Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold49
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: 1668912
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 42860 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:1107351 original size:13 final size:13
Alignment explanation
Indices: 1107333--1107357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1107323 ACCAAGATCA
1107333 TGTATCAATACAG
1 TGTATCAATACAG
1107346 TGTATCAATACA
1 TGTATCAATACA
1107358 AAGCAATATG
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:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
TGTATCAATACAG
Found at i:1114100 original size:20 final size:19
Alignment explanation
Indices: 1114055--1114107 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1114045 TATAGTATAA
*
1114055 ATGTATCAATACAATTTTC
1 ATGTATCAATACAAATTTC
* *
1114074 ATATATCGATACAAATTTC
1 ATGTATCAATACAAATTTC
1114093 ATTGTATCAATACAA
1 A-TGTATCAATACAA
1114108 TCTGAAAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (19 bp):
ATGTATCAATACAAATTTC
Found at i:1119401 original size:20 final size:20
Alignment explanation
Indices: 1119378--1119425 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1119368 CATTTCAAGC
1119378 ATGTATAGATACATT-CACTT
1 ATGTATAGATACATTAC-CTT
*
1119398 ATGTATCGATACATTACCTT
1 ATGTATAGATACATTACCTT
1119418 ATTGTATA
1 A-TGTATA
1119426 AATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGTATAGATACATTACCTT
Found at i:1127475 original size:19 final size:18
Alignment explanation
Indices: 1127430--1127487 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
1127420 TACTGCCAGT
*
1127430 TCATGTATCTATACATATG
1 TCATGTATCGATACA-ATG
1127449 TGCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
1127468 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
1127487 T
1 T
1127488 ATCGATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 21 0.58
20 14 0.39
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:1127489 original size:13 final size:13
Alignment explanation
Indices: 1127471--1127530 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
1127461 TACAATGATC
1127471 ATGTATCGATACA
1 ATGTATCGATACA
1127484 ATGTATCGATACA
1 ATGTATCGATACA
*
1127497 A---AAC-AT--A
1 ATGTATCGATACA
1127504 ATGTATCGATACA
1 ATGTATCGATACA
1127517 ATGTATCGATACA
1 ATGTATCGATACA
1127530 A
1 A
1127531 AGCATAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
9 2 0.05
10 4 0.10
11 2 0.05
13 29 0.74
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1127549 original size:33 final size:33
Alignment explanation
Indices: 1127452--1127538 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
1127442 ACATATGTGC
* *
1127452 ATGTATCGATACAATG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
*
1127484 ATGTATCGATACAAAACATAATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
1127517 ATGTATCGATACAAAGCATAAT
1 ATGTATCGATACAAAGCATAAT
1127539 ATATTAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 14 0.28
33 36 0.72
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:1130061 original size:20 final size:20
Alignment explanation
Indices: 1130036--1130096 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1130026 GTAGCTCATG
1130036 TATCGATACAAAGAACATTA
1 TATCGATACAAAGAACATTA
*
1130056 TATCGATAC-----A-A-TG
1 TATCGATACAAAGAACATTA
1130069 TATCGATACAAAGAACATTA
1 TATCGATACAAAGAACATTA
1130089 TATCGATA
1 TATCGATA
1130097 TATCTGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 18 0.56
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (20 bp):
TATCGATACAAAGAACATTA
Found at i:1130075 original size:33 final size:33
Alignment explanation
Indices: 1130033--1130096 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1130023 ATAGTAGCTC
1130033 ATGTATCGATACAAAGAACATTATATCGATACA
1 ATGTATCGATACAAAGAACATTATATCGATACA
1130066 ATGTATCGATACAAAGAACATTATATCGATA
1 ATGTATCGATACAAAGAACATTATATCGATA
1130097 TATCTGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGAACATTATATCGATACA
Found at i:1133590 original size:20 final size:20
Alignment explanation
Indices: 1133565--1133638 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
1133555 TGTTTGGGAA
1133565 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
1133585 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
*
1133605 ATGTATCGATACAATGT-GTC
1 ATGTATCGATACAAT-TCTTC
*
1133625 ATGTATCAATACAA
1 ATGTATCGATACAA
1133639 ACAGTGGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTC
Found at i:1138889 original size:52 final size:52
Alignment explanation
Indices: 1138811--1138939 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1138801 CGAAATATGA
* *
1138811 AAATTTATCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* * *
1138863 AAATTTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1138915 AAATTTACCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
1138940 AAGATCGGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1138966 original size:13 final size:13
Alignment explanation
Indices: 1138948--1138972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1138938 CAAAGATCGG
1138948 TGTATCGATACAA
1 TGTATCGATACAA
1138961 TGTATCGATACA
1 TGTATCGATACA
1138973 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:1139041 original size:20 final size:19
Alignment explanation
Indices: 1139012--1139049 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1139002 GCAGTAGCTT
1139012 AAATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
1139031 AAATATGTATCGATACAAA
1 AAAT-TGTATCGATACAAA
1139050 TCGTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Found at i:1140684 original size:78 final size:79
Alignment explanation
Indices: 1140550--1140753 Score: 223
Period size: 80 Copynumber: 2.6 Consensus size: 79
1140540 GAGATAATAA
* * * * * ** * *
1140550 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAG-AAATCGATG
1 CGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAAATCAAT-
*
1140614 A-TTAGAAAAAAAAT
65 ATTTAGAAAAAAAAC
*
1140628 CGGGATTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
1 CGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
* * * *
1140693 TTTTGGGAATAAAGC
66 -TTTAGAAAAAAAAC
* *
1140708 CGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCC
1140754 GATGAAATAA
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 47 0.45
79 7 0.07
80 51 0.49
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
TTTAGAAAAAAAAC
Found at i:1140770 original size:28 final size:28
Alignment explanation
Indices: 1140711--1140779 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1140701 ATAAAGCCGG
** * * *
1140711 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
1140739 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
1140767 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1140780 TTGACTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:1140829 original size:108 final size:109
Alignment explanation
Indices: 1140693--1140942 Score: 360
Period size: 108 Copynumber: 2.3 Consensus size: 109
1140683 AAAATCAATA
* ** * * *
1140693 TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
**
1140758 AAATAACGAGGTTGGAGTATCCTTGACTGTGAA-AAATTGGT-AT
66 -AATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGAT
*
1140801 TTTTGGAAATAAAATCGGAGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
* * * *
1140866 ATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTT
66 AATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGAT
1140910 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1140943 GATTATAGAA
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
107 27 0.21
108 66 0.52
109 33 0.26
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (109 bp):
TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
AATAACGAGGTTGGAGTATCCCCGACTGTGAAGAAATTGGTGAT
Found at i:1140856 original size:28 final size:27
Alignment explanation
Indices: 1140820--1140890 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
1140810 TAAAATCGGA
* **
1140820 GTTGAAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
1140848 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
1140875 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
1140891 TTGTGAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:1140937 original size:54 final size:51
Alignment explanation
Indices: 1140875--1141005 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
1140865 GATTAACGGG
* ** *
1140875 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TCATGAAAATAAAATCGGA
*
1140929 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCATGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTCATGAAAATAAAATCGGA
*
