311901 ATTAAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAATTATT
Found at i:1311881 original size:21 final size:21
Alignment explanation
Indices: 1311852--1311915 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1311842 AAATTTTAAA
*
1311852 TAAATATTTTAAATTATTTTT
1 TAAAAATTTTAAATTATTTTT
1311873 TAAAAATTTTAAAAATTATTTTT
1 TAAAAATTTT--AAATTATTTTT
*
1311896 T--AAATATTAAATATATTTTT
1 TAAAAATTTTAAAT-TATTTTT
1311916 AATAATATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.11
20 7 0.18
21 15 0.39
23 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAAATTTTAAATTATTTTT
Found at i:1311922 original size:21 final size:21
Alignment explanation
Indices: 1311869--1311954 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
1311859 TTTAAATTAT
* *
1311869 TTTTTAAAAATTTTAAAAATTA
1 TTTTTAATAATATTAAAAA-TA
* *
1311891 TTTTTTA-AATATTAAATATA
1 TTTTTAATAATATTAAAAATA
* * *
1311911 TTTTTAATAATATGAAACATT
1 TTTTTAATAATATTAAAAATA
1311932 TTTTTAATTAA-ATTAAAAATA
1 TTTTTAA-TAATATTAAAAATA
1311953 TT
1 TT
1311955 AATTCTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
20 8 0.15
21 35 0.67
22 9 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTTTAATAATATTAAAAATA
Found at i:1312117 original size:16 final size:15
Alignment explanation
Indices: 1312090--1312130 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1312080 TCTTTAAAAT
1312090 TAATTTTAAAATTAA
1 TAATTTTAAAATTAA
1312105 TAATTTATAAAATT-A
1 TAATTT-TAAAATTAA
1312120 T-A-TTTAAAATT
1 TAATTTTAAAATT
1312131 TAAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.28
13 2 0.08
14 1 0.04
15 8 0.32
16 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTTTAAAATTAA
Found at i:1312129 original size:12 final size:13
Alignment explanation
Indices: 1312077--1312130 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 13
1312067 AAATGTTTGA
1312077 ATATCTTTAAAATT
1 ATAT-TTTAAAATT
1312091 A-ATTTTAAAATT
1 ATATTTTAAAATT
1312103 AATAATTTATAAAATT
1 -AT-ATTT-TAAAATT
1312119 ATA-TTTAAAATT
1 ATATTTTAAAATT
1312131 TAAAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 16 0.44
13 5 0.14
14 2 0.06
15 6 0.17
16 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTTTAAAATT
Found at i:1312141 original size:18 final size:19
Alignment explanation
Indices: 1312112--1312147 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1312102 TAATAATTTA
1312112 TAAAATTATATTTAAAATT
1 TAAAATTATATTTAAAATT
1312131 TAAAA-TATATTTAAAAT
1 TAAAATTATATTTAAAAT
1312148 ATTATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTATATTTAAAATT
Found at i:1312248 original size:21 final size:21
Alignment explanation
Indices: 1312222--1312261 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1312212 TAAAAATCAT
1312222 AATTT-AAAATATTATAAAACA
1 AATTTAAAAATATT-TAAAACA
1312243 AATTTAAAAATATTTAAAA
1 AATTTAAAAATATTTAAAA
1312262 TTTAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTTAAAAATATTTAAAACA
Found at i:1312360 original size:22 final size:21
Alignment explanation
Indices: 1312332--1312397 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
1312322 AAGATATTTA
1312332 AATATTTTATATTATTTAAAAAT
1 AATATTTTA-A-TATTTAAAAAT
1312355 -ATA-TTTAATATTTAAAAAT
1 AATATTTTAATATTTAAAAAT
* *
1312374 AATA-TTTAAAATTAAAAAAAT
1 AATATTTTAATATT-TAAAAAT
1312395 AAT
1 AAT
1312398 TTCAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 11 0.28
20 12 0.31
21 13 0.33
22 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATTTTAATATTTAAAAAT
Found at i:1312368 original size:19 final size:19
Alignment explanation
Indices: 1312331--1312391 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
1312321 TAAGATATTT
1312331 AAATAT-TTTATATTATTTAA
1 AAATATATTTA-A-TATTTAA
1312351 AAATATATTTAATATTTAA
1 AAATATATTTAATATTTAA
*
1312370 AAATAATATTTAA-AATTAA
1 AAAT-ATATTTAATATTTAA
1312389 AAA
1 AAA
1312392 AATAATTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 19 0.50
20 15 0.39
21 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATATTTAATATTTAA
Found at i:1312378 original size:13 final size:13
Alignment explanation
Indices: 1312360--1312384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312350 AAAATATATT
1312360 TAATATTTAAAAA
1 TAATATTTAAAAA
1312373 TAATATTTAAAA
1 TAATATTTAAAA
1312385 TTAAAAAAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:1312399 original size:19 final size:19
Alignment explanation
Indices: 1312349--1312404 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
1312339 TATATTATTT
*
1312349 AAAAATATATTTAATATTTAA
1 AAAAATA-ATTTAA-AATTAA
1312370 AAATAAT-ATTTAAAATTAA
1 AAA-AATAATTTAAAATTAA
1312389 AAAAATAATTTCAAAA
1 AAAAATAATTT-AAAA
1312405 ATATATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 12 0.39
20 10 0.32
21 3 0.10
22 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATAATTTAAAATTAA
Found at i:1312426 original size:135 final size:134
Alignment explanation
Indices: 1312125--1312426 Score: 318
Period size: 135 Copynumber: 2.2 Consensus size: 134
1312115 AATTATATTT
*
1312125 AAAATTTAAAATATAT-TTAAAATATTATAAATCAAGTAATAAATTTGAAAGGTCATATCTTTAA
1 AAAATTTAAAATATATATTAAAATATTATAAAACAAGTAATAAATTTGAAAGGTCATATCTTTAA
1312189 AAATAATATATCTTTGAATAATTTAAAAATCATAATTTAAAATATTATAAAACAAATTTAAAAAT
66 AAATAATATATCTTTGAATAATTTAAAAATCATAATTTAAAATATTATAAAACAAATTTAAAAAT
***
1312254 ATTT
131 AAAA
* * * *
1312258 AAAATTTAAAATGTACATTTAAAATATTATAAAACTAGTAATAAATTTGAAATGTCATATCTTTA
1 AAAATTTAAAATATATA-TTAAAATATTATAAAACAAGTAATAAATTTGAAAGGTCATATCTTTA
* * * *
1312323 AGATATTTAA-ATAT-TTT-ATATTATTTAAAAAT-AT-ATTTAATAT-TTA-AAAATAATATTT
65 A-A-A-ATAATATATCTTTGA-ATAATTTAAAAATCATAATTTAAAATATTATAAAACAA-ATTT
*
1312381 AAAATTAAAAA
125 AAAAAT-AAAA
1312392 AATAATTTCAAAAATATATATATAAAAT-TT-TAAAA
1 AA-AATTT--AAAATATATAT-TAAAATATTATAAAA
1312427 TATATATATT
