Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 292 of 770
Found at i:89077610 original size:85 final size:84
Alignment explanation
Indices: 89077456--89077699 Score: 294
Period size: 85 Copynumber: 2.8 Consensus size: 84
89077446 CTGGGAAAAT
* * *
89077456 TAGCGGCG-TTTTTAAAAAAGCGCCGCTAAAAGTACATGTCTTTAGCGGCGTTTTTTATAAAAGC
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGT-CCTGTCTTTAGCGGCTTTTTTTA-AAAAGC
89077520 GCCGCTAAAAGTACAGGTCTC
64 GCCGCTAAAAGTACAGGTCTC
* *
89077541 TAGCGGCGTTTTTTATAAAAGCGTCGCTAAAGGTCCTGGT-TTCTAGCGGCTTTTTTTAAAAAGC
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTCCT-GTCTT-TAGCGGCTTTTTTTAAAAAGC
* * * *
89077605 GCCGCTAAAGGTCCTGGTCTT
64 GCCGCTAAAAGTACAGGTCTC
* * * *
89077626 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAATGTCCTAATCTTTACCGGCGTTTTTTCTAAAAAA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTCCT-GTCTTTAGCGGC-TTTTTT-TAAAAAG
89077691 CGCCGCTAA
63 CGCCGCTAA
89077700 TTTTTGTGGC
Statistics
Matches: 138, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
85 77 0.56
86 46 0.33
87 15 0.11
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (84 bp):
TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTCCTGTCTTTAGCGGCTTTTTTTAAAAAGCGC
CGCTAAAAGTACAGGTCTC
Found at i:89077688 original size:128 final size:128
Alignment explanation
Indices: 89077456--89077688 Score: 344
Period size: 128 Copynumber: 1.8 Consensus size: 128
89077446 CTGGGAAAAT
89077456 TAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCTTTAGCGGCGTTTTTTATAAAAGCG
1 TAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCTTTAGCGGCGTTTTTTATAAAAGCG
* *
89077521 CCGCTAAAAGTACAGGTCTCTAGCGGCGTTTTTTATAAAAGCGTCGCTAAAGGTCCTGGTTTC
66 CCGCTAAAAGTACAGATCTCTACCGGCGTTTTTTATAAAAGCGTCGCTAAAGGTCCTGGTTTC
* * * *
89077584 TAGCGGCTTTTTTTAAAAAGCGCCGCTAAAGGT-CCTGGTCTTTAGCGGCGTTTTTTATAAAAGC
1 TAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAGTACAT-GTCTTTAGCGGCGTTTTTTATAAAAGC
* * * *
89077648 GCCGCTAAATGTCCTA-ATCTTTACCGGCGTTTTTTCTAAAA
65 GCCGCTAAAAGTAC-AGATCTCTACCGGCGTTTTTTATAAAA
89077689 AACGCCGCTA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
127 2 0.02
128 90 0.97
129 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (128 bp):
TAGCGGCGTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCTTTAGCGGCGTTTTTTATAAAAGCG
CCGCTAAAAGTACAGATCTCTACCGGCGTTTTTTATAAAAGCGTCGCTAAAGGTCCTGGTTTC
Found at i:89084093 original size:16 final size:16
Alignment explanation
Indices: 89084057--89084093 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
89084047 AATACTTTTT
*
89084057 AAAAATATTTTTGAAA
1 AAAAATATTTTTAAAA
89084073 AAAAATATTTTTAAAA
1 AAAAATATTTTTAAAA
89084089 AAAAA
1 AAAAA
89084094 ATTCTTAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAATATTTTTAAAA
Found at i:89084500 original size:19 final size:19
Alignment explanation
Indices: 89084476--89084515 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
89084466 AACCCCAATT
89084476 TAGTTTATTTATAAAACAA
1 TAGTTTATTTATAAAACAA
*
89084495 TAGTTTATTTATAAAGCAA
1 TAGTTTATTTATAAAACAA
89084514 TA
1 TA
89084516 ATAAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (19 bp):
TAGTTTATTTATAAAACAA
Found at i:89084837 original size:22 final size:22
Alignment explanation
Indices: 89084803--89084844 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
89084793 TATTTACCCT
89084803 TTAAAATGTATAAAATTATAAA
1 TTAAAATGTATAAAATTATAAA
89084825 TTAATAATG-ATAAAATTATA
1 TTAA-AATGTATAAAATTATA
89084845 TTTTGACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
TTAAAATGTATAAAATTATAAA
Found at i:89091487 original size:23 final size:23
Alignment explanation
Indices: 89091460--89091506 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
89091450 GATACTCGTT
*
89091460 GTTGGGTATTGATACCAAATTGA
1 GTTGGGTATCGATACCAAATTGA
89091483 GTTGGGTATCGATACCAAATTGA
1 GTTGGGTATCGATACCAAATTGA
89091506 G
1 G
89091507 CTACTGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (23 bp):
GTTGGGTATCGATACCAAATTGA
Found at i:89098675 original size:34 final size:34
Alignment explanation
Indices: 89098632--89098711 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
89098622 ATTGTTTAGC
*
89098632 GGACTGTATCACTTGACTG-ATAGTATCAT-CTAGT
1 GGACAGTATCACTTGAC-GAATAGTATC-TCCTAGT
* * *
89098666 GGATAGTATCGCTTGGCGAATAGTATCTCCTAGT
1 GGACAGTATCACTTGACGAATAGTATCTCCTAGT
*
89098700 GGACAATATCAC
1 GGACAGTATCAC
89098712 CCAGCGAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 2 0.05
34 35 0.95
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (34 bp):
GGACAGTATCACTTGACGAATAGTATCTCCTAGT
Found at i:89099558 original size:18 final size:18
Alignment explanation
Indices: 89099494--89099567 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
89099484 ACTATGCTGG
89099494 TGTGCGAACCTATACTATA
1 TGTGCGAACC-ATACTATA
* * * *
89099513 TGTGTGAACCCTACCATT
1 TGTGCGAACCATACTATA
* * *
89099531 TATGCAAACCAAACTATA
1 TGTGCGAACCATACTATA
*
89099549 TGTGCGAACCCTACTATA
1 TGTGCGAACCATACTATA
89099567 T
1 T
89099568 ATGTGATAAT
Statistics
Matches: 40, Mismatches: 15, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
18 31 0.77
19 9 0.22
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (18 bp):
TGTGCGAACCATACTATA
Found at i:89105444 original size:22 final size:22
Alignment explanation
Indices: 89105418--89105489 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
89105408 GTTCACATTC
89105418 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
89105440 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
89105464 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
89105487 ATC
1 ATC
89105490 TCATATATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:89105464 original size:47 final size:47
Alignment explanation
Indices: 89105400--89105565 Score: 264
Period size: 47 Copynumber: 3.5 Consensus size: 47
89105390 TAGTCACCAC
*
89105400 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
89105447 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
* *
89105494 ATATGCATGTTCACATTCATCACATTTGCCATTTGGCCTTATCTCAT
1 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
*
89105541 ATATACGCA--TTCACATTAATCACAT
1 ATAT--GCATGTTCACATTCATCACAT
89105566 AAAATCCTAA
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
47 110 0.97
49 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (47 bp):
ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
Found at i:89109440 original size:29 final size:28
Alignment explanation
Indices: 89109407--89109504 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 28
89109397 ATTAAAGAAT
89109407 TCGCACACATAGTACCTCAATTACCAATC
1 TCGCACACATAGT-CCTCAATTACCAATC
* * **
89109436 TCGCACACA-AGTGCTCGATTGAAGAA-C
1 TCGCACACATAGTCCTCAATT-ACCAATC
* **
89109463 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGT-CCTCAATTACCAATC
*
89109492 TGGCACACATAGT
1 TCGCACACATAGT
89109505 GCTTGGTTGG
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
27 16 0.30
28 11 0.20
29 27 0.50
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTCCTCAATTACCAATC
Found at i:89109452 original size:56 final size:57
Alignment explanation
Indices: 89109379--89109507 Score: 172
Period size: 56 Copynumber: 2.3 Consensus size: 57
89109369 CTGACTGATT
* *
89109379 TCGCACACATA-TCGCTCGATTAAAGAATTCGCACACATAGTACCTCAATTACCAATC
1 TCGCACACATAGT-GCTCGATTAAAGAACTCGCACACATAGTACCTCAACTACCAATC
* * **
89109436 TCGCACACA-AGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTAAAGAACTCGCACACATAGTACCTCAACTACCAATC
*
89109492 TGGCACACATAGTGCT
1 TCGCACACATAGTGCT
89109508 TGGTTGGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
56 47 0.75
57 16 0.25
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTAAAGAACTCGCACACATAGTACCTCAACTACCAATC
Found at i:89110936 original size:27 final size:29
Alignment explanation
Indices: 89110906--89111018 Score: 99
Period size: 30 Copynumber: 4.0 Consensus size: 29
89110896 ATACAAGAGC
*
89110906 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
89110933 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
89110962 ATATAATTTTCAGCTCGCACACTTAGTGCT
1 ATAT-ATGTGAAGCTCGCACACTTAGTGCT
* * *
89110992 A-ATA-ATCAAACTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
89111019 GTACAATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 24 0.32
28 4 0.05
29 21 0.28
30 26 0.35
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:89110973 original size:30 final size:30
Alignment explanation
Indices: 89110918--89111047 Score: 162
Period size: 30 Copynumber: 4.5 Consensus size: 30
89110908 ATAGTGAATC
*
89110918 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
89110947 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