1140980 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1141006 TTGAGAAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
51 34 0.51
52 4 0.06
53 10 0.15
54 19 0.28
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTCATGAAAATAAAATCGGA
Found at i:1143385 original size:13 final size:13
Alignment explanation
Indices: 1143367--1143392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1143357 ACAAAGATCC
1143367 ATGTATCGATACA
1 ATGTATCGATACA
1143380 ATGTATCGATACA
1 ATGTATCGATACA
1143393 CAGAAAAATG
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:1143388 original size:33 final size:33
Alignment explanation
Indices: 1143346--1143412 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1143336 AAAATTTCCA
***
1143346 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1143379 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1143412 A
1 A
1143413 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1143456 original size:19 final size:18
Alignment explanation
Indices: 1143432--1143499 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1143422 CAGTAGCTAA
1143432 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1143451 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1143466 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1143483 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1143500 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1143472 original size:13 final size:13
Alignment explanation
Indices: 1143454--1143478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1143444 ACAATACTTA
1143454 TGTATCGATACAT
1 TGTATCGATACAT
1143467 TGTATCGATACA
1 TGTATCGATACA
1143479 AAACTTATGT
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:1143476 original size:32 final size:32
Alignment explanation
Indices: 1143435--1143497 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1143425 TAGCTAATTA
*
1143435 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1143467 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1143498 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1146475 original size:78 final size:79
Alignment explanation
Indices: 1146341--1146544 Score: 216
Period size: 80 Copynumber: 2.6 Consensus size: 79
1146331 GAGATAATAA
* * ** * *
1146341 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAG-AAATCGAT
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAATCAAT
*
1146404 GA-TTAGAAAAAAAAT
65 -ATTTAGAAAAAAAAC
*
1146419 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
* * * *
1146484 TTTTGGGAATAAAGC
66 -TTTAGAAAAAAAAC
* * * *
1146499 CGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1146545 GATGAAATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
77 6 0.06
78 43 0.41
79 7 0.07
80 49 0.47
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAATCAATA
TTTAGAAAAAAAAC
Found at i:1146556 original size:108 final size:108
Alignment explanation
Indices: 1146419--1146733 Score: 323
Period size: 108 Copynumber: 2.9 Consensus size: 108
1146409 GAAAAAAAAT
* *
1146419 CGGGATTGGAGTATCCCTTCGA--AAATAACGGGGTTGGAGTATCCCCAATTATGAGAAAATCAA
1 CGGGGTTGGAGTATCCC--CGATGAAATAACGGGGTTGGAGTATCCCCAACTATGA-AAAATCAA
* * * *
1146482 TA-TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
63 TATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * *** * ***
1146527 TGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGACTGTGAAAAATTGGTAT
1 CGGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCAACTATGAAAAATCAATAT
*
1146592 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAA
66 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
* * * * * ***
1146635 CGGGGTTGGAGTATCCCTGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTG
1 CGGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCAACTATGAA-AAATCAAT-
* *
1146699 TTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
64 ATTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
1146734 GATTATAGAA
Statistics
Matches: 178, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
106 3 0.02
107 34 0.19
108 107 0.60
109 34 0.19
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.28
Consensus pattern (108 bp):
CGGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCAACTATGAAAAATCAATAT
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
Found at i:1146561 original size:28 final size:28
Alignment explanation
Indices: 1146502--1146570 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1146492 ATAAAGCCGG
** * * *
1146502 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
1146530 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
1146558 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1146571 TTGACTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:1146646 original size:28 final size:27
Alignment explanation
Indices: 1146611--1146679 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 27
1146601 TAAAATCGGA
1146611 GTTGGAGTATCCCCTCG-GAAATAACGGG
1 GTTGGAGTATCCCCT-GAG-AATAACGGG
*
1146639 GTTGGAGTAT-CCCTGATGATTAACGGG
1 GTTGGAGTATCCCCTGA-GAATAACGGG
1146666 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1146680 GATTGTGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 1 0.03
27 22 0.59
28 14 0.38
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (27 bp):
GTTGGAGTATCCCCTGAGAATAACGGG
Found at i:1146733 original size:54 final size:51
Alignment explanation
Indices: 1146666--1146796 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
1146656 GATTAACGGG
* * *
1146666 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TCTTGAAAATAAAATCGGA
*
1146720 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTCTTGAAAATAAAATCGGA
*
1146771 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1146797 TTGAGAAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
51 35 0.51
52 4 0.06
53 10 0.15
54 19 0.28
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTCTTGAAAATAAAATCGGA
Found at i:1149163 original size:20 final size:20
Alignment explanation
Indices: 1149136--1149190 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1149126 TAAAATTTCC
*
1149136 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1149156 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1149176 AAATGTATCGATACA
1 AAATGTATCGATACA
1149191 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1149234 original size:19 final size:18
Alignment explanation
Indices: 1149210--1149277 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1149200 CAGTAGCTAA
1149210 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1149229 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1149244 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1149261 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1149278 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1149250 original size:13 final size:13
Alignment explanation
Indices: 1149232--1149256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1149222 ACAATACTTA
1149232 TGTATCGATACAT
1 TGTATCGATACAT
1149245 TGTATCGATACA
1 TGTATCGATACA
1149257 AAACTTATGT
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:1149254 original size:32 final size:32
Alignment explanation
Indices: 1149213--1149275 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1149203 TAGCTAATTA
*
1149213 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1149245 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1149276 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1149357 original size:21 final size:21
Alignment explanation
Indices: 1149333--1149389 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1149323 CATTTGTAGG
1149333 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1149354 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1149375 ATGTATCGATACATT
1 ATGTATCGATACATT
1149390 TGGATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1150173 original size:55 final size:53
Alignment explanation
Indices: 1150080--1150257 Score: 230
Period size: 55 Copynumber: 3.2 Consensus size: 53
1150070 AAGAGGAAAA
* * * * *
1150080 TAAAGTGTATCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTT
1 TAAAG-GTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTT
*
1150135 TGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTT
*
1150190 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTT
1150245 TAAAAGGTGTCCT
1 T-AAAGGTGTCCT
1150258 CCACCTATAT
Statistics
Matches: 110, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
54 5 0.05
55 95 0.86
56 10 0.09
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (53 bp):
TAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTT
Found at i:1153005 original size:19 final size:19
Alignment explanation
