Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 115 of 295
Found at i:39499259 original size:47 final size:46
Alignment explanation
Indices: 39499163--39499291 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 46
39499153 GTGCATATAA
* * * *
39499163 TACCTTGATTTGGCTACGGCCATGGTATAGGTATTTAGAGAGGACT
1 TACCTTGATTTGGCTATGGCCATGGTATAGGTACTCAGAGAGAACT
* * * *
39499209 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTAT-GGCCATGGTATAGGTACTCAGAGAGAACT
**
39499256 TACCTTGATTTGGCTACTGGCCACAGTATAGGTACT
1 TACCTTGATTTGGCTA-TGGCCATGGTATAGGTACT
39499292 TATCGATTGA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
46 16 0.23
47 54 0.76
48 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (46 bp):
TACCTTGATTTGGCTATGGCCATGGTATAGGTACTCAGAGAGAACT
Found at i:39499942 original size:18 final size:18
Alignment explanation
Indices: 39499919--39499957 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
39499909 ATTGAGAAGG
39499919 TGTATGCTTGTGAATGAA
1 TGTATGCTTGTGAATGAA
39499937 TGTATGCTTGTGAATGAA
1 TGTATGCTTGTGAATGAA
39499955 TGT
1 TGT
39499958 TGGATGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (18 bp):
TGTATGCTTGTGAATGAA
Found at i:39500968 original size:241 final size:242
Alignment explanation
Indices: 39500507--39500985 Score: 782
Period size: 241 Copynumber: 2.0 Consensus size: 242
39500497 CCCACGGGCG
* * * *
39500507 TGTGACCTTTGAATGCTTGAAAATTTTATGTGTTTCCTAAAGTTTGCAAATGTTATCAGTTTAGT
1 TGTGACCCTTGAATACTTGAAAATTTTATGTGTTTCCTAAAGTTTACAAATGTTATCAATTTAGT
39500572 CCCGAACCTCTTCCAAGCATGTTTTAAGGTCTCGTAGAGGCTTATAAGGGACATTGTGATTATAT
66 CCCGAACCTCTTCCAAGCATGTTTTAAGGTCTCGTAGAGGCTTATAAGGGACATTGTGATTATAT
39500637 TTGATTAATGTTTATGTGAAAATGAATGATTTATGTTGTGATTGATCAGTAATGCCTAGTAACCC
131 TTGATTAATGTTTATGTGAAAATGAATGATTTATGTTGTGATTGATCAGTAATGCCTAGTAACCC
* * * * *
39500702 TATTCCGGTGACGGATACGGGTTAGGGGTGTTACATTTTATTGCTCA
196 TATTCCAGCGACGAATACAGGTTAGGGGTATTACATTTTATTGCTCA
*
39500749 TGTGACCCTTGAATACTTGAAAATTTTATGTGTTTGCTAAAGTTTACAAATGTTATCAATTTAGT
1 TGTGACCCTTGAATACTTGAAAATTTTATGTGTTTCCTAAAGTTTACAAATGTTATCAATTTAGT
* *
39500814 CCCGAACTTCTTCCAAGCATGTTTTAAGGTTTCGTA-A-GCTTTATAAGGGACATTGTGATTATA
66 CCCGAACCTCTTCCAAGCATGTTTTAAGGTCTCGTAGAGGC-TTATAAGGGACATTGTGATTATA
* * *
39500877 TTTGGTTAATGTTTATGTGAAAATGAATGATTTATGTTGTGATTGATCGGTAATGCCTCGTAACC
130 TTTGATTAATGTTTATGTGAAAATGAATGATTTATGTTGTGATTGATCAGTAATGCCTAGTAACC
* *
39500942 TTATTCCAGCGATGAATACAGGTTAGGGGTATTACATTTTATTG
195 CTATTCCAGCGACGAATACAGGTTAGGGGTATTACATTTTATTG
39500986 GTATCAAAGC
Statistics
Matches: 219, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
240 2 0.01
241 123 0.56
242 94 0.43
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (242 bp):
TGTGACCCTTGAATACTTGAAAATTTTATGTGTTTCCTAAAGTTTACAAATGTTATCAATTTAGT
CCCGAACCTCTTCCAAGCATGTTTTAAGGTCTCGTAGAGGCTTATAAGGGACATTGTGATTATAT
TTGATTAATGTTTATGTGAAAATGAATGATTTATGTTGTGATTGATCAGTAATGCCTAGTAACCC
TATTCCAGCGACGAATACAGGTTAGGGGTATTACATTTTATTGCTCA
Found at i:39503957 original size:94 final size:94
Alignment explanation
Indices: 39503845--39504030 Score: 363
Period size: 94 Copynumber: 2.0 Consensus size: 94
39503835 ACTGAAGCTC
39503845 TAGTGTTAGTATAGTTAGAATCGGGTAAAGAATTTGTGATCTCTAGTGATGCATCGTTGAATGGT
1 TAGTGTTAGTATAGTTAGAATCGGGTAAAGAATTTGTGATCTCTAGTGATGCATCGTTGAATGGT
39503910 CAGGGTTGTTTTTTGATGAAGGAAGGCTA
66 CAGGGTTGTTTTTTGATGAAGGAAGGCTA
39503939 TAGTGTTAGTATAGTTAGAATCGGGTAAAGAATTTGTGATCTCTAGTGATGCATCGTTGAATGGT
1 TAGTGTTAGTATAGTTAGAATCGGGTAAAGAATTTGTGATCTCTAGTGATGCATCGTTGAATGGT
*
39504004 CAGGGTTGTTTTTTGATGCAGGAAGGC
66 CAGGGTTGTTTTTTGATGAAGGAAGGC
39504031 AAAGTTATAG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36
Consensus pattern (94 bp):
TAGTGTTAGTATAGTTAGAATCGGGTAAAGAATTTGTGATCTCTAGTGATGCATCGTTGAATGGT
CAGGGTTGTTTTTTGATGAAGGAAGGCTA
Found at i:39506548 original size:41 final size:41
Alignment explanation
Indices: 39506501--39506579 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
39506491 AGTGATAAAG
* *
39506501 CATAGCCGAAGCTATTTCAATCTCACACACTAAGTGCCTTT
1 CATAGCCGAAGCTATCTCAACCTCACACACTAAGTGCCTTT
39506542 CATAGCCGAAGCTATCTCAACCTCACACACTAAGTGCC
1 CATAGCCGAAGCTATCTCAACCTCACACACTAAGTGCC
39506580 ATATATATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (41 bp):
CATAGCCGAAGCTATCTCAACCTCACACACTAAGTGCCTTT
Found at i:39506612 original size:41 final size:42
Alignment explanation
Indices: 39506502--39506628 Score: 138
Period size: 41 Copynumber: 3.0 Consensus size: 42
39506492 GTGATAAAGC
* *
39506502 ATAGCCGAAGCTATTTCAATCTCACACACTAAGTGCCT-T-T
1 ATAGCCGAAGCTATTCCAACCTCACACACTAAGTGCCTATAT
39506542 CATAGCCGAAGCTA-TCTCAACCTCACACACTAAGTGCCATATAT
1 -ATAGCCGAAGCTATTC-CAACCTCACACACTAAGTGCC-TATAT
* * *
39506586 ATAGCTG-AGCTATTCCAA-CTCGCACACTTAGTGCTCTATAT
1 ATAGCCGAAGCTATTCCAACCTCACACACTAAGTGC-CTATAT
39506627 AT
1 AT
39506629 CCGAAAGTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
40 1 0.01
41 54 0.72
42 10 0.13
43 9 0.12
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (42 bp):
ATAGCCGAAGCTATTCCAACCTCACACACTAAGTGCCTATAT
Found at i:39514523 original size:27 final size:26
Alignment explanation
Indices: 39514506--39514575 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
39514496 ATATTAAGTC
39514506 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
39514533 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
39514561 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
39514576 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:39514569 original size:28 final size:28
Alignment explanation
Indices: 39514506--39514603 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
39514496 ATATTAAGTC
*
39514506 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
39514533 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
39514561 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
