Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 78
Found at i:3074054 original size:45 final size:44
Alignment explanation
Indices: 3073982--3074070 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
3073972 AAACGAACAT
* * *
3073982 GTTCTTGAACACTAAATGAACATGTTCGTGAACGTTAAATGAAC
1 GTTCTTGAACAATAAATGAACACGTTCGTGAACATTAAATGAAC
3074026 GTTCTTGAACATATAAATGAACACGTTCGTGAACATTAAATGAAC
1 GTTCTTGAACA-ATAAATGAACACGTTCGTGAACATTAAATGAAC
3074071 ACATTAGCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 11 0.27
45 30 0.73
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (44 bp):
GTTCTTGAACAATAAATGAACACGTTCGTGAACATTAAATGAAC
Found at i:3074083 original size:23 final size:24
Alignment explanation
Indices: 3074031--3074077 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
3074021 TGAACGTTCT
* *
3074031 TGAACATATAAATGAACACGTTCG
1 TGAACATATAAATGAACACATTAG
3074055 TGAACAT-TAAATGAACACATTAG
1 TGAACATATAAATGAACACATTAG
3074078 CTAACAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (24 bp):
TGAACATATAAATGAACACATTAG
Found at i:3074188 original size:30 final size:30
Alignment explanation
Indices: 3074090--3074194 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
3074080 AACAATAATA
**
3074090 AAACGAACACAAACACCTTTAAAAATAAAT
1 AAACGAACATGAACACCTTTAAAAATAAAT
* * * *
3074120 AAACAAACATGAACACGATATTACAAAT--TT
1 AAACGAACATGAACAC-CT-TTAAAAATAAAT
*
3074150 AAACGAACATGAACACCTTTAAAAATAAAC
1 AAACGAACATGAACACCTTTAAAAATAAAT
* *
3074180 AAATGAACACGAACA
1 AAACGAACATGAACA
3074195 TAACTTTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
28 7 0.12
29 1 0.02
30 42 0.72
31 1 0.02
32 7 0.12
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (30 bp):
AAACGAACATGAACACCTTTAAAAATAAAT
Found at i:3077393 original size:18 final size:16
Alignment explanation
Indices: 3077369--3077408 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3077359 CAAAACAATT
3077369 AATAAAACTAATTAAAAA
1 AATAAAA-T-ATTAAAAA
*
3077387 TATAAAATATTAAAAA
1 AATAAAATATTAAAAA
3077403 AATAAA
1 AATAAA
3077409 CATAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 13 0.65
17 1 0.05
18 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAATATTAAAAA
Found at i:3084088 original size:21 final size:21
Alignment explanation
Indices: 3084064--3084116 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3084054 TTGTTCTTAC
*
3084064 AGTATCGATACCAATTGAACA
1 AGTATCGATACCAATTGAAAA
3084085 AGTATCGATACCAATTGAAAA
1 AGTATCGATACCAATTGAAAA
3084106 AGTATCGATAC
1 AGTATCGATAC
3084117 TCACTAGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (21 bp):
AGTATCGATACCAATTGAAAA
Found at i:3087328 original size:2 final size:2
Alignment explanation
Indices: 3087321--3087360 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3087311 CTAATCTGGA
3087321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3087361 TATTTAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3093570 original size:60 final size:60
Alignment explanation
Indices: 3093474--3093628 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 60
3093464 GAATTTGGGA
* ***
3093474 ATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAGAAAGATG-GTCATAGTTT-AGGG
1 ATGAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAGAAAGA-GAGTCATAGTTTGA-GG
* * *
3093534 ATGAAATTAAAATGTTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAGTTTGAGG
1 ATGAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAGAAAGAGAGTCATAGTTTGAGG
* * * * * *
3093594 CTCAAATTACAATCTTCAAAAATTTAAGGACCAAT
1 ATGAAATTAAAATATTCAAAAGTTTAAAGACCAAT
3093629 CTAAAATGTG
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 77 0.97
61 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (60 bp):
ATGAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAGAAAGAGAGTCATAGTTTGAGG
Found at i:3094446 original size:30 final size:30
Alignment explanation
Indices: 3094412--3094475 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 30
3094402 TTTTTTTAGA
3094412 TATAAA-ATAATCAAATATTAATAAATAT-AT
1 TATAAATATAAT-AAATA-TAATAAATATAAT
3094442 TATAAATATAATAAATATAATAAATATAAT
1 TATAAATATAATAAATATAATAAATATAAT
3094472 TATA
1 TATA
3094476 TCTTTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 10 0.31
30 17 0.53
31 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TATAAATATAATAAATATAATAAATATAAT
Found at i:3094455 original size:9 final size:9
Alignment explanation
Indices: 3094413--3094471 Score: 75
Period size: 9 Copynumber: 6.2 Consensus size: 9
3094403 TTTTTTAGAT
3094413 ATAAA-ATA
1 ATAAATATA
3094421 ATCAAATATTA
1 AT-AAATA-TA
3094432 ATAAATATA
1 ATAAATATA
3094441 TTATAAATATA
1 --ATAAATATA
3094452 ATAAATATA
1 ATAAATATA
3094461 ATAAATATA
1 ATAAATATA
3094470 AT
1 AT
3094472 TATATCTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.04
9 25 0.54
10 6 0.13
11 13 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAAATATA
Found at i:3094464 original size:18 final size:18
Alignment explanation
Indices: 3094413--3094471 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
3094403 TTTTTTAGAT
3094413 ATAAA-ATAATCAAATATTA
1 ATAAATATAAT-AAATA-TA
3094432 ATAAATATATTATAAATATA
1 ATAAATATA--ATAAATATA
3094452 ATAAATATAATAAATATA
1 ATAAATATAATAAATATA
3094470 AT
1 AT
3094472 TATATCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.30
19 5 0.14
20 14 0.38
21 5 0.14
22 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATATAATAAATATA
Found at i:3094470 original size:15 final size:15
Alignment explanation
Indices: 3094411--3094461 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
3094401 CTTTTTTTAG
3094411 ATATAAA-ATAATCAA
1 ATATAAATATAAT-AA
*
3094426 ATATTAATA-AATATA
1 ATATAAATATAATA-A
*
3094441 TTATAAATATAATAA
1 ATATAAATATAATAA
3094456 ATATAA
1 ATATAA
3094462 TAAATATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 23 0.79
16 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAATATAATAA
Found at i:3113965 original size:20 final size:20
Alignment explanation
Indices: 3113942--3114004 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
3113932 ATCTAAATTC
3113942 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
3113962 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
3113985 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
3114005 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:3114160 original size:24 final size:27
Alignment explanation
Indices: 3114099--3114152 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
3114089 CCAATATATA
*
3114099 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
3114126 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
3114153 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:3121933 original size:18 final size:19
Alignment explanation
Indices: 3121910--3121952 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3121900 CAGTAATTCT
3121910 ATTCC-CTAATAATCTTAC
1 ATTCCACTAATAATCTTAC
**
3121928 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTAATAATCTTAC
3121948 ATTCC
1 ATTCC
3121953 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTCCACTAATAATCTTAC
Found at i:3126920 original size:13 final size:13
Alignment explanation
Indices: 3126902--3126926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3126892 TTGATCATGT
3126902 TCTTCATGTTCTA
1 TCTTCATGTTCTA
3126915 TCTTCATGTTCT
1 TCTTCATGTTCT
3126927 GCTGAAGTCC
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTCATGTTCTA
Found at i:3147522 original size:52 final size:51
Alignment explanation
Indices: 3147420--3147583 Score: 158
Period size: 49 Copynumber: 3.3 Consensus size: 51
3147410 TAATTTGTGG
* * * * * * *
3147420 TTCAATCTCATTC-T-AAGCTTGTAATCTTTTGCTTTACTATAACATGTAA