Statistics
Matches: 142, Mismatches: 15, Indels: 22
0.79 0.08 0.12
Matches are distributed among these distances:
132 6 0.04
133 26 0.18
134 11 0.08
135 58 0.41
136 19 0.13
137 19 0.13
138 3 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (134 bp):
AAAATTTAAAATATATATTAAAATATTATAAAACAAGTAATAAATTTGAAAGGTCATATCTTTAA
AAATAATATATCTTTGAATAATTTAAAAATCATAATTTAAAATATTATAAAACAAATTTAAAAAT
AAAA
Found at i:1312433 original size:25 final size:25
Alignment explanation
Indices: 1312396--1312458 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1312386 TAAAAAAATA
1312396 ATTTCAAAA-ATATATA-TATAAAA-
1 ATTT-AAAATATATATATTATAAAAC
*
1312419 TTTTAAAATATATATATTATAAAAC
1 ATTTAAAATATATATATTATAAAAC
*
1312444 ATTTCAAATATATAT
1 ATTTAAAATATATAT
1312459 TTCAAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.12
23 10 0.29
24 7 0.21
25 13 0.38
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTTAAAATATATATATTATAAAAC
Found at i:1312459 original size:23 final size:22
Alignment explanation
Indices: 1312395--1312459 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
1312385 TTAAAAAAAT
*
1312395 AATTTCAAAAATATATATATAAA
1 AATTTCAAATATATAT-TATAAA
* *
1312418 ATTTTAAAATATATATATTATAAA
1 AATTT-CAA-ATATATATTATAAA
1312442 ACATTTCAAATATATATT
1 A-ATTTCAAATATATATT
1312460 TCAAGTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 13 0.38
24 11 0.32
25 10 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTCAAATATATATTATAAA
Found at i:1314970 original size:31 final size:31
Alignment explanation
Indices: 1314932--1314992 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1314922 TTGGGCCCAT
1314932 GCCTAGAAAACATGTCTAAAATTCTGCATAG
1 GCCTAGAAAACATGTCTAAAATTCTGCATAG
1314963 GCCTAGAAAACATGTCTAAAATTCTGCATA
1 GCCTAGAAAACATGTCTAAAATTCTGCATA
1314993 AGCCCGACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (31 bp):
GCCTAGAAAACATGTCTAAAATTCTGCATAG
Found at i:1317344 original size:54 final size:54
Alignment explanation
Indices: 1317283--1317389 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
1317273 ATATGTCTCG
*
1317283 ACTTGAAATATAAGTTTAATATTTTACCAAAATTTATCGATATATACACAACTA
1 ACTTGAAATATAAGTTTAATATTTTACCAAAATTTATCCATATATACACAACTA
*
1317337 ACTTGAAATATAAGTTTAATATTTTACCAAAATTTATCCATATGTACACAACT
1 ACTTGAAATATAAGTTTAATATTTTACCAAAATTTATCCATATATACACAACT
1317390 GTGAGTAGGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (54 bp):
ACTTGAAATATAAGTTTAATATTTTACCAAAATTTATCCATATATACACAACTA
Found at i:1319738 original size:3 final size:3
Alignment explanation
Indices: 1319730--1319906 Score: 180
Period size: 3 Copynumber: 58.7 Consensus size: 3
1319720 TGATAGTGAC
1319730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
1319778 AAT AAT AGT TAT AAGA AAT AAT ACT AGT AGT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1319824 -AT ACAT AAC AAT -AT ATT CAT GAGA- AAT AAC AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT -A-AT AAT AAT AAT AAT AAT AAT AAT
* *
1319869 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1319907 CATTGATAAT
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
2 5 0.03
3 133 0.92
4 5 0.03
5 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1320095 original size:15 final size:14
Alignment explanation
Indices: 1320077--1320127 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
1320067 AAAACGGAAA
1320077 TGATAATATTAATAT
1 TGATAATA-TAATAT
*
1320092 TGATAATA-AATAA
1 TGATAATATAATAT
*
1320105 TAATAATATAAATAT
1 TGATAATAT-AATAT
1320120 TGATAATA
1 TGATAATA
1320128 ATAGAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
TGATAATATAATAT
Found at i:1320137 original size:28 final size:28
Alignment explanation
Indices: 1320079--1320140 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1320069 AACGGAAATG
* *
1320079 ATAATATTAATATTGATAATAAATAATA
1 ATAATATAAATATTGATAATAAATAAAA
1320107 ATAATATAAATATTGATAAT-AATAGAAA
1 ATAATATAAATATTGATAATAAATA-AAA
1320135 ATAATA
1 ATAATA
1320141 ATGTTAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
ATAATATAAATATTGATAATAAATAAAA
Found at i:1320733 original size:106 final size:107
Alignment explanation
Indices: 1320592--1320807 Score: 425
Period size: 106 Copynumber: 2.0 Consensus size: 107
1320582 GTCATCCCCA
1320592 AAACGACGTCGTTTTGGGGCGTTTCAGGCCATTCCAAAACTACGCCGTTTTAATGCCCTATTTAA
1 AAACGACGTCGTTTTGGGGCGTTTCAGGCCATTCCAAAACTACGCCGTTTTAATGCCCTATTTAA
1320657 GCTAA-TTTTTTTTAAAAAAAATTCATTTCTCTCATTCATTT
66 GCTAATTTTTTTTTAAAAAAAATTCATTTCTCTCATTCATTT
1320698 AAACGACGTCGTTTTGGGGCGTTTCAGGCCATTCCAAAACTACGCCGTTTTAATGCCCTATTTAA
1 AAACGACGTCGTTTTGGGGCGTTTCAGGCCATTCCAAAACTACGCCGTTTTAATGCCCTATTTAA
1320763 GCTAATTTTTTTTTAAAAAAAATTCATTTCTCTCATTCATTT
66 GCTAATTTTTTTTTAAAAAAAATTCATTTCTCTCATTCATTT
1320805 AAA
1 AAA
1320808 AAAAAAAACA
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 70 0.64
107 39 0.36
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (107 bp):
AAACGACGTCGTTTTGGGGCGTTTCAGGCCATTCCAAAACTACGCCGTTTTAATGCCCTATTTAA
GCTAATTTTTTTTTAAAAAAAATTCATTTCTCTCATTCATTT
Found at i:1322895 original size:17 final size:17
Alignment explanation
Indices: 1322869--1322918 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1322859 TAGCTTGTAT
*
1322869 TAGTAAACGAATCTAAC
1 TAGTAGACGAATCTAAC
*
1322886 TAGTAGACGAATCTAAT
1 TAGTAGACGAATCTAAC
1322903 TAGTAGACGAATCTAA
1 TAGTAGACGAATCTAA
1322919 ACATGTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (17 bp):
TAGTAGACGAATCTAAC
Found at i:1323210 original size:40 final size:40
Alignment explanation
Indices: 1323155--1323235 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
1323145 ACATATCTAA
* *
1323155 ATCCTAAGTGGATAACATGCTATATATACATGACTCGTAT
1 ATCCTAAGTAGATAACAGGCTATATATACATGACTCGTAT
1323195 ATCCTAAGTAGATAACAGGCTATATATACATGACTCGTAT