89110977 CGCACACTTAGTGCTA-ATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
89111004 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
89111034 CGCACACTTAGTGC
1 CGCACACTTAGTGC
89111048 CGAGACCAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.02
27 18 0.20
28 3 0.03
29 23 0.26
30 43 0.48
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:89111017 original size:57 final size:58
Alignment explanation
Indices: 89110917--89111047 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 58
89110907 TATAGTGAAT
* * * * *
89110917 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
89110976 TCGCACACTTAGTGCTA-ATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
89111033 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
89111048 CGAGACCAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 2 0.03
57 42 0.67
58 3 0.05
59 16 0.25
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:89118848 original size:29 final size:29
Alignment explanation
Indices: 89118816--89118916 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 29
89118806 ATAGTGAATC
89118816 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
89118845 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
* *
89118875 CGCACACTTAGTGCTA-ATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AGCT
89118902 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89118917 GTACAATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
26 2 0.03
27 18 0.26
28 1 0.01
29 21 0.31
30 26 0.38
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:89118871 original size:30 final size:30
Alignment explanation
Indices: 89118816--89118944 Score: 153
Period size: 29 Copynumber: 4.5 Consensus size: 30
89118806 ATAGTGAATC
*
89118816 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
89118845 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
89118875 CGCACACTTAGTGCTA-ATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * *
89118902 CGCACACTTAGTGCTGTACAATTTTAAAC-
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
89118931 CCCACACTTAGTGC
1 CGCACACTTAGTGC
89118945 CGAGACCAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.02
27 18 0.20
28 3 0.03
29 36 0.40
30 29 0.33
31 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:89123006 original size:40 final size:40
Alignment explanation
Indices: 89122961--89123090 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
89122951 CGGAATACAA
89122961 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
89123001 CCGGATAGAACAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
89123041 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
89123081 CCGGATATAA
1 CCGGATATAA
89123091 TTTCCAGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:89131111 original size:32 final size:32
Alignment explanation
Indices: 89131068--89131130 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
89131058 GCGGGTTTGC
* *
89131068 AGCCATTAGTAGCGGTAATTTGATCGGCACAA
1 AGCCATCAGTAGCGGTAATATGATCGGCACAA
**
89131100 AGCCATCAGTAGTTGTAATATGATCGGCACA
1 AGCCATCAGTAGCGGTAATATGATCGGCACA
89131131 TAACCATAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (32 bp):
AGCCATCAGTAGCGGTAATATGATCGGCACAA
Found at i:89131196 original size:27 final size:27
Alignment explanation
Indices: 89131116--89131217 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 27
89131106 CAGTAGTTGT
* *
89131116 AATATGATCGGCACATAACCATAGGTA
1 AATATGATAGGCACATAGCCATAGGTA
* * * * * *
89131143 AATA-GGTCGACACAGAGTCATAAGTA
1 AATATGATAGGCACATAGCCATAGGTA
*
89131169 AATATGATAGGCACATAGCCACAGGTA
1 AATATGATAGGCACATAGCCATAGGTA
* *
89131196 AATACGATTA-GCACAAAGCCAT
1 AATATGA-TAGGCACATAGCCAT
89131218 GAACAAGATG
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
26 20 0.35
27 35 0.61
28 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.20
Consensus pattern (27 bp):
AATATGATAGGCACATAGCCATAGGTA
Found at i:89131653 original size:27 final size:26
Alignment explanation
Indices: 89131632--89131818 Score: 178
Period size: 27 Copynumber: 7.0 Consensus size: 26
89131622 ATTTTAACCT
* *
89131632 ACAGGGGTATTTTGGTAATTTTACACT
1 ACAGGGGTATTTCGGTAATTTTACA-A
* * *
89131659 ACAAGGGTATTTTGGTAATTTTACCA
1 ACAGGGGTATTTCGGTAATTTTACAA
* *
89131685 ACTAAGGGTATTTCGATAATTTTACAA
1 AC-AGGGGTATTTCGGTAATTTTACAA
* * *
89131712 ATAGTGGTATTTCGATAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
* *
89131738 ACTGAGGGTATTTTGGTAATTTTACAAA
1 ACAG-GGGTATTTCGGTAATTTTAC-AA
* *
89131766 ACGGGGGTATTTCGATAATTTTA-AA
1 ACAGGGGTATTTCGGTAATTTTACAA
*
89131791 ATCCAGAGGTATTTCGGTAATTTTACAA
1 A--CAGGGGTATTTCGGTAATTTTACAA
89131819 TCTAGGATCT
Statistics
Matches: 134, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.02
26 26 0.19
27 98 0.73
28 7 0.05
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (26 bp):
ACAGGGGTATTTCGGTAATTTTACAA
Found at i:89131731 original size:80 final size:80
Alignment explanation
Indices: 89131637--89131818 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 80
89131627 AACCTACAGG
* * *
89131637 GGTATTTTGGTAATTTTACACTAC-AAGGGTATTTTGGTAATTTTAC-CAACTAAGGGTATTTCG
1 GGTATTTCGGTAATTTTACA-AACTAAGGGTATTTTGGTAATTTTACAAAAC-AAGGGTATTTCG
*
89131700 ATAATTTTACAAAT-AGT
64 ATAATTTTA-AAATCAGA
* * **
89131717 GGTATTTCGATAATTTTACAAACTGAGGGTATTTTGGTAATTTTACAAAACGGGGGTATTTCGAT
1 GGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAAACAAGGGTATTTCGAT
89131782 AATTTTAAAATCCAGA
66 AATTTTAAAAT-CAGA
89131798 GGTATTTCGGTAATTTTACAA
1 GGTATTTCGGTAATTTTACAA
89131819 TCTAGGATCT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
79 6 0.07
80 58 0.65
81 25 0.28
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (80 bp):
GGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAAACAAGGGTATTTCGAT
AATTTTAAAATCAGA
Found at i:89135623 original size:27 final size:26
Alignment explanation
Indices: 89135557--89135772 Score: 172
Period size: 27 Copynumber: 8.1 Consensus size: 26
89135547 CCCTAAAGGT
* * * *
89135557 GTATTTTAGTAATTTTACACTATAAGG
1 GTATTTCAGTAATTTTAAAAT-TGAGG
89135584 G-ATTTC-GTTAATTTTATAAATTGAGG
1 GTATTTCAG-TAATTTTA-AAATTGAGG
*
89135610 GTATTTCAGTAATTTTACAAACTGAGG
1 GTATTTCAGTAATTTTA-AAATTGAGG
* *
89135637 GTATTTTAGTAATTTTACAAATTGGGG
1 GTATTTCAGTAATTTTA-AAATTGAGG
* * *
89135664 GTATTT-AGGTAATTTTACAATCCGGGG
1 GTATTTCA-GTAATTTTAAAAT-TGAGG
*
89135691 GTATTTC-GATAATTTTACAAATTGGGG
1 GTATTTCAG-TAATTTTA-AAATTGAGG
*
89135718 GTATTTCAGTAATTTTACAATCT-AGAG
1 GTATTTCAGTAATTTTAAAAT-TGAG-G
* *
89135745 GTATTTCGGTAATTTTAAAATTCAGG
1 GTATTTCAGTAATTTTAAAATTGAGG
89135771 GT
1 GT
89135773 CTTAACAACC
Statistics
Matches: 159, Mismatches: 17, Indels: 27
0.78 0.08 0.13
Matches are distributed among these distances:
25 1 0.01
26 30 0.19
27 123 0.77
28 5 0.03
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (26 bp):
GTATTTCAGTAATTTTAAAATTGAGG
Found at i:89135666 original size:54 final size:54
Alignment explanation
Indices: 89135557--89135766 Score: 225
Period size: 54 Copynumber: 3.9 Consensus size: 54
89135547 CCCTAAAGGT
* * * * * * *
89135557 GTATTTTAGTAATTTTACACTATAAGGG-A-TTTCGTTAATTTTATAAATTGAGG
1 GTATTTCAGTAATTTTACAATCTGAGGGTATTTTAG-TAATTTTACAAATTGGGG
*
89135610 GTATTTCAGTAATTTTACAAACTGAGGGTATTTTAGTAATTTTACAAATTGGGG
1 GTATTTCAGTAATTTTACAATCTGAGGGTATTTTAGTAATTTTACAAATTGGGG
* * *
89135664 GTATTT-AGGTAATTTTACAATCCGGGGGTA-TTTCGATAATTTTACAAATTGGGG
1 GTATTTCA-GTAATTTTACAATCTGAGGGTATTTTAG-TAATTTTACAAATTGGGG
**
89135718 GTATTTCAGTAATTTTACAATCT-AGAGGTATTTCGGTAATTTTA-AAATT
1 GTATTTCAGTAATTTTACAATCTGAG-GGTATTTTAGTAATTTTACAAATT
89135767 CAGGGTCTTA
Statistics
Matches: 134, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
53 34 0.25
54 92 0.69
55 8 0.06
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (54 bp):
GTATTTCAGTAATTTTACAATCTGAGGGTATTTTAGTAATTTTACAAATTGGGG
Found at i:89135707 original size:81 final size:81
Alignment explanation
Indices: 89135608--89135761 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
89135598 TATAAATTGA
* * *
89135608 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTTAGTAATTTTACAAAT-TGGGGGTATTTAG
1 GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTAC-AATCTAGAGGTATTTAG
89135672 GTAATTTTACAATCCGG
65 GTAATTTTACAATCCGG
* * *
89135689 GGGTATTTC-GATAATTTTACAAATTGGGGGTATTTCAGTAATTTTACAATCTAGAGGTATTTCG
1 GGGTATTTCAG-TAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAATCTAGAGGTATTTAG
89135753 GTAATTTTA
65 GTAATTTTA
89135762 AAATTCAGGG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 4 0.06
81 61 0.94
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.41
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAATCTAGAGGTATTTAGG
TAATTTTACAATCCGG
Found at i:89136002 original size:17 final size:18
