Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold99
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: 1377724
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 13826 characters in sequence are not A, C, G, or T
File 8 of 10
Found at i:994353 original size:20 final size:20
Alignment explanation
Indices: 994310--994383 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
994300 CACATGGTCC
* *
994310 TGTATCGATACATTTCAGGCA
1 TGTATCGATACA-TTCACGTA
994331 TGTATCGATACATTCACGTA
1 TGTATCGATACATTCACGTA
* *
994351 TGTATCAATACATTGC-CTTA
1 TGTATCGATACATT-CACGTA
994371 TTGTATCGATACA
1 -TGTATCGATACA
994384 AATTGTTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 22 0.48
21 24 0.52
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACGTA
Found at i:997156 original size:24 final size:25
Alignment explanation
Indices: 997129--997179 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
997119 CCAAAATTTT
997129 ATTCATC-GGAGATACTTCAACCCC
1 ATTCATCAGGAGATACTTCAACCCC
* *
997153 ATTCTTCTAAGGGGATACTTCAACCCC
1 ATTCATC--AGGAGATACTTCAACCCC
997180 GCTTTTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (25 bp):
ATTCATCAGGAGATACTTCAACCCC
Found at i:1003966 original size:13 final size:13
Alignment explanation
Indices: 1003948--1003973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1003938 TACAGCAAGT
1003948 ATGTATCGATACA
1 ATGTATCGATACA
1003961 ATGTATCGATACA
1 ATGTATCGATACA
1003974 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1005590 original size:12 final size:12
Alignment explanation
Indices: 1005573--1005597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1005563 AGACGATGAA
1005573 GTTGATGAAGAT
1 GTTGATGAAGAT
1005585 GTTGATGAAGAT
1 GTTGATGAAGAT
1005597 G
1 G
1005598 GTGACTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (12 bp):
GTTGATGAAGAT
Found at i:1006235 original size:21 final size:22
Alignment explanation
Indices: 1006189--1006233 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1006179 TTGCAAGTTG
1006189 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
1006211 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
1006231 AAA
1 AAA
1006234 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:1008056 original size:15 final size:15
Alignment explanation
Indices: 1008036--1008066 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1008026 TAAAAATGTC
*
1008036 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1008051 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1008066 C
1 C
1008067 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1010155 original size:13 final size:13
Alignment explanation
Indices: 1010137--1010162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1010127 ACATTTTTCT
1010137 TTGTATCGATACA
1 TTGTATCGATACA
1010150 TTGTATCGATACA
1 TTGTATCGATACA
1010163 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1010328 original size:20 final size:20
Alignment explanation
Indices: 1010285--1010330 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1010275 AAATCTTTTG
1010285 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1010306 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1010326 CAAAA
1 CAAAA
1010331 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1012743 original size:13 final size:13
Alignment explanation
Indices: 1012725--1012750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1012715 TACAGCAAGT
1012725 ATGTATCGATACA
1 ATGTATCGATACA
1012738 ATGTATCGATACA
1 ATGTATCGATACA
1012751 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1013870 original size:11 final size:11
Alignment explanation
Indices: 1013854--1013878 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1013844 AAGGTTCAAC
1013854 AAAAAAAAAGA
1 AAAAAAAAAGA
1013865 AAAAAAAAAGA
1 AAAAAAAAAGA
1013876 AAA
1 AAA
1013879 GAGAGAAAAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:1013887 original size:18 final size:16
Alignment explanation
Indices: 1013854--1013895 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
1013844 AAGGTTCAAC
1013854 AAAAA-AAAAGAAAAA
1 AAAAAGAAAAGAAAAA
1013869 AAAAAGAAAAGAGAGAAA
1 AAAAAGAAAAGA-A-AAA
*
1013887 AAATAGAAA
1 AAAAAGAAA
1013896 CAAAGAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 1 0.04
18 11 0.48
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:1013888 original size:21 final size:22
Alignment explanation
Indices: 1013862--1013915 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
1013852 ACAAAAAAAA
*
1013862 AGAAAAAAAAAAGAAAAGA-G-
1 AGAAAAAAAAAAAAAAAGAGGT
* *
1013882 AGAAAAAATAGAAACAAAGAGGT
1 AGAAAAAA-AAAAAAAAAGAGGT
1013905 AGAAAAAAAAA
1 AGAAAAAAAAA
1013916 GGCTAACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 8 0.30
21 8 0.30
22 3 0.11
23 8 0.30
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (22 bp):
AGAAAAAAAAAAAAAAAGAGGT
Found at i:1021880 original size:55 final size:57
Alignment explanation
Indices: 1021832--1021960 Score: 160
Period size: 55 Copynumber: 2.4 Consensus size: 57
1021822 CCGTGGTTTT
** * *
1021832 CCTTTT-AAGTCCACAACTTTGTGGCACCC-TTTAAAGTCTACAG-TTCCGTGGTAA
1 CCTTTTAAAGTCCACAACTCCGTAGCACCCTTTTAAAGTCCACAGCTTCCGTGGTAA
* *
1021886 CTTTTTAAAGTCCACAACTCCGTAGCACCCTTTTAAAGTCCACAGCTT-CGTGGCAA
1 CCTTTTAAAGTCCACAACTCCGTAGCACCCTTTTAAAGTCCACAGCTTCCGTGGTAA
*
1021942 CGTTTT-AAGTCCACAACTC
1 CCTTTTAAAGTCCACAACTC
1021961 TGGAGTCTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
54 5 0.08
55 33 0.51
56 25 0.38
57 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (57 bp):
CCTTTTAAAGTCCACAACTCCGTAGCACCCTTTTAAAGTCCACAGCTTCCGTGGTAA
Found at i:1021907 original size:28 final size:28
Alignment explanation
Indices: 1021832--1021960 Score: 120
Period size: 28 Copynumber: 4.7 Consensus size: 28
1021822 CCGTGGTTTT
**
1021832 CCTTTT-AAGTCCACAACTTTGTGGC-A
1 CCTTTTAAAGTCCACAACTCCGTGGCAA
* * ** *
1021858 CCCTTTAAAGTCTACAGTTCCGTGGTAA
1 CCTTTTAAAGTCCACAACTCCGTGGCAA
* * *
1021886 CTTTTTAAAGTCCACAACTCCGTAGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAA
* *
1021914 CCTTTTAAAGTCCACAGCTTCGTGGCAA
1 CCTTTTAAAGTCCACAACTCCGTGGCAA
*
1021942 CGTTTT-AAGTCCACAACTC
1 CCTTTTAAAGTCCACAACTC
1021961 TGGAGTCTTG
Statistics
Matches: 78, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
26 5 0.06
27 24 0.31
28 49 0.63
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (28 bp):
CCTTTTAAAGTCCACAACTCCGTGGCAA
Found at i:1022380 original size:15 final size:14
Alignment explanation
Indices: 1022356--1022405 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1022346 CTTCGTAAAG
1022356 AAAAAA-CAAAGATA
1 AAAAAATCAAA-ATA
1022370 AAAAAATCAAAATA
1 AAAAAATCAAAATA
* *
1022384 CAAAAAATAAAAACA
1 -AAAAAATCAAAATA
1022399 AAAAAAT
1 AAAAAAT
1022406 TAGTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (14 bp):
AAAAAATCAAAATA
Found at i:1024354 original size:29 final size:29
Alignment explanation
Indices: 1024301--1024358 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1024291 GCCAAGAAAT
*
1024301 GTATCGATACATTAGTCAATTTATCGATA
1 GTATCGATACATTACTCAATTTATCGATA
*
1024330 GTATCGATACATTTCTC-ATTGTATCGATA
1 GTATCGATACATTACTCAATT-TATCGATA
1024359 TATTCTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (29 bp):
GTATCGATACATTACTCAATTTATCGATA
Found at i:1027205 original size:26 final size:26
Alignment explanation
Indices: 1027175--1027264 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
1027165 TGAAATAACA
*
1027175 TCGAGTCGAAACCAATGAAACCAATG
1 TCGAGTCAAAACCAATGAAACCAATG
*
1027201 TCGAGTCAAAACCAATGACACCAATG
1 TCGAGTCAAAACCAATGAAACCAATG
*
1027227 TAGAGTCAAAACCAATGAAACCAATG
1 TCGAGTCAAAACCAATGAAACCAATG
1027253 TCGAGTCAAAAC
1 TCGAGTCAAAAC
1027265 ATAGCTAGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (26 bp):
TCGAGTCAAAACCAATGAAACCAATG
Found at i:1030417 original size:52 final size:52
Alignment explanation
Indices: 1030269--1030397 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1030259 CAAAATATGA
1030269 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1030321 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1030373 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1030398 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1030424 original size:13 final size:13
Alignment explanation
Indices: 1030406--1030430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1030396 CAAAGATCAG
1030406 TGTATCGATACAA
1 TGTATCGATACAA
1030419 TGTATCGATACA
1 TGTATCGATACA
1030431 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1030511 original size:32 final size:32
Alignment explanation
Indices: 1030468--1030568 Score: 148
Period size: 32 Copynumber: 3.1 Consensus size: 32
1030458 GGCAGTAGCT
1030468 TACATTGTATTGATACAAAACTTATGTATCGA
1 TACATTGTATTGATACAAAACTTATGTATCGA
* *
1030500 TACATTATATTGATACAACACTTATGTATCGA
1 TACATTGTATTGATACAAAACTTATGTATCGA
* **
1030532 TACATTGTATCGATACAATAGTTTATGTATCGA
1 TACATTGTATTGATACAA-AACTTATGTATCGA
1030565 TACA
1 TACA
1030569 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 46 0.75
33 15 0.25
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (32 bp):
TACATTGTATTGATACAAAACTTATGTATCGA
Found at i:1030542 original size:13 final size:13
Alignment explanation
Indices: 1030524--1030548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1030514 ACAACACTTA
1030524 TGTATCGATACAT
1 TGTATCGATACAT
1030537 TGTATCGATACA
1 TGTATCGATACA
1030549 ATAGTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1031477 original size:49 final size:49
Alignment explanation
Indices: 1031309--1031486 Score: 203
Period size: 49 Copynumber: 3.6 Consensus size: 49
1031299 CGAAGAATGA
* * * * *
1031309 CAATGTGCTGCTTCATGGCCAGCGACATTGATCTTAAAGATGATGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * ** * *
1031358 CAATATGCTGATTCAAAGCCACCGATACCGGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * *
1031407 CAATGTGCTGGTTCAAGGCCAGCGACATTGGTCTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* *
1031456 CAATATGCTGATTCAAGGCCAGTGATATTGG
1 CAATATGCTGATTCAAGGCCAGCGACATTGG
1031487 ATTTAGAAGA
Statistics
Matches: 103, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 103 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
Found at i:1031541 original size:31 final size:30
Alignment explanation
Indices: 1031500--1031617 Score: 97
Period size: 29 Copynumber: 4.1 Consensus size: 30
1031490 TAGAAGAAGA