1 TTCAATCTCATTCATAAAACTTGTAAACTTCTGATCTACAATAACATATAA
* * * *
3147469 TTCAATTTCATTCATACAAACTTG-AAAGCTTCTGGTTTACATTAACATATAA
1 TTCAATCTCATTCATA-AAACTTGTAAA-CTTCTGATCTACAATAACATATAA
* *
3147521 TTCAATCTCATT--TAAAACTTGTAAACTTCTGATCTACAATAACTTATGA
1 TTCAATCTCATTCATAAAACTTGTAAACTTCTGATCTACAATAACATATAA
3147570 TTCAATCTCATTCA
1 TTCAATCTCATTCA
3147584 AAATCTAACA
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
49 50 0.53
50 6 0.06
51 2 0.02
52 36 0.38
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (51 bp):
TTCAATCTCATTCATAAAACTTGTAAACTTCTGATCTACAATAACATATAA
Found at i:3148326 original size:2 final size:2
Alignment explanation
Indices: 3148321--3148349 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3148311 ATGCTTAATC
3148321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3148350 GAATGAGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3148677 original size:22 final size:22
Alignment explanation
Indices: 3148632--3148686 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3148622 GTTCACGAAC
*
3148632 GTGTTCATTTAGCGTTAGTGTA
1 GTGTTCGTTTAGCGTTAGTGTA
*
3148654 GTGTTCGTTTAGCGTTCA-TTTA
1 GTGTTCGTTTAGCGTT-AGTGTA
*
3148676 GTGTTTGTTTA
1 GTGTTCGTTTA
3148687 TTGTTCGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.25, T:0.51
Consensus pattern (22 bp):
GTGTTCGTTTAGCGTTAGTGTA
Found at i:3148686 original size:11 final size:11
Alignment explanation
Indices: 3148632--3148698 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
3148622 GTTCACGAAC
*
3148632 GTGTTCATTTA
1 GTGTTCGTTTA
* * *
3148643 GCGTTAGTGTA
1 GTGTTCGTTTA
3148654 GTGTTCGTTTA
1 GTGTTCGTTTA
* *
3148665 GCGTTCATTTA
1 GTGTTCGTTTA
*
3148676 GTGTTTGTTTA
1 GTGTTCGTTTA
*
3148687 TTGTTCGGTTTA
1 GTGTTC-GTTTA
3148699 TATTCAATTT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.13, C:0.09, G:0.25, T:0.52
Consensus pattern (11 bp):
GTGTTCGTTTA
Found at i:3148692 original size:33 final size:34
Alignment explanation
Indices: 3148634--3148698 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
3148624 TCACGAACGT
3148634 GTTCATTTAGCGTTAGTGTAGTGTTC-GTTTAGC
1 GTTCATTTAGCGTTAGTGTAGTGTTCGGTTTAGC
* * * *
3148667 GTTCATTTAGTGTTTGTTTATTGTTCGGTTTA
1 GTTCATTTAGCGTTAGTGTAGTGTTCGGTTTA
3148699 TATTCAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.14, C:0.09, G:0.25, T:0.52
Consensus pattern (34 bp):
GTTCATTTAGCGTTAGTGTAGTGTTCGGTTTAGC
Found at i:3149199 original size:37 final size:38
Alignment explanation
Indices: 3149127--3149200 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
3149117 ATATTAAAAT
* *
3149127 TTATATTTTAAAATAAAAAAATCACATTAATAAAATAA
1 TTATATTTTAAAATAAAAAAATCACACTAAGAAAATAA
*
3149165 TTATA-TTTAAAATATAAAAA-CTACACTAAGAAAATA
1 TTATATTTTAAAATAAAAAAATC-ACACTAAGAAAATA
3149201 GGCATGGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.03
37 26 0.81
38 5 0.16
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.32
Consensus pattern (38 bp):
TTATATTTTAAAATAAAAAAATCACACTAAGAAAATAA
Found at i:3155075 original size:23 final size:23
Alignment explanation
Indices: 3155048--3155091 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3155038 CCAAAAGACT
*
3155048 GAAAAACGTGCTATAAAGATAAC
1 GAAAAACGTACTATAAAGATAAC
* *
3155071 GAAAAATGTATTATAAAGATA
1 GAAAAACGTACTATAAAGATA
3155092 GAATTATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.23
Consensus pattern (23 bp):
GAAAAACGTACTATAAAGATAAC
Found at i:3155118 original size:30 final size:30
Alignment explanation
Indices: 3155083--3155147 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3155073 AAAATGTATT
* *
3155083 ATAAAGATA-GAATTATTAAAAATTAAAAAA
1 ATAAAGATATGAAATAATAAAAA-TAAAAAA
* *
3155113 ATAAAGATATTAAATAATAAAAATAAATAA
1 ATAAAGATATGAAATAATAAAAATAAAAAA
3155143 ATAAA
1 ATAAA
3155148 AATAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (30 bp):
ATAAAGATATGAAATAATAAAAATAAAAAA
Found at i:3155147 original size:14 final size:15
Alignment explanation
Indices: 3155099--3155155 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
3155089 ATAGAATTAT
*
3155099 TAAAAATTAAAAAAA
1 TAAAAATTAAATAAA
3155114 TAAAGATATTAAAT-AA
1 TAAA-A-ATTAAATAAA
3155130 TAAAAA-TAAATAAA
1 TAAAAATTAAATAAA
3155144 TAAAAA-TAAATA
1 TAAAAATTAAATA
3155156 TTGAAGATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 5 0.13
14 15 0.39
15 5 0.13
16 7 0.18
17 6 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
TAAAAATTAAATAAA
Found at i:3161297 original size:21 final size:21
Alignment explanation
Indices: 3161267--3161306 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3161257 TTTTTAATTT
*
3161267 TTTTTAAATTTATATATTTTAA
1 TTTTTAAATTAATA-ATTTTAA
3161289 TTTTT-AATTAATAATTTT
1 TTTTTAAATTAATAATTTT
3161307 TACCTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAAATTAATAATTTTAA
Found at i:3166768 original size:4 final size:4
Alignment explanation
Indices: 3166761--3166785 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3166751 TATATATATA
3166761 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
3166786 TATAGTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3167935 original size:23 final size:23
Alignment explanation
Indices: 3167909--3167972 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
3167899 CAGCTTGTAT
3167909 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
3167932 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
3167955 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
3167973 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:3168172 original size:100 final size:99
Alignment explanation
Indices: 3167988--3168194 Score: 319
Period size: 100 Copynumber: 2.1 Consensus size: 99
3167978 TAATGTCCAT
* * *
3167988 AAGGACCACATATCATTCCTTAAGGATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCA-ATACATATACCAAGGATCAAGTATGTGTCTCACCA
3168053 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATAC--ATATGT-CCG
* *
3168091 AAGGACCACATATCATTCCTTAAGAATC-ATACATTTGCCAAGGATC-AGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCAATACATATACCAAGGATCAAGTATGTGTCTCACCAG
3168154 ACTTCACACATGTTCCAAAGAATACATATGTCCG
66 ACTTCACACATGTTCCAAAGAATACATATGTCCG
3168188 AAGGACC
1 AAGGACC
3168195 GCGTAGACCC
Statistics
Matches: 99, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
97 10 0.10
98 6 0.06
100 42 0.42
101 14 0.14
103 27 0.27
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (99 bp):
AAGGACCACATATCATTCCTTAAGAATCAATACATATACCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATGTCCG
Found at i:3170831 original size:21 final size:20
Alignment explanation
Indices: 3170771--3170831 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
3170761 AAAAAAATTA
* *
3170771 TATAAATTTTTATATTATAAT
1 TATAAATTTTTTTAAT-TAAT
* * *
3170792 TATATATTATTTAAATTAAT
1 TATAAATTTTTTTAATTAAT
3170812 TATAAACTTTTTTTAATTAA
1 TATAAA-TTTTTTTAATTAA
3170832 AAAATATTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAAATTTTTTTAATTAAT
Found at i:3178713 original size:2 final size:2
Alignment explanation
Indices: 3178706--3178751 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3178696 ATGTATATGC
3178706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3178748 AT AT
1 AT AT
3178752 GCATTAATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3179037 original size:18 final size:18
Alignment explanation
Indices: 3179014--3179048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3179004 AGGGATTATC
*
3179014 AGTGGTCCTTCGAGACAT
1 AGTGGTCATTCGAGACAT
*
3179032 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGAGACA
3179049 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:3179629 original size:21 final size:22