Alignment explanation
Indices: 89135980--89136014 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
89135970 TATCCGTGTA
*
89135980 GGGCCCAC-GTGCCCATT
1 GGGCCCACACTGCCCATT
89135997 GGGCCCACACTGCCCATT
1 GGGCCCACACTGCCCATT
89136015 TAGCCCAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.43, G:0.26, T:0.17
Consensus pattern (18 bp):
GGGCCCACACTGCCCATT
Found at i:89154593 original size:42 final size:42
Alignment explanation
Indices: 89154546--89154627 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
89154536 TCTGGCAAGA
89154546 ACTCAAAAGAAAAGAGAATACAACTAGGCTAACCGAAAGCAG
1 ACTCAAAAGAAAAGAGAATACAACTAGGCTAACCGAAAGCAG
89154588 ACTCAAAAGAAAAGAGAATACAACTAGGCTAACCGAAAGC
1 ACTCAAAAGAAAAGAGAATACAACTAGGCTAACCGAAAGC
89154628 GGAAGTATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.52, C:0.20, G:0.18, T:0.10
Consensus pattern (42 bp):
ACTCAAAAGAAAAGAGAATACAACTAGGCTAACCGAAAGCAG
Found at i:89160739 original size:28 final size:29
Alignment explanation
Indices: 89160707--89160821 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
89160697 TACCTGTATC
* *
89160707 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
89160735 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
89160764 TGGCCTATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
89160793 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
89160821 T
1 T
89160822 TCATGCTCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 27 0.36
29 47 0.63
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:89160804 original size:58 final size:57
Alignment explanation
Indices: 89160698--89160808 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 57
89160688 AATTTCACAT
* *
89160698 ACCTGTATCTGGCCCATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
89160755 ACCTGTATATGGCCTATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAAGCCC-AATCACATTCATATGGCCCATTAGGCCCA
89160809 GTCACATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (57 bp):
ACCTGTATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:89162190 original size:16 final size:16
Alignment explanation
Indices: 89162164--89162201 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
89162154 ATAAAGAAAA
89162164 TTTGAGATTTCAGGATT
1 TTTG-GATTTCAGGATT
*
89162181 TTTGGATTTCGGGATT
1 TTTGGATTTCAGGATT
89162197 TTTGG
1 TTTGG
89162202 GGCGTTACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.16, C:0.05, G:0.29, T:0.50
Consensus pattern (16 bp):
TTTGGATTTCAGGATT
Found at i:89164294 original size:24 final size:24
Alignment explanation
Indices: 89164267--89164315 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
89164257 TGGCGATGTC
89164267 ACATGAAACTGTTTCTAAAAACTG
1 ACATGAAACTGTTTCTAAAAACTG
89164291 ACATGAAACTGTTTCTAAAAACTG
1 ACATGAAACTGTTTCTAAAAACTG
89164315 A
1 A
89164316 GTCATTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (24 bp):
ACATGAAACTGTTTCTAAAAACTG
Found at i:89170237 original size:27 final size:26
Alignment explanation
Indices: 89170207--89170318 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
89170197 AGGAAGCGTC
* *
89170207 CTGGTGGCTATACCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
89170234 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
89170261 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* ** * *
89170289 CTGGTGACTCTATCACATTCTCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
89170315 CTGG
1 CTGG
89170319 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:89170313 original size:54 final size:54
Alignment explanation
Indices: 89170207--89170318 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
89170197 AGGAAGCGTC
* *
89170207 CTGGTGGCTATACCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATACCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
* * * * *
89170261 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TCTCTGTT
1 CTGGTGGCTATACCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTGTT
89170315 CTGG
1 CTGG
89170319 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATACCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
Found at i:89174976 original size:39 final size:39
Alignment explanation
Indices: 89174920--89175113 Score: 289
Period size: 39 Copynumber: 5.0 Consensus size: 39
89174910 AAGACACTGA
*
89174920 AAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
89174959 AAATGTATTCGGACTAAAGTCCCGCAGACTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
89174998 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTTGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
89175037 AAATGTATCCGGGCCAAAGTCCCGCAGGTTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
89175076 AAATGTATCCGGGTTAAAGTCCCGTAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
89175114 ATAATATAAT
Statistics
Matches: 139, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 139 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:89181827 original size:27 final size:26
Alignment explanation
Indices: 89181787--89181898 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
89181777 AGGAAGCGTC
*
89181787 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
89181814 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
89181841 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
89181869 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
89181895 CTGG
1 CTGG
89181899 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.68
28 17 0.22
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:89181891 original size:54 final size:54
Alignment explanation
Indices: 89181787--89181898 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
89181777 AGGAAGCGTC
*
89181787 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
89181841 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
89181895 CTGG
1 CTGG
89181899 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:89183165 original size:21 final size:21
Alignment explanation
Indices: 89183124--89183171 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
89183114 TTTTCCTCTT
*
89183124 ATTTCTTTTTTTCTTATCTCA
1 ATTTCTTTTTTTCTTAGCTCA
*
89183145 ATTTCTTTTATTT-TTCGCTCA
1 ATTTCTTTT-TTTCTTAGCTCA
*
89183166 TTTTCT
1 ATTTCT
89183172 CTCATTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTCTTTTTTTCTTAGCTCA
Found at i:89183493 original size:26 final size:26
Alignment explanation
Indices: 89183457--89183513 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
89183447 GATACAAATT
89183457 GATAATAGGTTAGGTAAATGTTCCAC
1 GATAATAGGTTAGGTAAATGTTCCAC
* * *
89183483 GATAATGGGTTAGGTAAATGTTTCAT
1 GATAATAGGTTAGGTAAATGTTCCAC
89183509 GATAA
1 GATAA
89183514 GAATTTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (26 bp):
GATAATAGGTTAGGTAAATGTTCCAC
Found at i:89185012 original size:25 final size:26
Alignment explanation
Indices: 89184984--89185035 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
89184974 TTTACAGTTT
89184984 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
89185009 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
89185035 T
1 T
89185036 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:89190972 original size:40 final size:40
Alignment explanation
Indices: 89190926--89191038 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
89190916 TACAACCACA
* *
89190926 AGCACAATTGCCTTCGGGTCTTAACCCGGGTAT-AGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGGTATAAGC-ACT
* * * *
89190966 CGCACAAATGCCCTCGGGTCTTAGCCCGGATATAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGGTATAAGCACT
* *
89191006 AGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGGTAT
89191039 CATTCAAATG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 59 0.97
41 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGGTATAAGCACT
Found at i:89194786 original size:26 final size:26
Alignment explanation
Indices: 89194757--89194840 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
89194747 TGATACGAAT
* *
89194757 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
89194783 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
89194809 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
89194835 TGATAA
1 TGATAA
89194841 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:89196353 original size:26 final size:26
Alignment explanation
Indices: 89196324--89196376 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
89196314 TTTACAGTTT
89196324 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
89196350 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
89196376 T
1 T
89196377 GCATGTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:89200448 original size:40 final size:39