1 ATCCTAAGTAGATAACAGGCTATATATACATGACTCGTAT
1323235 A
1 A
1323236 ATTTGATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (40 bp):
ATCCTAAGTAGATAACAGGCTATATATACATGACTCGTAT
Found at i:1324991 original size:30 final size:30
Alignment explanation
Indices: 1324956--1325015 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1324946 TATTTTATTA
*
1324956 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* *
1324986 TTAATTTTATTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
1325016 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:1329825 original size:8 final size:9
Alignment explanation
Indices: 1329797--1329825 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1329787 TAATTCCAAC
1329797 ATGTTGATA
1 ATGTTGATA
1329806 ATGTTGATA
1 ATGTTGATA
1329815 ATGTT-ATA
1 ATGTTGATA
1329823 ATG
1 ATG
1329826 ATTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATGTTGATA
Found at i:1332913 original size:261 final size:263
Alignment explanation
Indices: 1332321--1333291 Score: 1499
Period size: 261 Copynumber: 3.7 Consensus size: 263
1332311 TAATGCTAAA
* * *
1332321 CAGGTGTTATTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTG
1 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGCGCTATCCCTATTCCCCCGAATCCGGTTTTCTTCG
** *
1332386 GACCGATTTCGGCGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTATATTGAC-A
66 GACCGATTTCGGCGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAA
* *
1332450 ATGCTTTAAATTGGATATGTATATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTG
131 ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATGTGTGTGTG
1332515 ATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCC
196 ATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCC
1332580 TAG
261 TAG
* * * * *
1332583 CA-GTGATGTTGGACTTTAGTCTCTTAAATGTCCCTAT-TCTATT--CCCTAATCCGGTTTTCTT
1 CAGGTGTTGTTGTACTTTAGTCTCTTAAA-G-CGCTATCCCTATTCCCCCGAATCCGGTTTTCTT
*
1332644 CGGACCGATTTCGGGGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGAC
64 CGGACCGATTTCGGCGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGAC
*
1332709 AAATGCTTTAAAATGGATATGTACATTCAGCTGTGAGAATGCATACATTTA-TT-TATGTGTGTG
129 AAATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATGTGTGTG
*
1332772 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCTCTGATCTCCATGCTTGTTT
194 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTT
1332837 CCTAG
259 CCTAG
* * * *
1332842 CAGGTGTTGTTGTACTTTAATCTCTTAAAGCGCTATCCCTGTTCCCCCTAATCCGGTTTTCTTCA
1 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGCGCTATCCCTATTCCCCCGAATCCGGTTTTCTTCG
* * * *
1332907 GACCGATTTTGGGGATGAATCAGAACTCTTTGTTACCTTGAAAATAAAAATTATTATATTGACAA
66 GACCGATTTCGGCGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAA
*
1332972 ATGCTTTAAATTGGATATGTACGTTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTG
131 ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTA-TT-TATATGTGTGTG
* *
1333037 TGATGCAATGCTGCTATGTTCGTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTT
194 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTT
1333102 CCTAG
259 CCTAG
* * * *
1333107 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCTCCGAATTCGGTTTTCTTTG
1 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGCGCTATCCCTATTCCCCCGAATCCGGTTTTCTTCG
* * * * * *
1333172 GACTGATTTCGTCAATAAATC-GAACTCTTTGTTACCTTGAAAAAAAATAATATTACATTGACAA
66 GACCGATTTCGGCGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAA
* *
1333236 ATGTTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATAT
131 ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATAT
1333292 TGACAAATGC
Statistics
Matches: 646, Mismatches: 52, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
258 5 0.01
259 85 0.13
260 102 0.16
261 199 0.31
262 13 0.02
263 7 0.01
264 86 0.13
265 149 0.23
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (263 bp):
CAGGTGTTGTTGTACTTTAGTCTCTTAAAGCGCTATCCCTATTCCCCCGAATCCGGTTTTCTTCG
GACCGATTTCGGCGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAA
ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATGTGTGTGTG
ATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCC
TAG
Found at i:1333325 original size:62 final size:62
Alignment explanation
Indices: 1333228--1333353 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
1333218 ATAATATTAC
*
1333228 ATTGACAAATGTTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTAT
1 ATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTAT
1333290 ATTGACAAATGCTTTAAATTGGATATGTACG-TTCAGCTGTGAGAATGCATACATTTATTTAT
1 ATTGACAAATGCTTTAAATTGGATATGTA-GATTCAGCTGTGAGAATGCATACATTTATTTAT
1333352 AT
1 AT
1333354 ATGTGTGTGA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 61 0.98
63 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (62 bp):
ATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTAT
Found at i:1333757 original size:263 final size:263
Alignment explanation
Indices: 1333290--1334111 Score: 1299
Period size: 263 Copynumber: 3.1 Consensus size: 263
1333280 ATTTATTTAT
1333290 ATTGACAAATGCTTTAAATTGGATATGTACGTTCAGCTGTGAGAATGCATACATTTATTTATATA
1 ATTGACAAATGCTTTAAATTGGATATGTACGTTCAGCTGTGAGAATGCATACATTTATTTATATA
1333355 TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGC
66 TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGC
1333420 TTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCTG-CCGAATC
131 TTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTC-GCCCGAATC
* *
1333484 CGGTTTTCTTTGGACTGATTTCGGCAATAAATCGGAACTCTTTGTTACCTTGAAAAAAAATAATA
195 CAGTTTTCTTTGGACTGATTTCGGCGATAAATCGGAACTCTTTGTTACCTTGAAAAAAAATAATA
1333549 TTAC
260 TTAC
* *
1333553 ATTGACAAATGTTTTAAATTGGATATGTA-GATTCAGCTGTGAGAATGGATACATTTATTTATAT
1 ATTGACAAATGCTTTAAATTGGATATGTACG-TTCAGCTGTGAGAATGCATACATTTATTTATAT
* *
