Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 136 of 141
Found at i:40809991 original size:20 final size:20
Alignment explanation
Indices: 40809949--40809991 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40809939 CCAACATTTC
* *
40809949 AATAAATCAAAAAAATGTCA
1 AATAAATCAAAAAAATATAA
40809969 AATAAATCAAAAACAA-ATAA
1 AATAAATCAAAAA-AATATAA
40809989 AAT
1 AAT
40809992 TACATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (20 bp):
AATAAATCAAAAAAATATAA
Found at i:40810164 original size:111 final size:102
Alignment explanation
Indices: 40810092--40810491 Score: 550
Period size: 102 Copynumber: 3.8 Consensus size: 102
40810082 TAAAGAACGC
* *
40810092 AAAAAATTTACATTTATAACAAGTCACAATAAACACTAAACTAAACACAAACAATTTATGACCTA
1 AAAAAATTTACATTTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTATGACCTA
*
40810157 ATAATAAATTACTAACAAAATAACTTTAAAATAATTTAAAGAA
66 ATCATAAATTACTAACAAAATAACTTTAAAATAA-TT-----A
* *
40810200 CGCAAAAAATTTACATTTATAACAAGTCACAATAAACACTAAACTAAACACAAACAATTTATGAC
1 ---AAAAAATTTACATTTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTATGAC
*
40810265 CTAATAATAAATTACTAACAAAATAACTTTAAAATAATTA
63 CTAATCATAAATTACTAACAAAATAACTTTAAAATAATTA
* * * *
40810305 AAAAATTTTACATTCATAAAAAATCACAATAAACATTAAACTAAACACAAAAAATTTATGACCTA
1 AAAAAATTTACATTTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTATGACCTA
* *
40810370 ATCATAAATTACTAGCAAAATAACTTTCAAATAATTA
66 ATCATAAATTACTAACAAAATAACTTTAAAATAATTA
** * * *
40810407 AAAAAATGCACATTTATAAAAAATCACAATAAACATTAAACTAAACACAAACAATTAATAACCTA
1 AAAAAATTTACATTTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTATGACCTA
*
40810472 ACCATAAATTACTAA-AAAAT
66 ATCATAAATTACTAACAAAAT
40810492 TGACTTTACA
Statistics
Matches: 271, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
101 5 0.02
102 164 0.61
105 1 0.00
110 2 0.01
111 99 0.37
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.26
Consensus pattern (102 bp):
AAAAAATTTACATTTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTATGACCTA
ATCATAAATTACTAACAAAATAACTTTAAAATAATTA
Found at i:40810357 original size:48 final size:48
Alignment explanation
Indices: 40810202--40810462 Score: 123
Period size: 48 Copynumber: 5.2 Consensus size: 48
40810192 TTAAAGAACG
* * * *
40810202 CAAAAAATTTACATTTATAACAAGTCACAATAAACACTAAACTAAACA
1 CAAAAAATTTACATTAATAAAAAATCACAATAAACATTAAACTAAACA
* * * * * * * **
40810250 CAAACAATTTATGACCTAATAATAAATTACTAACAAAATAACTTTAAAATAATTA
1 CAAAAAATTTA-CA-TTAATAA-AAA--A-TCACAATA-AACATTAAACTAAACA
* *
40810305 -AAAAATTTTACATTCATAAAAAATCACAATAAACATTAAACTAAACA
1 CAAAAAATTTACATTAATAAAAAATCACAATAAACATTAAACTAAACA
* * * * * * **
40810352 CAAAAAATTTATGACCTAATCATAAATTACTAGCAAAATAACTTTCAAA-TAATTA
1 CAAAAAATTTA-CA-TTAAT-AAAAAAT-C-A-CAATA-AACATT-AAACTAAACA
** *
40810407 -AAAAAATGCACATTTATAAAAAATCACAATAAACATTAAACTAAACA
1 CAAAAAATTTACATTAATAAAAAATCACAATAAACATTAAACTAAACA
*
40810454 CAAACAATT
1 CAAAAAATT
40810463 AATAACCTAA
Statistics
Matches: 148, Mismatches: 47, Indels: 36
0.64 0.20 0.16
Matches are distributed among these distances:
46 3 0.02
47 21 0.14
48 35 0.24
49 4 0.03
50 9 0.06
51 15 0.10
52 9 0.06
53 3 0.02
54 26 0.18
55 20 0.14
56 3 0.02
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.26
Consensus pattern (48 bp):
CAAAAAATTTACATTAATAAAAAATCACAATAAACATTAAACTAAACA
Found at i:40810504 original size:42 final size:43
Alignment explanation
Indices: 40810457--40810542 Score: 165
Period size: 42 Copynumber: 2.0 Consensus size: 43
40810447 CTAAACACAA
40810457 ACAATTAATAACCTAACCATAAATTACT-AAAAAATTGACTTT
1 ACAATTAATAACCTAACCATAAATTACTAAAAAAATTGACTTT
40810499 ACAATTAATAACCTAACCATAAATTACTAAAAAAATTGACTTT
1 ACAATTAATAACCTAACCATAAATTACTAAAAAAATTGACTTT
40810542 A
1 A
40810543 AAATAATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (43 bp):
ACAATTAATAACCTAACCATAAATTACTAAAAAAATTGACTTT
Found at i:40810531 original size:102 final size:102
Alignment explanation
Indices: 40810226--40810532 Score: 349
Period size: 102 Copynumber: 3.0 Consensus size: 102
40810216 TTATAACAAG
* *
40810226 TCACAATAAACACTAAACTAAACACAAACAATTTATGACCTAATAATAAATTACTAACAAAATAA
1 TCACAATAAACATTAAACTAAACACAAACAATTTATGACCTAATCATAAATTACTAA-AAAATAA
*** *
40810291 CTTTA-AAATAATTAAAAAATTTTACATT-CATAAAAAA
65 CTTTACAAATAATTAAAAAACCATAAATTAC-TAAAAAA
* *
40810328 TCACAATAAACATTAAACTAAACACAAAAAATTTATGACCTAATCATAAATTACTAGCAAAATAA
1 TCACAATAAACATTAAACTAAACACAAACAATTTATGACCTAATCATAAATTACTA-AAAAATAA
*
40810393 CTTT-CAAATAATTAAAAAA--ATGCACATTTA-TAAAAAA
65 CTTTACAAATAATTAAAAAACCAT--A-AATTACTAAAAAA
* * * *
40810430 TCACAATAAACATTAAACTAAACACAAACAATTAATAACCTAACCATAAATTACTAAAAAATTGA
1 TCACAATAAACATTAAACTAAACACAAACAATTTATGACCTAATCATAAATTACTAAAAAA-TAA
* **
40810495 CTTTACAATTAA-TAACCTAACCATAAATTACTAAAAAA
65 CTTTACAAATAATTAA-AAAACCATAAATTACTAAAAAA
40810533 ATTGACTTTA
Statistics
Matches: 176, Mismatches: 17, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
100 1 0.01
101 4 0.02
102 151 0.86
103 18 0.10
105 2 0.01
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (102 bp):
TCACAATAAACATTAAACTAAACACAAACAATTTATGACCTAATCATAAATTACTAAAAAATAAC
TTTACAAATAATTAAAAAACCATAAATTACTAAAAAA
Found at i:40810704 original size:107 final size:108
Alignment explanation
Indices: 40810499--40810725 Score: 323
Period size: 107 Copynumber: 2.1 Consensus size: 108
40810489 AATTGACTTT
* * * * *
40810499 ACAATTAATAACCTAACCATAAATTACTAAAAAAATTGACTTTAAAATAATTTAAAAAATAAAAA
1 ACAATTTATAACCTAACCAGAAATTACTAAAAAAA-TAACTATAAAATAATTAAAAAAATAAAAA
* *
40810564 ATTTTATATTAATAGAAAATCACAAAACACTAAACTAAACACAA
65 ATATTATATTAATAAAAAATCACAAAACACTAAACTAAACACAA
**
40810608 ACAATTTATAACCTAATTAGAAATTACTAACAAAAA-AACTATAAAATAATTAAAAAAATAAAAA
1 ACAATTTATAACCTAACCAGAAATTACTAA-AAAAATAACTATAAAATAATTAAAAAAATAAAAA
* *
40810672 A-ATTATATTCATAAAAAATTACAAAACACTAAACTAAACACAA
65 ATATTATATTAATAAAAAATCACAAAACACTAAACTAAACACAA
40810715 ACAATTTATAA
1 ACAATTTATAA
40810726 TAATTAATAA
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
107 49 0.46
108 26 0.25
109 26 0.25
110 5 0.05
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.26
Consensus pattern (108 bp):
ACAATTTATAACCTAACCAGAAATTACTAAAAAAATAACTATAAAATAATTAAAAAAATAAAAAA
TATTATATTAATAAAAAATCACAAAACACTAAACTAAACACAA
Found at i:40810752 original size:107 final size:107
Alignment explanation
Indices: 40810541--40810753 Score: 286
Period size: 107 Copynumber: 2.0 Consensus size: 107
40810531 AAATTGACTT
* * *
40810541 TAAAATAATTTAAAAAATAAAAAATTTTATATTAATAGAAAATCACAAAACACTAAACTAAACAC
1 TAAAATAATTAAAAAAATAAAAAATATTATATTAATAAAAAATCACAAAACACTAAACTAAACAC
** **
40810606 AAACAATTTATAACCTAATTAGAAATTACTAACAAAAAAACTA
66 AAACAATTTATAA-CTAATTAGAAAAAAAAAACAAAAAAACTA
* *
40810649 TAAAATAATTAAAAAAATAAAAAA-ATTATATTCATAAAAAATTACAAAACACTAAACTAAACAC
1 TAAAATAATTAAAAAAATAAAAAATATTATATTAATAAAAAATCACAAAACACTAAACTAAACAC
*
40810713 AAACAATTTATAA-TAATTAATAACAAAAAAAACATAAAAAA
66 AAACAATTTATAACTAATT-AGAA-AAAAAAAACA-AAAAAA
40810754 TAACGATCCC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 5 0.05
106 3 0.03
107 55 0.60
108 29 0.32
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.24
Consensus pattern (107 bp):
TAAAATAATTAAAAAAATAAAAAATATTATATTAATAAAAAATCACAAAACACTAAACTAAACAC
AAACAATTTATAACTAATTAGAAAAAAAAAACAAAAAAACTA
Found at i:40813048 original size:11 final size:11
Alignment explanation
Indices: 40813010--40813066 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
40813000 TAAATCCTTT
40813010 CTCTCAATTT-
1 CTCTCAATTTC
*
40813020 CTCTGTAATATT-
1 CTCT-CAAT-TTC
40813032 CTCTCAATTTC
1 CTCTCAATTTC
40813043 CTCTCAATTTC
1 CTCTCAATTTC
*
40813054 CTCTCAAATTC
1 CTCTCAATTTC
40813065 CT
1 CT
40813067 ATTTGAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 6 0.15
11 29 0.71
12 6 0.15
ACGTcount: A:0.21, C:0.32, G:0.02, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40814903 original size:18 final size:18
Alignment explanation
Indices: 40814880--40814922 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40814870 TGCCAGGTGC
* *
40814880 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
40814898 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
40814916 GTTTCCT
1 GTATCCT
40814923 TTTCCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:40815401 original size:49 final size:49
Alignment explanation
Indices: 40815346--40815463 Score: 218
Period size: 49 Copynumber: 2.4 Consensus size: 49
40815336 TACATTAATG
*
40815346 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATA
*
40815395 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATA
40815444 TAATAAAATACAAAATAGTT
1 TAATAAAATACAAAATAGTT
40815464 AATATTCTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (49 bp):
TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATA
Found at i:40818870 original size:124 final size:124
Alignment explanation
Indices: 40818546--40818951 Score: 600
Period size: 124 Copynumber: 3.3 Consensus size: 124
40818536 CATGCTACTG
* * *
40818546 TAGCAAAAGCGCGTCCACGTGAGAGTGATTTCAAAAATTCTTTTAATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGAAG
* *
40818611 CGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCTACTA
66 C--TTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCTACAA
* *
40818672 TACCAAAAGCGTGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGAAG
*
40818737 CGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTA-TTTTTCAGGACCTACAA
66 CTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCTACAA
* * * * *
40818795 TAGCAAAAGCGCGTCCACGAGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGCTTGAAA
1 TAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGAAG
*
40818860 CATTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCTA-ATG
66 C-TTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCTACA-A
* ** *
40818920 TATCAAAAATGCGTCCGCGTGGGAGCGATTTC
1 TAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
40818952 CTTAATAAAT
Statistics
Matches: 254, Mismatches: 23, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
123 75 0.30
124 78 0.31
125 40 0.16
126 61 0.24
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (124 bp):
TAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGAAG
CTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACCTACAA
Found at i:40822987 original size:41 final size:41
Alignment explanation
Indices: 40822877--40822989 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 41
40822867 CACTAGCACC
*** *
40822877 AAGCCTGCTAGGCATAAAGCCTGATAGGGTACACCGACATG
1 AAGCCTGCTAGGCATAAAGCCTGATACATTACACCGACATA
* * *
40822918 AAGCCTGCTAGGCTTAAAGCCTGATACATTTCACCGGCATA
1 AAGCCTGCTAGGCATAAAGCCTGATACATTACACCGACATA
40822959 AAGCCTGCTAGGCATAAAGCCTGATACATTA
1 AAGCCTGCTAGGCATAAAGCCTGATACATTA
40822990 ATATAAAGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (41 bp):
AAGCCTGCTAGGCATAAAGCCTGATACATTACACCGACATA
Found at i:40824119 original size:16 final size:14
Alignment explanation
Indices: 40824088--40824116 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40824078 ATTTCACAAA
40824088 AATTTCACACATAT
1 AATTTCACACATAT
40824102 AATTTCACACATAT
1 AATTTCACACATAT
40824116 A
1 A
40824117 TAACGCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTCACACATAT
Found at i:40828952 original size:13 final size:13
Alignment explanation
Indices: 40828934--40828961 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40828924 AAGCCATGAT
40828934 AAGGTGGTTAGTA
1 AAGGTGGTTAGTA
40828947 AAGGTGGTTAGTA
1 AAGGTGGTTAGTA
40828960 AA
1 AA
40828962 ACTAATTCAG
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:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGGTGGTTAGTA
Found at i:40832273 original size:18 final size:19
Alignment explanation
Indices: 40832245--40832284 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
40832235 TCATTTATAT
40832245 TTTATTTTATATATAAATA
1 TTTATTTTATATATAAATA
* *
40832264 TTTA-TTTATATTTATATA
1 TTTATTTTATATATAAATA
40832282 TTT
1 TTT