Alignment explanation
Indices: 89200404--89200529 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
89200394 GGGACTCAAC
*
89200404 CCGGATTTAGTAGCTTGCTCGAAAGCCTTCGGATCTTAGT
1 CCGGATTTAGTA-CTTGCACGAAAGCCTTCGGATCTTAGT
* * * *
89200444 CCGGATTTAGTAACTCGCACGTATGCCGTCGGATCTTAGT
1 CCGGATTTAGT-ACTTGCACGAAAGCCTTCGGATCTTAGT
*
89200484 CCGGATTTAGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGC
1 CCGGATTTAGT-ACTT-GCACGAAAGCCTTC-GGATCTTAGT
89200524 CCGGAT
1 CCGGAT
89200530 ATCATTCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 64 0.89
41 8 0.11
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (39 bp):
CCGGATTTAGTACTTGCACGAAAGCCTTCGGATCTTAGT
Found at i:89202955 original size:38 final size:39
Alignment explanation
Indices: 89202882--89203063 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
89202872 AATGTTCGAG
89202882 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
89202921 TGATATCCGGGCTAAG-CCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
89202959 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
89202998 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
89203038 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
89203064 GTTTGAACGA
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 37 0.30
39 49 0.40
40 38 0.31
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:89211725 original size:40 final size:39
Alignment explanation
Indices: 89211681--89211806 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
89211671 GGGACTCAAC
*
89211681 CCGGATTTAGTAGCTTGCTCGAAAGCCTTCGGATCTTAGT
1 CCGGATTTAGTA-CTTGCACGAAAGCCTTCGGATCTTAGT
* * * *
89211721 CCGGATTTAGTAACTCGCACGTATGCCGTCGGATCTTAGT
1 CCGGATTTAGT-ACTTGCACGAAAGCCTTCGGATCTTAGT
*
89211761 CCGGATTTAGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGC
1 CCGGATTTAGT-ACTT-GCACGAAAGCCTTC-GGATCTTAGT
89211801 CCGGAT
1 CCGGAT
89211807 ATCATTCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 64 0.89
41 8 0.11
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (39 bp):
CCGGATTTAGTACTTGCACGAAAGCCTTCGGATCTTAGT
Found at i:89211765 original size:80 final size:80
Alignment explanation
Indices: 89211620--89211806 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
89211610 GCTACACATT
* * *
89211620 CAAATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTCAACCCG
*
89211684 GATTTAGT-AGCTT-GCT
64 GATTTAGTCA-CTTAGCA
* * * **
89211700 CGAAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTAGTCC
1 C-AAAGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTCAACCC
89211763 GGATTTAGTCACTTAGCA
63 GGATTTAGTCACTTAGCA
89211781 CAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAAGCCTTCGGGACTTAGCCCGGAT
89211807 ATCATTCGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 6 0.07
80 72 0.80
81 12 0.13
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTCAACCCGGA
TTTAGTCACTTAGCA
Found at i:89214203 original size:23 final size:21
Alignment explanation
Indices: 89214164--89214207 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
89214154 ATTTTATATG
89214164 TTAAAAATTTATTTAATTAAAA
1 TTAAAAATTTATTTAA-TAAAA
89214186 TTAAAACATTT-TTATAATAAAA
1 TTAAAA-ATTTATT-TAATAAAA
89214208 CAAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAATTTATTTAATAAAA
Found at i:89220237 original size:28 final size:28
Alignment explanation
Indices: 89220172--89220272 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
89220162 ATAGTGAATC
*
89220172 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
89220201 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
89220229 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
89220259 CGCACACTTAGTGC
1 CGCACACTTAGTGC
89220273 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:89228187 original size:28 final size:28
Alignment explanation
Indices: 89228122--89228222 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
89228112 ATAGTGAATC
*
89228122 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
89228151 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
89228179 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
89228209 CGCACACTTAGTGC
1 CGCACACTTAGTGC
89228223 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:89230589 original size:40 final size:40
Alignment explanation
Indices: 89230487--89230670 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
89230477 AAATTGAATG
* * * * *
89230487 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
89230527 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
89230567 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
89230607 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
89230647 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
89230671 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:89238629 original size:39 final size:40
Alignment explanation
Indices: 89238571--89238671 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
89238561 AAATTGAATG
* *
89238571 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
89238610 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
89238650 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
89238672 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:89238664 original size:40 final size:40
Alignment explanation
Indices: 89238571--89238752 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
89238561 AAATTGAATG
* * * * *
89238571 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
89238610 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
89238650 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
89238690 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
89238730 ATATCCGGG-TAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
89238753 CTTGTGCGGG
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 44 0.36
40 75 0.62
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:89247925 original size:40 final size:39
Alignment explanation
Indices: 89247839--89248022 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 39
89247829 AAATTGAATG
* * * * *
89247839 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGAA-AATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC--AAGTAGT
* * *
89247879 ACATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAG-T
* *
89247919 ATATCCGGGCCAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAG-T
* * * *
89247959 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGT
* * *
89247998 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
89248023 CTTGGTGCGG
Statistics
Matches: 116, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.01
39 5 0.04
40 108 0.93
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGT
Found at i:89249596 original size:8 final size:8
Alignment explanation
Indices: 89249583--89249633 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
89249573 ATAGCCAAAC
89249583 TTTCGGCT
1 TTTCGGCT
89249591 TTTCGGCAT
1 TTTCGGC-T
89249600 TTT-GGCT
1 TTTCGGCT
*
89249607 TTTTGGCT
1 TTTCGGCT
* *
89249615 TTTCAGCA
1 TTTCGGCT
89249623 TTTCGGCT
1 TTTCGGCT
89249631 TTT
1 TTT
89249634 GCCGATACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 4 0.11
8 28 0.78
9 4 0.11
ACGTcount: A:0.06, C:0.20, G:0.22, T:0.53
Consensus pattern (8 bp):
TTTCGGCT
Found at i:89249614 original size:24 final size:24
Alignment explanation
Indices: 89249587--89249633 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
89249577 CCAAACTTTC
* *
89249587 GGCTTTTCGGCATTTTGGCTTTTT
1 GGCTTTTCAGCATTTCGGCTTTTT
89249611 GGCTTTTCAGCATTTCGGCTTTT
1 GGCTTTTCAGCATTTCGGCTTTT
89249634 GCCGATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.19, G:0.23, T:0.51
Consensus pattern (24 bp):
GGCTTTTCAGCATTTCGGCTTTTT
Found at i:89250213 original size:11 final size:11
Alignment explanation
Indices: 89250197--89250226 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
89250187 TATAAATTAA
89250197 AGAAGAAGGGT
1 AGAAGAAGGGT
89250208 AGAAGAAGGGT
1 AGAAGAAGGGT
89250219 AGAAGAAG
1 AGAAGAAG
89250227 AAATCGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (11 bp):
AGAAGAAGGGT
Found at i:89250873 original size:16 final size:16
Alignment explanation
Indices: 89250852--89250885 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
89250842 AGAAAATTCA
89250852 GGATTTCAGGATTCTT
1 GGATTTCAGGATTCTT
*
89250868 GGATTTCAGGATTTTT
1 GGATTTCAGGATTCTT
89250884 GG
1 GG
89250886 GGCGTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (16 bp):
GGATTTCAGGATTCTT
Found at i:89259961 original size:17 final size:18
Alignment explanation
Indices: 89259939--89259973 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
89259929 TCACATTGAA
89259939 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