Alignment explanation
Indices: 3179603--3179652 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
3179593 ACGAAATTAT
*
3179603 TGTAGCAGGGTATCGATA-CAC
1 TGTAGCAGGGTACCGATACCAC
3179624 TGTAGCAGGGTACCGATACCAC
1 TGTAGCAGGGTACCGATACCAC
3179646 TGTAGCA
1 TGTAGCA
3179653 TACTAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (22 bp):
TGTAGCAGGGTACCGATACCAC
Found at i:3191254 original size:18 final size:19
Alignment explanation
Indices: 3191212--3191254 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3191202 TATTTCATTG
3191212 ATTTTTGAACATAGGATTA
1 ATTTTTGAACATAGGATTA
3191231 ATTTTTGAACATAGGATTA
1 ATTTTTGAACATAGGATTA
3191250 ATTTT
1 ATTTT
3191255 AATTAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (19 bp):
ATTTTTGAACATAGGATTA
Found at i:3194637 original size:42 final size:41
Alignment explanation
Indices: 3194548--3194639 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
3194538 TCTTGAAATC
*
3194548 CCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATGTTTT
* *
3194589 CCGTGTTTGTTTCACGTAATTCATTTTTCGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATGTTTT
3194630 CCAGTGTTTG
1 CC-GTGTTTG
3194640 GTTAGAAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATGTTTT
Found at i:3194901 original size:22 final size:23
Alignment explanation
Indices: 3194870--3194916 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3194860 AAAATCTATT
3194870 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
3194893 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
3194915 TA
1 TA
3194917 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3194939 original size:53 final size:50
Alignment explanation
Indices: 3194882--3194980 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 50
3194872 TTAATATTTC
* *
3194882 TAATAATATAATAT-TATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAAGATATATA-TTTT-AT-TT-TAATAAAATAATAAATTATATTA
*
3194935 TAATAATATAAGATATATATTTTATTTTAATAATATAATAAATTAT
1 TAATAATATAAGATATATATTTTATTTTAATAAAATAATAAATTAT
3194981 TAATAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
50 17 0.40
51 2 0.05
52 2 0.05
53 17 0.40
54 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (50 bp):
TAATAATATAAGATATATATTTTATTTTAATAAAATAATAAATTATATTA
Found at i:3195500 original size:14 final size:14
Alignment explanation
Indices: 3195481--3195536 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
3195471 CCAGAAATAT
*
3195481 AATTCATTTTCCAG
1 AATTCAATTTCCAG
*
3195495 AATTCAAATTT-CATT
1 AATTC-AATTTCCA-G
* *
3195510 AATTCATTTTTCAG
1 AATTCAATTTCCAG
3195524 AATTCAATTTCCA
1 AATTCAATTTCCA
3195537 AAAAACCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.45
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:3195504 original size:20 final size:21
Alignment explanation
Indices: 3195467--3195509 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3195457 CCGAAAAACG
3195467 TTTTCCAGAAATATAA-TTCA
1 TTTTCCAGAAATATAATTTCA
*
3195487 TTTTCCAGAATTCA-AATTTCA
1 TTTTCCAGAAAT-ATAATTTCA
3195508 TT
1 TT
3195510 AATTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTCCAGAAATATAATTTCA
Found at i:3195524 original size:29 final size:28
Alignment explanation
Indices: 3195480--3195534 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
3195470 TCCAGAAATA
3195480 TAATTCATTTTCCAGAATTCAAATTTCAT
1 TAATTCATTTTCCAGAATTC-AATTTCAT
*
3195509 TAATTCATTTTTCAGAATTCAATTTC
1 TAATTCATTTTCCAGAATTCAATTTC
3195535 CAAAAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (28 bp):
TAATTCATTTTCCAGAATTCAATTTCAT
Found at i:3195533 original size:15 final size:14
Alignment explanation
Indices: 3195481--3195529 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3195471 CCAGAAATAT
*
3195481 AATTCATTTTCCAG
1 AATTCATTTTTCAG
** *
3195495 AATTCAAATTTCATT
1 AATTCATTTTTCA-G
3195510 AATTCATTTTTCAG
1 AATTCATTTTTCAG
3195524 AATTCA
1 AATTCA
3195530 ATTTCCAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (14 bp):
AATTCATTTTTCAG
Found at i:3197292 original size:28 final size:28
Alignment explanation
Indices: 3197260--3197316 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3197250 TTAATGGTCG
3197260 AAAACCATTGGATTTCCAATTGGCGTGT
1 AAAACCATTGGATTTCCAATTGGCGTGT
3197288 AAAACCATTGGATTTCCAATTGGCGTGT
1 AAAACCATTGGATTTCCAATTGGCGTGT
3197316 A
1 A
3197317 CATTTTCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (28 bp):
AAAACCATTGGATTTCCAATTGGCGTGT
Found at i:3198187 original size:14 final size:14
Alignment explanation
Indices: 3198168--3198197 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3198158 TTTTAAAAAA
*
3198168 TATTTGATTGACAT
1 TATTTGATTGAAAT
3198182 TATTTGATTGAAAT
1 TATTTGATTGAAAT
3198196 TA
1 TA
3198198 ATATATATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (14 bp):
TATTTGATTGAAAT
Found at i:3204587 original size:3 final size:3
Alignment explanation
Indices: 3204579--3204616 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3204569 CTACCAAAAA
3204579 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3204617 ACCAAGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3206219 original size:31 final size:30
Alignment explanation
Indices: 3206179--3206340 Score: 184
Period size: 30 Copynumber: 5.4 Consensus size: 30
3206169 GAAATTACTG
3206179 TTTAG-CCTTTTAACTTTCTATTTTTGCTAT
1 TTTAGTCC-TTTAACTTTCTATTTTTGCTAT
* *
3206209 TTTAGTCCTTTAACTTTTTATTTTTTTCTAT
1 TTTAGTCCTTTAACTTTCTA-TTTTTGCTAT
* * *
3206240 TTTAGTCCTTTAATTTTCTATTTTTACAAT
1 TTTAGTCCTTTAACTTTCTATTTTTGCTAT
* * * * *
3206270 TTTAATCCTTTAAGTTTCTGTTTTGGTTAT
1 TTTAGTCCTTTAACTTTCTATTTTTGCTAT
* *
3206300 TTTAGTCCTGTAAATTTCTATTTTTGCTA-
1 TTTAGTCCTTTAACTTTCTATTTTTGCTAT
3206329 TTTAGTCCTTTA
1 TTTAGTCCTTTA
3206341 TTTTACTAAG
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 11 0.10
30 70 0.64
31 29 0.26
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTAGTCCTTTAACTTTCTATTTTTGCTAT
Found at i:3206252 original size:61 final size:60
Alignment explanation
Indices: 3206179--3206340 Score: 193
Period size: 61 Copynumber: 2.7 Consensus size: 60
3206169 GAAATTACTG
* * **
3206179 TTTAG-CCTTTTAACTTTCTATTTTTGCTATTTTAGTCCTTTAACTTTTTATTTTTTTCTAT
1 TTTAGTCC-TTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTGGT-TAT
* * * * * *
3206240 TTTAGTCCTTTAATTTTCTATTTTTACAATTTTAATCCTTTAAGTTTCTGTTTTGGTTAT
1 TTTAGTCCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTGGTTAT
*
3206300 TTTAGTCCTGTAAATTTCTATTTTTGCTA-TTTAGTCCTTTA
1 TTTAGTCCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTA
3206341 TTTTACTAAG
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 11 0.13
60 28 0.33
61 45 0.52
62 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (60 bp):
TTTAGTCCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAACTTTCTATTTTGGTTAT
Found at i:3209449 original size:30 final size:30
Alignment explanation
Indices: 3209415--3209566 Score: 144
Period size: 30 Copynumber: 5.0 Consensus size: 30
3209405 TAGCCTTTTC
* *
3209415 ACTTTCTATTTTTGTTATTTCAGTTCTTTA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
*
3209445 ACTTTCTATTTTTTTTTCTATTTTAGTCCTTTA
1 ACTTTCTA--TTTTTGT-TATTTTAGTCCTTTA
* ** *
3209478 ACTTTTTATTTTTACTATTTTAATCCTTTA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
* * * * *
3209508 AGTTTCTGTTTTGGTTATTTTAGTCATATA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
* *
3209538 AATTTCTATTTTTGCTA-TTTAGTCCTTTA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
3209567 TTTTACTAAG
Statistics
Matches: 97, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
29 10 0.10
30 56 0.58
31 5 0.05
32 6 0.06
33 20 0.21
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (30 bp):