1031500 TGCCACCAACTTGTGTGGGCTTTTGATAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGA-A-GGT
1031532 TG-CACCAACTTGTGT--GCTTTTGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGGT
** * *
1031559 TGCCACTGAC-T-TGTGGGCTTTTGAAAAGA
1 TGCCACCAACTTGTGTGGGCTTTTG-AAGGT
* * *
1031588 TACCACTAAC-T-TGTGGGCTTTTCAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGGT
1031616 TG
1 TG
1031618 GCACTGACTT
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
26 3 0.04
27 6 0.08
28 17 0.24
29 31 0.43
31 13 0.18
32 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (30 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAGGT
Found at i:1031674 original size:58 final size:55
Alignment explanation
Indices: 1031513--1031966 Score: 417
Period size: 58 Copynumber: 7.8 Consensus size: 55
1031503 CACCAACTTG
** * *
1031513 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGA-A-GGTTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACTGACT
* * * * * * *
1031570 TGTGGGCTTTTGAAAAGATACCACTAACTTGTGGGCTTTTCAAGGTTGGCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACTGACT
* * *
1031627 TATGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTG---AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACTGACT
* * *
1031685 TGTGGGCTTTAGGAGAAGGGTGCCACTGATTTGTGGGC-TTTGAAAAAGAGTGCCACTGACT
1 TGTGGGCTTT----GAAGGTTGCCACTGACTTGTGGGCTTTTG---AAGGGTGCCACTGACT
* * *
1031746 TGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGGAAAAGGGTGCCACTGATT
1 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTT-TG--AAGGGTGCCACTGACT
* * * *
1031805 TGTGGGCTTTGAAGGTTGCCACTGACTTATGGGCTTTGGGAGAAGGGTGCCACTAATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT---TGAAGGGTGCCACTGACT
* * *
1031863 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGACTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT---TGAAGGGTGCCACTGACT
*
1031921 TATGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTG
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTG
1031967 AGGAATATCT
Statistics
Matches: 347, Mismatches: 34, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
55 8 0.02
56 6 0.02
57 51 0.15
58 207 0.60
59 47 0.14
60 3 0.01
61 21 0.06
62 4 0.01
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (55 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACTGACT
Found at i:1031738 original size:89 final size:86
Alignment explanation
Indices: 1031554--1031966 Score: 440
Period size: 89 Copynumber: 4.7 Consensus size: 86
1031544 TGTGCTTTTG
* * * * * ** * *
1031554 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATACCACTAACTTGTGGGCTTTTCAAGGTTGG
1 AAGGGTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTAGAAGGGTGC
*
1031619 CACTGACTTATGGGCTTTGAAA
65 CACTGACTTGTGGGCTTTGAAA
1031641 AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGGAGAAGGGT
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT---AGAAGGGT
*
1031706 GCCACTGATTTGTGGGCTTTGAAA
63 GCCACTGACTTGTGGGCTTTGAAA
* * *
1031730 AAGAGTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGGAAAAGGGT
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT---AGAAGGGT
*
1031795 GCCACTGATTTGTGGGCTTTG---
63 GCCACTGACTTGTGGGCTTTGAAA
* * * * * * *
1031816 AAGGTTGCCACTGACTTATGGGCTTTGGGAGAAGGGTGCCACTAATTTGTGGGCTTT-GAAGGTT
1 AAGGGTGCCACTGACTTGTGGGCTTT---TGAAGGTTGCCACTGACTTGTGGGCTTTAGAAGGGT
* * *
1031880 GCCACTGACTTGTGGACTTTGGGAG
63 GCCACTGACTTGTGGGCTTT-GAAA
* * *
1031905 AAGGGTGCCACTGATTTATGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGGTG
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGAAGGGTG
1031967 AGGAATATCT
Statistics
Matches: 281, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
85 47 0.17
86 53 0.19
87 27 0.10
88 2 0.01
89 152 0.54
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (86 bp):
AAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGAAGGGTGCC
ACTGACTTGTGGGCTTTGAAA
Found at i:1031784 original size:147 final size:145
Alignment explanation
Indices: 1031553--1031963 Score: 548
Period size: 147 Copynumber: 2.8 Consensus size: 145
1031543 GTGTGCTTTT
* * * * *
1031553 GAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGA-TACCACTAACTTGTGGGCTTTTCAAGGTT
1 GAAGGGTGCCACTGATTTGTGGGC-TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTTAAAGGTT
*
1031617 GGCACTGACTTATGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
65 GCCACTGACTTATGGGCTTTG-AAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
*
1031682 ACTTGTGGGCTTTAGGA
129 ACTTATGGGCTTTAGGA
1031699 GAAGGGTGCCACTGATTTGTGGGCTTTGAAAAAGAGTGCCACTGACTTGTGGGCTTTTAAAGGTT
1 GAAGGGTGCCACTGATTTGTGGGCTTTG-AAAAGAGTGCCACTGACTTGTGGGCTTTTAAAGGTT
* *
1031764 GCCACTGACTTGTGGGCTTTGGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGGTTGCCACT
65 GCCACTGACTTATGGGCTTT--GAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACT
*
1031828 GACTTATGGGCTTTGGGA
128 GACTTATGGGCTTTAGGA
* * *
1031846 GAAGGGTGCCACTAATTTGTGGGCTTTG--AAG-GTTGCCACTGACTTGTGGACTTTGGGAGAAG
1 GAAGGGTGCCACTGATTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTT--TA-AAG
* * *
1031908 GGTGCCACTGATTTATGGGCTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGG
62 GTTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGG
1031964 GTGAGGAATA
Statistics
Matches: 238, Mismatches: 18, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
143 22 0.09
144 31 0.13
145 5 0.02
146 29 0.12
147 126 0.53
148 24 0.10
149 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (145 bp):
GAAGGGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTTAAAGGTTG
CCACTGACTTATGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGAC
TTATGGGCTTTAGGA
Found at i:1033414 original size:1 final size:1
Alignment explanation
Indices: 1033410--1033523 Score: 75
Period size: 1 Copynumber: 114.0 Consensus size: 1
1033400 GTTGTTGTTG
* * * * * * * *
1033410 TTTTTTTTTTCTTTGTTTTTTTGTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * * * **
1033475 TTTTTCGTTTTTTTCTTCTTCTTTTTTTTGTTTATTTGGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1033524 GTGGAGGATG
Statistics
Matches: 82, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:1033436 original size:20 final size:19
Alignment explanation
Indices: 1033404--1033525 Score: 99
Period size: 20 Copynumber: 6.2 Consensus size: 19
1033394 CTTTTTGTTG
* *
1033404 TTGTTGTTTT-TTTTTTCT
1 TTGTTTTTTTGTTTTTTTT
1033422 TTGTTTTTTTGTTTTTGTTT
1 TTGTTTTTTTGTTTTT-TTT
1033442 TT-TGTTTTTTG-TTTTTTT
1 TTGT-TTTTTTGTTTTTTTT
1033460 TTGTTTTTTAT-TTTTTTTT
1 TTGTTTTTT-TGTTTTTTTT
* *
1033479 TCGTTTTTTTCTTCTTCTTTTTT
1 T--TGTTTTT-TTGTT-TTTTTT
*
1033502 TTGTTTATTTGGTTTTTTTT
1 TTGTTT-TTTTGTTTTTTTT
1033522 TTGT
1 TTGT
1033526 GGAGGATGCC
Statistics
Matches: 86, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
18 19 0.22
19 20 0.23
20 21 0.24
21 14 0.16
22 5 0.06
23 7 0.08
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.84
Consensus pattern (19 bp):
TTGTTTTTTTGTTTTTTTT
Found at i:1047559 original size:104 final size:105
Alignment explanation
Indices: 1047367--1047568 Score: 336
Period size: 104 Copynumber: 1.9 Consensus size: 105
1047357 TCGAAATATG
1047367 AAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGCAAATTTGCCTGC
1 AAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGCAAATTTGCCTGC
***
1047432 ATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
66 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
* *
1047472 AAAA-TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 AAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGCAAATTTGCCTGC
1047536 ATGTATCGATACA-AAGATCAGTGTATCGATACA
66 ATGTATCGATACATAAGAT-AGTGTATCGATACA
1047569 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
103 2 0.02
104 85 0.93
105 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (105 bp):
AAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGCAAATTTGCCTGC
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:1047568 original size:52 final size:52
Alignment explanation
Indices: 1047368--1047548 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
1047358 CGAAATATGA
* *
1047368 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1047420 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
1047472 AAAATTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1047524 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1047549 AAGATCAGTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1047575 original size:13 final size:13
Alignment explanation
Indices: 1047557--1047581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1047547 CAAAGATCAG
1047557 TGTATCGATACAA
1 TGTATCGATACAA
1047570 TGTATCGATACA
1 TGTATCGATACA
1047582 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1047648 original size:19 final size:18
Alignment explanation
Indices: 1047624--1047721 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1047614 TAGCTTACAT
1047624 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1047643 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1047656 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1047675 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1047688 TGTATCGATATAATACTTTA
1 TGTATCGATACAA-AC-TTA
1047708 TGTATCGATACAAA
1 TGTATCGATACAAA
1047722 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.38
20 12 0.19
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1047660 original size:32 final size:32
Alignment explanation
Indices: 1047619--1047719 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1047609 GGTAGTAGCT
1047619 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
1047651 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* *
1047683 TACATTGTATCGATATAATACTTTATGTATCGA
1 TACATTGTATCGATACAAAAC-TTATGTATCGA
1047716 TACA
1 TACA
1047720 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:1047661 original size:13 final size:13
Alignment explanation
Indices: 1047643--1047697 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
1047633 ACAAAACTTA
1047643 TGTATCGATACAT
1 TGTATCGATACAT
1047656 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1047674 ATGTATCGATACAT
1 -TGTATCGATACAT
1047688 TGTATCGATA
1 TGTATCGATA
1047698 TAATACTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
16 6 0.17
18 1 0.03
19 9 0.25
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1052232 original size:28 final size:29
Alignment explanation