89259956 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
89259974 CTTCTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:89261100 original size:28 final size:28
Alignment explanation
Indices: 89261057--89261174 Score: 132
Period size: 28 Copynumber: 4.2 Consensus size: 28
89261047 CACATACCTA
* *
89261057 TATATGGCCCACTAGACCC-AATTATAT
1 TATATGGCCCATTAGACCCAAATCATAT
*
89261084 TCACATGGCCCATTAGACCCAAATCATAAT
1 T-ATATGGCCCATTAGACCCAAATCAT-AT
* * *
89261114 TATATGGCCCTTTAGGCCCAAATCACATT
1 TATATGGCCCATTAGACCCAAATCATA-T
*
89261143 TATATGG-CCATTAGACCCAAATCACAT
1 TATATGGCCCATTAGACCCAAATCATAT
89261170 TATAT
1 TATAT
89261175 TCATGCTCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
27 7 0.09
28 34 0.44
29 34 0.44
30 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (28 bp):
TATATGGCCCATTAGACCCAAATCATAT
Found at i:89261118 original size:57 final size:56
Alignment explanation
Indices: 89261057--89261174 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 56
89261047 CACATACCTA
* *
89261057 TATATGGCCCACTAGACCC-AATTATATTCACATGGCCCATTAGACCCAAATCATAAT
1 TATATGGCCCACTAGACCCAAATCACATTCACATGG-CCATTAGACCCAAATCA-AAT
** * * * *
89261114 TATATGGCCCTTTAGGCCCAAATCACATTTATATGGCCATTAGACCCAAATCACAT
1 TATATGGCCCACTAGACCCAAATCACATTCACATGGCCATTAGACCCAAATCAAAT
89261170 TATAT
1 TATAT
89261175 TCATGCTCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
56 7 0.13
57 33 0.63
58 12 0.23
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (56 bp):
TATATGGCCCACTAGACCCAAATCACATTCACATGGCCATTAGACCCAAATCAAAT
Found at i:89261128 original size:29 final size:29
Alignment explanation
Indices: 89261057--89261174 Score: 127
Period size: 29 Copynumber: 4.2 Consensus size: 29
89261047 CACATACCTA
* *
89261057 TATATGGCCCACTAGACCC-AATTAT-AT
1 TATATGGCCCATTAGACCCAAATCATAAT
*
89261084 TCACATGGCCCATTAGACCCAAATCATAAT
1 T-ATATGGCCCATTAGACCCAAATCATAAT
* * * *
89261114 TATATGGCCCTTTAGGCCCAAATCACATT
1 TATATGGCCCATTAGACCCAAATCATAAT
*
89261143 TATATGG-CCATTAGACCCAAATCA-CAT
1 TATATGGCCCATTAGACCCAAATCATAAT
89261170 TATAT
1 TATAT
89261175 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
27 7 0.09
28 31 0.41
29 35 0.46
30 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGACCCAAATCATAAT
Found at i:89261410 original size:16 final size:16
Alignment explanation
Indices: 89261386--89261416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89261376 ATAGCCAAAC
89261386 TTTCAGCTTTTCGACA
1 TTTCAGCTTTTCGACA
*
89261402 TTTCGGCTTTTCGAC
1 TTTCAGCTTTTCGAC
89261417 TTTTGCCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:89274634 original size:41 final size:41
Alignment explanation
Indices: 89274589--89274706 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
89274579 TGAAAGATAA
89274589 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
89274630 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89274660 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89274701 ATGTAG
1 ATGTAG
89274707 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:89274645 original size:71 final size:71
Alignment explanation
Indices: 89274557--89274720 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
89274547 GAGATGTATC
89274557 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89274622 AGGACA
66 AGGACA
89274628 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89274693 AGGACA
66 AGGACA
89274699 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
89274721 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:89282213 original size:41 final size:41
Alignment explanation
Indices: 89282168--89282285 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
89282158 TGAAAGATAA
89282168 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
89282209 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89282239 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
89282280 ATGTAG
1 ATGTAG
89282286 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:89282224 original size:71 final size:71
Alignment explanation
Indices: 89282136--89282299 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
89282126 GAGATGTATC
89282136 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89282201 AGGACA
66 AGGACA
89282207 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
89282272 AGGACA
66 AGGACA
89282278 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
89282300 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:89283512 original size:40 final size:40
Alignment explanation
Indices: 89283453--89283660 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
89283443 CAATTGAATG
* * * *
89283453 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
89283493 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
89283533 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
89283573 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
89283613 GTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
89283653 ATATCCGG
1 ATATCCGG
89283661 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:89283591 original size:80 final size:80
Alignment explanation
Indices: 89283455--89283660 Score: 243
Period size: 80 Copynumber: 2.6 Consensus size: 80
89283445 ATTGAATGAT
* * ** * * *
89283455 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
89283520 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
89283535 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* **
89283600 TGTGCAAGTCGTTGT
66 TGTGCAAGTCGCTAC
* *
89283615 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
89283661 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:89288822 original size:40 final size:40
Alignment explanation
Indices: 89288763--89288970 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
89288753 CAATTGAATG
* * * *
89288763 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
89288803 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
89288843 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
89288883 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
89288923 GTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
89288963 ATATCCGG
1 ATATCCGG
89288971 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:89288901 original size:80 final size:80
Alignment explanation
Indices: 89288765--89288970 Score: 243
Period size: 80 Copynumber: 2.6 Consensus size: 80
89288755 ATTGAATGAT
* * ** * * *
89288765 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
89288830 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
89288845 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* **
89288910 TGTGCAAGTCGTTGT
66 TGTGCAAGTCGCTAC
* *
89288925 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
89288971 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 106 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:89293554 original size:40 final size:40
Alignment explanation
Indices: 89293480--89293621 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
89293470 CCGCACCAAG
* * * * * *
89293480 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
89293520 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * * *
89293560 GCCTTCGGGTCTTGGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
89293600 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
89293622 GTAATTTTCA
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:89295521 original size:76 final size:76
Alignment explanation
Indices: 89295395--89295547 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
89295385 CTATATTTCT
* *
89295395 CAATAGATTTATTCAAGATCCTCCTTTTGTTTCATTATTTCAATAAAAATATTACATGCAAAATC
1 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
89295460 GTTGTCGACCA
66 GTTGTCGACCA
*
89295471 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTGCATGCAAAATC
1 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
89295536 GTTGTCGACCA
66 GTTGTCGACCA
89295547 C
1 C
89295548 TTTTATTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (76 bp):
CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
GTTGTCGACCA
Found at i:89302801 original size:21 final size:21
Alignment explanation
Indices: 89302752--89302802 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
89302742 AGTGTCATTG
* *
89302752 AGTTAATATTAAAGTTTTGTT
1 AGTTAATTTTAAAGTTTTGAT
** *
89302773 AGAAAATTTTAACGTTTTGAT
1 AGTTAATTTTAAAGTTTTGAT
89302794 AGTTAATTT
1 AGTTAATTT
89302803 AGTAAACAGG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (21 bp):
AGTTAATTTTAAAGTTTTGAT
Found at i:89305187 original size:33 final size:33
Alignment explanation
Indices: 89305145--89305208 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
89305135 CCAATGTAAG