39514590 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39514604 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39515067 original size:12 final size:12
Alignment explanation
Indices: 39515050--39515075 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39515040 TGGGCATACT
39515050 TATGTATATATA
1 TATGTATATATA
39515062 TATGTATATATA
1 TATGTATATATA
39515074 TA
1 TA
39515076 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:39517524 original size:68 final size:67
Alignment explanation
Indices: 39517452--39517601 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
39517442 CATCATGTGT
* * * *
39517452 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
39517514 ATGTAG
62 ATGTAG
** * *
39517520 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
39517585 AG
66 AG
39517587 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
39517602 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:39517557 original size:64 final size:64
Alignment explanation
Indices: 39517476--39517659 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
39517466 AGACATTATG
* *
39517476 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
39517540 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
39517605 AA
63 AA
* * * *
39517607 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
39517660 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:39519445 original size:25 final size:25
Alignment explanation
Indices: 39519411--39519458 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39519401 CCTGGCCTCG
39519411 GATATGGGTAAGGGGTGTTACATCA
1 GATATGGGTAAGGGGTGTTACATCA
39519436 GATATGGGTAAGGGGTGTTACAT
1 GATATGGGTAAGGGGTGTTACAT
39519459 TTAGTGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.38, T:0.29
Consensus pattern (25 bp):
GATATGGGTAAGGGGTGTTACATCA
Found at i:39534556 original size:12 final size:12
Alignment explanation
Indices: 39534539--39534564 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39534529 AAAATAGGGC
39534539 TTTAGCGGCGTT
1 TTTAGCGGCGTT
39534551 TTTAGCGGCGTT
1 TTTAGCGGCGTT
39534563 TT
1 TT
39534565 ATCAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:39534631 original size:40 final size:38
Alignment explanation
Indices: 39534552--39534705 Score: 139
Period size: 41 Copynumber: 3.8 Consensus size: 38
39534542 AGCGGCGTTT
* *
39534552 TTAGCGGCGTTTTATCAAAAAACGCCAC-AAAAACCAGAGCA
1 TTAGCGGCGTTTT-TC--AAAACGCCGCTAAAAA-TAGAGCA
* * *
39534593 ATCGCGGCGTTTTTACTAAAACGCCGCGAAAAATAGAGCA
1 TTAGCGGCGTTTTT-C-AAAACGCCGCTAAAAATAGAGCA
*
39534633 TTAGCGGCGCTTTTGGCAAAACGCCGCTAAAAATCAGAGCA
1 TTAGCGGCG-TTTT-TCAAAACGCCGCTAAAAAT-AGAGCA
*
39534674 TTAGCGGCGCTTTTCGAAAAACGCCGCTAAAA
1 TTAGCGGCGTTTTTC--AAAACGCCGCTAAAA
39534706 GTCATATAAC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
39 1 0.01
40 42 0.44
41 52 0.55
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (38 bp):
TTAGCGGCGTTTTTCAAAACGCCGCTAAAAATAGAGCA
Found at i:39534877 original size:7 final size:7
Alignment explanation
Indices: 39534862--39534913 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
39534852 TTAATTATCA
*
39534862 TTATAGT
1 TTATGGT
39534869 TTATGGT
1 TTATGGT
39534876 TTATGGT
1 TTATGGT
* *
39534883 TTAAGAT
1 TTATGGT
*
39534890 ATATGGT
1 TTATGGT
*
39534897 TTAGGGT
1 TTATGGT
*
39534904 TTAAGGT
1 TTATGGT
39534911 TTA
1 TTA
39534914 AGAGTTAACT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:39535088 original size:7 final size:7
Alignment explanation
Indices: 39534972--39535089 Score: 62
Period size: 7 Copynumber: 16.6 Consensus size: 7
39534962 TTATGATTAA
39534972 TTAGGGT
1 TTAGGGT
*
39534979 TTAATGG-
1 TT-AGGGT
39534986 TTAGGG-
1 TTAGGGT
*
39534992 TTAGAGT
1 TTAGGGT
*
39534999 TTAAGGT
1 TTAGGGT
*
39535006 GTAAGGGT
1 -TTAGGGT
*
39535014 TTATGGT
1 TTAGGGT
*
39535021 TAAGGGT
1 TTAGGGT
*
39535028 TAAGGGT
1 TTAGGGT
*
39535035 TAAGGGT
1 TTAGGGT
*
39535042 TTAGAGT
1 TTAGGGT
*
39535049 TTAGTGT
1 TTAGGGT
39535056 TTATGGG-
1 TTA-GGGT
*
39535063 ATAGGGGT
1 TTA-GGGT
*
39535071 TAAGAGGT
1 TTAG-GGT
39535079 TTAGGGT
1 TTAGGGT
39535086 TTAG
1 TTAG
39535090 ATTAATTAGT
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
6 8 0.09
7 60 0.71
8 17 0.20
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (7 bp):
TTAGGGT
Found at i:39535195 original size:22 final size:22
Alignment explanation
Indices: 39535170--39535233 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
39535160 AAAATAGGTT
39535170 TTAAGGGGATAGGGGTTAGGCG
1 TTAAGGGGATAGGGGTTAGGCG
**
39535192 TTAAGGGGATAAAGGTTAGGCG
1 TTAAGGGGATAGGGGTTAGGCG
*
39535214 TTAAGGGGATTGGGGTTAGG
1 TTAAGGGGATAGGGGTTAGG
39535234 GGTTTATGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.03, G:0.47, T:0.25
Consensus pattern (22 bp):
TTAAGGGGATAGGGGTTAGGCG
Found at i:39535282 original size:14 final size:14
Alignment explanation
Indices: 39535263--39535319 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
39535253 AATATTTTAA
*
39535263 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
39535277 GGTTTAGGGATTAT
1 GGTTTAGGGATTAT
* *
39535291 -GTGTTAGGGTTTAA
1 GGT-TTAGGGATTAT
*
39535305 GGTTTAGGGGTTAT
1 GGTTTAGGGATTAT
39535319 G
1 G
39535320 TATTAAGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 2 0.06
14 32 0.89
15 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:39535318 original size:28 final size:28
Alignment explanation
Indices: 39535277--39535346 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
39535267 TATGGATTAT
* *
39535277 GGTTTAGGGATTATGTGTT-AGGGTTTAA
1 GGTTTAGGGGTTATGTATTAAGGGTTT-A
39535305 GGTTTAGGGGTTATGTATTAAGGGTTTA
1 GGTTTAGGGGTTATGTATTAAGGGTTTA
*
39535333 GGTTTTAAGGGTTA
1 GG-TTTAGGGGTTA
39535347 AGAGATATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.54
29 17 0.46
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (28 bp):
GGTTTAGGGGTTATGTATTAAGGGTTTA
Found at i:39535344 original size:15 final size:15