1333617 GTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTTGCCCCCGATCTCCATG
65 ATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATG
* * * *
1333682 CTTGTTTCCTAGCAGGTGTTATTGTACTTTAGTTTCTTAAAGTGCTATCCGTATTCGCCCTAATC
130 CTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCGCCCGAATC
* * ** *
1333747 CTGTTTTCTTTGGACTGATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAGGAATATTA
195 CAGTTTTCTTTGGACTGATTTCGGCGATAAATCGGAACTCTTTGTTACCTTGAAAAAAAATAATA
1333812 TTAC
260 TTAC
* * *
1333816 ATTGACAAATGCTTTAAATTGGATATATACGTTCAGCTGTGAGAATGCATACATTTCTTTACATA
1 ATTGACAAATGCTTTAAATTGGATATGTACGTTCAGCTGTGAGAATGCATACATTTATTTATATA
* *
1333881 TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTGCATGC
66 TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGC
* * *
1333946 TTGTTTCCTTGCAAGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
131 TTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCGCCCGAATCC
* * * *
1334011 AGTTTTCTTTGGACCGATTTCGACGATAAATTGGAATTCTTTGTTACCTT-AAAGAAAATATTAT
196 AGTTTTCTTTGGACTGATTTCGGCGATAAATCGGAACTCTTTGTTACCTTGAAA-AAAA-A-TA-
1334075 TTATCATTAC
257 --AT-ATTAC
1334085 ATTGACAAATGCTTTAAATTGGATATG
1 ATTGACAAATGCTTTAAATTGGATATG
1334112 CTGCTTTTTT
Statistics
Matches: 509, Mismatches: 40, Indels: 14
0.90 0.07 0.02
Matches are distributed among these distances:
262 5 0.01
263 468 0.92
264 2 0.00
265 2 0.00
268 1 0.00
269 31 0.06
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (263 bp):
ATTGACAAATGCTTTAAATTGGATATGTACGTTCAGCTGTGAGAATGCATACATTTATTTATATA
TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGC
TTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCGCCCGAATCC
AGTTTTCTTTGGACTGATTTCGGCGATAAATCGGAACTCTTTGTTACCTTGAAAAAAAATAATAT
TAC
Found at i:1337312 original size:16 final size:17
Alignment explanation
Indices: 1337281--1337313 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1337271 TTCATAAGTA
1337281 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
1337298 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
1337314 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:1337660 original size:46 final size:46
Alignment explanation
Indices: 1337576--1337745 Score: 218
Period size: 46 Copynumber: 3.7 Consensus size: 46
1337566 TCCCATCCAC
* * * * * *
1337576 GGTCTTATTTATTTT-TGACATGATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
*
1337621 GGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
* *
1337667 GGTCTTATTCA-TTTCATGTCACGCTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
* *
1337713 GGTCTTATTCATTTCCCGTCATGTTGCCATGGT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGT
1337746 TGTAGAAGCC
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
45 17 0.16
46 88 0.81
47 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.43
Consensus pattern (46 bp):
GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
Found at i:1338976 original size:3 final size:3
Alignment explanation
Indices: 1338970--1339202 Score: 60
Period size: 3 Copynumber: 78.0 Consensus size: 3
1338960 TTAAGTTTTT
* * * *
1338970 TTA TTA TATA TTG CTA TTA TT- TATA TTA TTA CTA TTA CTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * * *
1339016 TTA TT- TATA TTA TTA TTA -TG TTA -TA TTTA GTA TTA TTT TTA ATA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * *
1339060 TTA -CA TT- TTT TTA CTA TTA -TA TTA CTA TTA TCT- TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * **
1339101 TTC TCTA TTA ATA TTTA TTA CTCTA TTT TTA ACA TTA TTA TTA -TA TTA
1 TTA T-TA TTA TTA -TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1339149 -TA TT- TGTT TTT TTA -TA CCTTA TTA TTA TTG CTA GTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA --TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1339194 TCA TTA TTA
1 TTA TTA TTA
1339203 ACACATATAA
Statistics
Matches: 165, Mismatches: 40, Indels: 50
0.65 0.16 0.20
Matches are distributed among these distances:
2 20 0.12
3 126 0.76
4 15 0.09
5 4 0.02
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1338996 original size:15 final size:15
Alignment explanation
Indices: 1338970--1339194 Score: 90
Period size: 15 Copynumber: 14.3 Consensus size: 15
1338960 TTAAGTTTTT
**
1338970 TTATTATATATTGCTA
1 TTATT-TATATTATTA
1338986 TTATTTATATTATTA
1 TTATTTATATTATTA
*
1339001 CTA-TTACTATTATTA
1 TTATTTA-TATTATTA
1339016 TTATTTATATTATTA
1 TTATTTATATTATTA
*
1339031 TTATGTTATATTTAGTA
1 TTAT-TTATA-TTATTA
* *
1339048 TTATTTTTAATATTA
1 TTATTTATATTATTA
* * *
1339063 -CATTT-TTTTACTA
1 TTATTTATATTATTA
1339076 TTATATTACTATTATCT-
1 TTAT-TTA-TATTAT-TA
* *
1339093 TTA-TTATTTTCTCTA
1 TTATTTATATTAT-TA
1339108 TTAATATT-TATTACTCTA
1 TT-AT-TTATATTA-T-TA
*
1339126 TT-TTTAACATTATTA
1 TTATTT-ATATTATTA
1339141 TTATATTATATT-TGT-
1 TTAT-TTATATTAT-TA
*
1339156 TTTTTTATACCTTATTA
1 TTATTTATA--TTATTA
1339173 TTATTGCTAGTATTATTA
1 TTATT--TA-TATTATTA
1339191 TTAT
1 TTAT
1339195 CATTATTAAC
Statistics
Matches: 160, Mismatches: 23, Indels: 50
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.03
14 20 0.12
15 53 0.33
16 29 0.18
17 30 0.19
18 19 0.12
19 2 0.01
20 2 0.01
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTTATATTATTA
Found at i:1339493 original size:23 final size:23
Alignment explanation
Indices: 1339450--1339494 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1339440 CATACATACT
* *
1339450 TTTTTAATATTATTATGTATTTC
1 TTTTAAATATTATTATATATTTC
1339473 TTTTAAATA-TATGTATATATTT
1 TTTTAAATATTAT-TATATATTT
1339495 ATGTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTAAATATTATTATATATTTC
Found at i:1340287 original size:46 final size:46
Alignment explanation
Indices: 1340220--1340351 Score: 228
Period size: 46 Copynumber: 2.9 Consensus size: 46
1340210 CGTCGCTATA