ACTTTCTATTTTTGTTATTTTAGTCCTTTA
Found at i:3209467 original size:33 final size:32
Alignment explanation
Indices: 3209415--3209490 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
3209405 TAGCCTTTTC
*
3209415 ACTTTCTA--TTTTTGTTATTTCAGTTCTTTA
1 ACTTTCTATTTTTTTGTTATTTCAGTCCTTTA
* *
3209445 ACTTTCTATTTTTTTTTCTATTTTAGTCCTTTA
1 ACTTTCTATTTTTTTGT-TATTTCAGTCCTTTA
*
3209478 ACTTTTTATTTTT
1 ACTTTCTATTTTT
3209491 ACTATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 8 0.21
32 6 0.15
33 25 0.64
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.67
Consensus pattern (32 bp):
ACTTTCTATTTTTTTGTTATTTCAGTCCTTTA
Found at i:3213867 original size:23 final size:24
Alignment explanation
Indices: 3213837--3213881 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3213827 TGCATTTCAT
3213837 TTCTACGT-GCACTACGGTGCAAA
1 TTCTACGTGGCACTACGGTGCAAA
*
3213860 TTCTACGTGGCACTTCGGTGCA
1 TTCTACGTGGCACTACGGTGCA
3213882 TTTATACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
TTCTACGTGGCACTACGGTGCAAA
Found at i:3217329 original size:45 final size:45
Alignment explanation
Indices: 3217278--3217381 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
3217268 ATGCACAGGA
3217278 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
3217323 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
3217368 AGTGCATCGATGCA
1 AGTGCATCGATGCA
3217382 TAAGGAGTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
Found at i:3217391 original size:64 final size:63
Alignment explanation
Indices: 3217322--3217465 Score: 173
Period size: 64 Copynumber: 2.3 Consensus size: 63
3217312 CGAATGCAAT
* * *
3217322 TAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG
1 TAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGG
* ** * * *
3217387 -AGTGCATCGATGCACCCCCTTAAAATGAAAACATCAAAGGTGATTTGTGTATCGATGCATGGG
1 TAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGG
3217450 TAGTGCATCGATGCAC
1 TAGTGCATCGATGCAC
3217466 TTCAAGGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 60 0.88
65 5 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (63 bp):
TAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGG
Found at i:3220903 original size:21 final size:22
Alignment explanation
Indices: 3220857--3220905 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3220847 GTTATTTCTG
3220857 TATTA-TAAAAAAATCATCTAA
1 TATTATTAAAAAAATCATCTAA
* * *
3220878 AATTATTAAAAAAAT-ATGTGA
1 TATTATTAAAAAAATCATCTAA
3220899 TATTATT
1 TATTATT
3220906 TTTTGAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
TATTATTAAAAAAATCATCTAA
Found at i:3222444 original size:20 final size:20
Alignment explanation
Indices: 3222419--3222472 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3222409 GACCAACAAA
3222419 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
3222439 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
3222459 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
3222473 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:3222509 original size:21 final size:21
Alignment explanation
Indices: 3222480--3222526 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3222470 AATATGTAAA
*
3222480 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
*
3222501 TCGCGTTGCAATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
3222522 TCGCA
1 TCGCA
3222527 ACGCGATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:3222542 original size:20 final size:20
Alignment explanation
Indices: 3222517--3222586 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
3222507 TGCAATTTTC
3222517 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* * *
3222537 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
3222556 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* *
3222575 TAATTTCGCAAC
1 CAAATTCGCAAC
3222587 AGGTTTTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:3223499 original size:24 final size:24
Alignment explanation
Indices: 3223467--3223520 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3223457 GTATTCAAAA
*
3223467 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3223491 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3223515 TTTGAT
1 TTTGAT
3223521 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3226118 original size:20 final size:20
Alignment explanation
Indices: 3226042--3226128 Score: 97
Period size: 19 Copynumber: 4.5 Consensus size: 20
3226032 TGTTGCGATA
* *
3226042 AACGTGAAAGTCAAATTTGC
1 AACGCGAAAGTCAAATTCGC
*
3226062 AACGC-AAAGTCAAATTCAC
1 AACGCGAAAGTCAAATTCGC
* * *
3226081 AATGTGAAAGAC-AATTCGC
1 AACGCGAAAGTCAAATTCGC
*
3226100 AACGCGATAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
3226120 AACGCGAAA
1 AACGCGAAA
3226129 TCGCAAACTG
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 29 0.55
20 24 0.45
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGC
Found at i:3226163 original size:20 final size:20
Alignment explanation
Indices: 3226138--3226212 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
3226128 ATCGCAAACT
*
3226138 GAATTTGACTTTCGTGTTGC
1 GAATTTGACTTTCGCGTTGC
** *
3226158 GAATTTGACTACCGCGTAGC
1 GAATTTGACTTTCGCGTTGC
*
3226178 GAATTTGACTTTCGCGTTGT
1 GAATTTGACTTTCGCGTTGC
*
3226198 GAATTTGACTATCGC
1 GAATTTGACTTTCGC
3226213 AACGCTTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:3226260 original size:20 final size:19
Alignment explanation
Indices: 3226221--3226281 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
3226211 GCAACGCTTA
*
3226221 TTTCGCGTTGCAAATTACC
1 TTTCGCGTTGCAATTTACC
3226240 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGC-AATTTACC
* *
3226260 TTTTGCGTAGCAAATTTACC
1 TTTCGCGTTGC-AATTTACC
3226280 TT
1 TT
3226282 CAACAGGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 11 0.30
20 26 0.70
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (19 bp):
TTTCGCGTTGCAATTTACC
Found at i:3226806 original size:23 final size:24
Alignment explanation
Indices: 3226759--3226807 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
3226749 TCATATGTAA
* *
3226759 TTGAGTTTGAATTTAAATTTCAAT
1 TTGAGTTTGAATTTAAATATAAAT
*
3226783 TTGAG-TTGAATTTCAATATAAAT
1 TTGAGTTTGAATTTAAATATAAAT
3226806 TT
1 TT
3226808 CGGCTCCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (24 bp):
TTGAGTTTGAATTTAAATATAAAT
Found at i:3227132 original size:38 final size:39
Alignment explanation
Indices: 3227090--3227175 Score: 147
Period size: 38 Copynumber: 2.2 Consensus size: 39
3227080 TCCGATGCTC
3227090 ATCAAAATCCAAAGCTCATATGGTGCCAAGC-AAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
3227128 ATCAAAATCCAAATCTCATATTGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
3227167 ATCAAAATC
1 ATCAAAATC
3227176 TACAACATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 29 0.64
39 16 0.36
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.19
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3227519 original size:14 final size:14
Alignment explanation
Indices: 3227495--3227531 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
3227485 AAATCACTTT
3227495 ACAACATCAAATTAA
1 ACAA-ATCAAATTAA
3227510 ACAAATCAAATTAA
1 ACAAATCAAATTAA
3227524 AC-AATCAA
1 ACAAATCAA
3227532 CTTTTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (14 bp):
ACAAATCAAATTAA
Found at i:3227550 original size:12 final size:12
Alignment explanation
Indices: 3227524--3227559 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
3227514 ATCAAATTAA
3227524 ACAATCAACTTTT
1 ACAATCAA-TTTT
3227537 ACAATCAATTTT
1 ACAATCAATTTT
3227549 ACAAATCAATT
1 AC-AATCAATT
3227560 AATCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (12 bp):