Alignment explanation
Indices: 39535296--39535345 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
39535286 ATTATGTGTT
39535296 AGGGTTTAAGG-TTT-
1 AGGGTTT-AGGTTTTA
* * *
39535310 AGGGGTTATGTATTA
1 AGGGTTTAGGTTTTA
39535325 AGGGTTTAGGTTTTA
1 AGGGTTTAGGTTTTA
39535340 AGGGTT
1 AGGGTT
39535346 AAGAGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 18 0.64
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (15 bp):
AGGGTTTAGGTTTTA
Found at i:39535374 original size:7 final size:7
Alignment explanation
Indices: 39535365--39535398 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39535355 GGGTTATGGG
*
39535365 TTTAGGG
1 TTTAGGA
39535372 TTTAGGA
1 TTTAGGA
39535379 TTTAGGA
1 TTTAGGA
*
39535386 TTTAAGA
1 TTTAGGA
39535393 TTTAGG
1 TTTAGG
39535399 GGTAAAGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (7 bp):
TTTAGGA
Found at i:39535382 original size:14 final size:14
Alignment explanation
Indices: 39535294--39535399 Score: 65
Period size: 14 Copynumber: 7.4 Consensus size: 14
39535284 GGATTATGTG
39535294 TTAGGGTTTAAGG-T
1 TTAGGGTTT-AGGAT
* *
39535308 TTAGGGGTTATGTAT
1 TTAGGGTTTA-GGAT
* *
39535323 TAAGGGTTTAGGTT
1 TTAGGGTTTAGGAT
*
39535337 TTAAGGGTTAAGAGAT
1 TT-AGGGTTTAG-GAT
* *
39535353 AT-GGG-TTATGGGT
1 TTAGGGTTTA-GGAT
39535366 TTAGGGTTTAGGAT
1 TTAGGGTTTAGGAT
* *
39535380 TTAGGATTTAAGAT
1 TTAGGGTTTAGGAT
39535394 TTAGGG
1 TTAGGG
39535400 GTAAAGGATA
Statistics
Matches: 68, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
13 6 0.09
14 39 0.57
15 20 0.29
16 3 0.04
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
TTAGGGTTTAGGAT
Found at i:39535782 original size:75 final size:73
Alignment explanation
Indices: 39535608--39535807 Score: 312
Period size: 75 Copynumber: 2.7 Consensus size: 73
39535598 TGGCTTCCAA
*
39535608 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGGCG-TTTTTAAAAAAAAGCCAA
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGACGTTTTTTAAAAAAAAGCCAA
39535672 AAAACACT
66 AAAACACT
* * *
39535680 ATTATAACAAATAAAAATAAATATGAAAATTAAAAGATTAGTGACGTTTTTTTAAAAAACGCCAC
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGACGTTTTTTAAAAAAAAG-C-C
39535745 AAAAAACACT
64 AAAAAACACT
* * *
39535755 TTTATAACAAATAAAAATAAATATGAAAATTAAGATATTAGTAACGTTTTTTA
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGACGTTTTTTA
39535808 GCGTTTTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
72 44 0.38
73 12 0.10
74 1 0.01
75 59 0.51
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (73 bp):
ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGACGTTTTTTAAAAAAAAGCCAA
AAAACACT
Found at i:39539483 original size:19 final size:19
Alignment explanation
Indices: 39539461--39539501 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39539451 TTTATTGATA
39539461 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
39539479 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
39539498 TTTT
1 TTTT
39539502 GATTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:39548612 original size:16 final size:16
Alignment explanation
Indices: 39548591--39548621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39548581 TTGCTGAATC
39548591 TGAAATACCGAAAAGT
1 TGAAATACCGAAAAGT
*
39548607 TGAAATGCCGAAAAG
1 TGAAATACCGAAAAG
39548622 CCGAAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (16 bp):
TGAAATACCGAAAAGT
Found at i:39548950 original size:29 final size:29
Alignment explanation
Indices: 39548836--39548936 Score: 166
Period size: 29 Copynumber: 3.5 Consensus size: 29
39548826 GCAAGCATGA
39548836 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39548865 ATATGAATGTGGTTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
**
39548894 ATACAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
39548923 ATATGAATGAGATT
1 ATATGAATGTGATT
39548937 GAGCCTAGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:39562072 original size:27 final size:27
Alignment explanation
Indices: 39562034--39562090 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
39562024 AGGTTATCGA
39562034 GTAATCGATCCGATTCGTCAATTTCAT
1 GTAATCGATCCGATTCGTCAATTTCAT
*
39562061 GTAATCGATCCGATTTGTCAATTTCAT
1 GTAATCGATCCGATTCGTCAATTTCAT
39562088 GTA
1 GTA
39562091 CGAGGTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATCGATCCGATTCGTCAATTTCAT
Found at i:39567917 original size:47 final size:47
Alignment explanation
Indices: 39567865--39567960 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
39567855 GATAATTGTG
* * *
39567865 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGA
*
39567912 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGA
39567959 AT
1 AT
39567961 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:39568477 original size:25 final size:25
Alignment explanation
Indices: 39568443--39568493 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
39568433 TCCTGCTCAT
39568443 GATCACTAAATAAATCATAACTCGA
1 GATCACTAAATAAATCATAACTCGA
39568468 GATCACTAAATAAATCATAACTCGA
1 GATCACTAAATAAATCATAACTCGA
39568493 G
1 G
39568494 TTATGAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.24
Consensus pattern (25 bp):
GATCACTAAATAAATCATAACTCGA
Found at i:39580064 original size:13 final size:13
Alignment explanation
Indices: 39580039--39580072 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
39580029 AGAAAAAGTA
39580039 AATTAATAAATAAT
1 AATTAA-AAATAAT
39580053 AATTAAAAATAAT
1 AATTAAAAATAAT
39580066 AATTAAA
1 AATTAAA
39580073 TTGCAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:39581202 original size:13 final size:13
Alignment explanation
Indices: 39581184--39581237 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
39581174 GCTCAGCAGG
*
39581184 GACACGCCTGTGT
1 GACACGCCCGTGT
39581197 GACACGCCCGTGT
1 GACACGCCCGTGT
* **
39581210 GACTCGAACGTGT
1 GACACGCCCGTGT
* *
39581223 GACACTCTCGTGT
1 GACACGCCCGTGT