*
89305145 GGCTTAAATGGTATACTTATTCTTTTGTATAAA
1 GGCTTAAATGGTATAATTATTCTTTTGTATAAA
89305178 GGCTTAAATGGTATAATTATTCTTTTGTATA
1 GGCTTAAATGGTATAATTATTCTTTTGTATA
89305209 TGGCCATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.47
Consensus pattern (33 bp):
GGCTTAAATGGTATAATTATTCTTTTGTATAAA
Found at i:89310937 original size:20 final size:20
Alignment explanation
Indices: 89310912--89310951 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
89310902 TAAATATTTT
89310912 TTTCTATGAAAATTGAGTAA
1 TTTCTATGAAAATTGAGTAA
89310932 TTTCTATGAAAATTGAGTAA
1 TTTCTATGAAAATTGAGTAA
89310952 AATTTAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTCTATGAAAATTGAGTAA
Found at i:89322189 original size:14 final size:14
Alignment explanation
Indices: 89322170--89322198 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
89322160 AAAAAATTCG
89322170 ATTCACTTATTAAT
1 ATTCACTTATTAAT
89322184 ATTCACTTATTAAT
1 ATTCACTTATTAAT
89322198 A
1 A
89322199 ATTCTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTCACTTATTAAT
Found at i:89327177 original size:67 final size:67
Alignment explanation
Indices: 89327068--89327254 Score: 257
Period size: 67 Copynumber: 2.8 Consensus size: 67
89327058 ATGGGCTGTA
* * * * **
89327068 ATGGGGTATAATGTGTAAAACTATAGCTCGGCTATGGTAACATAGAGAGTTTGCCAAGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
89327133 AC
66 AC
* *
89327135 ATGGGATATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTCCACCAAGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
89327200 AC
66 AC
* * * * *
89327202 ATGGGGTATGATGTGTAAGACCATATCTCGACTATGACATCATATAGAGTTCA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCA
89327255 TCGAGGCAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 105 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (67 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
AC
Found at i:89349461 original size:27 final size:28
Alignment explanation
Indices: 89349405--89349474 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
89349395 AAATTTGTAC
89349405 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
89349433 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
89349460 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
89349475 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:89359345 original size:40 final size:40
Alignment explanation
Indices: 89359301--89359486 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
89359291 GCTACTCGTT
* * *
89359301 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
89359341 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
89359381 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
89359421 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
89359462 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89359487 CATCATTCGA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:89367398 original size:40 final size:40
Alignment explanation
Indices: 89367354--89367538 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
89367344 GCTACTCGTT
* * *
89367354 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
89367394 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
89367434 CAAATGCCTTC-GGATCTTAGTCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
89367474 CAAATGCCTTC-GGATCTTAGTCTGGATATAGTCACTCAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTC-GCA
89367515 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
89367539 CATCATTCGA
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 12 0.09
40 110 0.84
41 9 0.07
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:89370561 original size:40 final size:39
Alignment explanation
Indices: 89370498--89370583 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 39
89370488 TAACGACTTA
*
89370498 TCGGCTAAAATGGCACTTAGTGTGCAGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
* * *
89370537 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCT
89370577 TCGGCTA
1 TCGGCTA
89370584 TATATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:89372843 original size:23 final size:24
Alignment explanation
Indices: 89372810--89372855 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
89372800 GCATCACATT
*
89372810 TCATATACCAAAATCAAACCATAA
1 TCATATACCAAAACCAAACCATAA
*
89372834 TCATA-ACCAAAACCAAGCCATA
1 TCATATACCAAAACCAAACCATA
89372856 TCACATGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.17
Consensus pattern (24 bp):
TCATATACCAAAACCAAACCATAA
Found at i:89380317 original size:23 final size:24
Alignment explanation
Indices: 89380284--89380329 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
89380274 GCATCACATT
*
89380284 TCATATACCAAAATCAAACCATAA
1 TCATATACCAAAACCAAACCATAA
*
89380308 TCATA-ACCAAAACCAAGCCATA
1 TCATATACCAAAACCAAACCATA
89380330 TCGCATAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.52, C:0.28, G:0.02, T:0.17
Consensus pattern (24 bp):
TCATATACCAAAACCAAACCATAA
Found at i:89380570 original size:42 final size:43
Alignment explanation
Indices: 89380477--89380615 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 43
89380467 GCTCTCGATG
* * * * *
89380477 TGGTCTTACATGT-AATCAAATATAGATGCCACTATCCCAGACA
1 TGGTCTTACACGTAAATCATA-ATCGATGCCAATGTCCCAGACA
* ** * * *
89380520 GGGTCTTACTTG-AAATCA-AATCCGATTCCGATGTCCCAAACA
1 TGGTCTTACACGTAAATCATAAT-CGATGCCAATGTCCCAGACA
*
89380562 TGGTCTTACACGTAAATCATTAGTCGATGCCAATGTCCCAGACA
1 TGGTCTTACACGTAAATCA-TAATCGATGCCAATGTCCCAGACA
89380606 TGGTCTTACA
1 TGGTCTTACA
89380616 GAAAAACACA
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.03
42 24 0.32
43 21 0.28
44 27 0.36
45 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
TGGTCTTACACGTAAATCATAATCGATGCCAATGTCCCAGACA
Found at i:89383984 original size:26 final size:26
Alignment explanation
Indices: 89383948--89384012 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
89383938 ATTTATCCTA
89383948 GTAAAATTTTTGACAATTTTACCCC-T
1 GTAAAA-TTTTGACAATTTTACCCCTT
* * *
89383974 GATAAAATTTTAACGATTTTTCCCCTT
1 G-TAAAATTTTGACAATTTTACCCCTT
89384001 GTAAAATTTTGA
1 GTAAAATTTTGA
89384013 AAAAAATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 26 0.79
27 7 0.21
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (26 bp):
GTAAAATTTTGACAATTTTACCCCTT
Found at i:89384163 original size:6 final size:6
Alignment explanation
Indices: 89384156--89384201 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
89384146 TGCAAGTTTC
* *
89384156 CATTTC CATTTC CATTTT CATTTT CATTTT CATTTT CA-TTT CATTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTT
89384202 ATGTTTTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.17, C:0.22, G:0.00, T:0.61
Consensus pattern (6 bp):
CATTTT
Found at i:89385736 original size:30 final size:31
Alignment explanation
Indices: 89385696--89385754 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
89385686 ATTTTCGAGC
*
89385696 TTAGGTGCAAAATCGTAATTCTGT-AAAGGT
1 TTAGGGGCAAAATCGTAATTCTGTCAAAGGT
* *
89385726 TTAGGGGCAAAATTGTAATTTTGTCAAAG
1 TTAGGGGCAAAATCGTAATTCTGTCAAAG
89385755 TTTGAGTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (31 bp):
TTAGGGGCAAAATCGTAATTCTGTCAAAGGT
Found at i:89386575 original size:47 final size:47
Alignment explanation
Indices: 89386517--89386638 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
89386507 GTTTTGGCAC
* *
89386517 TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATTACATTTGG
1 TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGACATTTGA
* ** *
89386564 TAAGACAAGGATCCCATGTAAGACCATGTTTGGAACATGGCATTTGA
1 TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGACATTTGA
89386611 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGATAAGGATATCATGTAAGACCATG
89386639 CCAAGGCATG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (47 bp):
TAAGATAAGGATATCATGTAAGACCATGTTTGGAACATGACATTTGA
Found at i:89386681 original size:54 final size:54
Alignment explanation
Indices: 89386617--89386877 Score: 328
Period size: 54 Copynumber: 4.8 Consensus size: 54
89386607 TTGATAAGAT
*
89386617 AAGGATATCATGTAAGACCATGCCAAGGCATGGCACTGATAAGTTCTATAAGGC
1 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
89386671 AAGGAAATCATGTAAGACCATGCCAAGGCATGGTATTGATAAGTTCTATAAGGC
1 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * *
89386725 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTAATAAGTTACTATAAGGC
1 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGGC
** * *
89386780 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * * * * *
89386833 AACGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT
89386878 AAAAAAGGAA
Statistics
Matches: 182, Mismatches: 22, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
52 3 0.02
53 41 0.23