ACAATCAATTTT
Found at i:3228984 original size:21 final size:21
Alignment explanation
Indices: 3228960--3229055 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
3228950 GACGGGACCA
*
3228960 CTTGAACGATGATAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * * *
3228981 CTTGAACGGTGGGAAGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* * * *
3229002 CTTCAATGATAAGGGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
**
3229023 CTTGAACGAT-AGAAGGCACCT
1 CTTGAACGATGAG-AGGGGCCT
*
3229044 CTTGAATGATGA
1 CTTGAACGATGA
3229056 TAGGTGCATC
Statistics
Matches: 54, Mismatches: 19, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 2 0.04
21 51 0.94
22 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:3229052 original size:42 final size:42
Alignment explanation
Indices: 3228974--3229053 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
3228964 AACGATGATA
* * * *
3228974 GGGGCCTCTTGAACGGTGGGAAGGGCTTCTTCAATGATAAGG
1 GGGGCCTCTTGAACGATGAGAAGGACCTCTTCAATGATAAGG
*
3229016 GGGGCCTCTTGAACGAT-AGAAGGCACCTCTTGAATGAT
1 GGGGCCTCTTGAACGATGAGAAGG-ACCTCTTCAATGAT
3229054 GATAGGTGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 5 0.16
42 27 0.84
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.24
Consensus pattern (42 bp):
GGGGCCTCTTGAACGATGAGAAGGACCTCTTCAATGATAAGG
Found at i:3231270 original size:14 final size:14
Alignment explanation
Indices: 3231251--3231295 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3231241 TAGTTTCGCA
3231251 TTGCGAATTTGGTG
1 TTGCGAATTTGGTG
* *
3231265 TTGCG-ATTTCTGCG
1 TTGCGAATTT-GGTG
3231279 TTGCGAATTTGGTG
1 TTGCGAATTTGGTG
3231293 TTG
1 TTG
3231296 TGATTTAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (14 bp):
TTGCGAATTTGGTG
Found at i:3231570 original size:22 final size:22
Alignment explanation
Indices: 3231545--3231587 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3231535 GAGATAGATG
3231545 AATTTCGTCGGAAATAGGGACA
1 AATTTCGTCGGAAATAGGGACA
* *
3231567 AATTTCGTCGGAGATGGGGAC
1 AATTTCGTCGGAAATAGGGAC
3231588 GGATGTCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (22 bp):
AATTTCGTCGGAAATAGGGACA
Found at i:3231732 original size:20 final size:20
Alignment explanation
Indices: 3231707--3231882 Score: 123
Period size: 20 Copynumber: 8.8 Consensus size: 20
3231697 ATATTATGTT
3231707 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
3231727 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* * *
3231746 TCTGTGTTG-TAATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
3231766 TTCGCGTTGCGAATTTGACTT
1 -TCGCGTTGCGAATTTGACTA
* **
3231787 TCGCGTTACGAATTTAGAAAA
1 TCGCGTTGCGAATTT-GACTA
*
3231808 TCGCGTTGCGAAATTGGA--A
1 TCGCGTTGCG-AATTTGACTA
* * *
3231827 TCTGAGTTGCGAAATTGGAAT-
1 TC-GCGTTGCG-AATTTGACTA
* *
3231848 TCACGTTGCGAATTTGA-GA
1 TCGCGTTGCGAATTTGACTA
3231867 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
3231883 TTGGTCATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.02
19 31 0.25
20 64 0.51
21 22 0.18
22 6 0.05
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:3232948 original size:66 final size:66
Alignment explanation
Indices: 3232835--3233030 Score: 329
Period size: 66 Copynumber: 3.0 Consensus size: 66
3232825 ACTTAAGGTT
* * *
3232835 TATCACTTTTATTAAGTTAATCAATCAATGAAATAATTAAGAAGGAATGAATTGATAATTAAAAT
1 TATCACTTCTATTAAGTCAATCAATCAATGAAATAATTAAGAGGGAATGAATTGATAATTAAAAT
3232900 C
66 C
* * *
3232901 TATCACTTCTATTAAGTCAATCAATCAATGATATAATCAAGAGGGAATAAATTGATAATTAAAAT
1 TATCACTTCTATTAAGTCAATCAATCAATGAAATAATTAAGAGGGAATGAATTGATAATTAAAAT
3232966 C
66 C
*
3232967 TATCACTTCTATTAAATCAATCAATCAATGAAATAATTAAGAGGGAATGAATTGATAATTAAAA
1 TATCACTTCTATTAAGTCAATCAATCAATGAAATAATTAAGAGGGAATGAATTGATAATTAAAA
3233031 GTTTGGGATG
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 120 1.00
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.33
Consensus pattern (66 bp):
TATCACTTCTATTAAGTCAATCAATCAATGAAATAATTAAGAGGGAATGAATTGATAATTAAAAT
C
Found at i:3233856 original size:21 final size:21
Alignment explanation
Indices: 3233832--3233884 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3233822 ATTCTGACTA
3233832 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3233853 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3233874 TCGCAATGCGA
1 TCGCATTGCGA
3233885 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3233902 original size:20 final size:20
Alignment explanation
Indices: 3233874--3234028 Score: 193
Period size: 20 Copynumber: 7.7 Consensus size: 20
3233864 TTTTCCTAAT
3233874 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
3233894 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* ** *
3233915 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
3233936 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
3233956 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3233976 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3233996 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
3234016 TTGCAATGCGAAT
1 TCGCAATGCGAAT
3234029 CTGACTATTG
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
20 86 0.72
21 34 0.28
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3234042 original size:60 final size:60
Alignment explanation
Indices: 3233874--3234051 Score: 189
Period size: 60 Copynumber: 2.9 Consensus size: 60
3233864 TTTTCCTAAT
* * * **
3233874 TCGCAATGCGAATACGTAAATCACAATGCGAATTTGGAAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCT-G-AAATCGCAATGCGAATTACGAAAA
* *
3233936 TCGCAATGCGATTACGTAAATCGCAATGCGAATAC-GTAAATCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTG-AAATCGCAATGCGAATTACGAAAA
* * * * *
3233996 TCGCAATGCGAATACATAAATTGCAATGCGAATCTGACTATTGCAATGCGATTTAC
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGA-AATCGCAATGCGAATTAC
3234052 ATAGCGCCAT
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.02
60 47 0.48
61 18 0.18
62 31 0.32
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGAAATCGCAATGCGAATTACGAAAA
Found at i:3234252 original size:22 final size:22
Alignment explanation
Indices: 3234227--3234291 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
3234217 GCGACATCCA
*
3234227 TCCCCATCTCCAACGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
*
3234249 TCCCCATCGT-CGACGATATCAG
1 TCCCCATC-TCCGACGAAATCAG
* *
3234271 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
3234292 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAG
Found at i:3234699 original size:20 final size:20
Alignment explanation
Indices: 3234659--3234728 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
3234649 TGCGATTCTT
*
3234659 GCGTTGCGATAGTC-TAATTC
1 GCGTTGCGATAGTCAT-TTTC
3234679 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* **
3234699 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATAGTCATTTTC
*
3234719 GTGTTGCGAT
1 GCGTTGCGAT
3234729 TTAAAGTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:3234729 original size:20 final size:20
Alignment explanation
Indices: 3234676--3234730 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3234666 GATAGTCTAA
* **
3234676 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
3234696 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
3234716 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
3234731 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:3234738 original size:20 final size:20
Alignment explanation
Indices: 3234695--3234738 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3234685 CGATAGTCAT
** *
3234695 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
3234715 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