Indices: 1052180--1052237 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1052170 TTAATTAAAT
* **
1052180 ATTAAATTATATTATTTTATTTTTATTTA
1 ATTAAATTATAATATTAAATTTTTATTTA
1052209 ATTAAATT-TAATATTAAATTTTTATTTA
1 ATTAAATTATAATATTAAATTTTTATTTA
1052237 A
1 A
1052238 ATTTCTACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTAAATTATAATATTAAATTTTTATTTA
Found at i:1059231 original size:39 final size:39
Alignment explanation
Indices: 1059187--1059264 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1059177 ATTAGGCTTG
* **
1059187 TTTAAGATTGACTCTTATGTTTGATTTTAAATTTGATTA
1 TTTAAGATTGACTCTTACGTTTGATTGCAAATTTGATTA
* *
1059226 TTTAAGTTTGATTCTTACGTTTGATTGCAAATTTGATTA
1 TTTAAGATTGACTCTTACGTTTGATTGCAAATTTGATTA
1059265 GTTGTGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (39 bp):
TTTAAGATTGACTCTTACGTTTGATTGCAAATTTGATTA
Found at i:1059249 original size:13 final size:13
Alignment explanation
Indices: 1059188--1059251 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
1059178 TTAGGCTTGT
* *
1059188 TTAAGATTGACTC
1 TTAAGTTTGATTC
*
1059201 TTATGTTTGATT-
1 TTAAGTTTGATTC
* *
1059213 TTAAATTTGATTAT
1 TTAAGTTTGATT-C
1059227 TTAAGTTTGATTC
1 TTAAGTTTGATTC
*
1059240 TTACGTTTGATT
1 TTAAGTTTGATT
1059252 GCAAATTTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.24
13 20 0.49
14 11 0.27
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAAGTTTGATTC
Found at i:1061120 original size:20 final size:20
Alignment explanation
Indices: 1061095--1061149 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1061085 CTGCCAGTTT
**
1061095 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1061115 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1061134 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1061150 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1061139 original size:19 final size:19
Alignment explanation
Indices: 1061095--1061200 Score: 80
Period size: 20 Copynumber: 5.7 Consensus size: 19
1061085 CTGCCAGTTT
**
1061095 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1061115 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
1061134 CATGTATCGATAC-----A
1 CATGTATCGATACAATGAA
* *
1061148 -ATGTATCGATACAAAGTAG
1 CATGTATCGATACAATG-AA
* *
1061167 CATGTATCGATACAAAGTAG
1 CATGTATCGATACAATG-AA
1061187 CATGTATCGATACA
1 CATGTATCGATACA
1061201 TCTGGGTGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
13 12 0.16
14 1 0.01
19 14 0.19
20 47 0.64
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1061153 original size:13 final size:13
Alignment explanation
Indices: 1061135--1061161 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1061125 TACAATGAAC
1061135 ATGTATCGATACA
1 ATGTATCGATACA
1061148 ATGTATCGATACA
1 ATGTATCGATACA
1061161 A
1 A
1061162 AGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1061158 original size:52 final size:53
Alignment explanation
Indices: 1061096--1061200 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 53
1061086 TGCCAGTTTC
* * *
1061096 ATGTATCGATACAATTGT-CCATGTATTGATACAATG-AACATGTATCGATACA
1 ATGTATCGATACAA-AGTACCATGTATCGATACAAAGTAACATGTATCGATACA
* *
1061148 ATGTATCGATACAAAGTAGCATGTATCGATACAAAGTAGCATGTATCGATACA
1 ATGTATCGATACAAAGTACCATGTATCGATACAAAGTAACATGTATCGATACA
1061201 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 2 0.04
52 29 0.63
53 15 0.33
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (53 bp):
ATGTATCGATACAAAGTACCATGTATCGATACAAAGTAACATGTATCGATACA
Found at i:1061173 original size:20 final size:20
Alignment explanation
Indices: 1061148--1061200 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1061138 TATCGATACA
1061148 ATGTATCGATACAAAGTAGC
1 ATGTATCGATACAAAGTAGC
1061168 ATGTATCGATACAAAGTAGC
1 ATGTATCGATACAAAGTAGC
1061188 ATGTATCGATACA
1 ATGTATCGATACA
1061201 TCTGGGTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACAAAGTAGC
Found at i:1061176 original size:33 final size:32
Alignment explanation
Indices: 1061116--1061181 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1061106 ACAATTGTCC
* *
1061116 ATGTATTGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1061148 ATGTATCGATACAAAGTAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1061181 A
1 A
1061182 AGTAGCATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1061776 original size:37 final size:37
Alignment explanation
Indices: 1061719--1061810 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
1061709 GTTTTCGTTT
*
1061719 TTCTCCCTTTAAAAAATTCTCCCCTTTAAACGATTATC
1 TTCT-CCTTTAAAAAATTCTCCCCCTTAAACGATTATC
* *
1061757 -TCGTCTTTTAAAAAATTCTCCCCCTTAAGCGATTATC
1 TTC-TCCTTTAAAAAATTCTCCCCCTTAAACGATTATC
1061794 TTCTCCTTTAAAAAATT
1 TTCTCCTTTAAAAAATT
1061811 TATTTTCACA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 45 0.94
38 3 0.06
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.40
Consensus pattern (37 bp):
TTCTCCTTTAAAAAATTCTCCCCCTTAAACGATTATC
Found at i:1063206 original size:20 final size:20
Alignment explanation
Indices: 1063181--1063229 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1063171 CTACCCGGTT
1063181 GCGACCTGGGAGTGCCGATC
1 GCGACCTGGGAGTGCCGATC
1063201 GCGACCTGGGAGTGCCGATC
1 GCGACCTGGGAGTGCCGATC
1063221 GCGACCTGG
1 GCGACCTGG
1063230 AGAGGGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.41, T:0.14
Consensus pattern (20 bp):
GCGACCTGGGAGTGCCGATC
Found at i:1063678 original size:13 final size:13
Alignment explanation
Indices: 1063660--1063688 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1063650 AAATAGTACC
1063660 CAATGTATCGATA
1 CAATGTATCGATA
1063673 CAATGTATCGATA
1 CAATGTATCGATA
1063686 CAA
1 CAA
1063689 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1064569 original size:20 final size:20
Alignment explanation
Indices: 1064541--1064615 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1064531 TTTTACCTTG
1064541 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1064561 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1064581 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1064601 ATGTATCGATACATT
1 ATGTATCGATACATT
1064616 ATGTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1064608 original size:40 final size:39
Alignment explanation
Indices: 1064541--1064618 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1064531 TTTTACCTTG
* *
1064541 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1064581 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1064619 TTTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1067616 original size:13 final size:13
Alignment explanation
Indices: 1067598--1067623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1067588 TACACCAAGT
1067598 ATGTATCGATACA
1 ATGTATCGATACA
1067611 ATGTATCGATACA
1 ATGTATCGATACA
1067624 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1067621 original size:32 final size:33
Alignment explanation
Indices: 1067580--1067643 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1067570 TAGCCAAACT
* **
1067580 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1067612 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1067644 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1078663 original size:13 final size:13
Alignment explanation
Indices: 1078626--1078655 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1078616 ACCTTCCTTT
1078626 AAAAAATAAAAAC
1 AAAAAATAAAAAC
1078639 AAAAAATAAAAAC
1 AAAAAATAAAAAC
1078652 AAAA
1 AAAA
1078656 TAAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:1079765 original size:62 final size:62
Alignment explanation
Indices: 1079646--1079894 Score: 309
Period size: 62 Copynumber: 4.1 Consensus size: 62
1079636 AACCTTTTAT
* *
1079646 CCTTTTAGTCCTCAAAGAGCAGG--A-TGTCTTTTCCTT-TTAAAGACCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCGAAGAGCAGGACACT-TCTTTT--TTGTTAAAGCCCACACAAGTTGGTGGCA
*
1079707 CCTTTTAGTCCTCGAGGAGCAGGACACTTCTTTTTTGTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCGAAGAGCAGGACACTTCTTTTTTGTTAAAGCCCACACAAGTTGGTGGCA
*
1079769 CCTTTTAGTCCTCGAAGAGCAGGACACTTCTTTTCTGTTAAAG-CCAGCACAAGTTGGTGGCA
1 CCTTTTAGTCCTCGAAGAGCAGGACACTTCTTTTTTGTTAAAGCCCA-CACAAGTTGGTGGCA
* * * *
1079831 CCTTTTA-TCCTCAAAGAACAGG--ACGTCTTTTCCTT-TTAAAGCCCACACAAGTTGGCGGCA
1 CCTTTTAGTCCTCGAAGAGCAGGACACTTCTTTT--TTGTTAAAGCCCACACAAGTTGGTGGCA
1079891 CCTT
1 CCTT
1079895 GTAGACACTT
Statistics
Matches: 170, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
59 8 0.05
60 24 0.14
61 43 0.25
62 87 0.51
63 7 0.04
64 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (62 bp):
CCTTTTAGTCCTCGAAGAGCAGGACACTTCTTTTTTGTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1080183 original size:13 final size:13
Alignment explanation
Indices: 1080165--1080189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1080155 CATAAAGTGT
1080165 TGTATCGATACAA
1 TGTATCGATACAA
1080178 TGTATCGATACA
1 TGTATCGATACA
1080190 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1080200 original size:32 final size:33
Alignment explanation
Indices: 1080145--1080208 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
1080135 TCCAATGATT
1080145 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1080178 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
1080209 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1080202 original size:19 final size:19
Alignment explanation
Indices: 1080144--1080227 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
1080134 TTCCAATGAT
1080144 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
1080164 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1080178 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1080196 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1080215 TTGTATCGATACA
1 TTGTATCGATACA
1080228 ATTTAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1080288 original size:13 final size:13
Alignment explanation
Indices: 1080270--1080294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1080260 ATTACTCAAA
1080270 TGTATCGATACAT
1 TGTATCGATACAT
1080283 TGTATCGATACA
1 TGTATCGATACA
1080295 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1080347 original size:52 final size:52
Alignment explanation
Indices: 1080303--1080431 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1080293 CACTGATCTT
*