Indices: 1152978--1153027 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1152968 TCGATACACT
* *
1152978 GTATGGATACATGATCTTG
1 GTATCGATACACGATCTTG
1152997 GTATCGATACACGATCTTG
1 GTATCGATACACGATCTTG
1153016 GTATCGATACAC
1 GTATCGATACAC
1153028 AGCGAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (19 bp):
GTATCGATACACGATCTTG
Found at i:1153102 original size:20 final size:20
Alignment explanation
Indices: 1153077--1153143 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1153067 CTACCACTAT
1153077 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
1153097 TTGTATCGAT--A---T--A
1 TTGTATCGATACATGGTACA
1153110 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGGTACA
1153130 TTGTATCGATACAT
1 TTGTATCGATACAT
1153144 TGTATCGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
18 2 0.05
20 25 0.62
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGGTACA
Found at i:1153144 original size:13 final size:13
Alignment explanation
Indices: 1153093--1153156 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
1153083 CGATACATGG
1153093 TACATTGTATCGA
1 TACATTGTATCGA
*
1153106 TATATTGTATCGA
1 TACATTGTATCGA
1153119 TACA-TG----G-
1 TACATTGTATCGA
1153126 TACATTGTATCGA
1 TACATTGTATCGA
1153139 TACATTGTATCGA
1 TACATTGTATCGA
1153152 TACAT
1 TACAT
1153157 AGTGAAAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
12 3 0.07
13 33 0.77
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1153177 original size:33 final size:33
Alignment explanation
Indices: 1153077--1153156 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
1153067 CTACCACTAT
*
1153077 TTGTATCGATACATGGTACATTGTATCGATATA
1 TTGTATCGATACATGGTACATTGTATCGATACA
1153110 TTGTATCGATACATGGTACATTGTATCGATACA
1 TTGTATCGATACATGGTACATTGTATCGATACA
1153143 TTGTATCGATACAT
1 TTGTATCGATACAT
1153157 AGTGAAAAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGGTACATTGTATCGATACA
Found at i:1156513 original size:13 final size:13
Alignment explanation
Indices: 1156492--1156523 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1156482 TCGATACATT
*
1156492 ATACTTTGTATCG
1 ATACATTGTATCG
1156505 ATACATTGTATCG
1 ATACATTGTATCG
1156518 ATACAT
1 ATACAT
1156524 GTACAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (13 bp):
ATACATTGTATCG
Found at i:1156534 original size:33 final size:33
Alignment explanation
Indices: 1156478--1156543 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1156468 AACCCTTGTA
* *
1156478 TGTATCGATACATTATACTTTGTATCGATACAT
1 TGTATCGATACATTACACATTGTATCGATACAT
*
1156511 TGTATCGATACATGTACA-ATTGTATTGATACAT
1 TGTATCGATACAT-TACACATTGTATCGATACAT
1156544 GAAACTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTACACATTGTATCGATACAT
Found at i:1156598 original size:20 final size:19
Alignment explanation
Indices: 1156573--1156626 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1156563 CTACCACTGT
1156573 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
1156593 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
1156613 TTGTATCGATACAT
1 TTGTATCGATACAT
1156627 TGTCTCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1162623 original size:20 final size:20
Alignment explanation
Indices: 1162598--1162641 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1162588 CAAATACAGT
1162598 AAATAAAAAATAAAAAAACA
1 AAATAAAAAATAAAAAAACA
* * *
1162618 AAATAATAAATAAATAAATA
1 AAATAAAAAATAAAAAAACA
1162638 AAAT
1 AAAT
1162642 TAGATTTGAT
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:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAAAATAAAAAAACA
Found at i:1162793 original size:25 final size:25
Alignment explanation
Indices: 1162745--1162799 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1162735 GGTGTTGATG
* * *
1162745 ATTATAGATATAATTAATTTATTTT
1 ATTATAGATATAAATAATTAATTTA
1162770 ATTATAGATTATAAATAA-TAATTTA
1 ATTATAGA-TATAAATAATTAATTTA
1162795 ATTAT
1 ATTAT
1162800 TTAAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTATAGATATAAATAATTAATTTA
Found at i:1162897 original size:5 final size:5
Alignment explanation
Indices: 1162889--1163001 Score: 55
Period size: 5 Copynumber: 23.6 Consensus size: 5
1162879 AAAAAATTAA
* * *
1162889 AATAT AATAT AAAAT AATAT AA-ATT AA-AA AATAAT ATTAT AATAT AA-A-
1 AATAT AATAT AATAT AATAT AATA-T AATAT AAT-AT AATAT AATAT AATAT
* * * * *
1162937 AATAT -ATAG AAT-T TATAT AATAT AATTATT AATAT ATTAA AAT-T TATAT
1 AATAT AATAT AATAT AATAT AATAT AA-TA-T AATAT AATAT AATAT AATAT
1162986 AA-AT -ATAT AATAT AAT
1 AATAT AATAT AATAT AAT
1163002 TATTAAAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
3 3 0.04
4 16 0.20
5 51 0.64
6 7 0.09
7 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1162936 original size:20 final size:19
Alignment explanation
Indices: 1162870--1162938 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 19
1162860 TAAATTTTAA
* *
1162870 ATATATTATAAAAAATTAAA
1 ATATAATATAAAAAA-TAAT
1162890 ATATAATAT--AAAATAAT
1 ATATAATATAAAAAATAAT
1162907 ATA-AAT-TAAAAAATAAT
1 ATATAATATAAAAAATAAT
1162924 ATTATAATATAAAAA
1 A-TATAATATAAAAA
1162939 TATATAGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 1 0.02
16 3 0.07
17 15 0.36
18 6 0.14
19 3 0.07
20 14 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAATATAAAAAATAAT
Found at i:1162944 original size:35 final size:36
Alignment explanation
Indices: 1162878--1162949 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 36
1162868 AAATATATTA
1162878 TAAAAAATTAAAATATAATATAAAATAATATA-AAT
1 TAAAAAATTAAAATATAATATAAAATAATATAGAAT
*
1162913 TAAAAAA-TAATATTATAATATAAAA-ATATATAGAAT
1 TAAAAAATTAA-AATATAATATAAAATA-ATATAGAAT
1162949 T
1 T
1162950 TATATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 4 0.12
35 25 0.76
36 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (36 bp):
TAAAAAATTAAAATATAATATAAAATAATATAGAAT
Found at i:1162981 original size:31 final size:32
Alignment explanation
Indices: 1162921--1163009 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
1162911 ATTAAAAAAT
* *
1162921 AATATTATAATATAAAAATATATAGAATTTATAT-
1 AATA-TATAATAT-AATATAT-TAAAATTTATATA
*
1162955 AATATA-ATTATTAATATATTAAAATTTATATA
1 AATATATAATA-TAATATATTAAAATTTATATA
1162987 AATATATAATATAAT-TATTAAAA
1 AATATATAATATAATATATTAAAA
1163010 ATTAACGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
31 19 0.40
32 19 0.40
33 6 0.12
34 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
AATATATAATATAATATATTAAAATTTATATA
Found at i:1163002 original size:22 final size:20
Alignment explanation
Indices: 1162950--1163007 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
1162940 ATATAGAATT
1162950 TATATAATATAA-TTATTAA
1 TATATAATATAATTTATTAA
*
1162969 TATAT--TAAAATTTATATAAA
1 TATATAATATAATTTAT-T-AA
1162989 TATATAATATAA-TTATTAA
1 TATATAATATAATTTATTAA
1163008 AAATTAACGC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 8 0.25
20 8 0.25
21 4 0.12
22 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATAATATAATTTATTAA
Found at i:1163011 original size:22 final size:22
Alignment explanation
Indices: 1162950--1163011 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1162940 ATATAGAATT
*
1162950 TATATAATATAATTATT-AATA
1 TATATAATATAATTATTAAAAA
* *
1162971 TAT-TAA-A-ATTTA-TATAAA
1 TATATAATATAATTATTAAAAA
1162989 TATATAATATAATTATTAAAAA
1 TATATAATATAATTATTAAAAA
1163011 T
1 T
1163012 TAACGCCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
17 1 0.03
18 9 0.29
19 4 0.13
20 4 0.13
21 7 0.23
22 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATAATATAATTATTAAAAA
Found at i:1170035 original size:30 final size:30
Alignment explanation
Indices: 1170000--1170090 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
1169990 ATTTAAATTA
1170000 GATAGTGGTGCACTAGTCCTTAATTTAAGG
1 GATAGTGGTGCACTAGTCCTTAATTTAAGG
* * *
1170030 GATAGTGGTGTACTGGTCCTTAATCTAAGG
1 GATAGTGGTGCACTAGTCCTTAATTTAAGG
*
1170060 GATAGTGGTGCACTAGTACTTAATTT-AGG
1 GATAGTGGTGCACTAGTCCTTAATTTAAGG
1170089 GA
1 GA
1170091 ATTTAAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 5 0.09
30 49 0.91
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (30 bp):
GATAGTGGTGCACTAGTCCTTAATTTAAGG
Found at i:1170178 original size:20 final size:18
Alignment explanation
Indices: 1170138--1170173 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1170128 TTCTCCTATG
1170138 ATCTACTATATATACCTT
1 ATCTACTATATATACCTT
1170156 ATCTACTATATATACCTT
1 ATCTACTATATATACCTT
1170174 GTATCATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCTACTATATATACCTT
Found at i:1174501 original size:13 final size:13
Alignment explanation
Indices: 1174483--1174507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1174473 TATAAAGTGT
1174483 TGTATCGATACAA
1 TGTATCGATACAA