3234735 TTTC
1 TTTC
3234739 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:3236617 original size:20 final size:20
Alignment explanation
Indices: 3236592--3236751 Score: 132
Period size: 20 Copynumber: 8.7 Consensus size: 20
3236582 AAGAATAGTT
3236592 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3236612 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3236632 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
3236648 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
3236665 AAAATCACAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
3236681 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3236699 ACAATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
3236719 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
3236739 ACTATCACAATGC
1 ACTATCGCAATGC
3236752 AAATTTAGGG
Statistics
Matches: 117, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.11
16 10 0.09
17 8 0.07
18 5 0.04
19 6 0.05
20 75 0.64
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:3236756 original size:20 final size:20
Alignment explanation
Indices: 3236717--3236757 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3236707 AATGCGAAAA
* *
3236717 TGACTATCGCAATGCGAATT
1 TGACTATCACAATGCAAATT
3236737 TGACTATCACAATGCAAATT
1 TGACTATCACAATGCAAATT
3236757 T
1 T
3236758 AGGGATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (20 bp):
TGACTATCACAATGCAAATT
Found at i:3236941 original size:20 final size:20
Alignment explanation
Indices: 3236916--3237034 Score: 132
Period size: 21 Copynumber: 5.9 Consensus size: 20
3236906 GATTCGAGTT
3236916 CGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
3236936 CGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
*
3236956 CGA-TTACGTAATCGCATTG
1 CGATTTACGTATTCGCATTG
* ** *
3236975 CGATTTTCCAAATTCGCGTTG
1 CGA-TTTACGTATTCGCATTG
* ** *
3236996 CGATTTTCCAAATTCGCGTTG
1 CGA-TTTACGTATTCGCATTG
3237017 CGATTTACGTATTCGCAT
1 CGATTTACGTATTCGCAT
3237035 CGATCGCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 18 0.21
20 34 0.39
21 35 0.40
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (20 bp):
CGATTTACGTATTCGCATTG
Found at i:3236964 original size:19 final size:19
Alignment explanation
Indices: 3236920--3236979 Score: 102
Period size: 19 Copynumber: 3.1 Consensus size: 19
3236910 CGAGTTCGAT
3236920 TTACGTATTCGCATTGCGA
1 TTACGTATTCGCATTGCGA
3236939 TTTACGTATTCGCATTGCGA
1 -TTACGTATTCGCATTGCGA
*
3236959 TTACGTAATCGCATTGCGA
1 TTACGTATTCGCATTGCGA
3236978 TT
1 TT
3236980 TTCCAAATTC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 20 0.51
20 19 0.49
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (19 bp):
TTACGTATTCGCATTGCGA
Found at i:3237520 original size:2 final size:2
Alignment explanation
Indices: 3237515--3237542 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3237505 ATTTTAAAAA
3237515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3237543 TAGTAATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3238268 original size:20 final size:20
Alignment explanation
Indices: 3238243--3238335 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
3238233 TTTTCCCAAT
3238243 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3238263 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
3238283 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
3238304 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3238325 TCGCAATGCGA
1 TCGCAATGCGA
3238336 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3238285 original size:41 final size:41
Alignment explanation
Indices: 3238240--3238335 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
3238230 CGATTTTCCC
3238240 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3238281 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3238322 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3238336 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3238289 original size:21 final size:20
Alignment explanation
Indices: 3238243--3238335 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3238233 TTTTCCCAAT
*
3238243 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
3238263 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
3238283 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
3238304 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
3238325 TCGCAATGCGA
1 TCGCAATGCGA
3238336 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:3238349 original size:20 final size:20
Alignment explanation
Indices: 3238324--3238418 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
3238314 AATTGGGAAA
*
3238324 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3238344 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3238365 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
3238385 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3238405 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3238419 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3238398 original size:41 final size:41
Alignment explanation
Indices: 3238321--3238398 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3238311 GCGAATTGGG
* * **
3238321 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
3238362 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
3238399 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:3238629 original size:22 final size:22
Alignment explanation
Indices: 3238601--3238644 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3238591 CACTCTCTCA
3238601 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3238623 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3238645 TATCTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3239122 original size:21 final size:22
Alignment explanation
Indices: 3239078--3239122 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3239068 TGTTATTATT
*
3239078 GTTTTTGGTATATCTTCATGTA
1 GTTTTTGGTATATCTTAATGTA
*
3239100 GTTTTTGGTATATC-TAATTTA
1 GTTTTTGGTATATCTTAATGTA
3239121 GT
1 GT
3239123 ATGTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.56
Consensus pattern (22 bp):
GTTTTTGGTATATCTTAATGTA
Found at i:3240757 original size:20 final size:20
Alignment explanation
Indices: 3240732--3240775 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3240722 TAGTTTACTT
3240732 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
3240752 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3240772 TCGC
1 TCGC
3240776 TCTTCTTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3242583 original size:14 final size:14
Alignment explanation
Indices: 3242564--3242599 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3242554 ATTGTTTAAT
3242564 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3242578 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3242592 TGATTTGT
1 TGATTTGT
3242600 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3242724 original size:14 final size:15
Alignment explanation
Indices: 3242705--3242781 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
3242695 CGAAATGGCT
3242705 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
3242719 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
3242737 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
3242756 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
3242770 ATCGCAATGCGA
1 ATCGCAA-GCGA
3242782 TTTCATTTCG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:3242737 original size:19 final size:19
Alignment explanation
Indices: 3242715--3242781 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
3242705 ATCGCAACGA