39581236 GA
1 GA
39581238 ATCATGCTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.22
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:39584110 original size:18 final size:18
Alignment explanation
Indices: 39584071--39584112 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
39584061 TATATTAGGG
*
39584071 GCCCATGTGGGCCCACAC
1 GCCCATGTGGGCCCACAA
39584089 GCCCATGT-GGCCCACGAA
1 GCCCATGTGGGCCCAC-AA
39584107 GCCCAT
1 GCCCAT
39584113 ATATAGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.19, C:0.43, G:0.26, T:0.12
Consensus pattern (18 bp):
GCCCATGTGGGCCCACAA
Found at i:39588331 original size:56 final size:56
Alignment explanation
Indices: 39588245--39588377 Score: 203
Period size: 56 Copynumber: 2.4 Consensus size: 56
39588235 TCCCAGATAG
*** *
39588245 GGTCTTACTCGCACACATATATTGGAGTCACATATCAATTCCAACGTATAAAACGT
1 GGTCTTACTCGCACACATATATCAAAGTCACATATCAATGCCAACGTATAAAACGT
* * *
39588301 GGTCTTACTTGCACACATATATCAAAGTCACATATCGATGCCAATGTATAAAACGT
1 GGTCTTACTCGCACACATATATCAAAGTCACATATCAATGCCAACGTATAAAACGT
39588357 GGTCTTACTCGCACACATATA
1 GGTCTTACTCGCACACATATA
39588378 CCGATGCCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAAAGTCACATATCAATGCCAACGTATAAAACGT
Found at i:39588396 original size:31 final size:31
Alignment explanation
Indices: 39588356--39588433 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
39588346 GTATAAAACG
*
39588356 TGGTCTTACTCGCACACATATACCGATGCCA
1 TGGTCTTACTCGCACAAATATACCGATGCCA
* *
39588387 TGGTATTACTTGCACAAATATACCGATGCCA
1 TGGTCTTACTCGCACAAATATACCGATGCCA
39588418 TGGTCTTACTCGCACA
1 TGGTCTTACTCGCACA
39588434 TCACATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (31 bp):
TGGTCTTACTCGCACAAATATACCGATGCCA
Found at i:39589052 original size:15 final size:15
Alignment explanation
Indices: 39589029--39589059 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39589019 TCAAAAATTC
39589029 CAATACAAAACATAT
1 CAATACAAAACATAT
*
39589044 CAATCCAAAACATAT
1 CAATACAAAACATAT
39589059 C
1 C
39589060 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:39592200 original size:16 final size:16
Alignment explanation
Indices: 39592176--39592206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39592166 ACTTTCAATT
39592176 TTTCAGCATTTTGGCA
1 TTTCAGCATTTTGGCA
*
39592192 TTTCGGCATTTTGGC
1 TTTCAGCATTTTGGC
39592207 GTTTTTCCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (16 bp):
TTTCAGCATTTTGGCA
Found at i:39606445 original size:21 final size:21
Alignment explanation
Indices: 39606412--39606453 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39606402 TGTTCATATA
*
39606412 AGTCCATTTATTTCA-TATTTT
1 AGTCCATTAATTT-ATTATTTT
*
39606433 AGTCCCTTAATTTATTATTTT
1 AGTCCATTAATTTATTATTTT
39606454 TTCAATTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (21 bp):
AGTCCATTAATTTATTATTTT
Found at i:39612149 original size:40 final size:40
Alignment explanation
Indices: 39612093--39612276 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
39612083 TTGAATGCTG
* *
39612093 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTGA-T-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT-ACTAAT
* * * *
39612132 ATCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGATACTAAT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* **
39612173 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGACACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
39612213 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAT
39612253 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39612277 GAATGAGTTA
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.02
40 124 0.97
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:39612297 original size:39 final size:39
Alignment explanation
Indices: 39612173--39612323 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
39612163 AGATACTAAT
* ** ** *
39612173 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGACACT-AAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
39612213 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
39612253 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
39612293 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
39612324 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:39619431 original size:21 final size:20
Alignment explanation
Indices: 39619402--39619447 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
39619392 AGAAATGCAA
39619402 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
39619423 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
39619443 T-AACC
1 TCAACC
39619448 ATTTCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:39620310 original size:22 final size:22
Alignment explanation
Indices: 39620283--39620326 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39620273 AAAAATAATC
*
39620283 AAAATTAATAAAAATTTATTAT
1 AAAATTAATAAAAATTCATTAT
*
39620305 AAAATTAATTAAAATTCATTAT
1 AAAATTAATAAAAATTCATTAT
39620327 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATAAAAATTCATTAT
Found at i:39627481 original size:21 final size:22
Alignment explanation
Indices: 39627448--39627491 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
39627438 ATTTAACAAA
39627448 TAAGTAGGGGGAAAACCTATGT
1 TAAGTAGGGGGAAAACCTATGT
39627470 TAAGTA-GGGGAAAACCTATGT
1 TAAGTAGGGGGAAAACCTATGT
39627491 T
1 T
39627492 CTTTATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.25
Consensus pattern (22 bp):
TAAGTAGGGGGAAAACCTATGT
Found at i:39628890 original size:21 final size:18
Alignment explanation
Indices: 39628845--39628895 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
39628835 TCTTCAACAA
39628845 CAACTTCCTCTTCTACAGT
1 CAACTT-CTCTTCTACAGT
39628864 -AACTTCTACTTCTACAGCAT
1 CAACTTCT-CTTCTACAG--T
39628884 CAACTTC-CTTCT
1 CAACTTCTCTTCT
39628896 TAATAACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 14 0.50
19 5 0.18