1174496 TGTATCGATACA
1 TGTATCGATACA
1174508 TATTTTTTTT
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:1174589 original size:13 final size:13
Alignment explanation
Indices: 1174571--1174595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1174561 ATCACTTAAA
1174571 TGTATCGATACAT
1 TGTATCGATACAT
1174584 TGTATCGATACA
1 TGTATCGATACA
1174596 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:1174660 original size:52 final size:52
Alignment explanation
Indices: 1174604--1174732 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1174594 CACTGATCTT
* *
1174604 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
1174656 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTTAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1174708 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1174733 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1175662 original size:19 final size:19
Alignment explanation
Indices: 1175638--1175683 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1175628 TGAATGTTGT
1175638 TCATCATGTTCTTGCATGA
1 TCATCATGTTCTTGCATGA
1175657 TCATCATGTTCTTGCATGA
1 TCATCATGTTCTTGCATGA
1175676 TCATCATG
1 TCATCATG
1175684 CTTGTTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (19 bp):
TCATCATGTTCTTGCATGA
Found at i:1178575 original size:30 final size:30
Alignment explanation
Indices: 1178541--1178603 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1178531 ATTTAAATTA
* *
1178541 GATAGTGGTGTACTAGTCTTTAATCTAAGG
1 GATAGTGGTGCACTAGTCCTTAATCTAAGG
1178571 GATAGTGGTGCACTAGTCCTTAATCTAAGG
1 GATAGTGGTGCACTAGTCCTTAATCTAAGG
1178601 GAT
1 GAT
1178604 TTAAATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (30 bp):
GATAGTGGTGCACTAGTCCTTAATCTAAGG
Found at i:1183325 original size:21 final size:23
Alignment explanation
Indices: 1183280--1183325 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1183270 ATGTATTGGT
*
1183280 AAAATATCTTTATATATTAATAA
1 AAAATATCTTAATATATTAATAA
*
1183303 AAAATAT-TTAATATTTTAA-AA
1 AAAATATCTTAATATATTAATAA
1183324 AA
1 AA
1183326 CTTACAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATATCTTAATATATTAATAA
Found at i:1184713 original size:16 final size:16
Alignment explanation
Indices: 1184676--1184722 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1184666 GACCCGAATT
*
1184676 TGAAATGACTCGAACCC
1 TGAAATAACTCGAA-CC
1184693 T-AAATAACTCGAACC
1 TGAAATAACTCGAACC
*
1184708 TGAAATAACCCGAAC
1 TGAAATAACTCGAAC
1184723 TCGAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 23 0.85
17 1 0.04
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.17
Consensus pattern (16 bp):
TGAAATAACTCGAACC
Found at i:1184728 original size:16 final size:17
Alignment explanation
Indices: 1184694--1184735 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1184684 CTCGAACCCT
*
1184694 AAATAACTCGAACCTG-
1 AAATAACCCGAACCTGA
1184710 AAATAACCCGAA-CTCGA
1 AAATAACCCGAACCT-GA
1184727 AAATAACCC
1 AAATAACCC
1184736 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.14
Consensus pattern (17 bp):
AAATAACCCGAACCTGA
Found at i:1185136 original size:3 final size:3
Alignment explanation
Indices: 1185123--1185182 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
1185113 GGATAAATCA
*
1185123 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1185171 ATT ATT ATT ATT
1 ATT ATT ATT ATT
1185183 TATAATCCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1190478 original size:20 final size:21
Alignment explanation
Indices: 1190443--1190482 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1190433 GAACAGGAAC
1190443 AGAAAACAAAAAATAGAAAAT
1 AGAAAACAAAAAATAGAAAAT
*
1190464 AGAAAA-AAAAGATAGAAAA
1 AGAAAACAAAAAATAGAAAA
1190483 CAAAAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (21 bp):
AGAAAACAAAAAATAGAAAAT
Found at i:1190488 original size:14 final size:13
Alignment explanation
Indices: 1190462--1190499 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1190452 AAAATAGAAA
1190462 ATAGAAAAAAAAG
1 ATAGAAAAAAAAG
1190475 ATAGAAAACAAAAG
1 ATAGAAAA-AAAAG
*
1190489 -TTGAAAAAAAA
1 ATAGAAAAAAAA
1190500 AATGAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 14 0.61
14 5 0.22
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (13 bp):
ATAGAAAAAAAAG
Found at i:1194235 original size:104 final size:104
Alignment explanation
Indices: 1194055--1194257 Score: 352
Period size: 104 Copynumber: 2.0 Consensus size: 104
1194045 AGTTTCTTTT
* * *
1194055 AGAATTCTTTGTATTCTTTGTCTAGATGTTTGATATAACAACACTTTTTTTAAAGAATTTTCTTC
1 AGAATTCCTTGTATTCTTTGTCTAGATGCTTGATATAACAACACATTTTTTAAAGAATTTTCTTC
* *
1194120 TTGTTAGAGTTTTAAGGTCATTAGGATTGCCCATTAAAC
66 TTGTTAGAGTTTCAAGGTCATTACGATTGCCCATTAAAC
1194159 AGAATTCCTTGTATTCTTTGTCTAGATGCTTGATATAACAACACATTTTTTAAAGAATTTTCTTC
1 AGAATTCCTTGTATTCTTTGTCTAGATGCTTGATATAACAACACATTTTTTAAAGAATTTTCTTC
*
1194224 TTTTTAGAGTTTCAAGGTCATTACGATTGCCCAT
66 TTGTTAGAGTTTCAAGGTCATTACGATTGCCCAT
1194258 AAAATAGATG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (104 bp):
AGAATTCCTTGTATTCTTTGTCTAGATGCTTGATATAACAACACATTTTTTAAAGAATTTTCTTC
TTGTTAGAGTTTCAAGGTCATTACGATTGCCCATTAAAC
Found at i:1199431 original size:34 final size:35
Alignment explanation
Indices: 1199393--1199459 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1199383 CCTTACAACA
1199393 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1199427 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1199460 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1199937 original size:13 final size:13
Alignment explanation
Indices: 1199919--1199944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1199909 AATTTTTTGG
1199919 TGTATCGATACAT
1 TGTATCGATACAT
1199932 TGTATCGATACAT
1 TGTATCGATACAT
1199945 ACTTGGTGTA
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):
TGTATCGATACAT
Found at i:1201170 original size:636 final size:636
Alignment explanation
Indices: 1199958--1201798 Score: 3601
Period size: 636 Copynumber: 2.9 Consensus size: 636
1199948 TGGTGTATCG
* *
1199958 ATACAAGTTTGGCTACTGCCAAGAATTCCCAATTACATGTATCGATACATATTTTTCATGTATCG
1 ATACAAGTTTGGCTACTGCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
1200023 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
66 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
1200088 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
131 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
*
1200153 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAATATTTGGTGAATC
196 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
1200218 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
261 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
* * * *
1200283 AAATAATTTCCGGTTTTATTCAATCTTTTGTTATATCAAAACCAAGATCCTAACAATCTCTCCCT
326 AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
1200348 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
391 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
1200413 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
456 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
1200478 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCATTAATTATCTTTCTCGC
521 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCATTAATTATCTTTCTCGC
1200543 GTATTTATTTTATGGAAATGATGTTTATCTCTCTAAGAATACATTTTTGCT
586 GTATTTATTTTATGGAAATGATGTTTATCTCTCTAAGAATACATTTTTGCT
*
1200594 ATACAAGTTTGGCTACTTCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
1 ATACAAGTTTGGCTACTGCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
1200659 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
66 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
1200724 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
131 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
1200789 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
196 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
1200854 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
261 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
1200919 AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
326 AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
1200984 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
391 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
1201049 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
456 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
1201114 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCATTAATTATCTTTCTCGC
521 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCATTAATTATCTTTCTCGC
1201179 GTATTTATTTTATGGAAATGATGTTTATCTCTCTAAGAATACATTTTTGCT
586 GTATTTATTTTATGGAAATGATGTTTATCTCTCTAAGAATACATTTTTGCT
1201230 ATACAAGTTTGGCTACTGCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
1 ATACAAGTTTGGCTACTGCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
1201295 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
66 ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
1201360 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
131 TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
1201425 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
196 CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
1201490 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
261 AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
1201555 AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
326 AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
1201620 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
391 TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
*
1201685 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTTGTGTTGCAAT
456 TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
1201750 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCAT
521 CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCAT
1201799 AGCTTCAAGA
Statistics
Matches: 1195, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
636 1195 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (636 bp):
ATACAAGTTTGGCTACTGCTAAGAATTCCCAATTACATGTATCGATACATATTTTTCATTTATCG
ATACATTGCAACATGTATCGATACTTTGAATTGTGTATCGATACTTTTAAGGGTTTTGACAATTT
TAGCCTAAGTCAACCTTAATGTATCGATACAAACACCTATGTATCGATACTTTGATATATTTTAA
CTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTATCCTTAACTAGAAAACATTTGGTGAATC
AAAAATCATTTGGTACAAAATTTATAAAGCACTTAATTGAATAAAACATATTATTGTTATTTTCA
AAATAATTTCCGGCTTTATTCAATCCTTTGTTATATTAAAACCAAGATCCTAACAATCTCCCCCT
TTTTGATATAACAAAACTTAGAAAATAAATTTTGGTTGACTTTAATCCCTTTTGTTGGCATAATT
TTCAAACGTGTATTTTCGGGTATCATTTCATGATCTTACCATTATGTTCAAGCTCGTGTTGCAAT
CATTCTCCTTGTATCAATATATTTCTTTAACCTGTAATCTGACTTCCATTAATTATCTTTCTCGC
GTATTTATTTTATGGAAATGATGTTTATCTCTCTAAGAATACATTTTTGCT
Found at i:1201966 original size:21 final size:21
Alignment explanation
Indices: 1201923--1201968 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1201913 TAATTCACGC
* *
1201923 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
1201944 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
1201965 ATTC
1 ATTC
1201969 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:1206333 original size:34 final size:35
Alignment explanation
Indices: 1206295--1206361 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1206285 CCTTACAACA
1206295 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1206329 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1206362 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1209470 original size:63 final size:62
Alignment explanation
Indices: 1209267--1209471 Score: 232
Period size: 63 Copynumber: 3.3 Consensus size: 62
1209257 CGCAATTCAG
* * **
1209267 ATCACCATCATGGCATCAAAATCAGTGACACCAAGTCACTCCTATTAAGACTTTTTAAGTCTA
1 ATCACCATCATGGCATCAAAATCAGAGACACCAAGTCACTCC-ATTAGGACTTCATAAGTCTA
* * * *
1209330 ATCACCTTTATGGCATCAAAATCA-ACGACACCAAGTCACTCCCATTAGGACTTCATAAGTTTG
1 ATCACCATCATGGCATCAAAATCAGA-GACACCAAGTCACT-CCATTAGGACTTCATAAGTCTA
* * * * *
1209393 ATCACTACCATGGCATCACAATTAGAGACACCAAGTCACTCTCATTAGGACTTCAAAAGTCTA
1 ATCACCATCATGGCATCAAAATCAGAGACACCAAGTCACTC-CATTAGGACTTCATAAGTCTA
* *
1209456 ATCGCCATCTTGGCAT
1 ATCACCATCATGGCAT
1209472 TATACCCAGT
Statistics
Matches: 117, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
62 1 0.01
63 113 0.97
64 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.27
Consensus pattern (62 bp):
ATCACCATCATGGCATCAAAATCAGAGACACCAAGTCACTCCATTAGGACTTCATAAGTCTA
Found at i:1209486 original size:63 final size:63
Alignment explanation
Indices: 1209267--1209498 Score: 180
Period size: 63 Copynumber: 3.7 Consensus size: 63
1209257 CGCAATTCAG
* * * * * ***
1209267 ATCACCATCATGGCATCAAAATCAGTGACACCAAGTCACTC-CTATTAAGACTTTTTAAGTCTA
1 ATCACCACCATGGCATCACAACCAGAGACACCAAGTCACTCTC-ATTAGGACTTCAAAAGTCTA
*** * * * * * *
1209330 ATCACCTTTATGGCATCAAAATCA-ACGACACCAAGTCACTCCCATTAGGACTTCATAAGTTTG
1 ATCACCACCATGGCATCACAACCAGA-GACACCAAGTCACTCTCATTAGGACTTCAAAAGTCTA
* **
1209393 ATCACTACCATGGCATCACAATTAGAGACACCAAGTCACTCTCATTAGGACTTCAAAAGTCTA
1 ATCACCACCATGGCATCACAACCAGAGACACCAAGTCACTCTCATTAGGACTTCAAAAGTCTA
* * * * * * * *
1209456 ATCGCCATCTTGGCATTATACCCAGTGACACTAAGTCACTCTC
1 ATCACCACCATGGCATCACAACCAGAGACACCAAGTCACTCTC
1209499 TTCAAGCTAA
Statistics
Matches: 137, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
63 135 0.99
64 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (63 bp):
ATCACCACCATGGCATCACAACCAGAGACACCAAGTCACTCTCATTAGGACTTCAAAAGTCTA
Found at i:1213680 original size:20 final size:19
Alignment explanation
Indices: 1213602--1213682 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 19
1213592 TTAAAAACCC
* *
1213602 AGAATGTATCGATACAATG
1 AGAATGTATCGATACATTT
1213621 AGAAATGTATCGATACAATTGT
1 AG-AATGTATCGATAC-ATT-T
*
1213643 AAGCATGTATCGATACATTT
1 -AGAATGTATCGATACATTT
1213663 AGTAATGTATCGATACATTT
1 AG-AATGTATCGATACATTT
1213683 CCTTGGAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.08
20 30 0.57
21 5 0.09
22 12 0.23
23 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
AGAATGTATCGATACATTT
Found at i:1213752 original size:21 final size:20
Alignment explanation
Indices: 1213704--1213779 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
1213694 TACAGGGTGG
**
1213704 TTTTGTATCGATACA-AAAC
1 TTTTGTATCGATACATTTAC
*
1213723 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACATTTAC
1213743 TATTTGTATCGATACATTTAC
1 T-TTTGTATCGATACATTTAC
1213764 TGTTTGTATCGATACA
1 T-TTTGTATCGATACA
1213780 AATTGTAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
19 14 0.28
20 3 0.06
21 33 0.66
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTTGTATCGATACATTTAC
Found at i:1219708 original size:21 final size:21
Alignment explanation
Indices: 1219683--1219722 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1219673 ATTTTAGAGG
1219683 TTTTGAAATCCTA-AAAATAAA
1 TTTTGAAAT-CTACAAAATAAA
1219704 TTTTGAAATCTACAAAATA
1 TTTTGAAATCTACAAAATA
1219723 CCAGAGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
TTTTGAAATCTACAAAATAAA
Found at i:1220862 original size:5 final size:5
Alignment explanation
Indices: 1220852--1220879 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1220842 GTTAATTGAC
1220852 TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTA
1220880 AAAATCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:1222270 original size:13 final size:14
Alignment explanation
Indices: 1222252--1222281 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1222242 TTTTTTTCTC
1222252 TTTTTCTT-TCTTT
1 TTTTTCTTCTCTTT
1222265 TTTTTCTTCTCTTT
1 TTTTTCTTCTCTTT
1222279 TTT
1 TTT
1222282 CCTCTCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTCTCTTT
Found at i:1222282 original size:12 final size:12
Alignment explanation
Indices: 1222242--1222287 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1222232 AATTTGTTTA
1222242 TTTTT-TTCTC-
1 TTTTTCTTCTCT
*
1222252 TTTTTCTTTCTTT
1 TTTTTC-TTCTCT
1222265 TTTTTCTTCTCT
1 TTTTTCTTCTCT
*
1222277 TTTTTCCTCTC
1 TTTTTCTTCTC
1222288 CACTTTCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 5 0.17
12 19 0.63
13 6 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTCTCT
Found at i:1222282 original size:21 final size:21
Alignment explanation
Indices: 1222242--1222282 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1222232 AATTTGTTTA
*
1222242 TTTTTTTCTCTTTTTCTTTCT
1 TTTTTTTCTCTCTTTCTTTCT
1222263 TTTTTTTCTTCTCTTT-TTTC
1 TTTTTTTC-TCTCTTTCTTTC
1222283 CTCTCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTCTCTTTCTTTCT
Found at i:1222868 original size:163 final size:164
Alignment explanation
Indices: 1222686--1223051 Score: 463
Period size: 164 Copynumber: 2.2 Consensus size: 164
1222676 AGATGAATTA
* * **** *
1222686 AAAAATCTCCCCGAAAATATTTATGGAATAGAAAACTC-AGTTTTTCGGAAATAGGAA-AATTT-
1 AAAAATCTCCCCGAAAATATTTAAGGAGTAGAAAACTCTA-AAGCTCGAAAATA-GAAGAATTTC
* *
1222748 AA-AAAAAATGAAAAACTTATGAAAATAAATAAAATTTTAAAAAATGATTTACGATGAATTAAAT
64 AAGAAAAAATGAAAAACTTAAG-AAATAAATAAAATTTTAAAAAATGATTTAAGATGAATTAAAT
* *
1222812 AATATTATTTAATGAATTTTAAAAATTAAAAACTAAG
128 AATAATATTTAATGAATTTTAAAAATTAAAAAATAAG
*
1222849 AAAAATC-CCTCCGAAAATATTTAAAGAGTAGAAAACTCTAAAGCTCGAAAATAGAAGAATTTCA
1 AAAAATCTCC-CCGAAAATATTTAAGGAGTAGAAAACTCTAAAGCTCGAAAATAGAAGAATTTCA
* * * * * *
1222913 AGGAAAAATGAAAAACTTAAGAAATGAATAAATTTTTGAAAATTGATTTAATATGAATTAAATAA
65 AGAAAAAATGAAAAACTTAAGAAATAAATAAAATTTTAAAAAATGATTTAAGATGAATTAAATAA
*