3242715 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3242734 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3242752 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3242766 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3242782 TTTCATTTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3242848 original size:19 final size:20
Alignment explanation
Indices: 3242806--3242855 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
3242796 GCGATATTCT
* *
3242806 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
3242826 CGTTGCGATAGCCA-TTTCA
1 CGTTGCGATAGCCATTTTCA
3242845 CGTTGCGATAG
1 CGTTGCGATAG
3242856 TCAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:3244707 original size:12 final size:12
Alignment explanation
Indices: 3244690--3244714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3244680 TCATAATCCT
3244690 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3244702 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3244714 G
1 G
3244715 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3247001 original size:19 final size:19
Alignment explanation
Indices: 3246979--3247076 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
3246969 GGAAATTACT
3246979 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3246998 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3247012 ATCGC-ATAGCGAAATGAAA
1 ATCGCAAT-GCGAAATGAAA
**
3247031 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3247045 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3247064 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3247077 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
13 1 0.02
14 17 0.28
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 29 0.48
20 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3247024 original size:33 final size:33
Alignment explanation
Indices: 3246979--3247072 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
3246969 GGAAATTACT
3246979 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3247012 ATCGC-ATAGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAAT-GCGAAATGAAAATCGCAACGAGAGA
3247045 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3247073 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3247094 original size:19 final size:20
Alignment explanation
Indices: 3247072--3247114 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3247062 AAATCGCAAC
3247072 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
3247091 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
3247111 GCGA
1 GCGA
3247115 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:3247099 original size:14 final size:14
Alignment explanation
Indices: 3247100--3247133 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3247090 TGCGATTTTC
3247100 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
3247114 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
3247128 ATTTTC
1 ATTTTC
3247134 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:3247268 original size:14 final size:14
Alignment explanation
Indices: 3247249--3247284 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3247239 TTAACATCAA
3247249 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3247263 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3247277 AC-AATCAA
1 ACAAATCAA
3247285 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3248398 original size:20 final size:20
Alignment explanation
Indices: 3248313--3248406 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
3248303 CGCTAAGTAA
*
3248313 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
3248333 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
3248353 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
3248374 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
3248394 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
3248407 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:3248425 original size:41 final size:41
Alignment explanation
Indices: 3248395--3248490 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
3248385 ATAGTCAGTA
* * *
3248395 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
3248436 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
3248477 TCGCATTGCGAATT
1 TCGCATTGCGAATT
3248491 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:3248439 original size:20 final size:20
Alignment explanation
Indices: 3248395--3248487 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3248385 ATAGTCAGTA
* **
3248395 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
3248416 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
3248436 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
3248457 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
3248477 TCGCATTGCGA
1 TCGCATTGCGA
3248488 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:3254713 original size:43 final size:43
Alignment explanation
Indices: 3254639--3254722 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
3254629 CGTTTACCGT
3254639 TGATAGTTCATTTCTTCTAAGCTTGAAGGATAATTATGATTGC
1 TGATAGTTCATTTCTTCTAAGCTTGAAGGATAATTATGATTGC
* * *
3254682 TGATGGTTTATTTCTTCTAA-TTTGAATGGATAATTATGATT
1 TGATAGTTCATTTCTTCTAAGCTTGAA-GGATAATTATGATT
3254723 AATGAAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 5 0.14
43 32 0.86
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.46
Consensus pattern (43 bp):
TGATAGTTCATTTCTTCTAAGCTTGAAGGATAATTATGATTGC
Found at i:3262503 original size:35 final size:35
Alignment explanation
Indices: 3262457--3262528 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
3262447 AAAAAAAAAA
3262457 TAGTGATTGTTTGAGCTAGAAGTTAACCTATTGAT
1 TAGTGATTGTTTGAGCTAGAAGTTAACCTATTGAT
* *
3262492 TAGTGATTGTTTGAGTTAGATGTTAACCTATTGAT
1 TAGTGATTGTTTGAGCTAGAAGTTAACCTATTGAT
3262527 TA
1 TA
3262529 AGATATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (35 bp):
TAGTGATTGTTTGAGCTAGAAGTTAACCTATTGAT
Found at i:3263077 original size:14 final size:15
Alignment explanation
Indices: 3263058--3263086 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3263048 CATTGTTAAT
3263058 AATATTTT-TTAAAA
1 AATATTTTATTAAAA
3263072 AATATTTTATTAAAA
1 AATATTTTATTAAAA
3263087 TGACAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTATTAAAA
Found at i:3263588 original size:49 final size:49
Alignment explanation
Indices: 3263516--3263614 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
3263506 CGAGCAAGCA
3263516 CATATAACCTTTTGTTCCCCCCCCCCCCCCGTAGATAATGAGTTCAAAT
1 CATATAACCTTTTGTTCCCCCCCCCCCCCCGTAGATAATGAGTTCAAAT
*
3263565 CATATAACCTTTTGTTCCCCCCCCCCCCCGGTAGATAATGAGTTCAAAT
1 CATATAACCTTTTGTTCCCCCCCCCCCCCCGTAGATAATGAGTTCAAAT
3263614 C
1 C
3263615 TATTAAAAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.24, C:0.36, G:0.11, T:0.28
Consensus pattern (49 bp):
CATATAACCTTTTGTTCCCCCCCCCCCCCCGTAGATAATGAGTTCAAAT
Found at i:3272969 original size:2 final size:2
Alignment explanation
Indices: 3272947--3272989 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3272937 AGCATGTTTG
* *
3272947 TA TA TA T- TA TA T- TA AA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3272987 TA T
1 TA T
3272990 TTGTATTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3273938 original size:21 final size:21
Alignment explanation
Indices: 3273913--3273955 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3273903 TTCTAAACCC
*
3273913 TAAATTCTAAAATACTTTAAT
1 TAAATTCTAAAATACTTCAAT
3273934 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
3273955 T
1 T
3273956 TAAGGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:3274114 original size:14 final size:16
Alignment explanation