54 93 0.51
55 41 0.23
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
Found at i:89386988 original size:7 final size:7
Alignment explanation
Indices: 89386976--89387003 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
89386966 TAAGGCTTAT
89386976 TTAAGTA
1 TTAAGTA
89386983 TTAAGTA
1 TTAAGTA
89386990 TTAAGTA
1 TTAAGTA
89386997 TTAAGTA
1 TTAAGTA
89387004 AGTGATGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
TTAAGTA
Found at i:89392721 original size:40 final size:39
Alignment explanation
Indices: 89392676--89392883 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 39
89392666 CGGAATACAA
*
89392676 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
89392716 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
89392756 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
89392796 CCGGATGTAGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
89392836 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
89392876 CCGGATAT
1 CCGGATAT
89392884 CATTCAATTG
Statistics
Matches: 143, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
39 4 0.03
40 136 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:89392816 original size:80 final size:81
Alignment explanation
Indices: 89392676--89392881 Score: 240
Period size: 80 Copynumber: 2.6 Consensus size: 81
89392666 CGGAATACAA
* * *
89392676 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCAC-AAT
*
89392740 -GCCTTCGGGTATTAGC
65 GGCCTTCGGGTATTAAC
* *
89392756 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAT
*
89392819 GGCCTTCGGGTCTTAAC
65 GGCCTTCGGGTATTAAC
** * ** * *
89392836 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
89392882 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
79 3 0.03
80 101 0.94
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAATG
GCCTTCGGGTATTAAC
Found at i:89399915 original size:40 final size:39
Alignment explanation
Indices: 89399870--89400077 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
89399860 CGGAATACAA
*
89399870 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
89399910 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
89399950 CCAGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
89399990 CCGGATGTAGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
89400030 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
89400070 CCGGATAT
1 CCGGATAT
89400078 CATTCAATTG
Statistics
Matches: 141, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.03
40 134 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:89400018 original size:80 final size:81
Alignment explanation
Indices: 89399873--89400075 Score: 225
Period size: 80 Copynumber: 2.5 Consensus size: 81
89399863 AATACAACCG
* * *
89399873 GATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAATGCC
1 GATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAATGCC
*
89399937 TTCGGGTATTAGCCCA
66 TTCGGGTATTAACCCA
* *
89399953 GATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCAC-AATGG
1 GATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAAT-G
* *
89400015 CCTTCGGGTCTTAACCCG
64 CCTTCGGGTATTAACCCA
** * ** * *
89400033 GATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 GATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
89400076 ATCATTCAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
79 3 0.03
80 97 0.93
81 1 0.01
82 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
GATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAATGCC
TTCGGGTATTAACCCA
Found at i:89405048 original size:41 final size:41
Alignment explanation
Indices: 89404991--89405073 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
89404981 AGAAAAGTTT
89404991 TACAATGGAACACAATGAAGTATACCAAGGATCGTACCTAA
1 TACAATGGAACACAATGAAGTATACCAAGGATCGTACCTAA
89405032 TACAATGGAACACAATGAAGTATACCAAGGATCGTACCTAA
1 TACAATGGAACACAATGAAGTATACCAAGGATCGTACCTAA
89405073 T
1 T
89405074 GGAGGATGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.20
Consensus pattern (41 bp):
TACAATGGAACACAATGAAGTATACCAAGGATCGTACCTAA
Found at i:89411310 original size:13 final size:13
Alignment explanation
Indices: 89411292--89411324 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
89411282 TAGTGTATCC
*
89411292 TTAATGTTTTTAA
1 TTAATGTGTTTAA
89411305 TTAATGTGTTTAA
1 TTAATGTGTTTAA
89411318 TTAATGT
1 TTAATGT
89411325 CCCTTCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (13 bp):
TTAATGTGTTTAA
Found at i:89411814 original size:52 final size:50
Alignment explanation
Indices: 89411738--89411858 Score: 179
Period size: 50 Copynumber: 2.4 Consensus size: 50
89411728 ATGAACAAAT
* * * *
89411738 GAGTTACTTAATTCATGACTTAATTTAATGATGTAAACTTTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTT-ATGATGCAAAC-TTAACTAACATGA
*
89411790 GAGTTACATAATGCATGTCATAATTTATGATGCAAACTTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTTATGATGCAAACTTAACTAACATGA
89411840 GAGTTACATAATGCATGAC
1 GAGTTACATAATGCATGAC
89411859 TTTATTAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 31 0.49
51 10 0.16
52 22 0.35
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (50 bp):
GAGTTACATAATGCATGACATAATTTATGATGCAAACTTAACTAACATGA
Found at i:89414471 original size:19 final size:19
Alignment explanation
Indices: 89414444--89414490 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
89414434 TGGTATTAGA
*
89414444 ATTAGTTTTCTA-TTCAAGT
1 ATTATTTTTCTATTTCAA-T
*
89414463 ATTATTTTTTTATTTTCAAT
1 ATTATTTTTCTA-TTTCAAT
89414483 ATTATTTT
1 ATTATTTT
89414491 AAAAAAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 5 0.21
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTATTTTTCTATTTCAAT
Found at i:89419765 original size:71 final size:71
Alignment explanation
Indices: 89419678--89419841 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
89419668 CGATTTGTCT
89419678 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
89419743 CTTTCA
66 CTTTCA
* *
89419749 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
89419814 CTTTCA
66 CTTTCA
89419820 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
89419842 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:89419879 original size:71 final size:70
Alignment explanation
Indices: 89419678--89419875 Score: 267
Period size: 71 Copynumber: 2.8 Consensus size: 70
89419668 CGATTTGTCT
* * * *
89419678 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
89419743 CTTTCA
65 CTTTCA
* * *
89419749 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
89419814 CTTTCA
65 CTTTCA
* *
89419820 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
89419876 TACAGGGTGT
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 94 0.79
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:89427340 original size:71 final size:71
Alignment explanation
Indices: 89427256--89427419 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
89427246 CGATTTGTCT
89427256 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
89427321 CTTTCA
66 CTTTCA
89427327 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
89427392 CTTTCA
66 CTTTCA
89427398 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
89427420 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:89427457 original size:71 final size:70
Alignment explanation
Indices: 89427256--89427453 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
89427246 CGATTTGTCT
* * * *
89427256 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
89427321 CTTTCA
65 CTTTCA
* * * *
89427327 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
89427392 CTTTCA
65 CTTTCA
* *
89427398 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
89427454 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:89429459 original size:23 final size:24
Alignment explanation
Indices: 89429428--89429486 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
89429418 TAGGGGTGTG
* *
89429428 AAAACATGAGAGTTTGA-AA-GAA
1 AAAAAATGAGAGATTGATAAGGAA
89429450 AAGAAAATGAGAGATTGATAATGGAA
1 AA-AAAATGAGAGATTGATAA-GGAA
89429476 AAAAAATGAGA
1 AAAAAATGAGA
89429487 AGAAAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 13 0.42
24 2 0.06
25 9 0.29
26 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.17
Consensus pattern (24 bp):
AAAAAATGAGAGATTGATAAGGAA
Found at i:89430125 original size:76 final size:76
Alignment explanation
Indices: 89429999--89430151 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
89429989 TAGCTAGGGT
89429999 TTCTTCAACTTTCAAGCTTCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTT
1 TTCTTCAACTTTCAAGCTTCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTT
89430064 TGAAATCCCGG
66 TGAAATCCCGG