40832285 TGTTCACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTTATATATAAATA
Found at i:40832280 original size:16 final size:16
Alignment explanation
Indices: 40832231--40832280 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
40832221 AAACATAAAT
40832231 TATTTCATTTATATTT-
1 TATTT-ATTTATATTTA
* **
40832247 TATTT-TATATATAAA
1 TATTTATTTATATTTA
40832262 TATTTATTTATATTTA
1 TATTTATTTATATTTA
40832278 TAT
1 TAT
40832281 ATTTTGTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
16 15 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTTATATTTA
Found at i:40832540 original size:88 final size:87
Alignment explanation
Indices: 40832407--40832708 Score: 362
Period size: 86 Copynumber: 3.5 Consensus size: 87
40832397 AATATATTTT
* * * * *
40832407 TTAAAAGTCAATAAAATCTGTTTCGGGATCTATTCCCGCCATTCAACGGATTTTATTCCAATTTT
1 TTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATT-CAATTTT
* *
40832472 GATTTTATTTCCAAAACAAG-TA
65 GATTTTATTTCCAAAACGAGAAA
* * * * *
40832494 TTAAAATTAAAATAAAAACTGTCTCGGGATTTATTCCAGCCGTTCAACAAATTTTATTCATTTTT
1 TTAAAATT-AAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTTT
*
40832559 TATTTTATTTCC-AAACGAGAAA
65 GATTTTATTTCCAAAACGAGAAA
* *
40832581 TTAAAGTTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAATGAATTTTATT-ACA-TTT
1 TTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCA-ATTTT
*
40832644 GATTTTGTTTCCAAAACGAGAAA
65 GATTTTATTTCCAAAACGAGAAA
* * * *
40832667 TTAAAATTAAAT-AAATCTATTTCCGGCTTTATTCTCGCCGTT
1 TTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTT
40832709 TAACAATATT
Statistics
Matches: 184, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
85 40 0.22
86 71 0.39
87 32 0.17
88 41 0.22
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (87 bp):
TTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGAATTTTATTCAATTTTG
ATTTTATTTCCAAAACGAGAAA
Found at i:40832897 original size:159 final size:159
Alignment explanation
Indices: 40832587--40832905 Score: 478
Period size: 159 Copynumber: 2.0 Consensus size: 159
40832577 GAAATTAAAG
40832587 TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAATGAATTTTATTACATTTGATTTTGT
1 TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAATGAATTTTATTACATTTGATTTTGT
* * * *
40832652 TTCCAAAACGAGAAATTAAAATTAAATAAATCTATTTCCGGCTTTATTCTCGCCGTTTAACAATA
66 TTCCAAAACGAGAAATTAAAATTAAATAAATCTATTTCCGGATTTATTCCCGCCATTTAACAAGA
* * * *
40832717 TTTGATTTGATTTTAATTTTGTTTTCAAA
131 TTTGATTCGATATTAAGTTTGTTTACAAA
*
40832746 TTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAATGAATTTTATTACATTTGATTTTGT
1 TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAATGAATTTTATTACATTTGATTTTGT
* * ** *
40832811 TTCCAAAACGAGAAATTAAAGTTAAATAAAATCTGTTTTGGGATTTATTCCCGCTATTTAACAAG
66 TTCCAAAACGAGAAATTAAAATTAAAT-AAATCTATTTCCGGATTTATTCCCGCCATTTAACAAG
* *
40832876 ATTTTATTCGATATT-GGTTTGTTTACAAA
130 ATTTGATTCGATATTAAGTTTGTTTACAAA
40832905 T
1 T
40832906 GAAGACTTAA
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
159 102 0.71
160 41 0.29
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (159 bp):
TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAATGAATTTTATTACATTTGATTTTGT
TTCCAAAACGAGAAATTAAAATTAAATAAATCTATTTCCGGATTTATTCCCGCCATTTAACAAGA
TTTGATTCGATATTAAGTTTGTTTACAAA
Found at i:40832999 original size:35 final size:35
Alignment explanation
Indices: 40832927--40833000 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
40832917 CAAATAATTC
* * *
40832927 TATTTCGGGATTTATTCCCGCTGTTTAACAGACTT
1 TATTTCGGGATTTATTCCCACCGTTCAACAGACTT
* * *
40832962 TATTTTGGGATTTATTCCCACCGTTCAACGGATTT
1 TATTTCGGGATTTATTCCCACCGTTCAACAGACTT
40832997 TATT
1 TATT
40833001 CCTTTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.45
Consensus pattern (35 bp):
TATTTCGGGATTTATTCCCACCGTTCAACAGACTT
Found at i:40833144 original size:87 final size:88
Alignment explanation
Indices: 40832962--40833285 Score: 460
Period size: 87 Copynumber: 3.7 Consensus size: 88
40832952 TAACAGACTT
* * * * * * *
40832962 TATTTTGGGATTTATTCCCACCGTTCAACGGATTTTATTCCTTTTTTTTATTTTTTTTCCAAA-C
1 TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTAC-TATTTTGATTTTGTTGCCAAATC
40833026 GAGAAATTAAAATTAAATAAAATC
65 GAGAAATTAAAATTAAATAAAATC
40833050 TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTAC-ATTTTGATTTTGTTGCCAAATCG
1 TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTACTATTTTGATTTTGTTGCCAAATCG
40833114 AGAAATTAAAATTAAATAAAATC
66 AGAAATTAAAATTAAATAAAATC
40833137 TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTAC-ATTTTGATTTTGTTGCCAAATCG
1 TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTACTATTTTGATTTTGTTGCCAAATCG
40833201 AGAAATTAAAATTAAATAAAATC
66 AGAAATTAAAATTAAATAAAATC
* * * * * * * *
40833224 TGTTTTGGGATTTATTCTCGCCGTTTAACTAGATTTTATT-CGATATTGA-TTTGTTTCCAAAT
1 TATTTTGAGATTTATTCCCGCCGTTCAAC-GGATTTTATTACTATTTTGATTTTGTTGCCAAAT
40833286 GATGACTTCA
Statistics
Matches: 219, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
86 16 0.07
87 150 0.68
88 53 0.24
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (88 bp):
TATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTACTATTTTGATTTTGTTGCCAAATCG
AGAAATTAAAATTAAATAAAATC
Found at i:40833366 original size:35 final size:35
Alignment explanation
Indices: 40833309--40833380 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
40833299 AATAATTCTG
40833309 TTTCAGGATTTATTCCACCCGTTTAACAAACTTTA
1 TTTCAGGATTTATTCCACCCGTTTAACAAACTTTA
* * *
40833344 TTTCGGGATTTATTCC-CGCCGTTTAACAGATTTTA
1 TTTCAGGATTTATTCCAC-CCGTTTAACAAACTTTA
40833379 TT
1 TT
40833381 CATTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTCAGGATTTATTCCACCCGTTTAACAAACTTTA
Found at i:40833449 original size:291 final size:293
Alignment explanation
Indices: 40833058--40833638 Score: 900
Period size: 292 Copynumber: 2.0 Consensus size: 293
40833048 TCTATTTTGA
* *
40833058 GATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTGATTTTGTTGCCAAATCGAGAAATTAA
1 GATTTATTCCCGCCGTTCAACAGATTTTATTACATTTTGATTTTATTGCCAAATCGAGAAATTAA
*
40833123 AATTAAATAAAATCTATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTACA-TTTTGATT
66 AATTAAATAAAATCTATTTCGAGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTTGATT
* * * *
40833187 TTGTTGCCAAATCGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCCGTTTAA
131 TTGTTGCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTAA
* * * *
40833252 CTAGATTTTATTCGATATTGATTTGTTTCCAAATGATGACTTCATCAAATAATTCTGTTTCAGGA
196 CAAGATTTTATTCGATATTGATTTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTCAGGA
*
40833317 TTTATTCCAC-CCGTTTAACAAACTTTATTTCGG
261 TTTATT-CACGCCATTTAACAAACTTTATTTCGG
* * * *
40833350 GATTTATTCCCGCCGTTTAACAGATTTTATT-CATTTTTTATTTTATTTCTAAA-CGAGAAATTA
1 GATTTATTCCCGCCGTTCAACAGATTTTATTACA-TTTTGATTTTATTGCCAAATCGAGAAATTA
* * * * *
40833413 AAGTTAGATAAAATCTGTTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTTTAT
65 AAATTAAATAAAATCTATTTCGAGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTTGAT
40833478 TTTGTTGCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTA
130 TTTGTTGCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTA
*
40833543 ACAAGATTTTATTCGATATTGATTTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTCGGG
195 ACAAGATTTTATTCGATATTGATTTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTCAGG
* *
40833608 ATTTATTCACGTCATTTAATAAACTTTATTT
260 ATTTATTCACGCCATTTAACAAACTTTATTT
40833639 TGATTTAATT
Statistics
Matches: 262, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
291 67 0.26
292 195 0.74
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (293 bp):
GATTTATTCCCGCCGTTCAACAGATTTTATTACATTTTGATTTTATTGCCAAATCGAGAAATTAA
AATTAAATAAAATCTATTTCGAGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTTGATT
TTGTTGCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTAA
CAAGATTTTATTCGATATTGATTTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTCAGGA
TTTATTCACGCCATTTAACAAACTTTATTTCGG
Found at i:40833524 original size:88 final size:86
Alignment explanation
Indices: 40833344--40833556 Score: 327
Period size: 88 Copynumber: 2.4 Consensus size: 86
40833334 ACAAACTTTA
* *
40833344 TTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCATTTTTTATTTTATTTCTAAACGAGAA
1 TTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCATTTTTTATTTTATTCCAAAACGAGAA
* *
40833409 ATTAAAGTTAGATAAAATCTG
66 ATTAAAATTAAATAAAATCTG
* * *
40833430 TTTCGGGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTTTATTTTGTTGCCAAAACGAG
1 TTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT-CATTTTTTATTTTATT-CCAAAACGAG
40833495 AAATTAAAATTAAATAAAATCTG
64 AAATTAAAATTAAATAAAATCTG
*
40833518 TTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTC
1 TTTCGGGATTTATTCCCGCCGTTTAAC-AGATTTTATTC
40833557 GATATTGATT
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 35 0.31
87 15 0.13
88 55 0.48
89 9 0.08
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (86 bp):
TTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCATTTTTTATTTTATTCCAAAACGAGAA
ATTAAAATTAAATAAAATCTG
Found at i:40833553 original size:380 final size:380
Alignment explanation
Indices: 40832743--40833626 Score: 1243
Period size: 380 Copynumber: 2.3 Consensus size: 380
40832733 TTTTGTTTTC
*
40832743 AAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAA-TGAATTTTATTACA-TTTGAT
1 AAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAG-ATTTTATTACATTTTGAT
* *
40832806 TTTGTTTCCAAAACGAGAAATTAAAGTTAAATAAAATCTGTTTTGGGATTTATTCCCGCTATTTA
65 TTTGTTTCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCATTTA
* *
40832871 ACAAGATTTTATTCGATATTGGTTTGTTTACAAATGAAGACTTAATCAAATAATTCTATTTCGGG
130 ACAAGATTTTATTCGATATTGATTTGTTTACAAATGAAGACTTAATCAAATAATTCTATTTCAGG
* * * *
40832936 ATTTATTCCCGCTGTTTAACAGACTTTATTTTGGGATTTATTCCCACCGTTCAACGGATTTTATT
195 ATTTATTCCCGCCGTTTAACAAACTTTATTTCGGGATTTATTCCCACCGTTCAACAGATTTTATT
* * *
40833001 CCTTTTTTTTATTTTTTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTTGAGATTTATT
260 CCTATTTTTTATTTTATTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGAGATTTATT
*
40833066 CCCGCCGTTCAACGGATTTTATTACATTTTGATTTTGTTGCCAAATCGAGAAATTA
325 CCCGCCGTTCAACGGATTTTATTACATTTTGATTTTGTTGCCAAAACGAGAAATTA
* * *
40833122 AAATTAAATAAAATCTATTTTGAGATTTATTCCCGCCGTTCAACGGATTTTATTACATTTTGATT
1 AAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTACATTTTGATT
* * * *
40833187 TTGTTGCCAAATCGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCCGTTTAA
66 TTGTTTCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCATTTAA
* * * * *
40833252 CTAGATTTTATTCGATATTGATTTGTTTCCAAATGATGACTTCATCAAATAATTCTGTTTCAGGA
131 CAAGATTTTATTCGATATTGATTTGTTTACAAATGAAGACTTAATCAAATAATTCTATTTCAGGA
* *
40833317 TTTATTCCAC-CCGTTTAACAAACTTTATTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATT
196 TTTATTCC-CGCCGTTTAACAAACTTTATTTCGGGATTTATTCCCACCGTTCAACAGATTTTATT
* * * * *
40833381 -C-ATTTTTTATTTTATTTCTAAACGAGAAATTAAAGTTAGATAAAATCTGTTTCGGGATTTATT
260 CCTATTTTTTATTTTATTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGAGATTTATT
*
40833444 CCCGCCGTTCAACGGATTTTATTACATTTTTTATTTTGTTGCCAAAACGAGAAATTA
325 CCCGCCGTTCAACGGATTTTATTACA-TTTTGATTTTGTTGCCAAAACGAGAAATTA
* * * *
40833501 AAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATT-CGATATTGA
1 AAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAAC-AGATTTTATTAC-ATTTTGA
* * * * * *
40833565 -TTTGTTTCC-AAACGA-AGACTT--AATCAAAT-AATTCTGTTTCGGGATTTATTCACGTCATT
64 TTTTGTTTCCAAAACGAGA-AATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCATT
40833624 TAA
128 TAA
40833627 TAAACTTTAT
Statistics
Matches: 450, Mismatches: 48, Indels: 18
0.87 0.09 0.03
Matches are distributed among these distances:
375 28 0.06
376 7 0.02
377 1 0.00
378 88 0.20
379 129 0.29
380 196 0.44
381 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (380 bp):
AAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTCAACAGATTTTATTACATTTTGATT
TTGTTTCCAAAACGAGAAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCATTTAA
CAAGATTTTATTCGATATTGATTTGTTTACAAATGAAGACTTAATCAAATAATTCTATTTCAGGA
TTTATTCCCGCCGTTTAACAAACTTTATTTCGGGATTTATTCCCACCGTTCAACAGATTTTATTC
CTATTTTTTATTTTATTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGAGATTTATTC
CCGCCGTTCAACGGATTTTATTACATTTTGATTTTGTTGCCAAAACGAGAAATTA
Found at i:40833713 original size:59 final size:59
Alignment explanation
Indices: 40833592--40833717 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 59
40833582 ACTTAATCAA
* * * * * * *
40833592 ATAATTCTGTTTCGGGATTTATTCACGTCATTTAATAAACTTTATTTTGATTTAATTAC
1 ATAATTTTGTTTAGGGATTTAATCACGCCATTTAACAAAATTGATTTTGATTTAATTAC
** ** *
40833651 ATAATTTTGTTTAGGGATTTAATCTTGCCATTTAACAAAATTGATTTTGATTTTGTTTC
1 ATAATTTTGTTTAGGGATTTAATCACGCCATTTAACAAAATTGATTTTGATTTAATTAC
40833710 ATAATTTT
1 ATAATTTT
40833718 AATTCTGTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.51
Consensus pattern (59 bp):
ATAATTTTGTTTAGGGATTTAATCACGCCATTTAACAAAATTGATTTTGATTTAATTAC
Found at i:40856975 original size:9 final size:9
Alignment explanation
Indices: 40856954--40856988 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
40856944 TCATCTATGT
40856954 TAAAAAACTA
1 TAAAAAAC-A
40856964 TAAAAAACA
1 TAAAAAACA
*
40856973 TAAAAAACG
1 TAAAAAACA
40856982 TAAAAAA
1 TAAAAAA
40856989 AAATGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (9 bp):
TAAAAAACA
Found at i:40856978 original size:19 final size:19
Alignment explanation
Indices: 40856954--40856999 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
40856944 TCATCTATGT
*
40856954 TAAAAAAC-TATAAAAAACA
1 TAAAAAACGTA-AAAAAAAA
40856973 TAAAAAACGTAAAAAAAAA
1 TAAAAAACGTAAAAAAAAA
*
40856992 TGAAAAAC
1 TAAAAAAC
40857000 AAAAAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (19 bp):
TAAAAAACGTAAAAAAAAA
Found at i:40864392 original size:62 final size:62
Alignment explanation
Indices: 40864277--40864456 Score: 165
Period size: 62 Copynumber: 2.9 Consensus size: 62
40864267 AGAGGGCCTA
* * * * *
40864277 TCAAAA-TTTTGGGAAATTATGATTTTTCC-TTGAA-TTTTTAGTAAATTTTAATTAGGC-CC
1 TCAAAATTTTTGGAAAATTATCA-TTTTCCTTTAAAGTTTTTAGAAAATTTTAATTAGACTCC
40864336 TCCAAAATTTTTGGAAAATT-TCATTTCTCCTTTAAAGTTTTTAGAAAATTTTAATTAGACTCC
1 T-CAAAATTTTTGGAAAATTATCATTT-TCCTTTAAAGTTTTTAGAAAATTTTAATTAGACTCC
* * * * * *
40864399 TC-AATTTTTTTGAAATTTCTCATTTTACCTTTTAATGTTTTTTTGAAAATTTTAATTA
1 TCAAAATTTTTGGAAAATTATCATTTT-CC-TTTAAAG-TTTTTAGAAAATTTTAATTA
40864457 AGCTCACTTA
Statistics
Matches: 101, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
59 4 0.04
60 10 0.10
61 29 0.29
62 30 0.30
63 9 0.09
64 19 0.19
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (62 bp):
TCAAAATTTTTGGAAAATTATCATTTTCCTTTAAAGTTTTTAGAAAATTTTAATTAGACTCC
Found at i:40864512 original size:21 final size:22
Alignment explanation
Indices: 40864478--40864518 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40864468 AATGTTTGAA
*
40864478 AAAAATTCTCATTA-ATCTCAC
1 AAAAATTCTAATTAGATCTCAC
*
40864499 AAAAATTTTAATTAGATCTC
1 AAAAATTCTAATTAGATCTC
40864519 CAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAAATTCTAATTAGATCTCAC
Found at i:40874417 original size:11 final size:11
Alignment explanation
Indices: 40874409--40874433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40874399 TAGTTTTTCT
40874409 TTTGGTTTTAA
1 TTTGGTTTTAA
40874420 TTTGGTTTTAA
1 TTTGGTTTTAA
40874431 TTT
1 TTT
40874434 TATTTTCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTGGTTTTAA
Found at i:40876535 original size:16 final size:16
Alignment explanation
Indices: 40876514--40876550 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40876504 TTTGTCTTCG
* *
40876514 TATTTTAAATTTTTAT
1 TATTTTAAATATATAT
40876530 TATTTTAAATATATAT
1 TATTTTAAATATATAT
40876546 TATTT
1 TATTT
40876551 AGATGGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTAAATATATAT
Found at i:40876926 original size:31 final size:31
Alignment explanation
Indices: 40876863--40876927 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
40876853 AAGTCTCGTG
* * *
40876863 CAAAGATATAATCAGTACAAGACAAACTATA
1 CAAAAATATAATCAATACAAGACAAACCATA
*
40876894 CAAAAATATAATTAATACAAGA-AAAGCCATA
1 CAAAAATATAATCAATACAAGACAAA-CCATA
40876925 CAA
1 CAA
40876928 GACAAATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.18
Consensus pattern (31 bp):
CAAAAATATAATCAATACAAGACAAACCATA
Found at i:40879444 original size:31 final size:31
Alignment explanation
Indices: 40879409--40879475 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
40879399 GTTACAAAAT
*
40879409 AGTCATTGAATTATTTGAAACTT-TTCATTTA
1 AGTCATTAAATTATTTGAAACTTATT-ATTTA
*
40879440 AGTCATTAAATTATTTGAAAGTTATTATTTA
1 AGTCATTAAATTATTTGAAACTTATTATTTA
40879471 AGTCA
1 AGTCA
40879476 CTGGTTGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTCATTAAATTATTTGAAACTTATTATTTA
Found at i:40890116 original size:21 final size:21
Alignment explanation
Indices: 40890092--40890132 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40890082 TATATGGTCA
*
40890092 GTATGATCTGTAATATGATAT
1 GTATGATCTATAATATGATAT
40890113 GTATGATCTATAATATGATA
1 GTATGATCTATAATATGATA
40890133 ACTATGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (21 bp):
GTATGATCTATAATATGATAT
Found at i:40890138 original size:21 final size:21
Alignment explanation
Indices: 40890093--40890140 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
40890083 ATATGGTCAG
* **
40890093 TATGATCTGTAATATGATATG
1 TATGATCTATAATATGATAAC
40890114 TATGATCTATAATATGATAAC
1 TATGATCTATAATATGATAAC
40890135 TATGAT
1 TATGAT
40890141 ATGTTATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (21 bp):
TATGATCTATAATATGATAAC
Found at i:40903753 original size:16 final size:16
Alignment explanation
Indices: 40903734--40903766 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40903724 AATTATTTAT
*
40903734 TTATTTTTGTAAGGTA
1 TTATTTTGGTAAGGTA
40903750 TTATTTTGGTAAGGTA
1 TTATTTTGGTAAGGTA
40903766 T
1 T
40903767 GTTTATGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (16 bp):
TTATTTTGGTAAGGTA
Found at i:40903794 original size:21 final size:21
Alignment explanation
Indices: 40903770--40903811 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40903760 AAGGTATGTT
*
40903770 TATGTTTTATTT-TTTGATTCA
1 TATGTTTT-TTTATTAGATTCA
40903791 TATGTTTTTTTATTAGATTCA
1 TATGTTTTTTTATTAGATTCA
40903812 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.21, C:0.05, G:0.10, T:0.64
Consensus pattern (21 bp):
TATGTTTTTTTATTAGATTCA
Found at i:40912981 original size:16 final size:17
Alignment explanation
Indices: 40912947--40912985 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
40912937 ATTTTAAATT
40912947 AAAAAATAATACATTTTA
1 AAAAAATAATACA-TTTA
40912965 AAAAAATAATACA-TTA
1 AAAAAATAATACATTTA
40912981 AAAAA
1 AAAAA
40912986 TATTCATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAATAATACATTTA
Found at i:40912983 original size:15 final size:15
Alignment explanation
Indices: 40912944--40912987 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 15
40912934 AAAATTTTAA
40912944 ATTAAAAAATAATAC
1 ATTAAAAAATAATAC
40912959 ATTTTAAAAAAATAATAC
1 A--TT-AAAAAATAATAC
40912977 ATTAAAAAATA
1 ATTAAAAAATA
40912988 TTCATAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.35
16 2 0.08
17 2 0.08
18 13 0.50
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAAAATAATAC
Found at i:40918765 original size:17 final size:17
Alignment explanation
Indices: 40918731--40918765 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40918721 CCCCCATTCT
*
40918731 AATCCCTAACAACTCTA
1 AATCCCTAACAACCCTA
*
40918748 AATCCCTAAGAACCCTA
1 AATCCCTAACAACCCTA
40918765 A
1 A
40918766 CAAATTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.20
Consensus pattern (17 bp):
AATCCCTAACAACCCTA
Found at i:40920145 original size:17 final size:17
Alignment explanation
Indices: 40920109--40920146 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40920099 TGGTATGATG
*
40920109 TGATGAAAATTCATGAA
1 TGATGAAAATACATGAA
40920126 TGATGGAAAATACATG-A
1 TGAT-GAAAATACATGAA
40920143 TGAT
1 TGAT
40920147 TAACTTATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (17 bp):
TGATGAAAATACATGAA
Found at i:40920459 original size:6 final size:6
Alignment explanation
Indices: 40920448--40920482 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
40920438 TATTTCTAAA
*
40920448 TTCATT TTCATT TTCATT TTCATT ATTAATT TTCA
1 TTCATT TTCATT TTCATT TTCATT -TTCATT TTCA
40920483 GATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (6 bp):
TTCATT
Found at i:40922968 original size:11 final size:11
Alignment explanation
Indices: 40922952--40923000 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
40922942 TGCAGGTTAT
40922952 TTTTGGTGTTG
1 TTTTGGTGTTG
40922963 TTTTGGTGTTG
1 TTTTGGTGTTG
* *
40922974 ATTTTGGGTGGTA
1 -TTTT-GGTGTTG
*
40922987 TTTTAGTGTTG
1 TTTTGGTGTTG
40922998 TTT
1 TTT
40923001 CGCTGTCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 18 0.58
12 8 0.26
13 5 0.16
ACGTcount: A:0.06, C:0.00, G:0.33, T:0.61
Consensus pattern (11 bp):
TTTTGGTGTTG
Found at i:40925722 original size:2 final size:2
Alignment explanation
Indices: 40925709--40925746 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
40925699 GTTTAATTTG
*
40925709 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40925747 GTTTCAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40926245 original size:17 final size:17
Alignment explanation
Indices: 40926223--40926257 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
40926213 AGTGAGTAGG
*
40926223 TTAATCTATTGTGTTTA
1 TTAATCTATTATGTTTA
40926240 TTAATCTATTATGTTTA
1 TTAATCTATTATGTTTA
40926257 T
1 T
40926258 CTTCGCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (17 bp):
TTAATCTATTATGTTTA
Found at i:40927107 original size:64 final size:64
Alignment explanation
Indices: 40927006--40927127 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
40926996 GGTTTCGTGA
*
40927006 CCACACGGGCGTGTGCAGCGCACGGGATTAGGGATTTGGGCGAATGTTGGTGCCACACGGGTGG
1 CCACACGGGCGTGTGCAACGCACGGGATTAGGGATTTGGGCGAATGTTGGTGCCACACGGGTGG
*
40927070 CCACACGGGCGTGTGCAACGCACGGGGTTAGGGATTTGGGCGAATGTTGGTGCCACAC
1 CCACACGGGCGTGTGCAACGCACGGGATTAGGGATTTGGGCGAATGTTGGTGCCACAC
40927128 AGCTTGACCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.18, C:0.23, G:0.40, T:0.19
Consensus pattern (64 bp):
CCACACGGGCGTGTGCAACGCACGGGATTAGGGATTTGGGCGAATGTTGGTGCCACACGGGTGG
Found at i:40929034 original size:20 final size:20
Alignment explanation
Indices: 40928996--40929036 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40928986 GGTGTTGGAA
* *
40928996 TATGAAATTGATGTAAATTG
1 TATGAAAATGATATAAATTG
*
40929016 TATGAAAATGATATCAATTG
1 TATGAAAATGATATAAATTG
40929036 T
1 T
40929037 TTGTGTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (20 bp):
TATGAAAATGATATAAATTG
Found at i:40940467 original size:37 final size:37
Alignment explanation
Indices: 40940426--40940534 Score: 87
Period size: 37 Copynumber: 3.1 Consensus size: 37
40940416 GATATAAAAC
40940426 TTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAA
1 TTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAA
* *
40940463 TTAAT-GACTA---A-ATT--GTAA--AAGAT--ATAGAA
1 TTAATCG-CTATTGACTTTCAGTAATTAA-ATGGTTA-AA
40940492 CTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAA
1 -TTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAA
40940530 TTAAT
1 TTAAT
40940535 GATTGAGGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 30
0.61 0.05 0.34
Matches are distributed among these distances:
28 2 0.04
29 4 0.08
30 10 0.19
31 5 0.09
33 3 0.06
34 3 0.06
36 5 0.09
37 15 0.28
38 4 0.08
39 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (37 bp):
TTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAA
Found at i:40940479 original size:67 final size:67
Alignment explanation
Indices: 40940401--40940536 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
40940391 AATTAAAATG