** *
1340220 ATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGTTGCC
1 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGAC
*
1340266 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGAT
1 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGAC
1340312 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1340352 AGAGCACACT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (46 bp):
ATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGAC
Found at i:1341083 original size:7 final size:7
Alignment explanation
Indices: 1341071--1341095 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1341061 ATTATTATAT
1341071 TATATTA
1 TATATTA
1341078 TATATTA
1 TATATTA
1341085 TATATTA
1 TATATTA
1341092 TATA
1 TATA
1341096 AATAAGTAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:1342368 original size:15 final size:15
Alignment explanation
Indices: 1342348--1342410 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
1342338 TATGCGATGA
1342348 ATTTATTGAATTTAT
1 ATTTATTGAATTTAT
*
1342363 ATTTATTGAAATTAT
1 ATTTATTGAATTTAT
1342378 -TTTGATTGAATTTAT
1 ATTT-ATTGAATTTAT
*
1342393 ATTGATTGAATTATAT
1 ATTTATTGAATT-TAT
1342409 AT
1 AT
1342411 ATATATGACT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 3 0.07
15 32 0.76
16 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (15 bp):
ATTTATTGAATTTAT
Found at i:1342808 original size:23 final size:23
Alignment explanation
Indices: 1342778--1342864 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
1342768 GCTTTATCGA
1342778 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
1342801 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATT
1342822 TCAGGCA---TATCGTGT-GTCATT
1 TCAGGCACTTTAT-GTGTCGT-ATT
*
1342843 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
1342865 ACTGATCAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
18 3 0.06
19 5 0.10
21 13 0.26
23 24 0.48
24 5 0.10
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:1342825 original size:21 final size:22
Alignment explanation
Indices: 1342790--1342839 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1342780 AGGCACTTTA
*
1342790 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACATCG
*
1342813 TGTGTCGTA-TCAGGCATATCG
1 TGTGTCGTATTCAGGCACATCG
1342834 TGTGTC
1 TGTGTC
1342840 ATTTTAGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.64
23 9 0.36
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACATCG
Found at i:1343416 original size:36 final size:36
Alignment explanation
Indices: 1343314--1343417 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
1343304 TAAGGTATAA
* * *
1343314 AATAACTGATTATTACTGAATAATTGACTGTTACTG
1 AATAACTGATTATTACTGAATAATTAATTGTTACCG
* * *
1343350 AATAACTGGTTATTACTGAATATTTTATTGTTACCG
1 AATAACTGATTATTACTGAATAATTAATTGTTACCG
* * *
1343386 AATAACTGACTGTTACTGAATAAATAATTGTT
1 AATAACTGATTATTACTGAATAATTAATTGTT
1343418 CTGAGAGTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAATTAATTGTTACCG
Found at i:1343417 original size:18 final size:18
Alignment explanation
Indices: 1343314--1343421 Score: 101
Period size: 18 Copynumber: 6.1 Consensus size: 18
1343304 TAAGGTATAA
*
1343314 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* *
1343332 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
1343350 AATAACTGGTTATTACTG
1 AATAACTGATTGTTACTG
** * *
1343368 AATATTTTATTGTTACCG
1 AATAACTGATTGTTACTG
*
1343386 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
1343404 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
1343421 A
1 A
1343422 GAGTTAATGA
Statistics
Matches: 69, Mismatches: 21, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
17 4 0.06
18 65 0.94
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:1348787 original size:15 final size:15
Alignment explanation
Indices: 1348767--1348828 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
1348757 TATGCGATGA
1348767 ATTTATTGAATTTAT
1 ATTTATTGAATTTAT
*
1348782 ATTTATTGAAATTAT
1 ATTTATTGAATTTAT
1348797 -TTTGATTGAATTTAT
1 ATTT-ATTGAATTTAT
*
1348812 ATTGATTGAATTCTAT
1 ATTTATTGAATT-TAT
1348828 A
1 A
1348829 ATATATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 3 0.07
15 32 0.78
16 6 0.15
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTTATTGAATTTAT
Found at i:1349226 original size:23 final size:23
Alignment explanation
Indices: 1349200--1349286 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
1349190 GCTTTATTGA
*
1349200 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* *
1349223 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTCATGTGTCGTATT
* *
1349244 TCAGGCACATCGTGTGTC--ATT
1 TCAGGCACTTCATGTGTCGTATT
* *
1349265 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTCATGTGTCGTAT
1349287 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
21 31 0.60
23 20 0.38
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACTTCATGTGTCGTATT
Found at i:1349838 original size:36 final size:36
Alignment explanation
Indices: 1349736--1349839 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
1349726 TAAGGTATAA
* *
1349736 AATAACTGATTATTACTGAATAATTGACTGTTACTG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* *
1349772 AATAACTGGTTATTACTGAATATTTGATTGTTACCG
1 AATAACTGATTATTACTGAATAATTGATTGTTACCG
* * * *
1349808 AATAACTGACTGTTACTGAATAAATAATTGTT
1 AATAACTGATTATTACTGAATAATTGATTGTT
1349840 CTGAGAGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAATTGATTGTTACCG
Found at i:1349839 original size:18 final size:18
Alignment explanation
Indices: 1349736--1349843 Score: 110
Period size: 18 Copynumber: 6.1 Consensus size: 18
1349726 TAAGGTATAA
*
1349736 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* *
1349754 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
1349772 AATAACTGGTTATTACTG
1 AATAACTGATTGTTACTG