Indices: 3274078--3274114 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3274068 TATTAATGTA
3274078 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
3274095 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
3274110 T-AATA
1 TGAATA
3274115 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:3274804 original size:127 final size:125
Alignment explanation
Indices: 3274554--3274810 Score: 399
Period size: 127 Copynumber: 2.0 Consensus size: 125
3274544 AATTTTCTTC
* *
3274554 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
3274619 CCTGATAAATGATTAATTTATTAAATTTTATTTATTTAGGACCAAATTGATAGCATATATAA
66 CCTAATAAATGATTAATTTATTAAATTTTATTTATTTAGGACCAAATTGATA-CATATA-AA
* * * *
3274681 TAATTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
3274746 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT-TATATAAA
66 CCTAA-TAAATGATTAATTTATTAAATTTTATTT-ATTTAGGACCAAATTGATACATATAAA
3274807 TAAT
1 TAAT
3274811 AAAGACTGAA
Statistics
Matches: 120, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
126 6 0.05
127 68 0.57
128 28 0.23
129 18 0.15
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (125 bp):
TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATAAATGATTAATTTATTAAATTTTATTTATTTAGGACCAAATTGATACATATAAA
Found at i:3275245 original size:34 final size:33
Alignment explanation
Indices: 3275207--3275274 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
3275197 TTTAAGTATT
*
3275207 TTGGAATTTAGGGTTTAGAATAAAATTGAATTAC
1 TTGGAAATTAGGGTTTAGAATAAAATTG-ATTAC
* *
3275241 TTGGAAATTGGGGTTTAGAATGAAATTGATTAC
1 TTGGAAATTAGGGTTTAGAATAAAATTGATTAC
3275274 T
1 T
3275275 GTTTTGCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 6 0.19
34 25 0.81
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (33 bp):
TTGGAAATTAGGGTTTAGAATAAAATTGATTAC
Found at i:3287106 original size:48 final size:48
Alignment explanation
Indices: 3287033--3287129 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
3287023 CATCGCGTAG
*
3287033 GAACCGAGTTATCATCCTTCTTAAAGATGACCAAGAACTCTTCATCAC
1 GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
*
3287081 GAACCGAGTTATCATCTTTCCTAAAGATGACCAAGAACTCTTCATCAC
1 GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
3287129 G
1 G
3287130 TATGAGCAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (48 bp):
GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
Found at i:3288636 original size:28 final size:30
Alignment explanation
Indices: 3288569--3288636 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
3288559 TATATAATTT
3288569 ATATTAATA-AGTATTTATAATTAATAATA
1 ATATTAATATAGTATTTATAATTAATAATA
* *
3288598 A-AATAAT-TA-TATATTATAATTAATATTA
1 ATATTAATATAGTAT-TTATAATTAATAATA
3288626 ATATTAATATA
1 ATATTAATATA
3288637 AAATATAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 3 0.09
28 21 0.66
29 6 0.19
30 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATTAATATAGTATTTATAATTAATAATA
Found at i:3288643 original size:28 final size:28
Alignment explanation
Indices: 3288584--3288643 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3288574 AATAAGTATT
* *
3288584 TATAATTAATAATAAAATAATTATATAT
1 TATAATTAATAATAAAATAATTATAAAA
* *
3288612 TATAATTAATATTAATATTAA-TATAAAA
1 TATAATTAATAATAA-AATAATTATAAAA
3288640 TATA
1 TATA
3288644 GTCTATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TATAATTAATAATAAAATAATTATAAAA
Found at i:3288657 original size:31 final size:31
Alignment explanation
Indices: 3288622--3288683 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3288612 TATAATTAAT
3288622 ATTAATATTAATATAAAATATA-GTCTATAAA
1 ATTAATATTAATATAAAATATATGT-TATAAA
* *
3288653 ATTAATATTGATATAAACTATATGTTATAAA
1 ATTAATATTAATATAAAATATATGTTATAAA
3288684 TTATATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (31 bp):
ATTAATATTAATATAAAATATATGTTATAAA
Found at i:3288720 original size:126 final size:127
Alignment explanation
Indices: 3288586--3288836 Score: 282
Period size: 126 Copynumber: 2.0 Consensus size: 127
3288576 TAAGTATTTA
* * *
3288586 TAATTAATAATAAAATAATTATA-TATTAT-AATTA-ATATTAATATTAATATAAAATATAGTCT
1 TAATTAATAATAAAACAA-TATAGT-TTATAAACTATATACT-ATATTAATATAAAATATAGT-T
* * ** * *
3288648 ATA-A-AATTAATATTGATATAAACTATAT-G-TTATAAATTATATAGTATAGTTTATAAATTAT
62 A-AGATAATTAACATTAATATAAACTATATAGAACATAAA-TATAAACTATAGTTTATAAATTAT
3288709 AGT
125 AGT
* * *
3288712 TAATTAATATTAATACAATATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGA
1 TAATTAATAATAAAACAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGA
*
3288777 TAATTAACATTAATATAAACTATATAGAACATTAATATAAACTATAGTTTATAAATTATA
66 TAATTAACATTAATATAAACTATATAGAACATAAATATAAACTATAGTTTATAAATTATA
3288837 TACTATAGGT
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
124 1 0.01
125 11 0.10
126 61 0.58
127 28 0.27
128 4 0.04
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (127 bp):
TAATTAATAATAAAACAATATAGTTTATAAACTATATACTATATTAATATAAAATATAGTTAAGA
TAATTAACATTAATATAAACTATATAGAACATAAATATAAACTATAGTTTATAAATTATAGT
Found at i:3288769 original size:15 final size:15
Alignment explanation
Indices: 3288751--3288801 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3288741 AACTATATAC
3288751 TATATTAATATAAAT
1 TATATTAATATAAAT
*
3288766 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
3288781 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
3288797 TATAT
1 TATAT
3288802 AGAACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:3288841 original size:21 final size:21
Alignment explanation
Indices: 3288812--3288863 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3288802 AGAACATTAA
*
3288812 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAT
* *
3288833 TATATACTATAGGTTAT-AAG
1 TATAAACTATAGGTTATAAAT
3288853 TATAAACTATA
1 TATAAACTATA
3288864 TAGTACACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAT
Found at i:3288878 original size:22 final size:21
Alignment explanation
Indices: 3288787--3288884 Score: 69
Period size: 22 Copynumber: 4.6 Consensus size: 21
3288777 TAATTAACAT
*
3288787 TAATATAAACTATATAGAACA
1 TAATATAAACTATATAGTACA
**
3288808 TTAATATAAAC--TATAGTTTA
1 -TAATATAAACTATATAGTACA
* * *
3288828 TAAATTATATACTATA-GGT-TA
1 T-AA-TATAAACTATATAGTACA
3288849 TAAGTATAAACTATATAGTACA
1 TAA-TATAAACTATATAGTACA
3288871 CTAATATAAACTAT
1 -TAATATAAACTAT
3288885 TGATTATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.02
20 20 0.33
21 11 0.18
22 23 0.38
23 5 0.08
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (21 bp):
TAATATAAACTATATAGTACA
Found at i:3288990 original size:18 final size:17
Alignment explanation
Indices: 3288906--3289016 Score: 76
Period size: 18 Copynumber: 6.8 Consensus size: 17
3288896 TATAGGTTAC
* *
3288906 ATATATAGTTTATAGCTT
1 ATATATA-TATATAGTTT
* *
3288924 ATA-A-ATATATTGTAT
1 ATATATATATATAGTTT
*
3288939 ATATACATACTATA-TGTT
1 ATATATATA-TATAGT-TT
3288957 ATATAT-T-TATA--TT
1 ATATATATATATAGTTT
3288970 ATATA-ATATATAGTTT
1 ATATATATATATAGTTT
*
3288986 ATATACTATAGATAGTTT
1 ATATA-TATATATAGTTT
3289004 ATATATATATATA
1 ATATATATATATA
3289017 CATAAGTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
13 8 0.11
14 4 0.05
15 13 0.18
16 9 0.12
17 13 0.18
18 27 0.36
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (17 bp):
ATATATATATATAGTTT
Found at i:3289026 original size:21 final size:22
Alignment explanation
Indices: 3288985--3289031 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3288975 ATATATAGTT
*
3288985 TATATACTATAGATAGTTTATA
1 TATATACTATACATAGTTTATA
3289007 TATATA-TATACATAAG-TTATA
1 TATATACTATACAT-AGTTTATA
3289028 TATA
1 TATA
3289032 GTTTACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TATATACTATACATAGTTTATA
Done.