40940401 GACTAAATTGTAAAAGATATAAAACTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAATTA
1 GACTAAATTGTAAAAGATATAAAACTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAATTA
40940466 AT
66 AT
*
40940468 GACTAAATTGTAAAAGATATAGAACTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAATTA
1 GACTAAATTGTAAAAGATATAAAACTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAATTA
40940533 AT
66 AT
40940535 GA
1 GA
40940537 TTGAGGGAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (67 bp):
GACTAAATTGTAAAAGATATAAAACTTAATCGCTATTGACTTTCAGTAATTAAATGGTTAAATTA
AT
Found at i:40942732 original size:21 final size:21
Alignment explanation
Indices: 40942693--40942732 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40942683 CTTGCTTCCC
*
40942693 AAATTTTCATGTTTTTTTCTA
1 AAATTTTCATGTTTGTTTCTA
40942714 AAATTTTCTAT-TTTGTTTC
1 AAATTTTC-ATGTTTGTTTC
40942733 AATTTCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
AAATTTTCATGTTTGTTTCTA
Found at i:40943598 original size:75 final size:75
Alignment explanation
Indices: 40943506--40943656 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
40943496 TGGTGTAGGG
*
40943506 ACGTGTTGGATATAAAAAACGAGGGAGAAGGGACCAAACGAAAGGGTATCATGATATCCAAACAT
1 ACGTGTTGGAGATAAAAAACGAGGGAGAAGGGACCAAACGAAAGGGTATCATGATATCCAAACAT
40943571 TGGAATGGCA
66 TGGAATGGCA
*
40943581 ACGTGTTGGAGATAAAAAACGAGGGAGAATGGACCAAACGAAAGGGTATCATGATATCCAAACAT
1 ACGTGTTGGAGATAAAAAACGAGGGAGAAGGGACCAAACGAAAGGGTATCATGATATCCAAACAT
40943646 TGGAATGGCA
66 TGGAATGGCA
40943656 A
1 A
40943657 TATCTCTAAC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.42, C:0.13, G:0.28, T:0.17
Consensus pattern (75 bp):
ACGTGTTGGAGATAAAAAACGAGGGAGAAGGGACCAAACGAAAGGGTATCATGATATCCAAACAT
TGGAATGGCA
Found at i:40948394 original size:18 final size:18
Alignment explanation
Indices: 40948373--40948426 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
40948363 CCCCTTTAAA
40948373 TCTCTTTCAATTTTCTTT-
1 TCTCTTTC-ATTTTCTTTC
*
40948391 TCTCTTTTCTTTTTTCTTTC
1 TCTC-TTTC-ATTTTCTTTC
*
40948411 TTTCTTTCATTTTCTT
1 TCTCTTTCATTTTCTT
40948427 CTTTTGCAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 11 0.37
19 16 0.53
20 3 0.10
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTCTTTCATTTTCTTTC
Found at i:40948408 original size:12 final size:12
Alignment explanation
Indices: 40948383--40948431 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
40948373 TCTCTTTCAA
*
40948383 TTTTCTTTTCTC
1 TTTTCTTTTTTC
40948395 TTTTCTTTTTTC
1 TTTTCTTTTTTC
40948407 -TTTCTTTCTTTC
1 TTTTCTTT-TTTC
40948419 ATTTTCTTCTTTT
1 -TTTTCTT-TTTT
40948432 GCAGGTATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
14 9 0.28
15 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:40949038 original size:15 final size:15
Alignment explanation
Indices: 40949015--40949055 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
40949005 GTTATTTCGG
40949015 TTTATGTTTAGGG-TCT
1 TTTA-GTTTAGGGAT-T
40949031 TTTAGTTTAGGGATT
1 TTTAGTTTAGGGATT
40949046 TTT-GTTTAGG
1 TTTAGTTTAGG
40949056 TTGTTGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 12 0.50
16 5 0.21
ACGTcount: A:0.15, C:0.02, G:0.27, T:0.56
Consensus pattern (15 bp):
TTTAGTTTAGGGATT
Found at i:40950158 original size:57 final size:56
Alignment explanation
Indices: 40950055--40950208 Score: 159
Period size: 57 Copynumber: 2.8 Consensus size: 56
40950045 TGTAATGAAG
* * * *
40950055 GTGTTGAGGTTGCTGGTAGTAAAGGTGGTGAACGTGTTGTAAGTTTAAATGGAGACA
1 GTGTTGAGGTTGCTGGCAATAAAGGTGGTGAAGGTGGTG-AAGTTTAAATGGAGACA
* ** * **
40950112 GTGTTGAGGTTGCTGGCAATAAAGGTGGTGAGGGTGGTGAATGTTTAGGTGGGGAGG
1 GTGTTGAGGTTGCTGGCAATAAAGGTGGTGAAGGTGGTGAA-GTTTAAATGGAGACA
* * *
40950169 GTGTTGA-GTTGTTAGCAATAAAGATGGT-AAGGTGGTGAAG
1 GTGTTGAGGTTGCTGGCAATAAAGGTGGTGAAGGTGGTGAAG
40950209 GTGGTGAGGG
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
54 1 0.01
55 10 0.12
56 20 0.24
57 51 0.62
ACGTcount: A:0.25, C:0.04, G:0.42, T:0.30
Consensus pattern (56 bp):
GTGTTGAGGTTGCTGGCAATAAAGGTGGTGAAGGTGGTGAAGTTTAAATGGAGACA
Found at i:40951786 original size:31 final size:31
Alignment explanation
Indices: 40951748--40951812 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
40951738 AAGGTAAATA
* *
40951748 ATGCTATTTATTTTTCACCAATTTTTTACTG
1 ATGCTATTTATTTTGCACCAATTTATTACTG
*
40951779 ATGCTATTTATTTTGCACGAATTTATTACTG
1 ATGCTATTTATTTTGCACCAATTTATTACTG
40951810 ATG
1 ATG
40951813 TTTTACTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (31 bp):
ATGCTATTTATTTTGCACCAATTTATTACTG
Found at i:40961116 original size:22 final size:20
Alignment explanation
Indices: 40961069--40961104 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
40961059 AAGTAGAGAT
40961069 AATT-TATTTTCTAAGTATA
1 AATTCTATTTTCTAAGTATA
40961088 AATTCTATTTTC-AAGTA
1 AATTCTATTTTCTAAGTA
40961105 ATCACAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (20 bp):
AATTCTATTTTCTAAGTATA
Found at i:41003135 original size:20 final size:21
Alignment explanation
Indices: 41003110--41003153 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41003100 CAATTATCAC
*
41003110 AATTAGATTGA-CAAAATAAA
1 AATTAGAGTGACCAAAATAAA
41003130 AATTAGAGTGACCAAAATAAA
1 AATTAGAGTGACCAAAATAAA
41003151 AAT
1 AAT
41003154 GGTACTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (21 bp):
AATTAGAGTGACCAAAATAAA
Found at i:41011622 original size:24 final size:25
Alignment explanation
Indices: 41011568--41011622 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
41011558 GTTGCGCAAT
41011568 TATTAATATGAATGTTTGTATAACA
1 TATTAATATGAATGTTTGTATAACA
*
41011593 TGATTAA-A-GAATGTTTGTATTAGCA
1 T-ATTAATATGAATGTTTGTA-TAACA
41011618 TATTA
1 TATTA
41011623 CTTGCTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 15 0.56
25 7 0.26
26 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (25 bp):
TATTAATATGAATGTTTGTATAACA
Found at i:41018553 original size:3 final size:3
Alignment explanation
Indices: 41018545--41018620 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
41018535 ATAAATAAGT
* * *
41018545 ATA ATA ATA TATC AT- ATA ATA ATA A-A CTA ATA ACA ATA CAGTA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA
* * *
41018591 ATA AT- ATA AAA ATA TTA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41018621 ATAAAAAACT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
2 5 0.09
3 45 0.80
4 4 0.07
5 2 0.04
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:41018582 original size:14 final size:14
Alignment explanation
Indices: 41018560--41018645 Score: 50
Period size: 14 Copynumber: 6.1 Consensus size: 14
41018550 AATATATCAT
41018560 ATAATAATAAACTA
1 ATAATAATAAACTA
* * *
41018574 ATAACAATACAGTA
1 ATAATAATAAACTA
*
41018588 ATAATAATATAA-AA
1 ATAATAATA-AACTA
* * *
41018602 ATATTAAAAATAATA
1 ATAATAATAA-ACTA
*
41018617 ATAAATAAAAAACTA
1 AT-AATAATAAACTA
*
41018632 A-AATAACAAACTA
1 ATAATAATAAACTA
41018645 A
1 A
41018646 AGGTTAAGTA
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
13 13 0.23
14 28 0.50
15 8 0.14
16 7 0.12
ACGTcount: A:0.67, C:0.07, G:0.01, T:0.24
Consensus pattern (14 bp):
ATAATAATAAACTA
Found at i:41022464 original size:75 final size:72
Alignment explanation
Indices: 41022322--41022471 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 72
41022312 CAGTTGTCCC
* *
41022322 ATAATTTTTTGACGTCATAGGAAACAGGTTGACATGTTTGCAACGTGTTGACTGCTTCTATTAGG
1 ATAATTTTTTGACGTCATAGGAAACAGGTTGACATGATCGCAACGTGTTGACTGCTTCTATTAGG
41022387 ATTTTGT
66 ATTTTGT
* *
41022394 ATAATTTTTTGACGTCAT-GTGAAACAGGTTGACAACATGATCGCAACTTGTTGACTGCTTCTGT
1 ATAATTTTTTGACGTCATAG-GAAACAGGTTG---ACATGATCGCAACGTGTTGACTGCTTCTAT
41022458 TAGGATTTTGT
62 TAGGATTTTGT
41022469 ATA
1 ATA
41022472 TAAATTACTA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
71 1 0.01
72 29 0.41
75 40 0.57
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (72 bp):
ATAATTTTTTGACGTCATAGGAAACAGGTTGACATGATCGCAACGTGTTGACTGCTTCTATTAGG
ATTTTGT
Found at i:41022845 original size:105 final size:108
Alignment explanation
Indices: 41022663--41023413 Score: 474
Period size: 108 Copynumber: 6.8 Consensus size: 108
41022653 GACAAAAATT
* * * *
41022663 TATCCTAACCTTTTTAAGTTTGCCTTAGACGAGTTTA-CCCTAACCTTTTTAAGGTTGCCTTAGA
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCC-AACCTTTTTAAGGTTGCCTTAAA
** * *
41022727 TGAGTTTATCCCAA-CTTTTT-TAAGTTACCTTGGA-AAAGGTC
65 TGAGTCAATCCCAACCTTTTTAAAAGTTACCTTAGACAAAGGTC
* * * * *
41022768 TATCCCAACATTTTTAAGGTTGCTTTAAACGAGTCTATCCCAACATTTTTAAGGTTGTCTTAAAT
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTAAGGTTGCCTTAAAT
*
41022833 GAGTCAATCCCAACCTTTTTAAAAGTTGCCTTAGACAAAGGTC
66 GAGTCAATCCCAACCTTTTTAAAAGTTACCTTAGACAAAGGTC
* * * * * *
41022876 TATCCCCACCTTTTTAAGGTTACCTTAGACAAGTCTATCCCAACCTTTTTAAGGTTGCTTTAGAC
1 TATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTAAGGTTGCCTTAAAT
* * * * * *
41022941 AAGTCTATCCTAACCTTTTTTGAAGGTTTCCTTAGAC-AAGGTC
66 GAGTCAATCCCAACC-TTTTTAAAAGTTACCTTAGACAAAGGTC
* ** * *
41022984 TATCCTAATTTTTTTTAAAAGGTTGCCTTAAACTG-GTCTATCCTAACCTTTTTTAAAGGTTGCC
1 TATCCCAA-CCTTTTT--AAGGTTGCCTTAGAC-GAGTCTATCCCAACC-TTTTT-AAGGTTGCC
* * * *
41023048 TTAGACAAG-GTCTATCCCAA-CTTTGTTAAAAGGTTGCCTTAGAC-TA-GTC
60 TTA-A-ATGAGTCAATCCCAACCTTT-TTAAAA-GTTACCTTAGACAAAGGTC
* * * * * *
41023097 CATCTCAACCTTTTTTAAAAGTTGTCTTAGACAATGTCTATCCAAACCTTTTTAAGGTTGCCTTA
1 TATCCCAACC-TTTTT-AAGGTTGCCTTAGACGA-GTCTATCCCAACCTTTTTAAGGTTGCCTTA
* * * * * * *
41023162 GACA-GTGTCTATCCAAACCTTTTT-AAGGTTGCCTTAGAC-GA-TTC
63 -A-ATGAGTCAATCCCAACCTTTTTAAAAGTTACCTTAGACAAAGGTC
* * * * *
41023206 TATCCCAATCTTTTTTAAAGGTTTCCTTAGACAAGGTCTATCCCAACTGTTTTTTAAAGGTTACC
1 TATCCCAA-CCTTTTT-AAGGTTGCCTTAGACGA-GTCTATCCCAAC--CTTTTT-AAGGTTGCC
* * * * * *
41023271 CTAGACAAG-GTCTATCCCAACTTTTTTTAAAGGTTGCCTTAGAC-AAGGTC
60 TTA-A-ATGAGTCAATCCCAAC-CTTTTTAAAAGTTACCTTAGACAAAGGTC
** * ** *
41023321 TATCTTAACTTTTTTTAAAAGGTTATCTTAGACTG-GTCTATCCCAACCTCTTTAAGGTTGCCTT
1 TATCCCAAC-CTTTTT--AAGGTTGCCTTAGAC-GAGTCTATCCCAACCTTTTTAAGGTTGCCTT
* * * * * *
41023385 AGACGGGTCTATACCAACCTTTTTCAAAG
62 AAATGAGTCAATCCCAACCTTTTTAAAAG
41023414 GTTGGCCTTG
Statistics
Matches: 522, Mismatches: 92, Indels: 59
0.78 0.14 0.09
Matches are distributed among these distances:
105 63 0.12
106 9 0.02
107 11 0.02
108 85 0.16
109 75 0.14
110 14 0.03
111 69 0.13
112 65 0.12
113 51 0.10
114 39 0.07
115 27 0.05
116 14 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (108 bp):
TATCCCAACCTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAACCTTTTTAAGGTTGCCTTAAAT
GAGTCAATCCCAACCTTTTTAAAAGTTACCTTAGACAAAGGTC
Found at i:41022887 original size:38 final size:37
Alignment explanation
Indices: 41022663--41023441 Score: 658
Period size: 35 Copynumber: 21.3 Consensus size: 37
41022653 GACAAAAATT
* * * *
41022663 TATCCTAACCTTTTT-AAGTTTGCCTTAGACGA-GTT
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
** *
41022698 TA-CCCTAACCTTTTT-AAGGTTGCCTTAGATGA-GTT
1 TATCCC-AACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* * * *
41022733 TATCCCAA-CTTTTTTAA-GTTACCTTGGAAAAGGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* * * *
41022768 TATCCCAACATTTTT-AAGGTTGCTTTAAACGA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* * *
41022803 TATCCCAACATTTTT-AAGGTTGTCTTA-A-ATGAGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAG-GTC
* *
41022838 AATCCCAACCTTTTTAAAAGTTGCCTTAGACAAAGGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGAC-AAGGTC
* *
41022876 TATCCCCACCTTTTT-AAGGTTACCTTAGACAA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
*
41022911 TATCCCAACCTTTTT-AAGGTTGCTTTAGACAA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* * *
41022946 TATCCTAACCTTTTTTGAAGGTTTCCTTAGACAAGGTC
1 TATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTC
* ** * *
41022984 TATCCTAATTTTTTTTAAAAGGTTGCCTTAAAC-TGGTC
1 TATCCCAA-CCTTTTT-AAAGGTTGCCTTAGACAAGGTC
*
41023022 TATCCTAACCTTTTTTAAAGGTTGCCTTAGACAAGGTC
1 TATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTC
*
41023060 TATCCCAA-CTTTGTTAAAAGGTTGCCTTAGACTA-GTC
1 TATCCCAACCTTT-TT-AAAGGTTGCCTTAGACAAGGTC
* * * * *
41023097 CATCTCAACCTTTTTTAAAAGTTGTCTTAGACAATGTC
1 TATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGTC
*
41023135 TATCCAAACCTTTTT-AAGGTTGCCTTAGAC-AGTGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAG-GTC
* * *
41023171 TATCCAAACCTTTTT-AAGGTTGCCTTAGACGA-TTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* *
41023206 TATCCCAATCTTTTTTAAAGGTTTCCTTAGACAAGGTC
1 TATCCCAA-CCTTTTTAAAGGTTGCCTTAGACAAGGTC
* * *
41023244 TATCCCAACTGTTTTTTAAAGGTTACCCTAGACAAGGTC
1 TATCCCAAC--CTTTTTAAAGGTTGCCTTAGACAAGGTC
*
41023283 TATCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTC
1 TATCCCAAC-CTTTTTAAAGGTTGCCTTAGACAAGGTC
** * ** *
41023321 TATCTTAACTTTTTTTAAAAGGTTATCTTAGAC-TGGTC
1 TATCCCAAC-CTTTTT-AAAGGTTGCCTTAGACAAGGTC
* *
41023359 TATCCCAACCTCTTT-AAGGTTGCCTTAGAC-GGGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
* *
41023394 TATACCAACCTTTTTCAAAGGTTGGCCTT-GACTAGGTC
1 TATCCCAACCTTTTT-AAAGGTT-GCCTTAGACAAGGTC
* *
41023432 TTTTCCAACC
1 TATCCCAACC
41023442 CTTCAATAAG
Statistics
Matches: 623, Mismatches: 85, Indels: 69
0.80 0.11 0.09
Matches are distributed among these distances:
34 19 0.03
35 175 0.28
36 88 0.14
37 106 0.17
38 168 0.27
39 67 0.11
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (37 bp):
TATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGTC
Found at i:41023278 original size:223 final size:223
Alignment explanation
Indices: 41022704--41023432 Score: 750
Period size: 223 Copynumber: 3.3 Consensus size: 223
41022694 AGTTTACCCT
* * * * * *
41022704 AACCTTTTTAAGGTTGCCTTAGA-TGAGTTTATCCCAA-CTTTTTTAA-GTTACCTTGGAAAAGG
1 AACCTTTTTAAGGTTGCCTTAGACAGAGTCTAT-CCAACCTTTTTAAAGGTTGCCTTAGACAAGG
* * * *
41022766 TCTATCCCAA-CATTTTT--AAGGTTGCTTTAAAC-GAGTCTATCCCAA-CATTTTT-AAGGTTG
65 TCTATCCCAATCTTTTTTAAAAGGTTGCCTTAAACAG-GTCTATCCCAACCTTTTTTAAAGGTTA
* * * * * *
41022825 TCTTA-A-ATGAGTCAATCCCAACCTTTTTAAAA-GTTGCCTTAGACAAAGGTCTATCCCCACC-
129 CCCTAGACAAG-GTCTATCCCAA-CTTTTTAAAAGGTTGCCTTAGAC-AAGGTCTATCTCAACCT
* *
41022886 TTTTT-AAGGTTACCTTAGACAA-GTCTATCCC
191 TTTTTAAAAGTTATCTTAGACAATGTCTATCCC
* * *
41022917 AACCTTTTTAAGGTTGCTTTAGACA-AGTCTATCCTAACCTTTTTTGAAGGTTTCCTTAGACAAG
1 AACCTTTTTAAGGTTGCCTTAGACAGAGTCTATCC-AACC-TTTTTAAAGGTTGCCTTAGACAAG
* * * * *
41022981 GTCTATCCTAATTTTTTTTAAAAGGTTGCCTTAAACTGGTCTATCCTAACCTTTTTTAAAGGTTG
64 GTCTATCCCAATCTTTTTTAAAAGGTTGCCTTAAACAGGTCTATCCCAACCTTTTTTAAAGGTTA
* * *
41023046 CCTTAGACAAGGTCTATCCCAACTTTGTTAAAAGGTTGCCTTAGACTA-GTCCATCTCAACCTTT
129 CCCTAGACAAGGTCTATCCCAACTTT-TTAAAAGGTTGCCTTAGACAAGGTCTATCTCAACCTTT
* *
41023110 TTTAAAAGTTGTCTTAGACAATGTCTATCCA
193 TTTAAAAGTTATCTTAGACAATGTCTATCCC
* * *
41023141 AACCTTTTTAAGGTTGCCTTAGACAGTGTCTATCCAAACCTTTTT-AAGGTTGCCTTAGACGA-T
1 AACCTTTTTAAGGTTGCCTTAGACAGAGTCTATCC-AACCTTTTTAAAGGTTGCCTTAGACAAGG
* * *
41023204 TCTATCCCAATCTTTTTT-AAAGGTTTCCTTAGACAAGGTCTATCCCAACTGTTTTTTAAAGGTT
65 TCTATCCCAATCTTTTTTAAAAGGTTGCCTTAAAC-AGGTCTATCCCAAC-CTTTTTTAAAGGTT
* * *
41023268 ACCCTAGACAAGGTCTATCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCTTAACTTT
128 ACCCTAGACAAGGTCTATCCCAAC-TTTTTAAAAGGTTGCCTTAGACAAGGTCTATCTCAACCTT
41023333 TTTTAAAAGGTTATCTTAGAC--TGGTCTATCCC
192 TTTTAAAA-GTTATCTTAGACAAT-GTCTATCCC
* * *
41023365 AACCTCTTTAAGGTTGCCTTAGAC-GGGTCTATACCAACCTTTTTCAAAGGTTGGCCTT-GACTA
1 AACCTTTTTAAGGTTGCCTTAGACAGAGTCTAT-CCAACCTTTTT-AAAGGTT-GCCTTAGACAA
41023428 GGTCT
63 GGTCT
41023433 TTTCCAACCC
Statistics
Matches: 436, Mismatches: 50, Indels: 47
0.82 0.09 0.09
Matches are distributed among these distances:
212 2 0.00
213 30 0.07
214 1 0.00
215 7 0.02
216 22 0.05
217 5 0.01
219 24 0.06
220 7 0.02
221 39 0.09
222 51 0.12
223 114 0.26
224 93 0.21
225 33 0.08
226 8 0.02
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (223 bp):
AACCTTTTTAAGGTTGCCTTAGACAGAGTCTATCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
CTATCCCAATCTTTTTTAAAAGGTTGCCTTAAACAGGTCTATCCCAACCTTTTTTAAAGGTTACC
CTAGACAAGGTCTATCCCAACTTTTTAAAAGGTTGCCTTAGACAAGGTCTATCTCAACCTTTTTT
AAAAGTTATCTTAGACAATGTCTATCCC
Found at i:41023388 original size:260 final size:254
Alignment explanation
Indices: 41022663--41023422 Score: 837
Period size: 260 Copynumber: 3.0 Consensus size: 254
41022653 GACAAAAATT
* * * *
41022663 TATCCTAACCTTTTTAAGTTTGCCTTAGACGAGTT-TA-CCCTAACCTTTTTAAGGTTGCCTTAG
1 TATCCAAACCTTTTTAAGGTTGCCTTAGACGA-TTCTATCCC-AACTTTTTTAAGGTTTCCTTAG
** * * * *
41022726 ATGA-GTTTATCCCAAC-TTTTTT-AA-GTTACCTTGGAAAAGGTCTATCCCAACATTTTT-AAG
64 ACAAGGTCTATCCCAACTTTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACTTTTTTAAAG
* * * * *
41022786 GTTGCTTTAAACGA-GTCTATCCCAACATTTTT--AAGGTTGTCTTA-AATGAGTCAATCCCAAC
129 GTTGCCTTAGACAAGGTCTATCCCAACTTTTTTAAAAGGTTGTCTTAGACTG-GTCAATCCCAAC
* *
41022847 CTTTTTAAAAGTTGCCTTAGACAAAGGTCTATCCCCACCTTTTTAAGGTTACCTTAGACAAGTC
193 CTTTTTAAAAGTTGCCTTAGAC-AAGGTCTAT-CCAACCTTTTTAAGGTTGCCTTAGACAAGTC
* * * * *
41022911 TATCCCAACCTTTTTAAGGTTGCTTTAGACAAGTCTATCCTAACCTTTTTTGAAGGTTTCCTTAG
1 TATCCAAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAA-CTTTTTT-AAGGTTTCCTTAG
* * * * * *
41022976 ACAAGGTCTATCCTAATTTTTTTTAAAAGGTTGCCTTAAAC-TGGTCTATCCTAACCTTTTTTAA
64 ACAAGGTCTATCCCAACTTTTTTT-AAAGGTTACCTTAGACAAGGTCTATCCCAA-CTTTTTTAA
* * * * *
41023040 AGGTTGCCTTAGACAAGGTCTATCCCAACTTTGTTAAAAGGTTGCCTTAGACTAGTCCATCTCAA
127 AGGTTGCCTTAGACAAGGTCTATCCCAACTTTTTTAAAAGGTTGTCTTAGACTGGTCAATCCCAA
* * *
41023105 CCTTTTTTAAAAGTTGTCTTAGACAATGTCTATCCAAACCTTTTTAAGGTTGCCTTAGACAGTGT
192 CC-TTTTTAAAAGTTGCCTTAGACAAGGTCTATCC-AACCTTTTTAAGGTTGCCTTAGACA-AGT
41023170 C
254 C
41023171 TATCCAAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAATCTTTTTTAAAGGTTTCCTTAG
1 TATCCAAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAA-CTTTTTT-AAGGTTTCCTTAG
*
41023236 ACAAGGTCTATCCCAACTGTTTTTTAAAGGTTACCCTAGACAAGGTCTATCCCAACTTTTTTTAA
64 ACAAGGTCTATCCCAACT-TTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAAC-TTTTTTAA
** * *
41023301 AGGTTGCCTTAGACAAGGTCTATCTTAACTTTTTTTAAAAGGTTATCTTAGACTGGTCTATCCCA
127 AGGTTGCCTTAGACAAGGTCTATCCCAAC-TTTTTTAAAAGGTTGTCTTAGACTGGTCAATCCCA
* * *
41023366 ACCTCTTT-AAGGTTGCCTTAGAC-GGGTCTATACCAACCTTTTTCAAAGGTTGGCCTT
191 ACCTTTTTAAAAGTTGCCTTAGACAAGGTCTAT-CCAACCTTTTT--AAGGTT-GCCTT
41023423 GACTAGGTCT
Statistics
Matches: 424, Mismatches: 62, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
247 1 0.00
248 32 0.08
249 8 0.02
250 14 0.03
251 9 0.02
252 6 0.01
254 13 0.03
255 14 0.03
256 14 0.03
257 16 0.04
258 2 0.00
259 68 0.16
260 128 0.30
261 62 0.15
262 37 0.09
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (254 bp):
TATCCAAACCTTTTTAAGGTTGCCTTAGACGATTCTATCCCAACTTTTTTAAGGTTTCCTTAGAC
AAGGTCTATCCCAACTTTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACTTTTTTAAAGGT
TGCCTTAGACAAGGTCTATCCCAACTTTTTTAAAAGGTTGTCTTAGACTGGTCAATCCCAACCTT
TTTAAAAGTTGCCTTAGACAAGGTCTATCCAACCTTTTTAAGGTTGCCTTAGACAAGTC
Found at i:41029373 original size:21 final size:21
Alignment explanation
Indices: 41029349--41029391 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41029339 AATAATAACT
41029349 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
41029370 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
41029391 A
1 A
41029392 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:41037390 original size:26 final size:26
Alignment explanation
Indices: 41037354--41037406 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41037344 CAAAATACTG
41037354 TAGCAAATGTCTATTTTCATAATTAA
1 TAGCAAATGTCTATTTTCATAATTAA
41037380 TAGCAAATGTCTATTTTCATAATTAA
1 TAGCAAATGTCTATTTTCATAATTAA
41037406 T
1 T
41037407 CTATTTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (26 bp):
TAGCAAATGTCTATTTTCATAATTAA
Found at i:41039208 original size:240 final size:240
Alignment explanation
Indices: 41038772--41039256 Score: 832
Period size: 240 Copynumber: 2.0 Consensus size: 240
41038762 ATATCCATTA
* *
41038772 TCACATTTGTTTTTTGCAGATGATTTGGTTCTTTTTGCTAAGGCAGATTTGAAACATGGTTTGGT
1 TCACACTTGTTTTTTGCAGATGATTTGGTTCTTTTTGCTAAGGCAGATTTGAAACATAGTTTGGT
41038837 CCTTAAGGAAATTTTGGATAACTTCTATAATATCTTAGGGCATCGGGTCAACAACCGAAAAACAA
66 CCTTAAGGAAATTTTGGATAACTTCTATAATATCTTAGGGCATCGGGTCAACAACCGAAAAACAA
41038902 TTATGTATTTCTCAAAAGGCGTGGAGGAGGATATAAGAAATAGTTTCAATCATACTCTTAGTTTT
131 TTATGTATTTCTCAAAAGGCGTGGAGGAGGATATAAGAAATAGTTTCAATCATACTCTTAGTTTT
41038967 CAAAAAGTGAGTAATCTTGGTACTTATTTGGGTGTA-CCCTTTTT
196 CAAAAAGTGAGTAATCTTGGTACTTATTTGGGTGTACCCCTTTTT
*
41039011 TCACACTTGTTTTTTTGCA-AGTGATTTGGTTTTTTTTTGCTAAGGCAGATTTGAAACATAGTTT
1 TCACACTTG-TTTTTTGCAGA-TGATTTGG-TTCTTTTTGCTAAGGCAGATTTGAAACATAGTTT
*
41039075 GGTCCTTAAGGAAATTTTGGATAACTTCTATAATATCTTAGGGCATTGGGTCAACAACCGAAAAA
63 GGTCCTTAAGGAAATTTTGGATAACTTCTATAATATCTTAGGGCATCGGGTCAACAACCGAAAAA
* ** * *
41039140 -AATTATGTATTTCTCAAAAGGCGTGGAGGAGGATTTAAGTGATAGTTTCAATCGTACTCTTGGT
128 CAATTATGTATTTCTCAAAAGGCGTGGAGGAGGATATAAGAAATAGTTTCAATCATACTCTTAGT
*
41039204 TTTCAATAAGTGAGTAATCTTGGTACTTATTTGGGTGTACCCCTTTTT
193 TTTCAAAAAGTGAGTAATCTTGGTACTTATTTGGGTGTACCCCTTTTT
41039252 TCACA
1 TCACA
41039257 ATAGGGTCAC
Statistics
Matches: 232, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
239 9 0.04
240 114 0.49
241 109 0.47
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (240 bp):
TCACACTTGTTTTTTGCAGATGATTTGGTTCTTTTTGCTAAGGCAGATTTGAAACATAGTTTGGT
CCTTAAGGAAATTTTGGATAACTTCTATAATATCTTAGGGCATCGGGTCAACAACCGAAAAACAA
TTATGTATTTCTCAAAAGGCGTGGAGGAGGATATAAGAAATAGTTTCAATCATACTCTTAGTTTT
CAAAAAGTGAGTAATCTTGGTACTTATTTGGGTGTACCCCTTTTT
Found at i:41044633 original size:24 final size:24
Alignment explanation
Indices: 41044600--41044654 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
41044590 AAGTTTTTGG
* *
41044600 AAAAAAATTTTGAATAGTAATTTTT
1 AAAAAATTTTTGAAT-CTAATTTTT
* *
41044625 AAAATATTTTTTAATCTAATTTTT
1 AAAAAATTTTTGAATCTAATTTTT
41044649 AAAAAA
1 AAAAAA
41044655 GGAATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
AAAAAATTTTTGAATCTAATTTTT
Found at i:41045950 original size:24 final size:25
Alignment explanation
Indices: 41045906--41045953 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
41045896 TGAGTATATA
41045906 AACATAAAAAATTAATAATTTAAAC
1 AACATAAAAAATTAATAATTTAAAC
*
41045931 AACAT-AATAATTAACT-ATTTAAA
1 AACATAAAAAATTAA-TAATTTAAA
41045954 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (25 bp):
AACATAAAAAATTAATAATTTAAAC
Found at i:41047687 original size:16 final size:17
Alignment explanation
Indices: 41047654--41047693 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41047644 TATAATATTT
41047654 AAAAGTTAAAACTAAAAA
1 AAAAG-TAAAACTAAAAA
*
41047672 TAAAGTAAAA-TAAAAA
1 AAAAGTAAAACTAAAAA
41047688 AAAAGT
1 AAAAGT
41047694 CAGAGAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAAGTAAAACTAAAAA
Found at i:41048642 original size:5 final size:5
Alignment explanation
Indices: 41048628--41048661 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
41048618 AATTATGCAA
*
41048628 AAAAG TAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
41048662 CAATTTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:41048646 original size:15 final size:14
Alignment explanation
Indices: 41048628--41048661 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41048618 AATTATGCAA
*
41048628 AAAAGTAAAGAAAAG
1 AAAAGAAAAG-AAAG
41048643 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
41048657 AAAAG
1 AAAAG
41048662 CAATTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:41053423 original size:19 final size:19
Alignment explanation
Indices: 41053399--41053455 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
41053389 AATCTTCAAG
41053399 GATATGCAATCATAGATAT
1 GATATGCAATCATAGATAT
*
41053418 GATATGCAATCTTAGAGGATAT
1 GATATGCAATC--ATA-GATAT
*
41053440 GATATGCAATCTTAGA
1 GATATGCAATCATAGA
41053456 GGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 13 0.41
20 1 0.03
21 2 0.06
22 16 0.50