** *
1349790 AATATTTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
1349808 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
1349826 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
1349843 A
1 A
1349844 GAGTTAATGA
Statistics
Matches: 71, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
17 4 0.06
18 67 0.94
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:1354000 original size:12 final size:12
Alignment explanation
Indices: 1353983--1354027 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
1353973 GCGATTTTTA
1353983 TTATTATTATAT
1 TTATTATTATAT
1353995 TTATTATATATAT
1 TTATTAT-TATAT
1354008 TTATTTATT-TAT
1 TTA-TTATTATAT
1354020 TTATTATT
1 TTATTATT
1354028 TCTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.16
12 13 0.42
13 9 0.29
14 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:1354012 original size:4 final size:4
Alignment explanation
Indices: 1353986--1354042 Score: 57
Period size: 4 Copynumber: 14.5 Consensus size: 4
1353976 ATTTTTATTA
* *
1353986 TTAT TATAT TTAT TATAT ATAT TTAT TTAT TTAT TTA- TTAT TTCT TT-T
1 TTAT T-TAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1354034 TT-T TTAT TT
1 TTAT TTAT TT
1354043 TTTGATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
3 9 0.20
4 30 0.65
5 7 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1360240 original size:525 final size:523
Alignment explanation
Indices: 1359051--1360704 Score: 2342
Period size: 525 Copynumber: 3.1 Consensus size: 523
1359041 AACAGTAGTG
* * * ** * *
1359051 GTTGTACTTTAGTCTCTTAAAGTGCTATACCTACTCCCTCGTTTCTGGGTTCCTTTGGACCGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTCCTTTGGACCGATT
* * * *
1359116 TCGGCGATGACTCGGAACTCTTTGATACCTTGAAAAATAATATTATTACATT-ATTAAATGCTTT
66 TCGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGA-CAAATGCTTT
*
1359180 AAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
130 AAATTGGATATGTACATTCAACTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
* *
1359245 ATGTTGCTATGTTCTTACTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAGCA
195 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAGCA
* * * *
1359310 GGTGTTGTTGTACTTTAGTCTCTTAAAG-GACAATCCCTATTTCCCCGAATCCGGTTTTCTTTGG
260 -GAG-TGTTGTACTTTAGTCTCTTAAAGTG-CTATCCCTATTCCCCCAAATCCGGTTTTCTTTGG
* *
1359374 ACAGA----GCAATGAATTGGAACTCTTTGTTACCTTGAAAAAAAT-TTATTACATTGAGAAATG
322 ACAGATTTGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATG
*
1359434 CTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATGTATGTCTGTGTGA
387 CTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATG--TGTGTGA
*
1359499 TGCACTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAG-CCCCGATCTCCATGCTTGTTTCCT
450 TGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCT
*
1359563 AGCTAGTGTT
515 AGC-AGTGGT
*
1359573 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGTATCCGGTTTCCTTTGGACCGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTCCTTTGGACCGATT
* * * *
1359638 TCGGCGATAAATTGGAACTCTTTATTACCTTGAAAAATAATATTATTACATTGGCCAATGCTTTA
66 TCGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTTA
* * *
1359703 AATTGAATATGTACATTCAACTGTGAAAATGCATACATTTATTTATATATGTGTGTGTGATGCAC
131 AATTGGATATGTACATTCAACTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAA
*
1359768 TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCTATGCTTGTTTCCTAGCA-
196 TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAGCAG
1359832 AGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCAAATCCGGTTTTCTTTGGACAG
261 AGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCAAATCCGGTTTTCTTTGGACAG
*
1359897 ATTTGGGCGATGAATTGGAAATCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCT
326 ATTT-GGCGATGAATTGGAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGCT
*
1359962 TTAAATTGGATATGTGCATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCA
389 TTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCA
* * *
1360027 ATGCTGCTATGTTCTTGGTGTTTATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTTGCA
454 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
1360092 GCTGGT
519 G-TGGT
* * * * **
1360098 GTTGTACTTTAGTTTCTTATAGTGCTATCCCTATTCCCCTGAATTCGGTTTTTTTTGGACCGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTCCTTTGGACCGATT
* * * *
1360163 TTGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAA-AACTTTTATTACATTGACAAACGCTTT
66 TCGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAATAA-TATTATTACATTGACAAATGCTTT
* * *
1360227 AAATTGGATATGTAGATTCATCTGTGAGAATGCATACATTTATTTATATATGTGAGTGTGATGCA
130 AAATTGGATATGTACATTCAACTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
* * * * *
1360292 ATACTGTTATGTTCTTAGTGTTGGTTGAACCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
195 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAGCA
* * * ***
1360357 GGTGGTGTTGTACTTTAGTCTCTTAAAGTTCTATCCCTATTCCCCTAAATCTTATTTTCTTTGGA
260 -G-AGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCAAATCCGGTTTTCTTTGGA
** * * *
1360422 CCA-ATTTCGGCGATGAATCAGAGCTCTTTGTTACCTTTAAAAAGAATATTATCACATTGACAAA
323 -CAGATTT-GGCGATGAATTGGAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAA
* * * * *
1360486 TGTTTTCAATTGAATATGTACGTTCAGCTGTGAGAATGCATACACTTATTTATATATGTGTGTGT
385 TGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATA--TGTGTGT
1360551 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCC-ATCTCCATGCTTGTTTC
448 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTC
* *
1360615 CTAGTAGGAGGT
513 CTAGCA-GTGGT
** * **
1360627 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTCCTTTGGACCGATT
*
1360692 TCGACGATGAATT
66 TCGGCGATGAATT
1360705 TTAGTGTTGA
Statistics
Matches: 1016, Mismatches: 97, Indels: 31
0.89 0.08 0.03
Matches are distributed among these distances:
519 59 0.06
520 2 0.00
522 237 0.23
524 80 0.08
525 261 0.26
526 71 0.07
528 159 0.16
529 94 0.09
530 53 0.05
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (523 bp):
GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTCCTTTGGACCGATT
TCGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTTA
AATTGGATATGTACATTCAACTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAA
TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAGCAG
AGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCAAATCCGGTTTTCTTTGGACAG
ATTTGGCGATGAATTGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTT
AAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGT
GGT
Found at i:1360436 original size:265 final size:265
Alignment explanation
Indices: 1359051--1360704 Score: 2274
Period size: 265 Copynumber: 6.3 Consensus size: 265
1359041 AACAGTAGTG
* * * * * *
1359051 GTTGTACTTTAGTCTCTTAAAGTGCTATACCTACTCCCTCGT--TTCTGGGTTCCTTTGGACCGA
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCC-C-TAAATCCGGTTTTCTTTGGACCGA
* * * * *
1359114 TTTCGGCGATGACTCGGAACTCTTTGATACCTTGAAAAATAATATTATTACATT-ATTAAATGCT
64 TTTCGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGA-CAAATGCT
1359178 TTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATG
128 TTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATG
* * *
1359243 CAATGTTGCTATGTTCTTACTGTTGATTGAATCATTAGCCCCCAATCTCCATGCTTGTTTCCTAG
193 CAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAG
*
1359308 CAGGTGTT
258 CAGGTGGT
* * *
1359316 GTTGTACTTTAGTCTCTTAAAG-GACAATCCCTATTTCCCC-GAATCCGGTTTTCTTTGGACAGA
1 GTTGTACTTTAGTCTCTTAAAGTG-CTATCCCTA-TTCCCCTAAATCCGGTTTTCTTTGGACCGA
* * *
1359379 -----GCAATGAATTGGAACTCTTTGTTACCTTGAAAAA-AAT-TTATTACATTGAGAAATGCTT
64 TTTCGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTT
* *
1359437 TAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATGTATGTCTGTGTGATGC
129 TAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGC
*
1359502 ACTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAG-CCCCGATCTCCATGCTTGTTTCCTAGC
194 AATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGC
*
1359566 TA-GTGTT
259 -AGGTGGT
*** *
1359573 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGTATCCGGTTTCCTTTGGACCGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
* * * * *
1359638 TCGGCGATAAATTGGAACTCTTTATTACCTTGAAAAATAATATTATTACATTGGCCAATGCTTTA
66 TCGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTTA
* * * *
1359703 AATTGAATATGTACATTCAACTGTGAAAATGCATACATTTATTTATATATGTGTGTGTGATGCAC
131 AATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAA
* *
1359768 TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCAATCTCTATGCTTGTTTCCTAGCA-
196 TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAG
*
1359832 --AGT
261 GTGGT
* *
1359835 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCAAATCCGGTTTTCTTTGGACAGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
*
1359900 TGGGCGATGAATTGGAAA-TCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTT
66 TCGGCGATGAATT-GAAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTT
*
1359964 AAATTGGATATGTGCATTCAGCTGTGAGAATGCATACATTTATTTATATA--TGTGTGTGATGCA
130 AAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
* * *
1360027 ATGCTGCTATGTTCTTGGTGTTTATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTTGCA
195 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
*
1360092 GCTGGT
260 GGTGGT
* * * * *
1360098 GTTGTACTTTAGTTTCTTATAGTGCTATCCCTATTCCCCTGAATTCGGTTTTTTTTGGACCGATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
* * *
1360163 TTGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAA-AACTTTTATTACATTGACAAACGCTTT
66 TCGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAATAA-TATTATTACATTGACAAATGCTTT
* * *
1360227 AAATTGGATATGTAGATTCATCTGTGAGAATGCATACATTTATTTATATATGTGAGTGTGATGCA
130 AAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
* * * *
1360292 ATACTGTTATGTTCTTAGTGTTGGTTGAACCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
195 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
1360357 GGTGGT
260 GGTGGT
* *** *
1360363 GTTGTACTTTAGTCTCTTAAAGTTCTATCCCTATTCCCCTAAATCTTATTTTCTTTGGACCAATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
* * * * * *
1360428 TCGGCGATGAA-TCAGAGCTCTTTGTTACCTTTAAAAAGAATATTATCACATTGACAAATGTTTT
66 TCGGCGATGAATTGA-AACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTT
* * * *
1360492 CAATTGAATATGTACGTTCAGCTGTGAGAATGCATACACTTATTTATATATGTGTGTGTGATGCA
130 AAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCA
*
1360557 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCC-ATCTCCATGCTTGTTTCCTAGTA
195 ATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCA
*
1360621 GGAGGT
260 GGTGGT
** * * **
1360627 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATT
1 GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
*
1360692 TCGACGATGAATT
66 TCGGCGATGAATT
1360705 TTAGTGTTGA
Statistics
Matches: 1240, Mismatches: 122, Indels: 54
0.88 0.09 0.04
Matches are distributed among these distances:
256 6 0.00
257 81 0.07
258 117 0.09
259 4 0.00
260 102 0.08
262 199 0.16
263 166 0.13
264 212 0.17
265 347 0.28
266 6 0.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (265 bp):
GTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCTAAATCCGGTTTTCTTTGGACCGATT
TCGGCGATGAATTGAAACTCTTTGTTACCTTGAAAAATAATATTATTACATTGACAAATGCTTTA
AATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAA
TGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAG
GTGGT
Found at i:1360812 original size:135 final size:134
Alignment explanation
Indices: 1360571--1360838 Score: 509
Period size: 135 Copynumber: 2.0 Consensus size: 134
1360561 TGCTATGTTC
1360571 TTAGTGTTGATTGAATCATTAGCCCCCATCTCCATGCTTGTTTCCTAGTAGGAGGTGTTGTACTT