20 1 0.04
21 6 0.21
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (18 bp):
CAACTTCTCTTCTACAGT
Found at i:39630898 original size:26 final size:26
Alignment explanation
Indices: 39630862--39630916 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39630852 AACAAACCAA
* * *
39630862 TATCGTAGCAAGGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCAAGTAACAG
*
39630888 TATCGCAGCAAAGCTGCAAGTATCAG
1 TATCGCAGCAAAGCTGCAAGTAACAG
39630914 TAT
1 TAT
39630917 ATGTGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCAAGTAACAG
Found at i:39643813 original size:23 final size:24
Alignment explanation
Indices: 39643777--39643821 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39643767 AATTCAATAC
39643777 TCAAATCCATATC-ATTTATCTAT
1 TCAAATCCATATCAATTTATCTAT
39643800 TCAAATACCA-ATCAATTTATCT
1 TCAAAT-CCATATCAATTTATCT
39643822 TACTTTACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAAATCCATATCAATTTATCTAT
Found at i:39648152 original size:6 final size:5
Alignment explanation
Indices: 39648130--39648200 Score: 54
Period size: 5 Copynumber: 13.2 Consensus size: 5
39648120 TGTCTTCTTG
* * *
39648130 TTTTA TCTTA CTTCTA TTTCTA TTTTTG TTTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA -TTTTA TTT-TA -TTTTA TTT-TA TTTTA TTTTA TTTTA
39648178 TTTTTA TTTTA TTTATA TTTTA T
1 -TTTTA TTTTA TTT-TA TTTTA T
39648201 GTTTCTTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.08
5 27 0.51
6 19 0.36
7 3 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:39648167 original size:5 final size:5
Alignment explanation
Indices: 39648159--39648200 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
39648149 CTATTTTTGT
39648159 TTTTA TTTTA TTTTA -TTTA TTTTTA TTTTA TTTATA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTT-TA TTTTA T
39648201 GTTTCTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.12
5 21 0.62
6 9 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:39648172 original size:11 final size:11
Alignment explanation
Indices: 39648153--39648200 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
39648143 CTATTTCTAT
*
39648153 TTTTGTTTTTA
1 TTTTATTTTTA
39648164 TTTTA-TTTTA
1 TTTTATTTTTA
39648174 -TTTATTTTTA
1 TTTTATTTTTA
*
39648184 TTTTATTTATA
1 TTTTATTTTTA
39648195 TTTTAT
1 TTTTAT
39648201 GTTTCTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 4 0.12
10 10 0.30
11 19 0.58
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:39648184 original size:15 final size:15
Alignment explanation
Indices: 39648160--39648200 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
39648150 TATTTTTGTT
39648160 TTTA-TTTTATTTTA
1 TTTATTTTTATTTTA
39648174 TTTATTTTTATTTTA
1 TTTATTTTTATTTTA
39648189 TTTATATTTTAT
1 TTTAT-TTTTAT
39648201 GTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTTTATTTTA
Found at i:39648187 original size:26 final size:26
Alignment explanation
Indices: 39648150--39648200 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
39648140 CTTCTATTTC
*
39648150 TATTTTTGTTTTTATTT-TATTTTATT
1 TATTTTT-ATTTTATTTATATTTTATT
39648176 TATTTTTATTTTATTTATATTTTAT
1 TATTTTTATTTTATTTATATTTTAT
39648201 GTTTCTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (26 bp):
TATTTTTATTTTATTTATATTTTATT
Found at i:39648210 original size:31 final size:32
Alignment explanation
Indices: 39648130--39648210 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 32
39648120 TGTCTTCTTG
* * *
39648130 TTTTATCTTACTTCTATTTCTATTTTTGTTTTTA
1 TTTTATTTTAC-T-TATTTCTATTTTTATTTATA
* *
39648164 TTTTATTTTATTTATTTTTA-TTTTATTTATA
1 TTTTATTTTACTTATTTCTATTTTTATTTATA
39648195 TTTTATGTTT-CTTATT
1 TTTTAT-TTTACTTATT
39648211 ATCTTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 20 0.50
32 10 0.25
33 1 0.03
34 9 0.22
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (32 bp):
TTTTATTTTACTTATTTCTATTTTTATTTATA
Found at i:39654491 original size:13 final size:12
Alignment explanation
Indices: 39654473--39654514 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
39654463 CCAAAAACAT
*
39654473 AAAAAAACAAAG
1 AAAAAAAAAAAG
*
39654485 AAAAAAAAAAGG
1 AAAAAAAAAAAG
39654497 AAAAAAAAAAGAG
1 AAAAAAAAAA-AG
39654510 AAAAA
1 AAAAA
39654515 GAATTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:39658313 original size:49 final size:49
Alignment explanation
Indices: 39658200--39658378 Score: 154
Period size: 50 Copynumber: 3.7 Consensus size: 49
39658190 GTATAATGCT
* ***
39658200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-C--AT-CAATTC
1 GATGCCATGT-CCAGACATGGTCTTACACTGACT-ATCACAAATCCAGGCC
* **
39658247 GATGCCATGTCCTAGACATGGGCTTACACTGACTATCA-AAATTGAGGCC
1 GATGCCATGTCC-AGACATGGTCTTACACTGACTATCACAAATCCAGGCC
* * * *
39658296 GATGCCATGTCTCAGACATGGTCTTACACT-AGCTCTCACATATCCATGCT
1 GATGCCATGTC-CAGACATGGTCTTACACTGA-CTATCACAAATCCAGGCC
*
39658346 GATCCCATGTCCCAGACATGGTCTTACACTGAC
1 GATGCCATGT-CCAGACATGGTCTTACACTGAC
39658379 ACATCTCGTA
Statistics
Matches: 108, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
46 5 0.05
47 29 0.27
48 3 0.03
49 34 0.31
50 35 0.32
51 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (49 bp):
GATGCCATGTCCAGACATGGTCTTACACTGACTATCACAAATCCAGGCC
Found at i:39658445 original size:46 final size:49
Alignment explanation
Indices: 39658200--39658562 Score: 287
Period size: 46 Copynumber: 7.7 Consensus size: 49
39658190 GTATAATGCT
* ***
39658200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCA--TC-AATTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TACATCTCGAGGCC
* * * * *
39658247 GATGCCATGTCCTAGACATGGGCTTACACTGACTATCAAAAT-T-GAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTACATCTCGAGGCC
* * * * * *
39658296 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCACATATCCATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-ACATCTCGAGGCC
* *
39658346 GATCCCATGTCCCAGACATGGTCTTACACT-G-AC-ACATCTCGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTCG-AGGCC