1222978 TAATATTTGATGAATTTTAAAAATTAAAAAATAAG
130 TAATATTTAATGAATTTTAAAAATTAAAAAATAAG
* * *
1223013 AAAAATCTCCCTGAAAATATTTACGGAGTAAAAAACTCT
1 AAAAATCTCCCCGAAAATATTTAAGGAGTAGAAAACTCT
1223052 GTATTTTGCA
Statistics
Matches: 174, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
162 5 0.03
163 45 0.26
164 105 0.60
165 19 0.11
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (164 bp):
AAAAATCTCCCCGAAAATATTTAAGGAGTAGAAAACTCTAAAGCTCGAAAATAGAAGAATTTCAA
GAAAAAATGAAAAACTTAAGAAATAAATAAAATTTTAAAAAATGATTTAAGATGAATTAAATAAT
AATATTTAATGAATTTTAAAAATTAAAAAATAAG
Found at i:1224200 original size:16 final size:16
Alignment explanation
Indices: 1224146--1224200 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1224136 TGTGTTCAGG
* *
1224146 TCATTTCGAGTTTGAA
1 TCATTTCGGGTTTGGA
1224162 TCATTTCGGGTTTGGA
1 TCATTTCGGGTTTGGA
** *
1224178 TTGTTTCGGGTTCGGA
1 TCATTTCGGGTTTGGA
1224194 TCATTTC
1 TCATTTC
1224201 AGATTCGAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (16 bp):
TCATTTCGGGTTTGGA
Found at i:1224273 original size:15 final size:16
Alignment explanation
Indices: 1224231--1224273 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1224221 TAACGTTCGA
*
1224231 GTCAATCAGG-TTCAG
1 GTCAATCTGGATTCAG
*
1224246 GTCATTCTGGATTCAG
1 GTCAATCTGGATTCAG
1224262 GTCAAT-TGGATT
1 GTCAATCTGGATT
1224274 TAACATTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (16 bp):
GTCAATCTGGATTCAG
Found at i:1224723 original size:51 final size:51
Alignment explanation
Indices: 1224668--1224781 Score: 228
Period size: 51 Copynumber: 2.2 Consensus size: 51
1224658 AACCCTTGAA
1224668 TGTATCGATACAACCAGATGTATCGATACATTATGCTTCATACCGATACAT
1 TGTATCGATACAACCAGATGTATCGATACATTATGCTTCATACCGATACAT
1224719 TGTATCGATACAACCAGATGTATCGATACATTATGCTTCATACCGATACAT
1 TGTATCGATACAACCAGATGTATCGATACATTATGCTTCATACCGATACAT
1224770 TGTATCGATACA
1 TGTATCGATACA
1224782 TGTTCATTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (51 bp):
TGTATCGATACAACCAGATGTATCGATACATTATGCTTCATACCGATACAT
Found at i:1224812 original size:20 final size:19
Alignment explanation
Indices: 1224766--1224822 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1224756 TCATACCGAT
*
1224766 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1224785 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1224804 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1224823 AAACTGGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1224876 original size:20 final size:20
Alignment explanation
Indices: 1224851--1224903 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1224841 TTACTACTGT
*
1224851 TTGTATCAATACAC-ATCACA
1 TTGTATCGATACACGATCA-A
*
1224871 TTGTATCGATACACGATGAA
1 TTGTATCGATACACGATCAA
1224891 TTGTATCGATACA
1 TTGTATCGATACA
1224904 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (20 bp):
TTGTATCGATACACGATCAA
Found at i:1226338 original size:32 final size:32
Alignment explanation
Indices: 1226288--1226380 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
1226278 GGGTTAATTG
*** *
1226288 TTCAGGTCATTGCAGGTTCAGATCATTTTGGA
1 TTCAGGTCATTTTGGGTTCGGATCATTTTGGA
**
1226320 TTTGGGTCATTTTGGGTTCGGATCATTTTGGA
1 TTCAGGTCATTTTGGGTTCGGATCATTTTGGA
1226352 TTCAGGTCATTTTGGGTTCGGATCATTTT
1 TTCAGGTCATTTTGGGTTCGGATCATTTT
1226381 TTGGTTCAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.44
Consensus pattern (32 bp):
TTCAGGTCATTTTGGGTTCGGATCATTTTGGA
Found at i:1226387 original size:17 final size:16
Alignment explanation
Indices: 1226302--1226380 Score: 97
Period size: 16 Copynumber: 4.9 Consensus size: 16
1226292 GGTCATTGCA
*
1226302 GGTTCAGATCATTTTG
1 GGTTCGGATCATTTTG
* * *
1226318 GATTTGGGTCATTTTG
1 GGTTCGGATCATTTTG
1226334 GGTTCGGATCATTTTG
1 GGTTCGGATCATTTTG
*
1226350 GATTCAGG-TCATTTTG
1 GGTTC-GGATCATTTTG
1226366 GGTTCGGATCATTTT
1 GGTTCGGATCATTTT
1226381 TTGGTTCAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
15 2 0.04
16 48 0.92
17 2 0.04
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.46
Consensus pattern (16 bp):
GGTTCGGATCATTTTG
Found at i:1227767 original size:6 final size:6
Alignment explanation
Indices: 1227756--1227838 Score: 55
Period size: 6 Copynumber: 13.0 Consensus size: 6
1227746 AAAATCATCG
*
1227756 TAAATT TAAATTT TAAATTT TAAATT TAAATT CT-AATT GT--ATT TAGATTT
1 TAAATT TAAA-TT TAAA-TT TAAATT TAAATT -TAAATT -TAAATT TA-AATT
*
1227806 TCAGAATC TAAATT TAAATTT TAAATT TAAATT
1 T-A-AATT TAAATT TAAA-TT TAAATT TAAATT
1227839 CTATCTAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 1 0.02
5 3 0.05
6 32 0.49
7 24 0.37
8 5 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:1227825 original size:51 final size:45
Alignment explanation
Indices: 1227769--1227878 Score: 170
Period size: 45 Copynumber: 2.4 Consensus size: 45
1227759 ATTTAAATTT
* *
1227769 TAAATTTTAAA-TTTAAATTCT-AATTGTATTTAGATTTTCAGAATC
1 TAAA-TTTAAATTTTAAATT-TAAATTCTATCTAGATTTTCAGAATC
1227814 TAAATTTAAATTTTAAATTTAAATTCTATCTAGATTTTCAGAATC
1 TAAATTTAAATTTTAAATTTAAATTCTATCTAGATTTTCAGAATC
1227859 TAAATTTAAATTTTAAATTT
1 TAAATTTAAATTTTAAATTT
1227879 TAAAATTTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
44 7 0.11
45 54 0.89
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (45 bp):
TAAATTTAAATTTTAAATTTAAATTCTATCTAGATTTTCAGAATC
Found at i:1227886 original size:8 final size:7
Alignment explanation
Indices: 1227756--1227882 Score: 52
Period size: 7 Copynumber: 17.6 Consensus size: 7
1227746 AAAATCATCG
1227756 TAAA-TT
1 TAAATTT
1227762 TAAATTT
1 TAAATTT
1227769 TAAATTT
1 TAAATTT
1227776 TAAA-TT
1 TAAATTT
*
1227782 TAAATTC
1 TAAATTT
*
1227789 TAATTGTATT
1 TAA--AT-TT
*
1227799 TAGATTT
1 TAAATTT
*
1227806 TCAGAA-TC
1 T-A-AATTT
1227814 TAAA-TT
1 TAAATTT
1227820 TAAATTT
1 TAAATTT
1227827 TAAA-TT
1 TAAATTT
1227833 TAAATTCTAT
1 TAAA-T-T-T
*
1227843 CTAGATTT
1 -TAAATTT
*
1227851 TCAGAA-TC
1 T-A-AATTT
1227859 TAAA-TT
1 TAAATTT
1227865 TAAATTT
1 TAAATTT
1227872 TAAATTT
1 TAAATTT
1227879 TAAA
1 TAAA
1227883 ATTTGAATAG
Statistics
Matches: 93, Mismatches: 12, Indels: 31
0.68 0.09 0.23
Matches are distributed among these distances:
6 30 0.32
7 42 0.45
8 8 0.09
9 5 0.05
10 5 0.05
11 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (7 bp):
TAAATTT
Found at i:1228953 original size:20 final size:19
Alignment explanation
Indices: 1228909--1228964 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
1228899 GTTTACCTAG
1228909 ATGTATCGATACATTGCTTA
1 ATGTATCGATACATT-CTTA
*
1228929 TTGTATCGATACATT-TTACA
1 ATGTATCGATACATTCTT--A
1228949 ATGTATCGATACATTC
1 ATGTATCGATACATTC
1228965 AGGCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 2 0.06
20 29 0.94
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTCTTA
Found at i:1231302 original size:51 final size:51
Alignment explanation
Indices: 1231237--1231390 Score: 182
Period size: 51 Copynumber: 3.0 Consensus size: 51
1231227 ATTTTTCATC
* * ** **
1231237 TCGGGGATACTCCAACCCCGGTTCCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGCAA
* * * * *
1231288 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATATATCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGCAA
* * *
1231339 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGCAA
1231390 T
1 T
1231391 TGGAGATATT
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCGCAA
Found at i:1231434 original size:28 final size:28
Alignment explanation
Indices: 1231403--1231465 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
1231393 GAGATATTCT
*
1231403 AACCCCGTTATTTCATCA-AGGATACTCC
1 AACCCCGTTATTTCAT-AGAGCATACTCC
*
1231431 AACCCCGTTATTTCCTAGAGCATACTCC
1 AACCCCGTTATTTCATAGAGCATACTCC
1231459 AACCCCG
1 AACCCCG
1231466 GCTTTATATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.25
Consensus pattern (28 bp):
AACCCCGTTATTTCATAGAGCATACTCC
Found at i:1231538 original size:28 final size:28
Alignment explanation
Indices: 1231499--1231554 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1231489 TTTTTTCATA
*
1231499 ATCGGAGGTACTCCAACCCCGTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
* *
1231527 ATCGGAGATACTCCAATCCTGTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
1231555 CAAGGGGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (28 bp):
ATCGGAGATACTCCAACCCCGTTATTTC
Found at i:1231564 original size:28 final size:28
Alignment explanation
Indices: 1231502--1231575 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
1231492 TTTCATAATC
* *
1231502 GGAGGTACTCCAACCCCGTTATTTCATC
1 GGAGATACTCCAACCCCGTTATTTCATA
* *
1231530 GGAGATACTCCAATCCTGTTATTTCCA-A
1 GGAGATACTCCAACCCCGTTATTT-CATA
* *
1231558 GGGGATACTCTAACCCCG
1 GGAGATACTCCAACCCCG
1231576 ATTTTATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 35 0.95
29 2 0.05