1 TTAGTGTTGATTGAATCATTAGCCCCCATCTCCATGCTTGTTTCCTAGTAGGAGGTGTTGTACTT
*
1360636 TAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATTTCGACGATG
66 CAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATTTCGACGATG
1360701 AATT
131 AATT
*
1360705 TTAGTGTTGATTGGATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGTAGGAGGTGTTGTACT
1 TTAGTGTTGATTGAATCATTAG-CCCCCATCTCCATGCTTGTTTCCTAGTAGGAGGTGTTGTACT
1360770 TCAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATTTCGACGAT
65 TCAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATTTCGACGAT
1360835 GAAT
130 GAAT
1360839 CGGAATTCTT
Statistics
Matches: 131, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
134 21 0.16
135 110 0.84
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (134 bp):
TTAGTGTTGATTGAATCATTAGCCCCCATCTCCATGCTTGTTTCCTAGTAGGAGGTGTTGTACTT
CAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTGTTTGAACTAATTTCGACGATG
AATT
Found at i:1364038 original size:18 final size:18
Alignment explanation
Indices: 1364015--1364071 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1364005 TACAACCATT
1364015 TACGGTACTATTTACGTA
1 TACGGTACTATTTACGTA
1364033 TACGGTACTATTTACGTA
1 TACGGTACTATTTACGTA
* * *
1364051 TACAGTACTGTTCACGTA
1 TACGGTACTATTTACGTA
1364069 TAC
1 TAC
1364072 AGTAGTTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (18 bp):
TACGGTACTATTTACGTA
Found at i:1370534 original size:26 final size:25
Alignment explanation
Indices: 1370470--1370534 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
1370460 TGTAATTTCA
* *
1370470 TATATGATATAATGATTCTATGGTCC
1 TATATGATATAAT-ATACTATGATCC
* *
1370496 TATGTGAT-T-ATATACATTTGATCC
1 TATATGATATAATATAC-TATGATCC
1370520 TATATGATATAATAT
1 TATATGATATAATAT
1370535 TGATATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 3 0.10
24 15 0.48
25 2 0.06
26 11 0.35
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (25 bp):
TATATGATATAATATACTATGATCC
Found at i:1374158 original size:18 final size:19
Alignment explanation
Indices: 1374111--1374162 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1374101 GCCGGAGCTC
* *
1374111 CCCCTCCCCTCTCTTCTTT
1 CCCCTCCCCTCTTTTCTCT
*
1374130 CCCCGCTCCCTCTTTTCTCT
1 CCCCTC-CCCTCTTTTCTCT
1374150 -CCCTCCCCT-TTTT
1 CCCCTCCCCTCTTTT
1374163 TTTTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 4 0.14
18 4 0.14
19 9 0.32
20 11 0.39
ACGTcount: A:0.00, C:0.56, G:0.02, T:0.42
Consensus pattern (19 bp):
CCCCTCCCCTCTTTTCTCT
Found at i:1375114 original size:23 final size:22
Alignment explanation
Indices: 1375082--1375127 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
1375072 ATAAGTTTTA
1375082 ATTATTATATTTT-ATATATATT
1 ATTATTATATTTTAATAT-TATT
1375104 ATTATGTATATTTTAATATTATT
1 ATTAT-TATATTTTAATATTATT
1375127 A
1 A
1375128 GGTATCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTATTATATTTTAATATTATT
Found at i:1375140 original size:23 final size:22
Alignment explanation
Indices: 1375087--1375132 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
1375077 TTTTAATTAT
*
1375087 TATATTTTATATATATTATTATG
1 TATATTTT-TATATATTATTAGG
1375110 TATA-TTTTA-ATATTATTAGG
1 TATATTTTTATATATTATTAGG
1375130 TAT
1 TAT
1375133 CTATTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 3 0.14
23 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (22 bp):
TATATTTTTATATATTATTAGG
Found at i:1375435 original size:25 final size:23
Alignment explanation
Indices: 1375407--1375453 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1375397 ACACTACTAC
*
1375407 TATTTAAAATATATATATATATACA
1 TATTT-AAATAT-TACATATATACA
*
1375432 TATTTATATATTACATATATAC
1 TATTTAAATATTACATATATAC
1375454 TCTTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAATATTACATATATACA
Found at i:1382121 original size:12 final size:12
Alignment explanation
Indices: 1382106--1382151 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1382096 TTTATTTTTT
1382106 TTTTTTTTCGTA-
1 TTTTTTTT-GTAC
1382118 TTTTTTTTGTAC
1 TTTTTTTTGTAC
*
1382130 TTTTTTTAT-CAC
1 TTTTTTT-TGTAC
1382142 TTTTTTTTGT
1 TTTTTTTTGT
1382152 GGGAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 4 0.14
12 24 0.83
13 1 0.03
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGTAC
Found at i:1384184 original size:3 final size:3
Alignment explanation
Indices: 1384178--1384219 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1384168 ACTACTATAT
1384178 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1384220 TAGAAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1384334 original size:3 final size:3
Alignment explanation
Indices: 1384320--1384358 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
1384310 AAATATACAC
*
1384320 TAA TATA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1384359 TTAAAATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1385645 original size:23 final size:24
Alignment explanation
Indices: 1385602--1385646 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1385592 GTAGTTCTAA
*
1385602 TTTGGGCTAGTTTTAGGTATTGGG
1 TTTGGGCTAGGTTTAGGTATTGGG
*
1385626 TTTGGG-TAGGTTTAGTTATTG
1 TTTGGGCTAGGTTTAGGTATTG
1385647 TAATTGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.13, C:0.02, G:0.36, T:0.49
Consensus pattern (24 bp):
TTTGGGCTAGGTTTAGGTATTGGG
Found at i:1389037 original size:34 final size:34
Alignment explanation
Indices: 1388999--1389067 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1388989 TAACAAATGC
1388999 TTTAAATTGGATATGCTTATTTTCTGAATCCCAA
1 TTTAAATTGGATATGCTTATTTTCTGAATCCCAA
*
1389033 TTTAAATTGGATATGCTTGTTTTCTGAATCCCAA
1 TTTAAATTGGATATGCTTATTTTCTGAATCCCAA
1389067 T
1 T
1389068 GGATCATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (34 bp):
TTTAAATTGGATATGCTTATTTTCTGAATCCCAA
Done.