* *
39658392 AATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTCGAGGCC
* * ** * *
39658438 GATG-CATGTCCCAGACAT-GTCTTATACTAGCTCT-TGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTCGAGGCC
* * *
39658484 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACAT-CTCGAGGCC
39658532 GATG-CATGTCCCAGACAT-GTCTTACACTGGC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC
39658563 ACACAAATAA
Statistics
Matches: 253, Mismatches: 47, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
44 10 0.04
45 16 0.06
46 73 0.29
47 60 0.24
48 27 0.11
49 36 0.14
50 31 0.12
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATCTCGAGGCC
Found at i:39658508 original size:94 final size:93
Alignment explanation
Indices: 39658200--39658565 Score: 288
Period size: 94 Copynumber: 3.9 Consensus size: 93
39658190 GTATAATGCT
* * * ** *
39658200 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-ATC-CATCAATTC-GATGCCATGTCCTAG
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTA-CATATCGAGGCTGATG-CATGTCCCAG
* * **
39658262 ACATGGGCTTACACTGAC-TATCAAAATTGAGGCC
64 ACAT-GTCTTACACTGACACATC-TCA-T-A-GCC
* * * *
39658296 GATGCCATGT-CTCAGACATGGTCTTACACTAGCTCTCACATATCCATGCTGATCCCATGTCCCA
1 GATGCCATGTCCT-AGACATGGTCTTACACTGGCTCT-ACATATCGAGGCTGAT-GCATGTCCCA
*
39658360 GACATGGTCTTACACTGACACATCTCGTAGCC
63 GACAT-GTCTTACACTGACACATCTCATAGCC
* * *
39658392 AATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGAGGCTGATGCATGTCCCAGAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTACATATCGAGGCTGATGCATGTCCCAGAC
* * *
39658454 ATGTCTTATACT-AGCTCTTGTCTCA-ATGCC
66 ATGTCTTACACTGA-CAC--ATCTCATA-GCC
* *
39658484 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGA
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTACAT-ATCGAGGCTGATGCATGTCCCAGA
*
39658547 CATGTCTTACACTGGCACA
65 CATGTCTTACACTGACACA
39658566 CAAATAACCC
Statistics
Matches: 221, Mismatches: 32, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
89 1 0.00
90 11 0.05
91 15 0.07
92 23 0.10
93 14 0.06
94 63 0.29
95 14 0.06
96 38 0.17
97 2 0.01
98 8 0.04
99 29 0.13
100 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTACATATCGAGGCTGATGCATGTCCCAGAC
ATGTCTTACACTGACACATCTCATAGCC
Found at i:39658543 original size:140 final size:143
Alignment explanation
Indices: 39658194--39658562 Score: 402
Period size: 140 Copynumber: 2.6 Consensus size: 143
39658184 CATAGGGTAT
39658194 AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAT-T--CGATGCCATG
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-CAT-AATGTGCCGATG-CATG
* * * *
39658256 TCCTAGACATGGGCTTACACTGACTATCAAAATTGAGGCCGATGCCATGTCTCAGACATGGTCTT
63 TCCCAGACAT-GTCTTACACTGGCTAT-AAAATTGAGGCCGATGCCATGTCCCAGACATGGTCTT
39658321 ACACTAGCTCTCACATATC
126 ACACTAGCTCT-ACATATC
* * * * * *
39658340 CATGCTGATCCCATGTCCCAGACATGGTCTTACACTGACACATC-T--CGTAGCCAATGCATGTC
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGT-GCCGATGCATGTC
* * *
39658402 CCAGACATGTCTTACACTGGCT-T-ACATCTCGAGGCTGATG-CATGTCCCAGACAT-GTCTTAT
65 CCAGACATGTCTTACACTGGCTATAAAAT-T-GAGGCCGATGCCATGTCCCAGACATGGTCTTAC
** *
39658463 ACTAGCTCT-TGTCTC
128 ACTAGCTCTACATATC
* *
39658478 AATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTC-TCATAATGTGGCCGATGCATGTC
1 AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGT-GCCGATGCATGTC
39658542 CCAGACATGTCTTACACTGGC
65 CCAGACATGTCTTACACTGGC
39658563 ACACAAATAA
Statistics
Matches: 189, Mismatches: 25, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
137 2 0.01
138 39 0.21
140 53 0.28
141 14 0.07
142 11 0.06
143 12 0.06
144 14 0.07
145 5 0.03
146 39 0.21
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (143 bp):
AATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATAATGTGCCGATGCATGTCC
CAGACATGTCTTACACTGGCTATAAAATTGAGGCCGATGCCATGTCCCAGACATGGTCTTACACT
AGCTCTACATATC
Found at i:39660660 original size:27 final size:26
Alignment explanation
Indices: 39660622--39660936 Score: 269
Period size: 27 Copynumber: 11.7 Consensus size: 26
39660612 AGACCTCGTG
* *
39660622 TTGTAAAATTACTGAAATATCCCCAGC
1 TTGTAAAATTACCGAAATA-CCCCAGT
39660649 TTGTAAAATTACCGAAATACCCCTAGGT
1 TTGTAAAATTACCGAAATACCCC-A-GT
39660677 TT-TAAAATTACCGAAATACCCCTTA-T
1 TTGTAAAATTACCGAAATACCCC--AGT
* * * *
39660703 TTGTAAACTTACCAAAATACCCTTAGA
1 TTGTAAAATTACCGAAATACCC-CAGT
* *
39660730 TTGTAAAACTATCGAAATACCCCCGAG-
1 TTGTAAAATTACCGAAATA-CCCC-AGT
39660757 TTGTAAAATTACCGAAATACCCCAGT
1 TTGTAAAATTACCGAAATACCCCAGT
* * *
39660783 TTGTAAAATTACCAAAATACCTTCAGA
1 TTGTAAAATTACCGAAATACC-CCAGT
* * * *
39660810 TTATAAAATTATCAAAATACTCTC-GAT
1 TTGTAAAATTACCGAAATAC-CCCAG-T
39660837 TTGTAAAATTACCGAAATACCCCTAGT
1 TTGTAAAATTACCGAAATACCCC-AGT
* * ** *
39660864 TTGTAACATTATCGAAATACCCTTGGA
1 TTGTAAAATTACCGAAATACCC-CAGT
**
39660891 TTGTAAAATTACTAAAATACCCCCAGT
1 TTGTAAAATTACCGAAATA-CCCCAGT
*
39660918 TTGTAAAATTATCGAAATA
1 TTGTAAAATTACCGAAATA
39660937 TATTTGTAGT
Statistics
Matches: 234, Mismatches: 38, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.01
26 35 0.15
27 182 0.78
28 15 0.06
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (26 bp):
TTGTAAAATTACCGAAATACCCCAGT
Found at i:39660764 original size:81 final size:81
Alignment explanation
Indices: 39660649--39660936 Score: 338
Period size: 81 Copynumber: 3.6 Consensus size: 81
39660639 TATCCCCAGC
* * * *
39660649 TTGTAAAATTACCGAAATA-CCCCTAGGTTTTAAAATTACCGAAATACCCCTTA-TTTGTAAACT
1 TTGTAAAATTATCAAAATACCCCCGA-GTTGTAAAATTACCGAAATACCCC-TAGTTTGTAAACT
39660712 TACCAAAATACCCTTAGA
64 TACCAAAATACCCTTAGA
* * *
39660730 TTGTAAAACTATCGAAATACCCCCGAGTTGTAAAATTACCGAAATACCCC-AGTTTGTAAAATTA
1 TTGTAAAATTATCAAAATACCCCCGAGTTGTAAAATTACCGAAATACCCCTAGTTTGTAAACTTA
39660794 CCAAAATA-CCTTCAGA
66 CCAAAATACCCTT-AGA
* * * *
39660810 TTATAAAATTATCAAAATACTCTCGATTTGTAAAATTACCGAAATACCCCTAGTTTGT-AACATT