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (19 bp):
GATATGCAATCATAGATAT
Found at i:41053477 original size:23 final size:22
Alignment explanation
Indices: 41053413--41053479 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
41053403 TGCAATCATA
41053413 GATATGATATGCAATCTTAGAG
1 GATATGATATGCAATCTTAGAG
41053435 GATATGATATGCAATCTTAGAG
1 GATATGATATGCAATCTTAGAG
* *
41053457 GATATGATTTTGTAATCTTAGAG
1 GATATGA-TATGCAATCTTAGAG
41053480 ATTTAATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 29 0.69
23 13 0.31
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (22 bp):
GATATGATATGCAATCTTAGAG
Found at i:41053491 original size:21 final size:23
Alignment explanation
Indices: 41053425--41053491 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
41053415 TATGATATGC
* *
41053425 AATCTTAGAGGATATG-ATATGC
1 AATCTTAGAGGATATGAATTTGT
*
41053447 AATCTTAGAGGATATGATTTTGT
1 AATCTTAGAGGATATGAATTTGT
*
41053470 AATCTTAGA-GAT-TTAATTTGT
1 AATCTTAGAGGATATGAATTTGT
41053491 A
1 A
41053492 GATATCCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.21
22 19 0.49
23 12 0.31
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
AATCTTAGAGGATATGAATTTGT
Found at i:41054095 original size:37 final size:37
Alignment explanation
Indices: 41054019--41054095 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
41054009 CATACATACG
*
41054019 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
41054057 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
41054094 TT
1 TT
41054096 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:41054201 original size:27 final size:27
Alignment explanation
Indices: 41054171--41054231 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
41054161 ATGTATTTTT
41054171 TATTTTT-TTATAAT-TCACATACATATA
1 TATTTTTCTTAT-ATGT-ACATACATATA
*
41054198 TATTTTTCTTATATGTACATATATATA
1 TATTTTTCTTATATGTACATACATATA
41054225 TATTTTT
1 TATTTTT
41054232 ATATTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTTTTCTTATATGTACATACATATA
Found at i:41058822 original size:47 final size:44
Alignment explanation
Indices: 41058766--41058859 Score: 143
Period size: 47 Copynumber: 2.1 Consensus size: 44
41058756 AAGCTCAAGG
* *
41058766 AAATGAGGCTCGCCCGATATCGTGGTAAGGATAAAAGAAAAAGTTA
1 AAATGAGGCTCGCCCGATATCATGCTAAGGAT-AAA-AAAAAGTTA
41058812 AANATGAGGCTCGCCCGATATCATGCTAAGGATAAAAAAAAGTTA
1 AA-ATGAGGCTCGCCCGATATCATGCTAAGGATAAAAAAAAGTTA
41058857 AAA
1 AAA
41058860 AGTAATTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 1 0.02
45 11 0.24
46 5 0.11
47 28 0.62
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (44 bp):
AAATGAGGCTCGCCCGATATCATGCTAAGGATAAAAAAAAGTTA
Found at i:41060090 original size:61 final size:61
Alignment explanation
Indices: 41060023--41060146 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
41060013 TGGAATAATG
41060023 ATTAATGGACTAATAAAACTTTCACAAGGGAAGTTTTGCATATTACTTTACAAGTTTCTAA
1 ATTAATGGACTAATAAAACTTTCACAAGGGAAGTTTTGCATATTACTTTACAAGTTTCTAA
*
41060084 ATTAATGGACTAATAAAACTTTCACAAGGGAAGTTTTGCATATTACTTTAGAAGTTTCTAA
1 ATTAATGGACTAATAAAACTTTCACAAGGGAAGTTTTGCATATTACTTTACAAGTTTCTAA
41060145 AT
1 AT
41060147 AATACAGGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (61 bp):
ATTAATGGACTAATAAAACTTTCACAAGGGAAGTTTTGCATATTACTTTACAAGTTTCTAA
Found at i:41060988 original size:44 final size:44
Alignment explanation
Indices: 41060939--41061053 Score: 171
Period size: 44 Copynumber: 2.6 Consensus size: 44
41060929 AGTGGTTCTG
*
41060939 TCTCCCTGGAAAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTA
1 TCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAA-TCCTA
*
41060983 TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTA
1 TCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAATCCTA
*
41061027 TCTCCCT-GAGCAGCAGTGGAGTAGGTT
1 TCTCCCTGGA-CAGCAGTGGAATAGGTT
41061054 AAAAATTACA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 62 0.95
45 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (44 bp):
TCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAATCCTA
Found at i:41061073 original size:44 final size:44
Alignment explanation
Indices: 41060978--41061091 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
41060968 AGATTGTAAG
* * * **
41060978 TCCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTGAA
1 TCCTATCTCCCTGAG-CAGCAGTGGAGTAGGTTAAAAATTCAGAA
41061022 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATTACAG-A
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATT-CAGAA
* * * *
41061066 TCTTATCTCCCTAAGTAGTAGTGGAG
1 TCCTATCTCCCTGAGCAGCAGTGGAG
41061092 CAGATCGAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 57 0.97
45 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATTCAGAA
Found at i:41061293 original size:128 final size:129
Alignment explanation
Indices: 41061020--41061295 Score: 385
Period size: 128 Copynumber: 2.1 Consensus size: 129
41061010 GAAGATTGTG
* *
41061020 AATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGTAGT
1 AATCCTATCTCCCTGAGCAACAGTGGAGTAGG---AAAATTACAGATCTTATCTCCCTAAGCAGT
* * *
41061085 AGTGGAGCAGATCGAAGACGGCGAATCTTATCCTCCCAAGGTAGTAGGCAAGTAGATTTAAGCCA
63 AGTGGAGCAGATCGAAGACAGCGAATCTTATCCTCCCAAGGTAGTAGGCAAGCAAATTTAAGCCA
41061150 CT
128 CT
* * *
41061152 -AGCCTTATATCCCTGAGTAACAGTGGAGTAGG-AAATTACAGATCTTATCTCCCTAAGCAGTAG
1 AATCC-TATCTCCCTGAGCAACAGTGGAGTAGGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* * * * *
41061215 TGGAGCAGATCGAAGACAGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTTAGTCAGT
65 TGGAGCAGATCGAAGACAGCGAATCTTATCCTCCCAAGGTAGTAGGCAAGCAAATTTAAGCCACT
41061280 AATCCTATCTCCCTGA
1 AATCCTATCTCCCTGA
41061296 AGTTGTAGTG
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
128 97 0.76
129 3 0.02
131 3 0.02
132 24 0.19
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (129 bp):
AATCCTATCTCCCTGAGCAACAGTGGAGTAGGAAAATTACAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACAGCGAATCTTATCCTCCCAAGGTAGTAGGCAAGCAAATTTAAGCCACT
Found at i:41061407 original size:50 final size:50
Alignment explanation
Indices: 41061353--41061620 Score: 275
Period size: 50 Copynumber: 5.4 Consensus size: 50
41061343 TTGGCATTAC
41061353 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
1 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
* * ** ****** *
41061403 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAATATTGC
1 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
** *
41061453 AGTTAAATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
1 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
* * ** ****** *
41061503 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAATATTGC
1 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
** *
41061553 AGTTAAATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
1 AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
*
41061603 AGTGGAATAGATTAAAGC
1 AGTGGAATAGATTGAAGC
41061621 TAAAGGTAGC
Statistics
Matches: 161, Mismatches: 57, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
50 161 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (50 bp):
AGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGT
Found at i:41061474 original size:100 final size:100
Alignment explanation
Indices: 41061358--41061644 Score: 504
Period size: 100 Copynumber: 2.9 Consensus size: 100
41061348 ATTACAGTGG
*
41061358 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
41061423 CAACGGCGAATCTTGTTTCCCCAATATTGCAGTTA
66 CAACGGCGAATCTTGTTTCCCCAATATTGCAGTTA
41061458 AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
41061523 CAACGGCGAATCTTGTTTCCCCAATATTGCAGTTA
66 CAACGGCGAATCTTGTTTCCCCAATATTGCAGTTA
* *
41061558 AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTAAAGCTA
1 AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *
41061623 -AAGGTAGCGTATCTTGTTTCCC
66 CAACG--GCGAATCTTGTTTCCC
41061645 TAGCGTTGCA
Statistics
Matches: 180, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
99 3 0.02
100 162 0.90
101 15 0.08
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (100 bp):
AATAGATTGAATCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
CAACGGCGAATCTTGTTTCCCCAATATTGCAGTTA
Found at i:41062435 original size:19 final size:19
Alignment explanation
Indices: 41062411--41062464 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
41062401 AATTTTCAAG
41062411 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41062430 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41062449 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
41062465 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41062735 original size:23 final size:23
Alignment explanation
Indices: 41062691--41062735 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41062681 TCTTATTTTG
* *
41062691 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
41062714 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
41062736 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:41063102 original size:38 final size:38
Alignment explanation
Indices: 41063025--41063102 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 38
41063015 CATACATACG
*
41063025 TTTTATAATATATACATATACGTACACATTTTTTAATTT
1 TTTTATAATATATACATATACG-ACACATTTTATAATTT
* *
41063064 TTTTATAA-ATATATATATAC-ACATACTTTTATATATTT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATTT
41063102 T
1 T
41063103 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.12
37 6 0.18
38 16 0.47
39 8 0.24
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTTATAATATATACATATACGACACATTTTATAATTT
Found at i:41067925 original size:24 final size:24
Alignment explanation
Indices: 41067880--41067925 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41067870 ATTGCATTTG
* *
41067880 TATCTAAATCTGAATATGCATCCA
1 TATCTAAATCTGAAAATACATCCA
41067904 TATCTAAATCTGAAAATACATC
1 TATCTAAATCTGAAAATACATC
41067926 TGATTCTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (24 bp):
TATCTAAATCTGAAAATACATCCA
Found at i:41071532 original size:30 final size:28
Alignment explanation
Indices: 41071492--41071562 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
41071482 ACAAACTATT
*
41071492 TTTTAGTAATTTTTTAATAACTTTTATAGA
1 TTTTA-TAATTTTTTAATAAATTTT-TAGA
* * *
41071522 TTCTTTTAA-TTATTAATAAATTTTTATA
1 TT-TTATAATTTTTTAATAAATTTTTAGA
41071550 TTTTATAATTTTT
1 TTTTATAATTTTT
41071563 ATAGTTAGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
27 5 0.15
28 8 0.24
29 13 0.39
30 5 0.15
31 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTATAATTTTTTAATAAATTTTTAGA
Found at i:41072761 original size:54 final size:55
Alignment explanation
Indices: 41072695--41072832 Score: 215
Period size: 55 Copynumber: 2.5 Consensus size: 55
41072685 AATCCATGTG
* * *
41072695 CATTTGCAAATGA-ATCATTTCTCATTTTCATTTTCATTTTGAGAAAATAACATT
1 CATTTCCAAATGATTTCATTTCTCATTTTCATTTTCATTTTGAGAAAACAACATT
*
41072749 CATTTCCAAATGATTTCATTTCTCATTTTCATTTTCATTTTGAGAAAACCACATT
1 CATTTCCAAATGATTTCATTTCTCATTTTCATTTTCATTTTGAGAAAACAACATT
*
41072804 CATTTTCAAATGATTTCATTTCTCCATTT
1 CATTTCCAAATGATTTCATTTCT-CATTT
41072833 CGGAGTAAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 12 0.16
55 60 0.78
56 5 0.06
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (55 bp):
CATTTCCAAATGATTTCATTTCTCATTTTCATTTTCATTTTGAGAAAACAACATT
Found at i:41074576 original size:23 final size:24
Alignment explanation
Indices: 41074541--41074609 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
41074531 TTACTACAAA
41074541 ATTGAGTGGCTTGTCCACAACGAT
1 ATTGAGTGGCTTGTCCACAACGAT
* * *
41074565 ATTG-GTGTCTTGTCCTCAACGCT
1 ATTGAGTGGCTTGTCCACAACGAT
** *
41074588 AACGAGTGGCTTGACCACAACG
1 ATTGAGTGGCTTGTCCACAACG
41074610 TAAATGAGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (24 bp):
ATTGAGTGGCTTGTCCACAACGAT
Found at i:41074618 original size:24 final size:24
Alignment explanation
Indices: 41074543--41074630 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 24