1080303 TGTATCGATACATGCAGGCAAATTTGCCCTGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1080355 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1080407 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1080432 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1083599 original size:61 final size:61
Alignment explanation
Indices: 1083532--1083856 Score: 377
Period size: 61 Copynumber: 5.5 Consensus size: 61
1083522 ATAGGACGTC
*
1083532 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCAAGATGCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATGCT
* * * *
1083593 TTTTCCTTTTAAAGCCCACATAAGTTGGTGGCACCTTTCAATCCTCAAAGAG-AAGGACGTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAA-GATGCT
** * *
1083654 TTTTCCTTTTAAAGCCCACACAAGTTGGCAGCACCTTTCAGTCCTTAAAGAGCAGGATGCT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATGCT
* ** *
1083715 TTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC-TT-AG--AGC--AG-G-ACG-T-C-
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATGCT
* * * **
1083765 TTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCTTTCAATGCTCTCAAAGAGCAATACACT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT-C-CTCAAAGAGCAAGATGCT
1083828 TTTTCCTTTTAAAGCCCACACAAGTTGGT
1 TTTTCCTTTTAAAGCCCACACAAGTTGGT
1083857 TGATGACAAC
Statistics
Matches: 220, Mismatches: 29, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
50 33 0.15
51 3 0.01
52 2 0.01
53 2 0.01
54 1 0.00
55 2 0.01
56 1 0.00
58 2 0.01
59 3 0.01
60 5 0.02
61 136 0.62
62 2 0.01
63 28 0.13
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (61 bp):
TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGATGCT
Found at i:1083728 original size:122 final size:121
Alignment explanation
Indices: 1083503--1083856 Score: 442
Period size: 122 Copynumber: 3.0 Consensus size: 121
1083493 CGTTACGACA
* **
1083503 CACCTTTTATCCTCAAAGAATAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 CACCTTTAATCCTCAAAGAATAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGCAGCACCT
*
1083568 TTCAGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTAAAGCCCACATAAGTTGGTGG
66 TTCAGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
*
1083624 CACCTTTCAATCCTCAAAGAGA-AGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGCAGCAC
1 CACCTTT-AATCCTCAAAGA-ATAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGCAGCAC
* *
1083688 CTTTCAGTCCTTAAAGAGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGG
64 CTTTCAGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
** * **
1083746 CACC-----T--T---AGAGCAGGACGTCTTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCT
1 CACCTTTAATCCTCAAAGAATAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGCAGCACCT
* * * **
1083801 TTCAATGCTCTCAAAGAGCAATACACTTTTTCCTTTTAAAGCCCACACAAGTTGGT
66 TTCAGT-C-CTTAAAGAGCAAGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGT
1083857 TGATGACAAC
Statistics
Matches: 209, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
111 48 0.23
112 1 0.00
113 41 0.20
114 1 0.00
116 1 0.00
121 7 0.03
122 109 0.52
123 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (121 bp):
CACCTTTAATCCTCAAAGAATAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGCAGCACCT
TTCAGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1083756 original size:50 final size:50
Alignment explanation
Indices: 1083702--1083801 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
1083692 CAGTCCTTAA
* * *
1083702 AGAGCAGGATG-CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 AGAGCAGGACGTC-TTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCTT
1083752 AGAGCAGGACGTCTTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCTT
1 AGAGCAGGACGTCTTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCTT
1083802 TCAATGCTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (50 bp):
AGAGCAGGACGTCTTTTCCTTTTAAAGCCAACACAAGTTGGTGGCACCTT
Found at i:1084994 original size:107 final size:107
Alignment explanation
Indices: 1084808--1085021 Score: 401
Period size: 107 Copynumber: 2.0 Consensus size: 107
1084798 TTCGAATACC
*
1084808 ACTTTCTTTCTTCCTTTGTTGGCATATTTTGCTTGTTGCTCTACTTTCTTTTCAATTTGAGCCTT
1 ACTTTCTTTCTTCCCTTGTTGGCATATTTTGCTTGTTGCTCTACTTTCTTTTCAATTTGAGCCTT
*
1084873 CACCTTTTCATGCAACTTCCTAACAAATTTAGCTTTGGCATT
66 CACCTTTTCATGCAACTTCCTAACAAATTCAGCTTTGGCATT
*
1084915 ACTTTCTTTCTTCCCTTGTTGGCATATTTTGCTTGTTGCTCTACTTTCTTTTTAATTTGAGCCTT
1 ACTTTCTTTCTTCCCTTGTTGGCATATTTTGCTTGTTGCTCTACTTTCTTTTCAATTTGAGCCTT
1084980 CACCTTTTCATGCAACTTCCTAACAAATTCAGCTTTGGCATT
66 CACCTTTTCATGCAACTTCCTAACAAATTCAGCTTTGGCATT
1085022 GCCATCCTGA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.17, C:0.24, G:0.11, T:0.48
Consensus pattern (107 bp):
ACTTTCTTTCTTCCCTTGTTGGCATATTTTGCTTGTTGCTCTACTTTCTTTTCAATTTGAGCCTT
CACCTTTTCATGCAACTTCCTAACAAATTCAGCTTTGGCATT
Found at i:1090218 original size:52 final size:52
Alignment explanation
Indices: 1090133--1090257 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1090123 ATATGAAAAG
* *
1090133 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATATATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1090185 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1090237 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1090258 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1090270 original size:52 final size:51
Alignment explanation
Indices: 1090133--1090277 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
1090123 ATATGAAAAG
*
1090133 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATATATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1090185 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1090237 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1090278 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1090284 original size:13 final size:13
Alignment explanation
Indices: 1090266--1090290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1090256 CAAAGATCAG
1090266 TGTATCGATACAA
1 TGTATCGATACAA
1090279 TGTATCGATACA
1 TGTATCGATACA
1090291 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1090357 original size:19 final size:18
Alignment explanation
Indices: 1090333--1090430 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1090323 TAGCTTAAAT
1090333 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1090352 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1090365 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1090384 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1090397 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1090417 TGTATCGATACAAA
1 TGTATCGATACAAA
1090431 TTGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1090370 original size:13 final size:13
Alignment explanation
Indices: 1090352--1090408 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1090342 ACAAAACTTA
1090352 TGTATCGATACAT
1 TGTATCGATACAT
1090365 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1090383 ATGTATCGATACAT
1 -TGTATCGATACAT
1090397 TGTATCGATACA
1 TGTATCGATACA
1090409 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1090372 original size:32 final size:32
Alignment explanation
Indices: 1090331--1090428 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
1090321 AGTAGCTTAA
*
1090331 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1090363 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1090395 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1090428 A
1 A
1090429 AATTGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1092708 original size:42 final size:43
Alignment explanation
Indices: 1092602--1092711 Score: 138
Period size: 42 Copynumber: 2.6 Consensus size: 43
1092592 TTCTTCTCTC
* * * *
1092602 CTCCTCCTATCATCCCTTCGC--TCTTTATTATCTCTCCTATTT
1 CTCCTCCTATCATCCCTTC-CTATCTCTACTATCCCTCCTATCT
*
1092644 CTCCTCCTATAATCCCTT-CTATCTCTACTATCCCTCCTATCT
1 CTCCTCCTATCATCCCTTCCTATCTCTACTATCCCTCCTATCT
1092686 CTCCTCCTATCAT-CCTTCCTATCTCT
1 CTCCTCCTATCATCCCTTCCTATCTCT
1092712 TCTTTCTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 4 0.07
42 54 0.92
ACGTcount: A:0.14, C:0.42, G:0.01, T:0.44
Consensus pattern (43 bp):
CTCCTCCTATCATCCCTTCCTATCTCTACTATCCCTCCTATCT
Found at i:1094429 original size:61 final size:61
Alignment explanation
Indices: 1094329--1094719 Score: 498
Period size: 61 Copynumber: 6.4 Consensus size: 61
1094319 GTTCTCATCA
* * * * * ** *
1094329 TTGGTAGCACCTTTTAGTCCTCGAAGACCAGGATGTCTTTTCTTTTTAAAGCCCACATAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
* * *
1094390 TTGGTGGCACATTTCAGTCCTCAAAGAGCATGACGTCTTTTCCTTTTAAAGCCCACACAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
* * * *
1094451 TTGGTGGCACCTTTCAGTCCTCGAAGAGCAGAACGCCTTTTCCCTTTAAAGCCCACATAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
* * ** * *
1094512 TTGGTGGCACATTTTAGTCCTCAAAGAGCAGGATATCTTTTCCGTTTAAAGCCCTCACAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
* * * *
1094573 TTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCTACACGAT
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
* * *
1094634 TTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACATCTTTT-CCTTTAAAGCTCACACAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
*
1094694 TTGGTGGCACC-TTCTAGTCCCCAAAG
1 TTGGTGGCACCTTTC-AGTCCTCAAAG
1094720 TGTAGGACAC
Statistics
Matches: 285, Mismatches: 44, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
59 3 0.01
60 36 0.13
61 246 0.86
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (61 bp):
TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAG
Found at i:1094648 original size:183 final size:182
Alignment explanation
Indices: 1094329--1094719 Score: 548
Period size: 183 Copynumber: 2.1 Consensus size: 182
1094319 GTTCTCATCA
* * * ** *
1094329 TTGGTAGCACCTTTTAGTCCTCGAAGACCAGGATGTCTTTTCTTTTTAAAGCCCACATAAGTTGG
1 TTGGTGGCACCTTTTAGTCCTCAAAGACCAGGATATCTTTTCCGTTTAAAGCCCACACAAGTTGG
* *
1094394 TGGCACATTTCAGTCCTCAAAGAGCATGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
66 TGGCACATTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAGTTGGTGGC
* * *
1094459 ACCTTTCAGTCCTCGAAGAGCAGAACGCCTTTTCCCTTTAAAGCCCACATAAG
131 ACCTTTCAGTCCTCAAAGAGCAGAACACCTTTT-CCTTTAAAGCCCACACAAG
* * *
1094512 TTGGTGGCACATTTTAGTCCTCAAAGAGCAGGATATCTTTTCCGTTTAAAGCCCTCACAAGTTGG
1 TTGGTGGCACCTTTTAGTCCTCAAAGACCAGGATATCTTTTCCGTTTAAAGCCCACACAAGTTGG
* * * * *
1094577 TGGCACCTTTCAGTCTTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCTACACGATTTGGTGGC
66 TGGCACATTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAGTTGGTGGC
* * * *
1094642 ACCTTTCAGTCCTCAAAGAGTAGGACATCTTTTCCTTTAAAGCTCACACAAG
131 ACCTTTCAGTCCTCAAAGAGCAGAACACCTTTTCCTTTAAAGCCCACACAAG
* *
1094694 TTGGTGGCACCTTCTAGTCCCCAAAG
1 TTGGTGGCACCTTTTAGTCCTCAAAG
1094720 TGTAGGACAC
Statistics
Matches: 182, Mismatches: 26, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
182 40 0.22
183 142 0.78
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (182 bp):
TTGGTGGCACCTTTTAGTCCTCAAAGACCAGGATATCTTTTCCGTTTAAAGCCCACACAAGTTGG
TGGCACATTTCAGTCCTCAAAGAGCAGGACGTCTTTTCCCTTTAAAGCCCACACAAGTTGGTGGC
ACCTTTCAGTCCTCAAAGAGCAGAACACCTTTTCCTTTAAAGCCCACACAAG
Found at i:1095610 original size:21 final size:21
Alignment explanation
Indices: 1095586--1095625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1095576 AAGGAGAAAA
1095586 TCCCATAATGCCC-TTAGCTTG
1 TCCCATAAT-CCCATTAGCTTG
*
1095607 TCCCTTAATCCCATTAGCT
1 TCCCATAATCCCATTAGCT
1095626 GAGCATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.35, G:0.10, T:0.35
Consensus pattern (21 bp):
TCCCATAATCCCATTAGCTTG
Found at i:1097244 original size:78 final size:79
Alignment explanation
Indices: 1097141--1097816 Score: 575
Period size: 78 Copynumber: 8.7 Consensus size: 79
1097131 ATTTATGTTT
* * *
1097141 TTATTTCCGAAGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCAATTTTCCATAATC-GGG
1 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCGATTTTCCATAATCAGGG
**
1097205 ATACTCCAACCTTG
66 ATACTCCAACCCCG
* * * * *
1097219 TT-TTTTCTGAGGGGATACTCTAACCCTAATTTTA-TTTAAAAAGCATCGATTTTTCATAATC--
1 TTATTTTC-GAGGGGATACTCCAACCCCAGTTTTATTTTCAAAA-CATCGATTTTCCATAATCAG
* *
1097280 GG-TACTTCAACCCTG
64 GGATACTCCAACCCCG
* * * ** *
1097295 TTATTTTCGAGGGGATACTCTAATCCC-GATTTTATTTTCAAAACATCAATTTTTTACAATCAGG
1 TTATTTTCGAGGGGATACTCCAACCCCAG-TTTTATTTTCAAAACATCGATTTTCCATAATCAGG
*
1097359 GATACTCTAACCCCG
65 GATACTCCAACCCCG
* *** * * * **
1097374 -TATTTTTGAGGGGATACTCCAACCGTGGTTTTATTTCCAAAACATTGATTTTTCATAATCAAAG
1 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCGATTTTCCATAATCAGGG
1097438 ATACTCCAACCCCG
66 ATACTCCAACCCCG
* ** * * *
1097452 TTA-TTAC-A-GGGATACTTAAACCTCAGTTTTATTTTTAAAATATCGATTTTCCATAATCAGGG
1 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCGATTTTCCATAATCAGGG
*
1097514 ATACTCCGACCCCG
66 ATACTCCAACCCCG
* * * * * * *
1097528 TTGTTTTCGAGAGGATACTCCAACCCCAGTTTTATTTCCAAAATA-CTGATTTTTC-TCAATTAA
1 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATC-GATTTTCCAT-AATCAG
1097591 GGATACTCCAACCCCG
64 GGATACTCCAACCCCG
* * * * *
1097607 TTA-TTTCTGAGAGGATACTCCAATCCCTA-TTTTATTTCCAAAACA-CTAATTTTTCA-AATC-
1 TTATTTTC-GAGGGGATACTCCAA-CCCCAGTTTTATTTTCAAAACATC-GATTTTCCATAATCA
* *
1097667 GGAGATACTCCGACCTCG
63 GG-GATACTCCAACCCCG
* * * * *
1097685 TTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAATA-CTGATTTTCCATAATCGGG
1 TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATC-GATTTTCCATAATCAGG
* *
1097749 GATACTTCAACTCCG
65 GATACTCCAACCCCG
* *
1097764 TTATTTTTGAAGGGG-TACTCCAACCTC-GATTTTATTTTCAAAACATCGATTTT
1 TTATTTTCG-AGGGGATACTCCAACCCCAG-TTTTATTTTCAAAACATCGATTTT
1097817 TTACGTTCGG
Statistics
Matches: 489, Mismatches: 83, Indels: 51
0.78 0.13 0.08
Matches are distributed among these distances:
76 107 0.22
77 33 0.07
78 171 0.35
79 167 0.34
80 11 0.02
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (79 bp):
TTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCGATTTTCCATAATCAGGG
ATACTCCAACCCCG
Found at i:1097595 original size:79 final size:77
Alignment explanation
Indices: 1097151--1097817 Score: 444
Period size: 79 Copynumber: 8.6 Consensus size: 77
1097141 TTATTTCCGA
* * *
1097151 AGGGATACTCCAACCCCAGTTTTATTTTCAAAACA-TCAATTTTC-CATAATC-GGGATACTCCA
1 AGGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTTCTC--AATCAGGGATACTCCA
**
1097213 ACCTTGTTTTTTCTG
64 ACCCCGTTTTTTC-G
* * * * *
1097228 AGGGGATACTCTAACCCTAATTTTATTT-AAAAAGCA-TCGATTTTTCAT-AATC--GG-TACTT
1 A-GGGATACTCCAACCCCAGTTTTATTTCCAAAA-CACT-GATTTTTC-TCAATCAGGGATACTC
*
1097287 CAACCCTGTTATTTTCG
62 CAACCCCGTT-TTTTCG
* * * *
1097304 AGGGGATACTCTAATCCC-GATTTTATTTTCAAAACA-TCAATTTTT-TACAATCAGGGATACTC
1 A-GGGATACTCCAACCCCAG-TTTTATTTCCAAAACACT-GATTTTTCT-CAATCAGGGATACTC
*
1097366 TAACCCCGTATTTTT-G
62 CAACCCCGT-TTTTTCG
*** * **
1097382 AGGGGATACTCCAACCGTGGTTTTATTTCCAAAACATTGATTTTTCAT-AATCAAAGATACTCCA
1 A-GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTTC-TCAATCAGGGATACTCCA
* *
1097446 ACCCCGTTATTAC-
64 ACCCCGTTTTTTCG
** * ** * * *
1097459 AGGGATACTTAAACCTCAGTTTTATTTTTAAAATA-TCGATTTTCCAT-AATCAGGGATACTCCG
1 AGGGATACTCCAACCCCAGTTTTATTTCCAAAACACT-GATTTTTC-TCAATCAGGGATACTCCA
1097522 ACCCCGTTGTTTTCG
64 ACCCCGTT-TTTTCG
* * *
1097537 AGAGGATACTCCAACCCCAGTTTTATTTCCAAAATACTGATTTTTCTCAATTAAGGATACTCCAA
1 AG-GGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTTCTCAATCAGGGATACTCCAA
*
1097602 CCCCGTTATTTCTG
65 CCCCGTTTTTTC-G
* * *
1097616 AGAGGATACTCCAATCCCTA-TTTTATTTCCAAAACACTAATTTTTC-AAATC-GGAGATACTCC
1 AG-GGATACTCCAA-CCCCAGTTTTATTTCCAAAACACTGATTTTTCTCAATCAGG-GATACTCC
* *
1097678 GACCTCGTTATTTTCG
63 AACCCCGTT-TTTTCG
* * * * *
1097694 AGGAGATACTCCAACCTCAGTTTTATTTCCAAAATACTGATTTTCCAT-AATCGGGGATACTTCA
1 AGG-GATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTTC-TCAATCAGGGATACTCCA
* *
1097758 ACTCCGTTATTTTTG
64 ACCCCGTT-TTTTCG
* * *
1097773 AAGGGGTACTCCAACCTC-GATTTTATTTTCAAAACA-TCGATTTTT
1 -AGGGATACTCCAACCCCAG-TTTTATTTCCAAAACACT-GATTTTT
1097818 TACGTTCGGG
Statistics
Matches: 479, Mismatches: 74, Indels: 72
0.77 0.12 0.12
Matches are distributed among these distances:
74 1 0.00
75 1 0.00
76 108 0.23
77 28 0.06
78 151 0.32
79 178 0.37
80 12 0.03
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (77 bp):
AGGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTTCTCAATCAGGGATACTCCAAC
CCCGTTTTTTCG
Found at i:1097817 original size:157 final size:157
Alignment explanation
Indices: 1097149--1097817 Score: 635
Period size: 157 Copynumber: 4.3 Consensus size: 157
1097139 TTTTATTTCC
* *
1097149 GAAGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCAATTTTCCATAATC-GGGATACTCCA
1 GAAGGGATACTCCAACCCGA-TTTTATTTTCAAAACATCAATTTTTCATAATCAGGGATACTCCA
** * * *
1097213 ACCTTGTT-TTTTCTGAGGGGATACTCTAACC-CTAATTTTATTT--AAAA-AGCATCGATTTTT
65 ACCCCGTTATTTTC-GAGGAGATACTCCAACCTC-AGTTTTATTTCCAAAATA-C-T-GATTTTT
* * *
1097273 CATAATC--GG-TACTTCAACCCTGTTATTTTC
125 CATAATCAAGGATACTCCAACCCCGTTATTTTT
* * * * *
1097303 GAGGGGATACTCTAATCCCGATTTTATTTTCAAAACATCAATTTTTTACAATCAGGGATACTCTA
1 GAAGGGATACTCCAA-CCCGATTTTATTTTCAAAACATCAATTTTTCATAATCAGGGATACTCCA
* * * * *
1097368 ACCCCG-TATTTTTGAGGGGATACTCCAACCGT-GGTTTTATTTCCAAAACATTGATTTTTCATA
65 ACCCCGTTATTTTCGAGGAGATACTCCAACC-TCAGTTTTATTTCCAAAATACTGATTTTTCATA
*
1097431 ATCAAAGATACTCCAACCCCGTTA---TT
129 ATCAAGGATACTCCAACCCCGTTATTTTT
** * * * *
1097457 -ACAGGGATACTTAAACCTC-AGTTTTATTTTTAAAATATCGATTTTCCATAATCAGGGATACTC
1 GA-AGGGATACTCCAACC-CGA-TTTTATTTTCAAAACATCAATTTTTCATAATCAGGGATACTC
* * *
1097520 CGACCCCGTTGTTTTCGA-GAGGATACTCCAACCCCAGTTTTATTTCCAAAATACTGATTTTTC-
63 CAACCCCGTTATTTTCGAGGA-GATACTCCAACCTCAGTTTTATTTCCAAAATACTGATTTTTCA
* *
1097583 TCAATTAAGGATACTCCAACCCCGTTATTTCT
127 T-AATCAAGGATACTCCAACCCCGTTATTTTT
* *
1097615 G-AGAGGATACTCCAATCCCTATTTTATTTCCAAAACA-CTAATTTTTCA-AATC-GGAGATACT
1 GAAG-GGATACTCCAA-CCCGATTTTATTTTCAAAACATC-AATTTTTCATAATCAGG-GATACT
* * *
1097676 CCGACCTCGTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAATACTGATTTTCCA
62 CCAACCCCGTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAATACTGATTTTTCA
** * *
1097741 TAATCGGGGATACTTCAACTCCGTTATTTTT
127 TAATCAAGGATACTCCAACCCCGTTATTTTT
* *
1097772 GAAGGGGTACTCCAACCTCGATTTTATTTTCAAAACATCGATTTTT
1 GAAGGGATACTCCAACC-CGATTTTATTTTCAAAACATCAATTTTT
1097818 TACGTTCGGG
Statistics
Matches: 423, Mismatches: 60, Indels: 61
0.78 0.11 0.11
Matches are distributed among these distances:
153 4 0.01
154 137 0.32
155 90 0.21
156 9 0.02
157 143 0.34
158 37 0.09
159 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (157 bp):
GAAGGGATACTCCAACCCGATTTTATTTTCAAAACATCAATTTTTCATAATCAGGGATACTCCAA
CCCCGTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAATACTGATTTTTCATAAT
CAAGGATACTCCAACCCCGTTATTTTT
Found at i:1099864 original size:12 final size:12
Alignment explanation
Indices: 1099847--1099878 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1099837 GGTGGTGTTT
1099847 TTTTATTTATTC
1 TTTTATTTATTC
1099859 TTTTATTTATTC
1 TTTTATTTATTC
*
1099871 ATTTATTT
1 TTTTATTT
1099879 TGTTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATTTATTC
Found at i:1105262 original size:51 final size:51
Alignment explanation
Indices: 1105168--1105335 Score: 228
Period size: 51 Copynumber: 3.3 Consensus size: 51
1105158 GAAAATGACG
* * *
1105168 GGGTTGGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAACCA
1 GGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAGCCA
* * * * * *
1105219 GGGTTGGAGCATCCCCGATTATGGGAAATTGATATTTTAGAAATAAAGCCG
1 GGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAGCCA
** *
1105270 GGGTTGGAGTATCCTTGATTGTGGAAAATCGATGTTTTAGAAATAAAGCTA
1 GGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAGCCA
1105321 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
1105336 TTCAGAAATA
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 98 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAGCCA
Found at i:1105351 original size:130 final size:127
Alignment explanation
Indices: 1105217--1105653 Score: 427
Period size: 130 Copynumber: 3.4 Consensus size: 127
1105207 GAAATAAAAC
* * * *
1105217 CAGGGTTGGAGCATCCCCGATTATGGGAAAT-TGATATTTTAGAAATAAAGCCGGGGTTGGAGTA
1 CAGGGTTGGAGTATCCCCGATTATGGAAAATCAG-TATTTTAGAAATAAA-CTGGGGTTGGAGTA
* * *
1105281 TCCTTGATTGTGGAAAATCGATGTTTTAGAAATAAAGCTAGGGTTGGAGTATCCCTTCAGAAATA
64 TCCTCGATTGTGGAAAAT-GATGGTTTAGAAATAAA-CTGGGGTTGGAGTATCCCTTCAGAAATA
1105346 A
127 A
* * *
1105347 CAGGGTTGAAGTATCCCCGATTATGGAAAATCAGTGTTTTGGAAATGAAACTGGGGTTGGAGTAT
1 CAGGGTTGGAGTATCCCCGATTATGGAAAATCAGTATTTTAGAAAT-AAACTGGGGTTGGAGTAT
* * * * *
1105412 CCTCGAATGT-GAAATATTGGTGGTTTAAAAATAAAACCGGGGTTAGAGTATCCCTTC-GAAAAT
65 CCTCGATTGTGGAAA-A-TGATGGTTTAGAAAT-AAACTGGGGTTGGAGTATCCCTTCAG-AAAT
1105475 AA
126 AA
* * * * * * * * *
1105477 CAGGGTTAGAGTATCTCCGATTGTAGAAAATCGGTGTTTTGGAAATAAAATGGGGTTAGAGTATT
1 CAGGGTTGGAGTATCCCCGATTATGGAAAATCAGTATTTTAGAAATAAACTGGGGTTGGAGTA-T