1 TTGTAAAATTATCAAAATACCCCCGAGTTGTAAAATTACCGAAATACCCCTAGTTTGTAAAC-TT
* * *
39660874 ATCGAAATACCCTTGGA
65 ACCAAAATACCCTTAGA
*
39660891 TTGTAAAATTA-CTAAAATACCCCC-AGTTTGTAAAATTATCGAAATA
1 TTGTAAAATTATC-AAAATACCCCCGAG-TTGTAAAATTACCGAAATA
39660937 TATTTGTAGT
Statistics
Matches: 179, Mismatches: 20, Indels: 16
0.83 0.09 0.07
Matches are distributed among these distances:
79 5 0.03
80 70 0.39
81 95 0.53
82 9 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (81 bp):
TTGTAAAATTATCAAAATACCCCCGAGTTGTAAAATTACCGAAATACCCCTAGTTTGTAAACTTA
CCAAAATACCCTTAGA
Found at i:39660949 original size:27 final size:27
Alignment explanation
Indices: 39660919--39660979 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
39660909 ACCCCCAGTT
* *
39660919 TGTAAAATTA-TCGAAATATATTTGTAG
1 TGTAAAATTACT-GAAATACACTTGTAG
39660946 TGTAAAATTACTGAAATACACTTGTAG
1 TGTAAAATTACTGAAATACACTTGTAG
39660973 -GTAAAAT
1 TGTAAAAT
39660980 GATTGTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
27 23 0.74
28 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.36
Consensus pattern (27 bp):
TGTAAAATTACTGAAATACACTTGTAG
Found at i:39663051 original size:10 final size:9
Alignment explanation
Indices: 39663027--39663052 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39663017 TTCAAGGATT
39663027 TCAAAAACA
1 TCAAAAACA
39663036 TCAAAAACA
1 TCAAAAACA
39663045 TCAAAAAC
1 TCAAAAAC
39663053 CAACACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (9 bp):
TCAAAAACA
Found at i:39664554 original size:17 final size:18
Alignment explanation
Indices: 39664513--39664562 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
39664503 ACATGTTTAT
*
39664513 TAATTAAGGATAATAAAG
1 TAATTTAGGATAATAAAG
39664531 TAATTTAGGA-AATAAA-
1 TAATTTAGGATAATAAAG
39664547 TAAGTTTA--ATAATAAA
1 TAA-TTTAGGATAATAAA
39664563 ACAAACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 1 0.03
16 9 0.31
17 10 0.34
18 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
TAATTTAGGATAATAAAG
Found at i:39665493 original size:43 final size:44
Alignment explanation
Indices: 39665444--39665594 Score: 175
Period size: 43 Copynumber: 3.5 Consensus size: 44
39665434 GATTACCGAA
* *
39665444 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGAATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
*
39665488 -TGTGATTACGTGTAAGACCATGT-TCGGGACATTGGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCT-GGGACATTGGCATCGTAT
* * * * *
39665530 ATATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
39665573 ATGTGATAACATATAAGACCAT
1 ATGTGATTACATGTAAGACCAT
39665595 ATTTGGGATA
Statistics
Matches: 90, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
42 2 0.02
43 87 0.97
44 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:39665602 original size:43 final size:42
Alignment explanation
Indices: 39665444--39665616 Score: 170
Period size: 43 Copynumber: 4.1 Consensus size: 42
39665434 GATTACCGAA
* *
39665444 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGAATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
*
39665486 ATTGTGATTACGTGTAAGACCATGT-TCGGGACATTGGCATCGTT
1 A-TGTGATTACATGTAAGACCATGTCT-GGGACATTGGCATCG-T
* * * * *
39665530 ATATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T
* * * * * *
39665573 ATGTGATAACATATAAGACCATATTTGGGATA-TGGCATTGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
39665614 ATG
1 ATG
39665617 AGCTTTATGT
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.04
42 9 0.08
43 93 0.85
44 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (42 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
Found at i:39667738 original size:27 final size:27
Alignment explanation
Indices: 39667708--39667799 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
39667698 ATTACCAAAG
*
39667708 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
**
39667735 TACCCTTTATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* **
39667762 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
39667789 TACCCTCGATT
1 TACCCTCGATT
39667800 GTGAAATTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:39667872 original size:54 final size:54
Alignment explanation
Indices: 39667812--39667953 Score: 135
Period size: 54 Copynumber: 2.6 Consensus size: 54
39667802 GAAATTATTG
* *
39667812 AAATACCCCTA-TAGGGTAGAATTACCAAAATACCCCTAAATTGTAAAATTACCA
1 AAATACCCCTAGT-GGGTAAAATTACCAAAATACCACTAAATTGTAAAATTACCA
** ** * * *
39667866 AAATACCCCTAGTTTGTAAAATTACCAAAATACCACTAGTTTGTGAAATTATCG
1 AAATACCCCTAGTGGGTAAAATTACCAAAATACCACTAAATTGTAAAATTACCA
* ** *
39667920 AAATA-CCCTCAATTTGTAAAATTACCGAAATACC
1 AAATACCCCT-AGTGGGTAAAATTACCAAAATACC
39667954 TTTGATTTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
53 4 0.05
54 70 0.93
55 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (54 bp):
AAATACCCCTAGTGGGTAAAATTACCAAAATACCACTAAATTGTAAAATTACCA
Found at i:39667961 original size:27 final size:27
Alignment explanation
Indices: 39667831--39668067 Score: 172
Period size: 27 Copynumber: 8.7 Consensus size: 27
39667821 TATAGGGTAG
* * * *
39667831 AATTACCAAAATACCCCTAAATTGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
* *
39667858 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCGAAATACCCTTGA-TTTGTAA
* * *
39667885 AATTACCAAAATACCACTAG-TTTGTGA
1 AATTACCGAAATACC-CTTGATTTGTAA
* **
39667912 AATTATCGAAATACCCTCAATTTGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
* **
39667939 AATTACCGAAATACCTTTGATTTACAA
1 AATTACCGAAATACCCTTGATTTGTAA
* *
39667966 AATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACCGAAATACCCTTGA-TTTGT-AA
** * * **
39667995 AATTATAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCCTTGATTTGTAA
* *
39668022 AATTACTGAAATACCCTTGGTTTGTAA
1 AATTACCGAAATACCCTTGATTTGTAA
* * *
39668049 ATTTACCAAAACACCCTTG
1 AATTACCGAAATACCCTTG
39668068 TAGGATGAAA
Statistics
Matches: 171, Mismatches: 33, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.02