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (28 bp):
GGAGATACTCCAACCCCGTTATTTCATA
Found at i:1231628 original size:51 final size:50
Alignment explanation
Indices: 1231558--1231729 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 50
1231548 TTATTTCCAA
* *
1231558 GGGGATACTCTAACCCCGATTTTATTTCTAAAATACTAATCTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACTGAT-TTTCACAATC
* * * *
1231609 GGAGATACTCCAACTCCGATTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACTGATTT-TCACAATC
* ***
1231660 GGGGGATACTTCAACCCCGGCCTTATTTCT-AAAT-CATCGATTTTTCACAATC
1 -GGGGATACTCCAACCCCGATTTTATTTCTAAAATAC-T-GA-TTTTCACAATC
1231712 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1231730 TTATTTTTGA
Statistics
Matches: 101, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
50 2 0.02
51 64 0.63
52 32 0.32
53 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACTGATTTTCACAATC
Found at i:1231636 original size:110 final size:108
Alignment explanation
Indices: 1231341--1231622 Score: 318
Period size: 110 Copynumber: 2.6 Consensus size: 108
1231331 TATCGCAATC
* * * * * * *
1231341 GGGGATACTCCAACTCCGATTTTATTT-TCAAAACACCAATTTTTCACAATTGGAGATATTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGAGATACTCCAA
*
1231405 CCCCGTTATTTCATCAAGGATACTCCAACCCCGTTATTTCCTA
66 CCCCGTTATTTCATCAAGGATACTCCAACCCCGTTATTTCCAA
* * ** * * * * *
1231448 GAGCATACTCCAACCCCGGCTTTATATCTAAAAATATTGATTTTTTTCATAATCGGAGGTACTCC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAAATACT-A-ATTTTTCACAATCGGAGATACTCC
* * *
1231513 AACCCCGTTATTTCATC-GGAGATACTCCAATCCTGTTATTTCCAA
64 AACCCCGTTATTTCATCAAG-GATACTCCAACCCCGTTATTTCCAA
* *
1231558 GGGGATACTCTAACCCCGATTTTATTTCT-AAAATACTAATCTTTCACAATCGGAGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGAGATACTCCAA
1231622 C
66 C
1231623 TCCGATTTTA
Statistics
Matches: 140, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
107 44 0.31
108 7 0.05
109 9 0.06
110 80 0.57
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGAGATACTCCAA
CCCCGTTATTTCATCAAGGATACTCCAACCCCGTTATTTCCAA
Found at i:1231860 original size:79 final size:79
Alignment explanation
Indices: 1231661--1231869 Score: 208
Period size: 79 Copynumber: 2.6 Consensus size: 79
1231651 CTCACAATCG
* *** * * * * *
1231661 GGGGATACTTCAACCCCGGCCTTA-TTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCGATTTTTCATAATCAGAGATACTCCAA
*
1231725 CCCCGTTATTTTTGA
65 CCCCGTTATTTTCGA
* *
1231740 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACTGA-TTTTCTATAATCAGAGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTTC-ATAATCAGAGATACTCCAA
*
1231804 CCCTGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * ***
1231819 GGGGATACTCCAAACTCTG-TTTTATTTTTGGAACACCGATTTTTCATAATC
1 GGGGATACTCC-AACCCCGATTTTATTTTCAAAACACCGATTTTTCATAATC
1231870 GAGGATATTC
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.05
79 87 0.82
80 14 0.13
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTTCATAATCAGAGATACTCCAAC
CCCGTTATTTTCGA
Found at i:1243959 original size:13 final size:13
Alignment explanation
Indices: 1243941--1243966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1243931 TACAGCAAGT
1243941 ATGTATCGATACA
1 ATGTATCGATACA
1243954 ATGTATCGATACA
1 ATGTATCGATACA
1243967 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:1246216 original size:21 final size:21
Alignment explanation
Indices: 1246183--1246227 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1246173 TTGCAAGTTG
*
1246183 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1246205 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1246225 AAA
1 AAA
1246228 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:1248051 original size:15 final size:15
Alignment explanation
Indices: 1248031--1248061 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1248021 TAAAAATGTC
*
1248031 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1248046 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1248061 C
1 C
1248062 TAAACAAAAT
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:1250099 original size:20 final size:20
Alignment explanation
Indices: 1250020--1250099 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1250010 AATGTCCAAA
*
1250020 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1250040 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1250065 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1250085 TTGTATCGATACATT
1 ATGTATCGATACATT
1250100 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1250103 original size:13 final size:13
Alignment explanation
Indices: 1250085--1250123 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1250075 ACATTTTTCT
1250085 TTGTATCGATACA
1 TTGTATCGATACA
1250098 TTGTATCGATACA
1 TTGTATCGATACA
*
1250111 CTGTATCGATACA
1 TTGTATCGATACA
1250124 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1250269 original size:21 final size:21
Alignment explanation
Indices: 1250245--1250291 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1250235 AAATCTTTTG
1250245 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1250266 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1250286 CAAAAT
1 CAAAAT
1250292 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1250288 original size:20 final size:19
Alignment explanation
Indices: 1250247--1250289 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1250237 ATCTTTTGCA
1250247 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1250267 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1250287 AAA
1 AAA
1250290 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1252683 original size:13 final size:13
Alignment explanation
Indices: 1252665--1252690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1252655 TACAGCAAGT
1252665 ATGTATCGATACA
1 ATGTATCGATACA
1252678 ATGTATCGATACA
1 ATGTATCGATACA
1252691 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:1253839 original size:12 final size:12
Alignment explanation
Indices: 1253822--1253854 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
1253812 CACCTTCTTT
1253822 AAAAAAAACAAA
1 AAAAAAAACAAA
1253834 AAAAAAAACAAA
1 AAAAAAAACAAA
1253846 AAAGAAAAA
1 AAA-AAAAA
1253855 AGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:1255799 original size:20 final size:21
Alignment explanation
Indices: 1255752--1255804 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1255742 TCCAATCACC
*
1255752 TGTATCGATACATTCTTTGTA
1 TGTATCGATACATTCTTGGTA
*
1255773 AGTATCGATACA-T-TTGGTCA
1 TGTATCGATACATTCTTGGT-A
1255793 TGTATCGATACA
1 TGTATCGATACA
1255805 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTTGGTA
Found at i:1255810 original size:13 final size:13
Alignment explanation
Indices: 1255792--1255816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1255782 ACATTTGGTC
1255792 ATGTATCGATACA
1 ATGTATCGATACA
1255805 ATGTATCGATAC
1 ATGTATCGATAC
1255817 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:1257832 original size:20 final size:22
Alignment explanation
Indices: 1257793--1257837 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1257783 GCTGTGAGAG
*
1257793 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
1257815 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
1257835 TGG
1 TGG
1257838 TGAGCGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.04, C:0.29, G:0.49, T:0.18
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCGACC
Found at i:1258136 original size:21 final size:22
Alignment explanation
Indices: 1258106--1258147 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1258096 CTGCTTTTGT
1258106 TGATGATTTTG-A-TGAAAAAA
1 TGATGATTTTGAAGTGAAAAAA
1258126 TGATGTATTTTGAAGTGAAAAA
1 TGATG-ATTTTGAAGTGAAAAA
1258148 CAAGAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 1 0.05
23 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (22 bp):
TGATGATTTTGAAGTGAAAAAA
Found at i:1258298 original size:13 final size:13
Alignment explanation
Indices: 1258280--1258317 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1258270 ATAAACCCTT
*
1258280 TGTATCGATACAC
1 TGTATCGATACAA
1258293 TGTATCGATACAA
1 TGTATCGATACAA
*
1258306 TGTATAGATACA
1 TGTATCGATACA
1258318 GAGAATGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1258533 original size:8 final size:8
Alignment explanation
Indices: 1258515--1258545 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1258505 TTTTCAACAT
1258515 CAAACATCA
1 CAAA-ATCA
1258524 CAAAATCA
1 CAAAATCA
1258532 CAAAATCA
1 CAAAATCA
1258540 CAAAAT
1 CAAAAT
1258546 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:1264426 original size:13 final size:13
Alignment explanation