* * * * * *
1105542 CC-CAATTATGAAAAATTAGTGGTTTGGAAATAAAATCGGGGTTGGAGTATCCC-TCAGAAATAA
65 CCTCGATTGTGGAAAATGA-TGGTTTAGAAATAAACT-GGGGTTGGAGTATCCCTTCAGAAATAA
**
1105605 C-GAGGTTGGAGTATCCCCGATGGTGGAAAATCAGTATTTTAGAAATAAA
1 CAG-GGTTGGAGTATCCCCGATTATGGAAAATCAGTATTTTAGAAATAAA
1105654 AACATGAATG
Statistics
Matches: 254, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
127 1 0.00
128 52 0.20
129 51 0.20
130 142 0.56
131 8 0.03
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (127 bp):
CAGGGTTGGAGTATCCCCGATTATGGAAAATCAGTATTTTAGAAATAAACTGGGGTTGGAGTATC
CTCGATTGTGGAAAATGATGGTTTAGAAATAAACTGGGGTTGGAGTATCCCTTCAGAAATAA
Found at i:1108193 original size:50 final size:50
Alignment explanation
Indices: 1108046--1108194 Score: 201
Period size: 50 Copynumber: 3.0 Consensus size: 50
1108036 TAGGTAACAG
* * * *
1108046 CTGGGTAAAACCCAGAATGTATGGATACATTG-AGAAATGTATCAACACAT
1 CTGGGTAAAACCCAGAATGTATCGATACAATGAAG-AATGTATCGATACAT
* *
1108096 CTGGGTAAAACCTAGAATGTATCGATACAATGAAGAATGTATTGATACAT
1 CTGGGTAAAACCCAGAATGTATCGATACAATGAAGAATGTATCGATACAT
* * *
1108146 CTGGGTAAAACCCAAAATGTATCGATGCAATGAAGGATGTATCGATACA
1 CTGGGTAAAACCCAGAATGTATCGATACAATGAAGAATGTATCGATACA
1108195 AATTATGGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 85 0.98
51 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (50 bp):
CTGGGTAAAACCCAGAATGTATCGATACAATGAAGAATGTATCGATACAT
Found at i:1108962 original size:180 final size:183
Alignment explanation
Indices: 1108693--1109176 Score: 635
Period size: 180 Copynumber: 2.7 Consensus size: 183
1108683 ACACTTTGGG
* * * * * * * *
1108693 GGACT-AAAAGGTGCCACCAAC-T-TATGGGCTTTGAAAGGAAAAGGCGTCTTGCTCTTTGAGGA
1 GGACTGAAAA-GTGCCACCAACTTGTGTGGGCATTAAAAGGAAAAGACGGCATGCTCTTTCAAGA
1108755 CTGAAAGGTG-C-CCAACTTGTGTGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGGACTAA
65 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGGACTAA
1108818 AATGTGCCACCAACTTGTGTCAACTTTAAAAGGAAAAGGTGTCCTACTTTTTGA
130 AATGTGCCACCAACTTGTGTCAACTTTAAAAGGAAAAGGTGTCCTACTTTTTGA
* *
1108872 GGACTGAAAAGTGTCACCAACTTGTGTGGGCATT-AAATGAAAA-A-GGCATGCT-TTTCACAGA
1 GGACTGAAAAGTGCCACCAACTTGTGTGGGCATTAAAAGGAAAAGACGGCATGCTCTTTCA-AGA
* * *
1108933 CTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGAACTAA
65 CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGGACTAA
* * *
1108998 AATGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGTGTCCTGCTTTTTGA
130 AATGTGCCACCAACTTGTGTCAACTTTAAAAGGAAAAGGTGTCCTACTTTTTGA
* * * * * * *
1109052 GGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTCTTTGAGGAC
1 GGACTGAAAAGTGCCACCAACTTGTGTGGGCATTAAAAGGAAAAGACGGCATGCTCTTTCAAGAC
* * ** *
1109117 TGAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGA
66 TGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGGA
1109177 TTGAAAGGAT
Statistics
Matches: 263, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
177 4 0.02
178 17 0.06
179 16 0.06
180 144 0.55
181 16 0.06
182 1 0.00
183 61 0.23
184 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (183 bp):
GGACTGAAAAGTGCCACCAACTTGTGTGGGCATTAAAAGGAAAAGACGGCATGCTCTTTCAAGAC
TGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGGAAAAGACGTCTTGCTCTTTGAGGACTAAA
ATGTGCCACCAACTTGTGTCAACTTTAAAAGGAAAAGGTGTCCTACTTTTTGA
Found at i:1109182 original size:61 final size:61
Alignment explanation
Indices: 1108674--1109184 Score: 570
Period size: 61 Copynumber: 8.5 Consensus size: 61
1108664 AAAAAGAGAG
* * * * * *
1108674 AGGCGTCCTACACTTTGGGGGACTAAAAGGTGCCACCAAC-T-TATGGGCTTTGAAAGGAAA
1 AGGCGTCCTGCTCTTT-GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
1108734 AGGCGTCTTGCTCTTTGAGGACTGAAAGGTG-C-CCAACTTGTGTGGGCTTTAAAGGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * * ***
1108793 AGACGTCTTGCTCTTTGAGGACTAAAATGTGCCACCAACTTGTGTCAACTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * * * * *
1108854 AGGTGTCCTACTTTTTGAGGACTGAAAAGTGTCACCAACTTGTGTGGGCATT-AAATGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * * * * *
1108914 AAG-G-CATGCT-TTTCACAGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAGGGAAA
1 AGGCGTCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * * * *
1108973 AGACGTCTTGCTCTTTGAGAACTAAAATGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * *
1109034 AGGTGTCCTGCTTTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
1109095 AGACGTCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* *
1109156 AGGTGTCCTGCTCTTTGAGGATTGAAAGG
1 AGGCGTCCTGCTCTTTGAGGACTGAAAGG
1109185 ATAAAAGGTT
Statistics
Matches: 374, Mismatches: 68, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
57 9 0.02
58 34 0.09
59 65 0.17
60 24 0.06
61 238 0.64
62 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (61 bp):
AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
Found at i:1110165 original size:9 final size:9
Alignment explanation
Indices: 1110143--1110206 Score: 67
Period size: 9 Copynumber: 7.0 Consensus size: 9
1110133 CTTAAACAGG
1110143 TTCTTTTCTT
1 TTCTTTT-TT
1110153 TTCTTTTTT
1 TTCTTTTTT
1110162 TTCTTTTTT
1 TTCTTTTTT
*
1110171 CTCTTTTTT
1 TTCTTTTTT
*
1110180 TTGTTTTTT
1 TTCTTTTTT
*
1110189 GTT-TTTTGT
1 -TTCTTTTTT
*
1110198 TTGTTTTTT
1 TTCTTTTTT
1110207 AGAAAAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
8 2 0.04
9 36 0.77
10 9 0.19
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1118029 original size:97 final size:97
Alignment explanation
Indices: 1117863--1118094 Score: 401
Period size: 97 Copynumber: 2.4 Consensus size: 97
1117853 AAAAAAAAAT
* *
1117863 GGGGTTGGAGTATCTCCTCGGAGGAATGGGGTCGGAGTGTCCCCAATGATGACAATTTAAGCAAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCAAG
1117928 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
66 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
* * * *
1117960 GGGGTCGGAGTATCCCCTCGGAGGAATGAGGTTGGAGTGTCCCCGATGATGACAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCAAG
1118025 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
66 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
*
1118057 GAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGT
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGT
1118095 ATCTCCGAGG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 126 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGCAAG
AATAAGATTTGAATCTTGACAAGTTTAAAAGC
Found at i:1120298 original size:20 final size:20
Alignment explanation
Indices: 1120273--1120349 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
1120263 GTAAAAAGAT
1120273 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1120293 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1120313 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1120333 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
1120350 CAGGGTACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1121380 original size:28 final size:28
Alignment explanation
Indices: 1121221--1121889 Score: 568
Period size: 28 Copynumber: 22.9 Consensus size: 28
1121211 TTTAAAAAAA
*
1121221 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAG
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAG-G
* * * *
1121253 TTGCCCCTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAGG
*
1121284 GTGCCACTGACTTGTGGGCTTTGAAAAAAG
1 GTGCCACTGACTTGTGGGCTTTG--AAAGG
* * * *
1121314 TTGCCACCGACTCATGTGGGTTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTG-AAAGG
1121345 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1121373 GTGCCACTGACTTATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1121401 ATGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
1121429 ATGCCACTAACTTGTGGGCTTTAAAAAGA
1 GTGCCACTGACTTGTGGGCTTT-GAAAGG
* *
1121458 ATGTCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1121486 GTGCCACTGACTTGTAGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1121514 GTGCCATTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1121542 ATGCCACTGACTTGT-GGCTTTGAAAAGAG
1 GTGCCACTGACTTGTGGGCTTTG-AAAG-G
* *
1121571 TTGCCA-TCGACTCGTGGGCTTTGAAAGG
1 GTGCCACT-GACTTGTGGGCTTTGAAAGG
* * *
1121599 ATGCCCCTAACTTGTGGGCTTTGAAAAGAG
1 GTGCCACTGACTTGTGGGCTTTG-AAAG-G
* ** *
1121629 TTGCCACCAACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTG-AAAGG
* * *
1121660 GTTCCACTAACTTATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
**
1121688 GTGCCACTGACTTGTGGGCTTTGAAAAAAA
1 GTGCCACTGACTTGTGGGCTTTG--AAAGG
* * **
1121718 TTGCCACCGACTCGTGTGGGCTTTGAAAAAAA
1 GTGCCACTGACT--TGTGGGCTTTG--AAAGG
* * * **
1121750 TTACCACCGACTCGTGTGGGCTTTGAAAATA
1 GTGCCACTGACT--TGTGGGCTTTG-AAAGG
* *
1121781 GTGCCATTGACTTGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1121809 GTGCCACTGGCTTGTGGGCTTTGAAAAG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
1121837 ATGCCATTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
1121865 GTGCCACTGACTTGTAGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
1121890 GAGATGAACG
Statistics
Matches: 543, Mismatches: 77, Indels: 38
0.83 0.12 0.06
Matches are distributed among these distances:
27 7 0.01
28 265 0.49
29 86 0.16
30 45 0.08
31 44 0.08
32 96 0.18
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:1121473 original size:113 final size:114
Alignment explanation
Indices: 1121215--1121895 Score: 669
Period size: 113 Copynumber: 5.8 Consensus size: 114
1121205 CTTTTTTTTA
* * * * *
1121215 AAAAAAGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCCCTAACTTGTGTGGGCTTTGAA
1 AAAAGAGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GATGCCACTGAC-T-TGTGGGCTTTGAA
* * *
1121280 AA-GAGTGCCACTGACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTCATGTGGGTTTTG
60 AAGGA-TGCCACTGACTTGTGGGCTTTG--AAAAGATGCCACTGACT--TGTGGGCTTTG
* *
1121339 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTG-AAAGGAT
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* * * *
1121403 GCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTA
66 GCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG
* * * *
1121452 AAAAGAATGTCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTAGGCTTTGAAAAGG-T
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
*
1121516 GCCATTGACTTGTGGGCTTTG-AAAGAATGCCACTGACTTGT-GGCTTTG
66 GCCACTGACTTGTGGGCTTTGAAAAG-ATGCCACTGACTTGTGGGCTTTG
* * *
1121564 AAAAGAGTTGCCA-TCGACTCGTGGGCTTTGAAAGGATGCCCCTAACTTGTGGGCTTTGAAAAGA
1 AAAAGAG-TGCCACT-GACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-