89430075 TTCTTCAACTTTCAAGCTTCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTT
1 TTCTTCAACTTTCAAGCTTCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTT
89430140 TGAAATCCCGG
66 TGAAATCCCGG
89430151 T
1 T
89430152 AACTCGGTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (76 bp):
TTCTTCAACTTTCAAGCTTCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTACGTTTT
TGAAATCCCGG
Found at i:89431082 original size:93 final size:92
Alignment explanation
Indices: 89430924--89431092 Score: 275
Period size: 93 Copynumber: 1.8 Consensus size: 92
89430914 GGATGGTTGA
* **
89430924 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGTT
*
89430989 GAGTCCGAGTTTGTGAGATGTAACTAG
66 GAGTCCAAGTTTGTGAGATGTAACTAG
* *
89431016 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
89431081 TGAGTCCAAGTT
65 TGAGTCCAAGTT
89431093 CACTTAGGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 24 0.34
93 46 0.66
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCAAGTTTGTGAGATGTAACTAG
Found at i:89432495 original size:23 final size:23
Alignment explanation
Indices: 89432449--89432496 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
89432439 ATCATAGAGA
* *
89432449 GAAAAGAACTTGAAAAAGAGAGT
1 GAAAAGAAATTGAAAAAGAAAGT
* *
89432472 GAAAAGAAATTTAAAGAGAAAGT
1 GAAAAGAAATTGAAAAAGAAAGT
89432495 GA
1 GA
89432497 GAGAAAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (23 bp):
GAAAAGAAATTGAAAAAGAAAGT
Found at i:89432540 original size:36 final size:37
Alignment explanation
Indices: 89432461--89432540 Score: 85
Period size: 36 Copynumber: 2.2 Consensus size: 37
89432451 AAAGAACTTG
* * *
89432461 AAAAAGAGAGTGAAAAGAAATTTAAAGAGAAAGTGAG
1 AAAAAAAGAGTGAAAAGAAATTTAAAGAGAAAATGAA
*
89432498 AGAAAAAGAG-GAAAAG-AATTTGAGAA-AGAAAATGAA
1 AAAAAAAGAGTGAAAAGAAATTT-A-AAGAGAAAATGAA
89432534 AAAAAAA
1 AAAAAAA
89432541 AAAAAATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
35 5 0.14
36 21 0.58
37 10 0.28
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.11
Consensus pattern (37 bp):
AAAAAAAGAGTGAAAAGAAATTTAAAGAGAAAATGAA
Found at i:89438135 original size:36 final size:36
Alignment explanation
Indices: 89438086--89438157 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
89438076 AGTATTTTTA
89438086 CTTGAACTAGATAATCCTAACTCTAATTCGAAGCCT
1 CTTGAACTAGATAATCCTAACTCTAATTCGAAGCCT
*
89438122 CTTGAACTGGATAATCCTAACTCTAATTCGAAGCCT
1 CTTGAACTAGATAATCCTAACTCTAATTCGAAGCCT
89438158 TTATATATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (36 bp):
CTTGAACTAGATAATCCTAACTCTAATTCGAAGCCT
Found at i:89447760 original size:93 final size:93
Alignment explanation
Indices: 89447632--89447802 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
89447622 GCCCCTAAGT
* *
89447632 GAACTCAGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
89447697 CGAGTTCGGATGCCTAGTTACATCTCTC
66 CGAGTTCGGATGCCTAGTTACATCTCTC
* * *
89447725 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCAGACTCAACTCA
89447789 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
89447803 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:89447799 original size:46 final size:45
Alignment explanation
Indices: 89447627--89447798 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 45
89447617 AACCCGCCCC
* * *
89447627 TAAGTGAACTCAGACTCAACTCAATGAGCTCAGGCGTTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTC-GGCATTCGCATCCA
* *
89447673 TAAGTGAACTCAGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA
*** *
89447719 TCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGT-GAACTCAGACTCAACTCAACGAGTTCGG-CATTCGCATCCA
*
89447766 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGG
89447799 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 62 0.59
47 32 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGCATTCGCATCCA
Found at i:89447818 original size:46 final size:45
Alignment explanation
Indices: 89447675--89447818 Score: 129
Period size: 46 Copynumber: 3.1 Consensus size: 45
89447665 CGCATCCATA
*
89447675 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* *
89447724 --CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
89447767 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATCCT
89447814 AGTGA
1 AGTGA
89447819 CATGTCACCT
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 6 0.08
44 1 0.01
46 34 0.43
47 29 0.36
48 5 0.06
49 1 0.01
50 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCCT
Found at i:89465164 original size:40 final size:39
Alignment explanation
Indices: 89464999--89465182 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
89464989 AAATTGAATG
* * *
89464999 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
89465039 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
89465079 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
89465119 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
89465158 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
89465183 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:89465207 original size:80 final size:81
Alignment explanation
Indices: 89465039--89465227 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
89465029 GCTGGAAATT
* * * *
89465039 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
89465104 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
89465120 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
89465183 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
89465199 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
89465228 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:89473277 original size:40 final size:39
Alignment explanation
Indices: 89473112--89473295 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
89473102 AAATTGAATG
* * *
89473112 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
89473152 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
89473192 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
89473232 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
89473271 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
89473296 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:89473320 original size:80 final size:81
Alignment explanation
Indices: 89473152--89473340 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
89473142 GCTGGAAATT
* * * *
89473152 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
89473217 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
89473233 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
89473296 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
89473312 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
89473341 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:89479706 original size:13 final size:13
Alignment explanation
Indices: 89479688--89479715 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
89479678 TGAAAATTCG
89479688 TTAATGGTACATT
1 TTAATGGTACATT
89479701 TTAATGGTACATT
1 TTAATGGTACATT
89479714 TT
1 TT
89479716 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:89489644 original size:21 final size:21
Alignment explanation
Indices: 89489620--89489663 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
89489610 GAATCTTTAG
*
89489620 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
89489641 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
89489662 TA
1 TA
89489664 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:89491923 original size:22 final size:22
Alignment explanation
Indices: 89491896--89491939 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
89491886 CTCTCGATTT
89491896 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
89491918 TTTTATTGCTCCTTTTCAATCA
1 TTTTATTGCTCCTTTTCAATCA
89491940 AAAGAGATAA
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:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTTATTGCTCCTTTTCAATCA
Found at i:89496094 original size:32 final size:32
Alignment explanation
Indices: 89496058--89496119 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
89496048 AGCTTTTGGT
89496058 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
89496090 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
89496120 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:89504308 original size:6 final size:6
Alignment explanation
Indices: 89504297--89504375 Score: 66
Period size: 5 Copynumber: 14.2 Consensus size: 6
89504287 GGGATCACTA
89504297 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
* *
89504340 A-GAAT A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
89504376 GAATAGAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
4 3 0.05
5 27 0.43
6 27 0.43
8 6 0.10
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (6 bp):
ACTAAT
Done.