Indices: 1264408--1264432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1264398 AATTTGGTCA
1264408 TGTATCGATACAT
1 TGTATCGATACAT
1264421 TGTATCGATACA
1 TGTATCGATACA
1264433 CCCAAGAGGT
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:1264540 original size:20 final size:21
Alignment explanation
Indices: 1264493--1264545 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1264483 GCCAATCACC
*
1264493 TGTATCGATACATTCTTTGTA
1 TGTATCGATACATTCTTGGTA
*
1264514 AGTATCGATACA-T-TTGGTCA
1 TGTATCGATACATTCTTGGT-A
1264534 TGTATCGATACA
1 TGTATCGATACA
1264546 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTTGGTA
Found at i:1264551 original size:13 final size:13
Alignment explanation
Indices: 1264533--1264557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1264523 ACATTTGGTC
1264533 ATGTATCGATACA
1 ATGTATCGATACA
1264546 ATGTATCGATAC
1 ATGTATCGATAC
1264558 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:1265015 original size:26 final size:26
Alignment explanation
Indices: 1264933--1265015 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
1264923 TGGCATTTTC
1264933 CAGTCCTCAAAGAGCAGGACGCCTTT
1 CAGTCCTCAAAGAGCAGGACGCCTTT
* * * ** *
1264959 CAAAGCCCACACA-AGTTGGTCGCACCTTT
1 C--AGTCCTCAAAGAGCAGGACG--CCTTT
1264988 CAGTCCTCAAAGAGCAGGACGCCTTT
1 CAGTCCTCAAAGAGCAGGACGCCTTT
1265014 CA
1 CA
1265016 AAGCCCACAC
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
26 8 0.20
27 13 0.32
28 13 0.32
29 6 0.15
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (26 bp):
CAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:1265022 original size:110 final size:110
Alignment explanation
Indices: 1264849--1265120 Score: 420
Period size: 111 Copynumber: 2.5 Consensus size: 110
1264839 GATCCTAACA
* * *
1264849 CAAAGTCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCAT
1 CAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCAC
1264914 ACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
65 ACAAGTTGGTGGCATTTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
* *
1264959 CAAAGCCCACACAAGTTGGTCGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
1 CAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCAC
** *
1265024 ACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTT
65 ACAAGTTGGTGGCATTTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
* *
1265070 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGACGC
1 CAAAGCCCACACAAGTTGGTGGCACTT-TCAGTCCTCAAAGAGCAAGACGC
1265121 TCTCTCCTTT
Statistics
Matches: 147, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
110 73 0.50
111 74 0.50
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (110 bp):
CAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACA
CAAGTTGGTGGCATTTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:1265075 original size:56 final size:55
Alignment explanation
Indices: 1264849--1265120 Score: 411
Period size: 55 Copynumber: 4.9 Consensus size: 55
1264839 GATCCTAACA
* *
1264849 CAAAGTCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
*
1264904 CAAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
* *
1264959 CAAAGCCCACACAAGTTGGTCGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
** *
1265014 CAAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTT
1 CAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1265070 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAAGACGC
1 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
1265121 TCTCTCCTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
55 147 0.75
56 50 0.25
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (55 bp):
CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:1265281 original size:150 final size:148
Alignment explanation
Indices: 1264978--1265275 Score: 411
Period size: 150 Copynumber: 2.0 Consensus size: 148
1264968 CACAAGTTGG
** *
1264978 TCGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTT
1 TCGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAATGGCACTTTT
* *
1265043 TTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCA
66 CTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCCAGTCCTCA
1265108 AAGAGCAAGACGCTCTCTCCTT
131 AAGAGCAAGACG----CTCCTT
*
1265130 TCGC-CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTAATGGCACTTTT
1 TCGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAATGGCACTTTT
* *
1265193 CTAGTCCTCAAAGAGCAGGATGCCTTTTCCTGTCAAAGCCCAAACAAGTTGGTGGCATTTTCCAG
66 CTAGTCCTCAAAGAGCAGGATGCC--TT--T-T-AAAGCCCAAACAAGTTGGTGGCACTTCCCAG
*
1265258 TCCTCAAAGAGCAGGACG
125 TCCTCAAAGAGCAAGACG
1265276 TCTTTCAAAG
Statistics
Matches: 131, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
150 73 0.56
151 5 0.04
152 6 0.05
154 1 0.01
155 1 0.01
156 45 0.34
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (148 bp):
TCGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAATGGCACTTTT
CTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCCAGTCCTCA
AAGAGCAAGACGCTCCTT
Found at i:1265309 original size:55 final size:56
Alignment explanation
Indices: 1265139--1265739 Score: 682
Period size: 55 Copynumber: 10.4 Consensus size: 56
1265129 TTCGCCCTTT
* ** *
1265139 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTAATGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
* *
1265195 AGTCCTCAAAGAGCAGGATGCCTTTTCCTGTCAAAGCCCAAACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCC---T--T-TCAAAGCCCACACAAGTTGGTGGCACTTTTCC
*
1265256 AGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
*
1265311 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
* * * **
1265366 AGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
*
1265422 AGTCCTCAAAGA-CTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCAC--TTCC
1 AGTCCTCAAAGAGC-AGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
* * *
1265476 AGTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
*
1265532 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGG--A-C---GCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
* *
1265593 AGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCC
1 AGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCC
* * *
1265654 AGTCTTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGT-GCACTTTT-T
1 AGTCCTCAAAGAGCAGGACG-----CC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
*
1265714 ATTCCTCAAAGAGCAGGACGCACTTT
1 AGTCCTCAAAGAGCAGGACGC-CTTT
1265740 ATTTTCCTCA
Statistics
Matches: 478, Mismatches: 37, Indels: 61
0.83 0.06 0.11
Matches are distributed among these distances:
54 50 0.10
55 133 0.28
56 90 0.19
58 2 0.00
59 8 0.02
60 27 0.06
61 115 0.24
62 53 0.11
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (56 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCC
Found at i:1265780 original size:42 final size:42
Alignment explanation
Indices: 1265716--1265916 Score: 203
Period size: 42 Copynumber: 4.7 Consensus size: 42
1265706 CACTTTTTAT
*
1265716 TCCTCAAAGAGCAGGACGCACTTTATTTTCCTCATTCCTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTG
* * * *
1265758 TCCTCAAAGAGTAGGACACACTTCA-TTCCCTTCTTTTCTCTTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTTCC-TC-TTTC-C-TTTG
* *
1265803 TCCTTAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTG
* * * *
1265845 TCCTCAAAGAGCAAGACGCA-TTTCGTTTTCCTTTTTTCCTTTA
1 TCCTCAAAGAGCAGGACGCACTTT-ATTTTCC-TCTTTCCTTTG
*
1265888 TCCTCGAAA-AGCAGGACGTACTTT-TTTTC
1 TCCTC-AAAGAGCAGGACGCACTTTATTTTC
1265917 ACTTTGTCCT
Statistics
Matches: 131, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
41 7 0.05
42 57 0.44
43 25 0.19
44 11 0.08
45 27 0.21
46 4 0.03
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (42 bp):
TCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTG
Found at i:1265882 original size:87 final size:85
Alignment explanation
Indices: 1265711--1265916 Score: 247
Period size: 87 Copynumber: 2.4 Consensus size: 85
1265701 TGGTGCACTT
* *
1265711 TTTATTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCATTCCTTTGTCCTCAAAGAGTAGGACA
1 TTTA-TCCTCAAAGAGCAGGACGCACTTTATTTTCCTCATTCCTTTGTCCTCAAAGAGCAAGACA
1265776 CACTTCATTCCCTTCTTTTCTC
65 CACTTCATTCCCTTCTTTTC-C
* * * * *
1265798 TTTTGTCCTTAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACG
1 -TTTATCCTCAAAGAGCAGGACGCACTTTATTTTCCTCATTCCTTTGTCCTCAAAGAGCAAGACA
* * *
1265863 CATTTCGTTTTCCTT-TTTTCC
65 CACTTC-ATTCCCTTCTTTTCC
*
1265884 TTTATCCTCGAAA-AGCAGGACGTACTTT-TTTTC
1 TTTATCCTC-AAAGAGCAGGACGCACTTTATTTTC
1265917 ACTTTGTCCT
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
84 5 0.05
85 21 0.20
86 4 0.04
87 64 0.62
88 9 0.09
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (85 bp):
TTTATCCTCAAAGAGCAGGACGCACTTTATTTTCCTCATTCCTTTGTCCTCAAAGAGCAAGACAC
ACTTCATTCCCTTCTTTTCC
Done.