41074533 ACTACAAAAT
* *
41074543 TGAGTGGCTTGTCCACAACG-ATAT
1 TGAGTGGCTTGACCACAACGTA-AA
* * *
41074567 TG-GTGTCTTGTCCTCAACGCT-AA
1 TGAGTGGCTTGACCACAACG-TAAA
*
41074590 CGAGTGGCTTGACCACAACGTAAA
1 TGAGTGGCTTGACCACAACGTAAA
*
41074614 TGAGTGGTTTGACCACA
1 TGAGTGGCTTGACCACA
41074631 CAGTGCAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
23 18 0.35
24 33 0.65
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (24 bp):
TGAGTGGCTTGACCACAACGTAAA
Found at i:41081291 original size:45 final size:45
Alignment explanation
Indices: 41081221--41081352 Score: 131
Period size: 45 Copynumber: 2.9 Consensus size: 45
41081211 CTATACGCCT
* * * * * *
41081221 AAAATGAGTAATACCATAGTTGAAAGACATTTTGAG-ATCATGATT
1 AAAATAAGTAAGACCATAGCTGAAAGACACTATG-GCATCATGATA
* *
41081266 AAGATAAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATA
1 AAAATAAGTAAGACCATAGCTGAAAGACACTATGGCATCATGATA
* * ** *
41081311 AAAATGAGTAAGACCATAGCTAAAAGACGGTATGACATCATG
1 AAAATAAGTAAGACCATAGCTGAAAGACACTATGGCATCATG
41081353 TGAAAGTATG
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 1 0.01
45 70 0.99
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (45 bp):
AAAATAAGTAAGACCATAGCTGAAAGACACTATGGCATCATGATA
Found at i:41085997 original size:353 final size:353
Alignment explanation
Indices: 41085351--41086059 Score: 1418
Period size: 353 Copynumber: 2.0 Consensus size: 353
41085341 TTAGGATCAG
41085351 AGTGCTTAGGATCAGACTCTGGCTTGGTCCCCTCAACTTCTAGGTATTTAATTATCCTGTATTTG
1 AGTGCTTAGGATCAGACTCTGGCTTGGTCCCCTCAACTTCTAGGTATTTAATTATCCTGTATTTG
41085416 AGTAGAAAACTTATAAGTTTGGAAAAATTTAGTGAGATCCACATATAGATTTTAAGAAGAAATTT
66 AGTAGAAAACTTATAAGTTTGGAAAAATTTAGTGAGATCCACATATAGATTTTAAGAAGAAATTT
41085481 TGATGTGTTCAGGTCAGATTTTTAACTCCCTAATAAACACGGTCATCATTTTTGGTGGGCGACGC
131 TGATGTGTTCAGGTCAGATTTTTAACTCCCTAATAAACACGGTCATCATTTTTGGTGGGCGACGC
41085546 TTGGTGATTTCCCAAGTGATTTCTACCTTTGGGTCATTCCCAGATTTCGTTGTCTTTACGGCCTT
196 TTGGTGATTTCCCAAGTGATTTCTACCTTTGGGTCATTCCCAGATTTCGTTGTCTTTACGGCCTT
41085611 GGAGTACTAGGGCTCACTAACAGCACTAAAACACTTGCTCTATCGATCTATTGCCAATTGAGGCT
261 GGAGTACTAGGGCTCACTAACAGCACTAAAACACTTGCTCTATCGATCTATTGCCAATTGAGGCT
41085676 TTTTAGGACTTGCAATTCAAATCTTTGA
326 TTTTAGGACTTGCAATTCAAATCTTTGA
41085704 AGTGCTTAGGATCAGACTCTGGCTTGGTCCCCTCAACTTCTAGGTATTTAATTATCCTGTATTTG
1 AGTGCTTAGGATCAGACTCTGGCTTGGTCCCCTCAACTTCTAGGTATTTAATTATCCTGTATTTG
41085769 AGTAGAAAACTTATAAGTTTGGAAAAATTTAGTGAGATCCACATATAGATTTTAAGAAGAAATTT
66 AGTAGAAAACTTATAAGTTTGGAAAAATTTAGTGAGATCCACATATAGATTTTAAGAAGAAATTT
41085834 TGATGTGTTCAGGTCAGATTTTTAACTCCCTAATAAACACGGTCATCATTTTTGGTGGGCGACGC
131 TGATGTGTTCAGGTCAGATTTTTAACTCCCTAATAAACACGGTCATCATTTTTGGTGGGCGACGC
41085899 TTGGTGATTTCCCAAGTGATTTCTACCTTTGGGTCATTCCCAGATTTCGTTGTCTTTACGGCCTT
196 TTGGTGATTTCCCAAGTGATTTCTACCTTTGGGTCATTCCCAGATTTCGTTGTCTTTACGGCCTT
41085964 GGAGTACTAGGGCTCACTAACAGCACTAAAACACTTGCTCTATCGATCTATTGCCAATTGAGGCT
261 GGAGTACTAGGGCTCACTAACAGCACTAAAACACTTGCTCTATCGATCTATTGCCAATTGAGGCT
41086029 TTTTAGGACTTGCAATTCAAATCTTTGA
326 TTTTAGGACTTGCAATTCAAATCTTTGA
41086057 AGT
1 AGT
41086060 TCAATAAGAG
Statistics
Matches: 356, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
353 356 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (353 bp):
AGTGCTTAGGATCAGACTCTGGCTTGGTCCCCTCAACTTCTAGGTATTTAATTATCCTGTATTTG
AGTAGAAAACTTATAAGTTTGGAAAAATTTAGTGAGATCCACATATAGATTTTAAGAAGAAATTT
TGATGTGTTCAGGTCAGATTTTTAACTCCCTAATAAACACGGTCATCATTTTTGGTGGGCGACGC
TTGGTGATTTCCCAAGTGATTTCTACCTTTGGGTCATTCCCAGATTTCGTTGTCTTTACGGCCTT
GGAGTACTAGGGCTCACTAACAGCACTAAAACACTTGCTCTATCGATCTATTGCCAATTGAGGCT
TTTTAGGACTTGCAATTCAAATCTTTGA
Found at i:41090717 original size:56 final size:52
Alignment explanation
Indices: 41090656--41090792 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 52
41090646 GAGACCACAT
* *
41090656 GTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCTAC
1 GTAAGACCATGTCTGGGACATGGCATTGGCATTACTGA-G--AT-AGAGGTCCCAC
* *
41090712 GTAAGACCATGTCTGGGACATGGCGTTGG---TACTGAGATAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCATTACTGAGATAGAGGTCCCAC
*
41090761 GTAAGACCATGTCTGGGACATGGCATGGGCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCAT
41090793 CGATATGAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
49 36 0.50
50 2 0.03
52 1 0.01
53 5 0.07
56 28 0.39
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (52 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCATTACTGAGATAGAGGTCCCAC
Found at i:41097615 original size:8 final size:8
Alignment explanation
Indices: 41097602--41097631 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41097592 CCATCCTAGA
41097602 AAAATTAT
1 AAAATTAT
41097610 AAAATTAT
1 AAAATTAT
41097618 AAAATTAT
1 AAAATTAT
41097626 AAAATT
1 AAAATT
41097632 CACCCCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:41112490 original size:52 final size:52
Alignment explanation
Indices: 41112412--41112511 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
41112402 GAGACTTTTC
41112412 ATATTTGGCCTTTAACTAGTACAATTACAAGCACTAATTTCATGTTTAGAGG
1 ATATTTGGCCTTTAACTAGTACAATTACAAGCACTAATTTCATGTTTAGAGG
* * *
41112464 ATATTTTGCCTTTAACTATTACAATTACAAGCACTAATTTCATTTTTA
1 ATATTTGGCCTTTAACTAGTACAATTACAAGCACTAATTTCATGTTTA
41112512 ACTCTTGTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (52 bp):
ATATTTGGCCTTTAACTAGTACAATTACAAGCACTAATTTCATGTTTAGAGG
Found at i:41114609 original size:209 final size:209
Alignment explanation
Indices: 41114249--41114671 Score: 756
Period size: 209 Copynumber: 2.0 Consensus size: 209
41114239 ATTTAAAAAA
* *
41114249 AAATCAAATAATATAAAAAAATGGATAGATTGTAAGTTAACAAGAATAAGATAGTAAGCATACCC
1 AAATCAAATAATATAAAAAAATGAATAGATTGTAAGTTAAAAAGAATAAGATAGTAAGCATACCC
* *
41114314 TTCAACTCACGAAAGTCATGAATTTAGGGTAGGTTCTGATGCATTCCAAGAAATGTCTAAACATT
66 TTCAACTCACAAAAGTCATGAATTTAGGGTAGGTTCTGATGCATTCCAAGAAAAGTCTAAACATT
41114379 GAATTGATTAAATAAGTTAATGTAGGAGTGATGTGCTAAAAATTTGAAACTATTAAATTAAAAAT
131 GAATTGATTAAATAAGTTAATGTAGGAGTGATGTGCTAAAAATTTGAAACTATTAAATTAAAAAT
41114444 AAATATACAATTTT
196 AAATATACAATTTT
* *
41114458 AAATCAAATAATATAAACAAATGAATAGATTGTAAGTTAAAAATAATAAGATAGTAAGCATACCC
1 AAATCAAATAATATAAAAAAATGAATAGATTGTAAGTTAAAAAGAATAAGATAGTAAGCATACCC
* *
41114523 TTCAACTCACAAAAGTCATGAGTTTAGGGTAGGTTTTGATGCATTCCAAGAAAAGTCTAAACATT
66 TTCAACTCACAAAAGTCATGAATTTAGGGTAGGTTCTGATGCATTCCAAGAAAAGTCTAAACATT
41114588 GAATTGATTAAATAAGTTAATGTAGGAGTGATGTGCTAAAAATTTGAAACTATTAAATTAAAAAT
131 GAATTGATTAAATAAGTTAATGTAGGAGTGATGTGCTAAAAATTTGAAACTATTAAATTAAAAAT
*
41114653 AAATATACCATTTT
196 AAATATACAATTTT
*
41114667 GAATC
1 AAATC
41114672 TTCTCAAGCT
Statistics
Matches: 204, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 204 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (209 bp):
AAATCAAATAATATAAAAAAATGAATAGATTGTAAGTTAAAAAGAATAAGATAGTAAGCATACCC
TTCAACTCACAAAAGTCATGAATTTAGGGTAGGTTCTGATGCATTCCAAGAAAAGTCTAAACATT
GAATTGATTAAATAAGTTAATGTAGGAGTGATGTGCTAAAAATTTGAAACTATTAAATTAAAAAT
AAATATACAATTTT
Found at i:41116756 original size:34 final size:35
Alignment explanation
Indices: 41116717--41116787 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
41116707 GTGGACATTC
41116717 TACAAG-AAAAATTATATAATAGATCAAAAAACAT
1 TACAAGAAAAAATTATATAATAGATCAAAAAACAT
* *
41116751 TACAAGAAAAAAATTATATAATAGATTAAAATACAT
1 TACAAG-AAAAAATTATATAATAGATCAAAAAACAT
41116787 T
1 T
41116788 TATAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 6 0.18
36 27 0.82
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.27
Consensus pattern (35 bp):
TACAAGAAAAAATTATATAATAGATCAAAAAACAT
Found at i:41122606 original size:50 final size:50
Alignment explanation
Indices: 41122420--41122610 Score: 197
Period size: 50 Copynumber: 3.8 Consensus size: 50
41122410 GATAATAACA
* ** * * *
41122420 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * ** * *
41122469 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAATTTTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
41122519 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
41122569 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41122611 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
49 38 0.33
50 78 0.67
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:41126381 original size:40 final size:41
Alignment explanation
Indices: 41126320--41126463 Score: 204
Period size: 41 Copynumber: 3.5 Consensus size: 41
41126310 AACTTTATGT
41126320 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
41126361 CTAGCAGGCT-AGTGCCGGTGATCTGAATTAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
41126401 CTAGTAGTCTAAGTGCCGATGATCTGAATCA-GTCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT-TATAAAC
41126442 CTAGC-GGACTAAGTGCCGGTGA
1 CTAGCAGG-CTAAGTGCCGGTGA
41126464 ATATGTTAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
40 40 0.44
41 51 0.56
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:41128993 original size:44 final size:43
Alignment explanation
Indices: 41128888--41129012 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
41128878 GTAATCAACT
* * * *
41128888 ATCGATGCC-ACTGTCCCAGACAGGGTCTTATAC-AAA-ATCAT
1 ATCGATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCTCAA
*
41128929 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA
1 AT-CGATGCCAACGTCCCAGACATGGTCTTACACG-AAATCTCAA
* *
41128974 ATCGATGCCAACGTCCCAGACGTGGTCCTACACGAAATC
1 ATCGATGCCAACGTCCCAGACATGGTCTTACACGAAATC
41129013 ACATATCGGA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.03
42 26 0.37
43 6 0.08
44 32 0.45
45 5 0.07
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
ATCGATGCCAACGTCCCAGACATGGTCTTACACGAAATCTCAA
Found at i:41131600 original size:40 final size:40
Alignment explanation
Indices: 41131552--41131732 Score: 202
Period size: 40 Copynumber: 4.5 Consensus size: 40
41131542 TTGTCAGATC
* * *
41131552 AACC-AAACACACCAGACAGAAGCTCATAAGAGCTAATCC
1 AACCGAAACACGCCAGACAGAAGCTCACAAGAGCTAATCT
* * * *
41131591 AACCGAAACACGCCAAAAAAAAGCTCACAAGAGTTAATCT
1 AACCGAAACACGCCAGACAGAAGCTCACAAGAGCTAATCT
* * *
41131631 AATCGAAACACGCTAGACAGAAGCTCACAAGAGTTAATCT
1 AACCGAAACACGCCAGACAGAAGCTCACAAGAGCTAATCT
* * * *
41131671 AATCGAAACACGCCAGACATAAGCTTATAAGAGCTAATCT
1 AACCGAAACACGCCAGACAGAAGCTCACAAGAGCTAATCT
* * *
41131711 AACTGAAACACACCAAACAGAA
1 AACCGAAACACGCCAGACAGAA
41131733 AGTATAACAC
Statistics
Matches: 119, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 4 0.03
40 115 0.97
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (40 bp):
AACCGAAACACGCCAGACAGAAGCTCACAAGAGCTAATCT
Found at i:41137704 original size:43 final size:42
Alignment explanation
Indices: 41137594--41137755 Score: 155
Period size: 43 Copynumber: 3.8 Consensus size: 42
41137584 TACCGTAACA
* * * *
41137594 ATGCCATATCCCAGATATGGTCTTACAAGTAATCTA-GTATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAATC-ACATATCG
* * * *
41137636 ATGCCAATAGCCTAGCCATGTTCTTACACGAAATCACATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * *
41137679 ATGCCAATGTCCCAGACATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * * *
41137722 ATGTCATATCCTAGATATGGTCTTACACGTAATC
1 ATGCCATATCCCAGACATGGTCTTACACGAAATC
41137756 TCAGTAACCC
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 30 0.31
43 67 0.69
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:41145310 original size:21 final size:21
Alignment explanation
Indices: 41145285--41145324 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
41145275 TATAATTACT
41145285 TCATG-CCAAAACATATATATA
1 TCATGTCCAAAAC-TATATATA
41145306 TCATGTCCAAAACTATATA
1 TCATGTCCAAAACTATATA
41145325 ACCCAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (21 bp):
TCATGTCCAAAACTATATATA
Found at i:41147572 original size:43 final size:43
Alignment explanation
Indices: 41147511--41147668 Score: 205
Period size: 43 Copynumber: 3.7 Consensus size: 43
41147501 TAACAATGCC
*
41147511 ATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGTCA
1 ATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGTCA
* * * *
41147554 ATATCCCAGCTATGGTCTTACACGAAATCACATATCGATGTCA
1 ATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGTCA
* * *
41147597 ATGTCCCAGATATGGTCTTACACG-AAGTCTTAG-ATCGATG-CC
1 ATATCCCAGATATGGTCTTACACGTAA-TC-TCGTATCGATGTCA
41147639 ATATCCCAGATATGGTCTTACACGTAATCT
1 ATATCCCAGATATGGTCTTACACGTAATCT
41147669 TGGAAACCCT
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 28 0.28
43 71 0.71
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (43 bp):
ATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGTCA
Found at i:41149046 original size:22 final size:22
Alignment explanation
Indices: 41149016--41149058 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41149006 AATTTCTAAA
*
41149016 TTTCAAAAGATATTAATAAATC
1 TTTCAAAAGATATTAAAAAATC
* *
41149038 TTTCCAAAGATGTTAAAAAAT
1 TTTCAAAAGATATTAAAAAAT
41149059 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (22 bp):
TTTCAAAAGATATTAAAAAATC
Found at i:41150971 original size:113 final size:114
Alignment explanation
Indices: 41150570--41151149 Score: 633
Period size: 114 Copynumber: 5.1 Consensus size: 114
41150560 AAAATAAGCA
* * * * * * *
41150570 TTAGCGGCG-TTTCCATAAAGCGCCGC-AAAATACCTAAGCACAACGACCCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * * *
41150633 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCCGGGCT
66 TCGAGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
41150682 TTAGTGGCGTTTTCGAGAAAGCGCCACCAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
41150747 TCGAGGATTTAGTGGCATTTTTTAGT-AGACGCCGCTAATGCTCAGGGCT
66 TCGAGGATTTAGTGGCGTTTTTAAGTAAG-CGCCGCTAATGCTCAGGGCT
* * * *
41150796 TTAGCGGCGTTTTCGGGAAAGCGCCGA-AAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCA
1 TTAGCGGCGTTTTCGAGAAAGCGCC-ACAAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCT
* * * * *
41150860 TTCGAGGATTTAGTGGTGTTTTTAGGTAAGTGCCACTAATGCTCA-AGCT
65 TTCGAGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * *
41150909 TTAGCAGCGCTTTT-GAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCATTTTTTGAGCT
1 TTAGCGGCG-TTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
41150973 TCCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGTTCAGGGCT
65 TTCGAGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * * * *
41151023 TTAGCGGCGTTTAT-GAGAAAGCGCCGCAACAAAAACTAAA-TCGAACTACACCGTTTTCTGA-C
1 TTAGCGGCGTTT-TCGAGAAAGCGCCACAA-AAAAACCAAAGCCCAACGACGCCGTTTTCTGAGC
* * * * *
41151085 AATTCGTGGGCTTTAGCGGCG-TTTTAAG-AATGCGCCGCTAATGCTTAGGGCT
64 -TTTCG-AGGATTTAGTGGCGTTTTTAAGTAA-GCGCCGCTAATGCTCAGGGCT
41151137 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
41151150 TGTTCAAGCG
Statistics
Matches: 397, Mismatches: 58, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
112 9 0.02
113 114 0.29
114 250 0.63
115 24 0.06
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGAGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:41151180 original size:227 final size:226
Alignment explanation
Indices: 41150570--41151151 Score: 687
Period size: 227 Copynumber: 2.6 Consensus size: 226
41150560 AAAATAAGCA
* * * * * * *
41150570 TTAGCGGCG-TTTCCATAAAGCGCCG-CAAAATACCTAAGCACAACGACCCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTCGAGAAAGCGCCGAAAAAATACCTAAACCCAACGACACCGTTTTCTGAGCAT
* * * *
41150633 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCCGGGCTTTAGTGGCGTTTTCGA
66 TCGGGGATTTAGCGGCGTTTTTAAG-AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* *
41150698 GAAAGCGCCACCAAAAAACCAAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAGTGGC
130 GAAAGCGCCA-CAAAAAACCAAAGCCCAACGACGCCATTTTCTGAGCTTCCGAGGATTTAGTGGC
*
41150763 ATTTTTTAGTAGACGCCGCTAATGCTCAGGGCT
194 ATTTTTAAGTAGACGCCGCTAATGCTCAGGGCT
* * *
41150796 TTAGCGGCGTTTTCGGGAAAGCGCCGAAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCAT
1 TTAGCGGCGTTTTCGAGAAAGCGCCGAAAAAATACCTAAACCCAACGACACCGTTTTCTGAGCAT
* * * * * * * * *
41150861 TCGAGGATTTAGTGGTGTTTTTAGGTAAGTGCCACTAATGCTCA-AGCTTTAGCAGCGCTTTTGA
66 TCGGGGATTTAGCGGCGTTTTTAAG-AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* *
41150925 GAAAGCGCCACAAAAAAACCAAAGCCCAACGACGCCATTTTTTGAGCTTCCGGGGATTTAGTGGC
130 GAAAGCGCCAC-AAAAAACCAAAGCCCAACGACGCCATTTTCTGAGCTTCCGAGGATTTAGTGGC
* *
41150990 GTTTTTAAGTA-AGCGCCGCTAATGTTCAGGGCT
194 ATTTTTAAGTAGA-CGCCGCTAATGCTCAGGGCT
* * *
41151023 TTAGCGGCGTTTAT-GAGAAAGCGCCGCAACAAAA-A-CTAAATCGAACTACACCGTTTTCTGA-
1 TTAGCGGCGTTT-TCGAGAAAGCGCCG-AA-AAAATACCTAAACCCAACGACACCGTTTTCTGAG
* *
41151084 CAATTCGTGGGCTTTAGCGGCG-TTTTAAGAATGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTT
63 C-ATTCG-GGGATTTAGCGGCGTTTTTAAGAA-GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTT
41151148 TTTG
125 TTTG
41151152 TTCAAGCGGC
Statistics
Matches: 300, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
226 14 0.05
227 183 0.61
228 99 0.33
229 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (226 bp):
TTAGCGGCGTTTTCGAGAAAGCGCCGAAAAAATACCTAAACCCAACGACACCGTTTTCTGAGCAT
TCGGGGATTTAGCGGCGTTTTTAAGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
AAAGCGCCACAAAAAACCAAAGCCCAACGACGCCATTTTCTGAGCTTCCGAGGATTTAGTGGCAT
TTTTAAGTAGACGCCGCTAATGCTCAGGGCT
Found at i:41151844 original size:14 final size:14
Alignment explanation
Indices: 41151800--41151845 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
41151790 TATTAAATAA
*
41151800 GGTTTAGGGTTAGT
1 GGTTTGGGGTTAGT
* *
41151814 AGTTAGGGGTTAGT
1 GGTTTGGGGTTAGT
*
41151828 GGTTTGGGGTTAAT
1 GGTTTGGGGTTAGT
41151842 GGTT
1 GGTT
41151846 AGAAGTTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.43, T:0.41
Consensus pattern (14 bp):
GGTTTGGGGTTAGT
Found at i:41152213 original size:14 final size:14
Alignment explanation
Indices: 41152194--41152242 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
41152184 GGAATATTAC
41152194 GGTTTAAGATTTGG
1 GGTTTAAGATTTGG
* *
41152208 GGTTTAGGGTTTGG
1 GGTTTAAGATTTGG
* *
41152222 GGTTT-GGTTTTGG
1 GGTTTAAGATTTGG
41152235 GGTTTAAG
1 GGTTTAAG
41152243 GTTTAGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (14 bp):
GGTTTAAGATTTGG
Found at i:41152235 original size:13 final size:14
Alignment explanation
Indices: 41152203--41152246 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
41152193 CGGTTTAAGA
41152203 TTTGGGGTTTAGGG
1 TTTGGGGTTTAGGG
*
41152217 TTTGGGGTTT-GGT
1 TTTGGGGTTTAGGG
*
41152230 TTTGGGGTTTAAGG
1 TTTGGGGTTTAGGG
41152244 TTT
1 TTT
41152247 AGAATTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TTTGGGGTTTAGGG
Found at i:41153603 original size:146 final size:146
Alignment explanation
Indices: 41153259--41153606 Score: 364
Period size: 146 Copynumber: 2.4 Consensus size: 146
41153249 AACTGTTGGG
* * * *
41153259 GAAACGACTTCG-TTTGAGCTTATAGTTAGTGGCGCTTTACTCAAAACGCTGCAAAATTGTTCTA
1 GAAACGACTTCGTTTTGA-CTTTTAGTTAGTGGCGC-TTACTTAAAACGCCGCAAAAATGTTCTA
** * * *
41153323 ACATTTATAGAAACGCTGCCATTTTGTAAATGTTATTAGTGGCGTTTTTGCAAAAACGCCACGGG
64 ACATTTATAGAAACGAGGCCATTTTGTAAATATTATTAGTGGCGTTTTTGCAAAAACACCACAGG
* * *
41153388 TTTGAGGTAAGTGTTGAT
129 TGTGAGCTAAGTATTGAT
* * * * *
41153406 GAAGCGACTGCGTTTTGA-TTTATAGTTTGTGGCGCTT-CGGTTAAAATGCCGCAAAAATGTTTT
1 GAAACGACTTCGTTTTGACTTT-TAGTTAGTGGCGCTTAC--TTAAAACGCCGCAAAAATGTTCT
* * * * *
41153469 AACATTTATTGATACGAGGCCGTTTTG-CAGTATTATTAGTGGCGTTTATT-CAAAAACACCACA
63 AACATTTATAGAAACGAGGCCATTTTGTAAATATTATTAGTGGCGTTT-TTGCAAAAACACCACA
**
41153532 GGTGTGAGCTATTTATTGAT
127 GGTGTGAGCTAAGTATTGAT
* *
41153552 GAAACGGCTTCGTTTTGACTTTTAGTTAGTGGCGCTTATTTATAAACGCCGCAAA
1 GAAACGACTTCGTTTTGACTTTTAGTTAGTGGCGCTTACTTA-AAACGCCGCAAA
41153607 TGGATAATTT
Statistics
Matches: 163, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
145 4 0.02
146 87 0.53
147 67 0.41
148 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (146 bp):
GAAACGACTTCGTTTTGACTTTTAGTTAGTGGCGCTTACTTAAAACGCCGCAAAAATGTTCTAAC
ATTTATAGAAACGAGGCCATTTTGTAAATATTATTAGTGGCGTTTTTGCAAAAACACCACAGGTG
TGAGCTAAGTATTGAT
Found at i:41154568 original size:15 final size:15
Alignment explanation
Indices: 41154548--41154579 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41154538 AGGGTTGAAG
*
41154548 TATTTGGTACTAGTT
1 TATTTGGTACTAATT
41154563 TATTTGGTACTAATT
1 TATTTGGTACTAATT
41154578 TA
1 TA
41154580 CTGTTATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (15 bp):
TATTTGGTACTAATT
Found at i:41155568 original size:13 final size:13
Alignment explanation
Indices: 41155552--41155663 Score: 109
Period size: 13 Copynumber: 8.5 Consensus size: 13
41155542 TTACTAAAAT
*
41155552 TTACTTTAATATA
1 TTACTTAAATATA
*
41155565 TTACTTTAATATA
1 TTACTTAAATATA
*
41155578 TTACTTAAATAAA
1 TTACTTAAATATA
*
41155591 TTACTTAAATACA
1 TTACTTAAATATA
*
41155604 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
41155618 TTGGTTAAATTTA
1 TTACTTAAATATA
*
41155631 TTACTTAAATATG
1 TTACTTAAATATA
*
41155644 TTACTTAAATACA
1 TTACTTAAATATA
41155657 TTACTTA
1 TTACTTA
41155664 CTAAAATTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
12 3 0.04
13 70 0.86
14 5 0.06
15 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:41155843 original size:29 final size:29
Alignment explanation
Indices: 41155805--41156003 Score: 100
Period size: 29 Copynumber: 6.4 Consensus size: 29
41155795 TATGTACAAG
41155805 AACTTACATAACTTATTAATATTTATATA
1 AACTTACATAACTTATTAATATTTATATA
* *
41155834 AACTTACATAAC-TATCACATAAACTTATATGTA
1 AACTTACATAACTTATTA-AT--A-TT-TATATA
* * * *
41155867 AACTTACATAATACATAACTT-ATATGTAAACA
1 AACTTACAT-A-AC-TTA-TTAATATTTATATA
* * *
41155899 TACATAATACATAACTTATAAATTTTTTTTATATA
1 AAC-T--TACATAACTTATTAA---TATTTATATA
* * ** *
41155934 AACTTACATAA-TACATTACT-TACATATT
1 AACTTACATAACT-TATTAATATTTATATA
41155962 AACTTACATAACTTATTAATATTTATATA
1 AACTTACATAACTTATTAATATTTATATA
41155991 AACTTACATAACT
1 AACTTACATAACT
41156004 ATCACATAAA
Statistics
Matches: 123, Mismatches: 27, Indels: 40
0.65 0.14 0.21
Matches are distributed among these distances:
28 25 0.20
29 34 0.28
31 3 0.02
32 20 0.16
33 18 0.15
34 4 0.03
35 15 0.12
36 2 0.02
37 1 0.01
38 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (29 bp):
AACTTACATAACTTATTAATATTTATATA
Found at i:41155949 original size:67 final size:64
Alignment explanation
Indices: 41155865--41156045 Score: 178
Period size: 67 Copynumber: 2.8 Consensus size: 64
41155855 AACTTATATG
*
41155865 TAAACTTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAATTTTTTTTA
1 TAAACTTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAA---TATTTA
41155930 TA
63 TA
* * ** *
41155932 TAAACTTACATAATACATTACTTACA--T-ATTA-AC-T--TACATAACTTATTAATATTTATA
1 TAAACTTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAATATTTATA
*
41155989 TAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTA
1 TAAACTTACAT-A--AT-ACAT-AACTTATATGTAAACATACATAATACATAACTTA
41156046 CATGTTAACT
Statistics
Matches: 91, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
57 18 0.20
58 1 0.01
60 16 0.18
61 4 0.04
62 7 0.08
63 2 0.02
64 3 0.03
65 2 0.02
66 2 0.02
67 25 0.27
69 11 0.12
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (64 bp):
TAAACTTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAATATTTATA
Found at i:41155965 original size:28 final size:28
Alignment explanation
Indices: 41155929--41156073 Score: 123
Period size: 28 Copynumber: 5.0 Consensus size: 28
41155919 AATTTTTTTT
*
41155929 ATATAAACTTACATAATACATTACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* * **
41155957 ATATTAACTTACATAACTTA-TTAA-TATTT
1 ATATAAACTTACATAA--TACATAACT-TAC
*
41155986 ATATAAACTTACATAACTATCACATAAACTTAT
1 ATATAAACTTACAT-A--AT-ACAT-AACTTAC
*
41156019 ATGTAAACTTACATAATACATAACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* *
41156047 ATGTTAACTTACATAATACATAACTTA
1 ATATAAACTTACATAATACATAACTTA
41156074 TAAAATTTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
28 48 0.50
29 20 0.21
30 6 0.06
31 1 0.01
32 3 0.03
33 17 0.18
34 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (28 bp):
ATATAAACTTACATAATACATAACTTAC
Done.