* ** * * *
1121628 GTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTTCCACTAACTTATGGGCTTTG
63 GATGCCACTGACT--TGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTG
* ** *
1121683 -AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAAATTGCCACCGACTCGTGTGGGCTTTGAAAA
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGA-TGCCACTGACT--TGTGGGCTTTGAAAA
** * * * *
1121747 AAATTACCACCGACTCGTGTGGGCTTTGAAAATAGTGCCATTGACTTGTGGGCTTTG
62 GGA-TGCCACTGACT--TGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTG
* * * *
1121804 AAAAG-GTGCCACTGGCTTGTGGGCTTTGAAAAGATGCCATTGACTTGTGGGCTTTG-AAAGGGT
1 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
* *
1121867 GCCACTGACTTGTAGGCTTTGAAGAGATG
66 GCCACTGACTTGTGGGCTTTGAAAAGATG
1121896 AACGTTCAAG
Statistics
Matches: 474, Mismatches: 64, Indels: 50
0.81 0.11 0.09
Matches are distributed among these distances:
112 18 0.04
113 157 0.33
114 6 0.01
115 30 0.06
116 3 0.01
117 66 0.14
118 37 0.08
119 25 0.05
120 14 0.03
121 87 0.18
122 15 0.03
123 1 0.00
124 15 0.03
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (114 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGAT
GCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:1122874 original size:13 final size:13
Alignment explanation
Indices: 1122856--1122913 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1122846 ATTACCCAAA
1122856 TGTATCGATACAT
1 TGTATCGATACAT
*
1122869 TGTATCGATACAC
1 TGTATCGATACAT
1122882 TG-ATC--T---T
1 TGTATCGATACAT
1122889 TGTATCGATACAT
1 TGTATCGATACAT
1122902 TGTATCGATACA
1 TGTATCGATACA
1122914 CTGATCTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1122893 original size:20 final size:20
Alignment explanation
Indices: 1122868--1122933 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1122858 TATCGATACA
1122868 TTGTATCGATACACTGATCT
1 TTGTATCGATACACTGATCT
1122888 TTGTATCGAT--AC--A---
1 TTGTATCGATACACTGATCT
1122901 TTGTATCGATACACTGATCT
1 TTGTATCGATACACTGATCT
1122921 TTGTATCGATACA
1 TTGTATCGATACA
1122934 TGCAGGCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 23 0.59
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACACTGATCT
Found at i:1122898 original size:33 final size:33
Alignment explanation
Indices: 1122856--1122934 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1122846 ATTACCCAAA
1122856 TGTATCGATACATTGTATCGATACACTGATCTT
1 TGTATCGATACATTGTATCGATACACTGATCTT
1122889 TGTATCGATACATTGTATCGATACACTGATCTT
1 TGTATCGATACATTGTATCGATACACTGATCTT
1122922 TGTATCGATACAT
1 TGTATCGATACAT
1122935 GCAGGCAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACACTGATCTT
Found at i:1122978 original size:52 final size:52
Alignment explanation
Indices: 1122922--1123050 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1122912 CACTGATCTT
*
1122922 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1122974 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1123026 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1123051 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1130223 original size:24 final size:24
Alignment explanation
Indices: 1130193--1130240 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1130183 AAAGGAAACA
1130193 AAACAAAA-AAAGAGAAAA-AAGAAG
1 AAACAAAAGAAA-A-AAAAGAAGAAG
1130217 AAACAAAAGAAAAAAAAGAAGAAG
1 AAACAAAAGAAAAAAAAGAAGAAG
1130241 GGAAAAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 15 0.68
25 3 0.14
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (24 bp):
AAACAAAAGAAAAAAAAGAAGAAG
Found at i:1130226 original size:21 final size:21
Alignment explanation
Indices: 1130200--1130239 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1130190 ACAAAACAAA
*
1130200 AAAAGAGAAAAAAGAAGAAAC
1 AAAAGAAAAAAAAGAAGAAAC
1130221 AAAAGAAAAAAAAGAAGAA
1 AAAAGAAAAAAAAGAAGAA
1130240 GGGAAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAGAAAC
Found at i:1130233 original size:30 final size:27
Alignment explanation
Indices: 1130180--1130235 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
1130170 GTTCTTTTCC
*
1130180 AAAAAAGGAAACAAAACAAAAAAAGAG
1 AAAAAAGGAAACAAAAAAAAAAAAGAG
1130207 AAAAAAGAAGAAACAAAAGAAAAAAAAGA
1 AAAAAAG--GAAACAAAA-AAAAAAAAGA
1130236 AGAAGGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAAGGAAACAAAAAAAAAAAAGAG
Found at i:1131222 original size:32 final size:35
Alignment explanation
Indices: 1131191--1131317 Score: 131
Period size: 34 Copynumber: 3.7 Consensus size: 35
1131181 ATACCTTCTT
* *
1131191 AAAGTCCACAACTCCGTGGC-TCCTTTTTTCTTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTTTC-TTTC
* *
1131226 AAAGCCCACAACTCCGTGGCA--CTTTTTTCTTTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTTTTC-TTTC
* *
1131260 AAAGTCCACGACTCAGTGGCATCC--TTCTC-TTC
1 AAAGTCCACAACTCAGTGGCATCCTTTTTTCTTTC
*
1131292 AAAGTCCACGACTCAGTGGCATCCTT
1 AAAGTCCACAACTCAGTGGCATCCTT
1131318 CTCTTCAAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
32 27 0.33
34 34 0.42
35 19 0.23
36 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (35 bp):
AAAGTCCACAACTCAGTGGCATCCTTTTTTCTTTC
Found at i:1131229 original size:35 final size:35
Alignment explanation
Indices: 1131189--1131285 Score: 133
Period size: 34 Copynumber: 2.8 Consensus size: 35
1131179 AAATACCTTC
1131189 TTAAAGTCCACAACTCCGTGGCTCCTTTTTTCTTT
1 TTAAAGTCCACAACTCCGTGGCTCCTTTTTTCTTT
* *
1131224 TTAAAGCCCACAACTCCGTGGC-ACTTTTTTCTTT
1 TTAAAGTCCACAACTCCGTGGCTCCTTTTTTCTTT
* * *
1131258 TCAAAGTCCACGACTCAGTGGCATCCTT
1 TTAAAGTCCACAACTCCGTGGC-TCCTT
1131286 CTCTTCAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.55
35 21 0.40
36 3 0.06
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (35 bp):
TTAAAGTCCACAACTCCGTGGCTCCTTTTTTCTTT
Found at i:1131318 original size:32 final size:32
Alignment explanation
Indices: 1131252--1131332 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
1131242 TGGCACTTTT
*
1131252 TTCTTTTCAAAGTCCACGACTCAGTGGCATCC
1 TTCTCTTCAAAGTCCACGACTCAGTGGCATCC
1131284 TTCTCTTCAAAGTCCACGACTCAGTGGCATCC
1 TTCTCTTCAAAGTCCACGACTCAGTGGCATCC
*
1131316 TTCTCTTCAAAGCCCAC
1 TTCTCTTCAAAGTCCAC
1131333 ACAAGTCGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.30
Consensus pattern (32 bp):
TTCTCTTCAAAGTCCACGACTCAGTGGCATCC
Found at i:1131361 original size:32 final size:32
Alignment explanation
Indices: 1131324--1131426 Score: 156
Period size: 32 Copynumber: 3.2 Consensus size: 32
1131314 CCTTCTCTTC
1131324 AAAGCCCACACAAGTCGGTGGCAACCCTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTTCT
* *
1131356 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTT-TCT
*
1131389 AAAGCCCACACAAGTCAGTGGCAACCC-TTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTTCT
1131420 -AAGCCCA
1 AAAGCCCA
1131427 ATATAGCTGG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
30 7 0.11
31 3 0.05
32 28 0.43
33 27 0.42
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTTCT
Found at i:1131395 original size:33 final size:33
Alignment explanation
Indices: 1131314--1131419 Score: 160
Period size: 33 Copynumber: 3.2 Consensus size: 33
1131304 TCAGTGGCAT
1131314 CCTTCTCTTCAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTC-T-AAAGCCCACACAAGTCGGTGGCAAC
*
1131349 CCTT-TCTAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1131381 CATTCTCTAAAGCCCACACAAGTCAGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1131414 CCTTCT
1 CCTTCT
1131420 AAGCCCAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
32 27 0.42
33 32 0.49
34 2 0.03
35 4 0.06
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1131581 original size:92 final size:92
Alignment explanation
Indices: 1131414--1132063 Score: 885
Period size: 92 Copynumber: 7.1 Consensus size: 92
1131404 CAGTGGCAAC
* *
1131414 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1131479 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1131507 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1131572 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1131599 CCTCTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
*
1131664 AGCTGGCCTTAAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
1131691 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
*
1131756 AGTTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1131783 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTTTAAGTCCAATA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCT-TCTTTAAGTCCAATG
* * *
1131847 TCGCTGGTCTTGAATCAGCATATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
1131875 CCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTC
* * *
1131934 CAATATCGCTGGCCTTGAATCAGCATATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1131967 CCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTC
* *
1132026 CAATATAGCTGGCCTTGAATCAGCATATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1132059 CCTTT
1 CCTTT
1132064 TCCATCTTTA
Statistics
Matches: 526, Mismatches: 23, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
86 4 0.01
88 1 0.00
91 1 0.00
92 476 0.90
93 4 0.01
96 1 0.00
98 39 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1131861 original size:233 final size:233
Alignment explanation
Indices: 1131419--1132107 Score: 961
Period size: 233 Copynumber: 2.9 Consensus size: 233
1131409 GCAACCCTTC
* * * *
1131419 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
* * * * *
1131484 GGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
60 GGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCAC
* *
1131543 ATTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----TC-
125 ATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCT
*
1131603 -TAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
184 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
*
1131652 TAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1131717 GAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGC
66 GAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGC
*
1131782 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATA
131 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATA
* *
1131847 TCGCTGGTCTTGAATCAGCATATTGGCACCTTCTTCTT
196 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
*
1131885 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1131950 GAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGC
66 GAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGC
*
1132015 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
131 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCA
* * * *
1132080 ATGTAGTTGGCCTTTAATCAGCACATTG
193 ATATAGCTGGCCTTGAATCAGCATATTG
1132108 ACATCCTTTT
Statistics
Matches: 415, Mismatches: 26, Indels: 27
0.89 0.06 0.06
Matches are distributed among these distances:
227 81 0.20
229 2 0.00
231 3 0.01
233 292 0.70
234 3 0.01
236 34 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (233 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGC
ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
Found at i:1132099 original size:52 final size:55
Alignment explanation
Indices: 1132017--1132163 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 55
1132007 ACATTGGCAC
*
1132017 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
* * * * *
1132069 CTTTAAGTTCAATGTAGTTGGCCTTTAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
* * * *
1132124 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGG
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGG
1132164 TATCTTTATC
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 36 0.47
53 2 0.03
54 5 0.06
55 34 0.44
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCATCCTTTTTCTCAT
Found at i:1132813 original size:20 final size:19
Alignment explanation
Indices: 1132783--1132838 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
1132773 GGCAGTAGCC
*
1132783 AAAATTGTATCGATACACC
1 AAAATTGTATCGATACACA
*
1132802 AAAGTATGTATCGATACACA
1 AAAAT-TGTATCGATACACA
1132822 AAAATTGTATCGATACA
1 AAAATTGTATCGATACA
1132839 TTGGATTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (19 bp):
AAAATTGTATCGATACACA
Found at i:1132823 original size:19 final size:20
Alignment explanation
Indices: 1132783--1132838 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1132773 GGCAGTAGCC
1132783 AAAATTGTATCGATACACC-
1 AAAATTGTATCGATACACCA
*
1132802 AAAGTATGTATCGATACA-CA
1 AAAAT-TGTATCGATACACCA
1132822 AAAATTGTATCGATACA
1 AAAATTGTATCGATACA
1132839 TTGGATTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (20 bp):
AAAATTGTATCGATACACCA
Found at i:1141615 original size:13 final size:13
Alignment explanation
Indices: 1141597--1141622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1141587 ACACCAAAGT
1141597 ATGTATCGATACA
1 ATGTATCGATACA
1141610 ATGTATCGATACA
1 ATGTATCGATACA
1141623 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1141620 original size:33 final size:33
Alignment explanation
Indices: 1141578--1141642 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1141568 TAGCCAAACT
* *
1141578 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
1141611 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1141643 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1142197 original size:44 final size:48
Alignment explanation
Indices: 1142148--1142298 Score: 148
Period size: 52 Copynumber: 3.1 Consensus size: 48
1142138 AGTTGTAAGG
*
1142148 TTTGCCCAGATAAATTGAT-C-T-T-TGTATCGATACATGCAGGCAAA
1 TTTGCCCAGATAAATCGATACATATATGTATCGATACATGCAGGCAAA
**
1142192 TTTGCCCAGATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAA
1 TTTGCCCAGATAAATCGATACA-TAT---ATGTATCGATACATGCAGGCAAA
** *
1142244 TTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATACAGGCAAA
1 TTTGCCCAGATAAATCGATACA-TAT---ATGTATCGATACATGCAGGCAAA
1142296 TTT
1 TTT
1142299 TCCATATTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
44 16 0.17
45 1 0.01
47 1 0.01
48 1 0.01
52 75 0.80
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (48 bp):
TTTGCCCAGATAAATCGATACATATATGTATCGATACATGCAGGCAAA
Found at i:1142248 original size:52 final size:52
Alignment explanation
Indices: 1142170--1142298 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1142160 AATTGATCTT
*
1142170 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1142222 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1142274 TGTATCGATACATACAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1142299 TCCATATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1146569 original size:11 final size:10
Alignment explanation
Indices: 1146553--1146630 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 10
1146543 GACCCCTTTC
1146553 TATTTTTTTGT
1 TATTTTTTT-T
*
1146564 TATTTTTTCCT
1 TATTTTTT-TT
**
1146575 TGGTTTTTTT
1 TATTTTTTTT
*
1146585 T-TGTTTTTT
1 TATTTTTTTT
*
1146594 TA-TATTTTT
1 TATTTTTTTT
*
1146603 T-TGTTTTTT
1 TATTTTTTTT
*
1146612 TGTTTTTTTT
1 TATTTTTTTT
1146622 TATTTTTTT
1 TATTTTTTT
1146631 CGGGTATGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
9 19 0.37
10 17 0.33
11 15 0.29
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:1146575 original size:25 final size:24
Alignment explanation
Indices: 1146547--1146594 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1146537 CATCTGGACC
*
1146547 CCTTTCTATTTTTTTGTTATTTTTT
1 CCTTGCTATTTTTTTGTT-TTTTTT
* *
1146572 CCTTGGTTTTTTTTTGTTTTTTT
1 CCTTGCTATTTTTTTGTTTTTTT
1146595 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.04, C:0.10, G:0.08, T:0.77
Consensus pattern (24 bp):
CCTTGCTATTTTTTTGTTTTTTTT
Found at i:1146582 original size:1 final size:1
Alignment explanation
Indices: 1146578--1146630 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
1146568 TTTTCCTTGG
* * * * * *
1146578 TTTTTTTTTGTTTTTTTATATTTTTTTGTTTTTTTGTTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1146631 CGGGTATGAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:1146603 original size:18 final size:18
Alignment explanation
Indices: 1146580--1146630 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1146570 TTCCTTGGTT
1146580 TTTTTTTGTTTTTTTATA
1 TTTTTTTGTTTTTTTATA
* *
1146598 TTTTTTTGTTTTTTTGTT
1 TTTTTTTGTTTTTTTATA
*
1146616 TTTTTTTATTTTTTT
1 TTTTTTTGTTTTTTT
1146631 CGGGTATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTATA
Found at i:1146609 original size:26 final size:26
Alignment explanation
Indices: 1146580--1146630 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1146570 TTCCTTGGTT
1146580 TTTTTTTGTTTTTTTATATTTTTTTG
1 TTTTTTTGTTTTTTTATATTTTTTTG
*
1146606 TTTTTTTGTTTTTTTTTATTTTTTT
1 TTTTTTTGTTTTTTTATATTTTTTT
1146631 CGGGTATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (26 bp):
TTTTTTTGTTTTTTTATATTTTTTTG
Found at i:1152336 original size:13 final size:13
Alignment explanation
Indices: 1152318--1152343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1152308 TACAGCAAGT
1152318 ATGTATCGATACA
1 ATGTATCGATACA
1152331 ATGTATCGATACA
1 ATGTATCGATACA
1152344 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1154580 original size:21 final size:21
Alignment explanation
Indices: 1154547--1154591 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1154537 TTGCAAGTTG
*
1154547 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1154569 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1154589 AAA
1 AAA
1154592 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1156414 original size:15 final size:15
Alignment explanation
Indices: 1156394--1156424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1156384 TAAAAATGTC
*
1156394 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1156409 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1156424 C
1 C
1156425 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1158521 original size:13 final size:13
Alignment explanation
Indices: 1158503--1158528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1158493 ACATTTTTCT
1158503 TTGTATCGATACA
1 TTGTATCGATACA
1158516 TTGTATCGATACA
1 TTGTATCGATACA
1158529 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1166242 original size:23 final size:22
Alignment explanation
Indices: 1166216--1166262 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1166206 AAAAATAATG
*
1166216 GAATGAATAGCAAGAAAAAAAAA
1 GAATGAACAGCAA-AAAAAAAAA
* *
1166239 GAATGAACATCAAACAAAAAAA
1 GAATGAACAGCAAAAAAAAAAA
1166261 GA
1 GA
1166263 GTGGCCTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (22 bp):
GAATGAACAGCAAAAAAAAAAA
Found at i:1168328 original size:96 final size:97
Alignment explanation
Indices: 1168170--1168379 Score: 377
Period size: 96 Copynumber: 2.2 Consensus size: 97
1168160 ATTGAAAAAA
* *
1168170 GGGGTTAGAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGACAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGAAAATTTAAGCGAG
1168235 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
66 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
* *
1168267 GGGGTTGGAGTATCCCCTCGGAGGAAT-GGGTTGGAGTGTTCCCGATGATGAAAATTTAAGCGAG
1 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGAAAATTTAAGCGAG
1168331 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
66 AATAAGATTTGAATCTTGACAAGTTTAAAAGC
1168363 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
1168380 GAGGAATAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
96 83 0.76
97 26 0.24
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.26
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGAAAATTTAAGCGAG
AATAAGATTTGAATCTTGACAAGTTTAAAAGC
Found at i:1170598 original size:20 final size:20
Alignment explanation
Indices: 1170572--1170626 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1170562 AAAAGGACAG
*
1170572 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
1170592 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
1170612 AATGTATCTATACAT
1 AATGTATCGATACAT
1170627 CTGGGTACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1172180 original size:13 final size:13
Alignment explanation
Indices: 1172162--1172189 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1172152 CATTATTCAA
1172162 TGTATCGATACAT
1 TGTATCGATACAT
1172175 TGTATCGATACAT
1 TGTATCGATACAT
1172188 TG
1 TG
1172190 ATCTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1179147 original size:11 final size:11
Alignment explanation
Indices: 1179127--1179185 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
1179117 AGTCATAAGT
*
1179127 AAAAACACAAA
1 AAAAAAACAAA
1179138 AAAAAAACAAA
1 AAAAAAACAAA
1179149 AAAAAAACAAA
1 AAAAAAACAAA
*
1179160 AACAAAA-AAA
1 AAAAAAACAAA
* * *
1179170 ACACACACAAA
1 AAAAAAACAAA
1179181 AAAAA
1 AAAAA
1179186 GAGTGCAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 6 0.15
11 33 0.85
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Done.