27 142 0.83
28 7 0.04
29 19 0.11
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGATTTGTAA
Found at i:39669047 original size:24 final size:25
Alignment explanation
Indices: 39668971--39669040 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
39668961 AGGAAGTGCT
* * * *
39668971 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
39668996 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
39669021 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39669041 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:39669053 original size:24 final size:24
Alignment explanation
Indices: 39668996--39669067 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
39668986 TAGTTTACCG
39668996 AAAAG-GGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
39669020 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
39669044 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
39669068 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:39669309 original size:31 final size:30
Alignment explanation
Indices: 39669260--39669342 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
39669250 CGCTTACAGT
*
39669260 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGCCCAGTGATATGATTTATGA
39669290 AAAGGCTTCGACCCAGTGATATGATTTATGA
1 AAAGGCTTCG-CCCAGTGATATGATTTATGA
*
39669321 AAAAGCTTCGGCCCAGT-ATATG
1 AAAGGCTTC-GCCCAGTGATATG
39669343 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 15 0.31
31 33 0.67
32 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGCCCAGTGATATGATTTATGA
Found at i:39672404 original size:14 final size:14
Alignment explanation
Indices: 39672385--39672415 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39672375 AGATGATACC
*
39672385 TTTTGTTTATGTTA
1 TTTTGTTTAAGTTA
39672399 TTTTGTTTAAGTTA
1 TTTTGTTTAAGTTA
39672413 TTT
1 TTT
39672416 ATTAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (14 bp):
TTTTGTTTAAGTTA
Found at i:39672446 original size:13 final size:14
Alignment explanation
Indices: 39672422--39672451 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39672412 ATTTATTAAT
39672422 TTACTAATTTAACC
1 TTACTAATTTAACC
39672436 TTACTAA-TTAACC
1 TTACTAATTTAACC
39672449 TTA
1 TTA
39672452 AAATCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (14 bp):
TTACTAATTTAACC
Found at i:39687724 original size:4 final size:4
Alignment explanation
Indices: 39687715--39687797 Score: 166
Period size: 4 Copynumber: 20.8 Consensus size: 4
39687705 AATAATAATA
39687715 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39687763 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
39687798 GCGATTTTTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 79 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:39689122 original size:12 final size:13
Alignment explanation
Indices: 39689086--39689123 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
39689076 AAATATTTGA
39689086 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
39689099 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
39689113 CTTG-TCTTAAT
1 CTTGTTCTTAAT
39689124 ATTCTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:39695070 original size:46 final size:45
Alignment explanation
Indices: 39694928--39695096 Score: 148
Period size: 46 Copynumber: 3.7 Consensus size: 45
39694918 TATCTGTGTT
*
39694928 GATGCCATGTCCCAGACATGGTCTTACACTG-ACACATCTCATAGCC
1 GATGCCATGTCCCAGACAT-GTCTTACACTGCACTCATCTCAT-GCC
* * * * * *
39694974 AAAG-CATGTCCCAGACATGTCTTACACTGGC-TTACGTCTCGAGGCT
1 GATGCCATGTCCCAGACATGTCTTACACT-GCACT-CATCTC-ATGCC
* *
39695020 GATG-CATGCCCCAGACATGTCTTACACTAGCACTCATCTCAATGTC
1 GATGCCATGTCCCAGACATGTCTTACACT-GCACTCATCTC-ATGCC
*
39695066 GATGCCATGTCCCAAACATGATCTTACACTG
1 GATGCCATGTCCCAGACATG-TCTTACACTG
39695097 GTTATCATAA
Statistics
Matches: 97, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
44 10 0.10
45 15 0.15
46 47 0.48
47 16 0.16
48 9 0.09
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (45 bp):
GATGCCATGTCCCAGACATGTCTTACACTGCACTCATCTCATGCC
Found at i:39695092 original size:94 final size:90
Alignment explanation
Indices: 39694927--39695137 Score: 230
Period size: 94 Copynumber: 2.3 Consensus size: 90
39694917 ATATCTGTGT
*
39694927 TGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCATAGCCAAAGCATGTCCCAGACAT
1 TGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCATAGCCAAAGCATGTCCCAAACAT
* *
39694992 GTCTTACACTGGCTTA-CGT-CTCGAGGC
64 GTCTTACACTGG-TTATCATAAT-GAGGC
* * * * *
39695019 TGATGCATGCCCCAGACATGTCTTACACTAGCACTCATCTCA-ATGTCGATGCCATGTCCCAAAC
1 TGATGCATGTCCCAGACATGTCTTACACT-G-ACACATCTCATA-GCCAAAG-CATGTCCCAAAC
**
39695083 ATGATCTTACACTGGTTATCATAATTTGGC
62 ATG-TCTTACACTGGTTATCATAATGAGGC
39695113 TGATGCATGTCCCAGACATGTCTTA
1 TGATGCATGTCCCAGACATGTCTTA
39695138 TGCTAGCTCA
Statistics
Matches: 101, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
90 10 0.10
91 15 0.15
92 18 0.18
93 17 0.17
94 40 0.40
95 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (90 bp):
TGATGCATGTCCCAGACATGTCTTACACTGACACATCTCATAGCCAAAGCATGTCCCAAACATGT
CTTACACTGGTTATCATAATGAGGC
Found at i:39697063 original size:43 final size:43
Alignment explanation
Indices: 39697007--39697173 Score: 160
Period size: 43 Copynumber: 3.9 Consensus size: 43
39696997 AGCTCGTACA
* * *
39697007 ATGCC-ATATCCCAGATATGGTCTTACATATTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATATAATCACATATCG
* * * * * *
39697049 ATGCCACTGTCCCAGACAGGGTCTTATACAAAATCA-ATTAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATATAATCACA-TATCG
* * *
39697092 ATGCCAATGTCCCAGACATGGTCTTACAGATAATCTCA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACATATAATCACATAT-CG
* * *
39697135 ATGCCAATCTTCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATATAATCACAT
39697174 CTCAATCACC
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 7 0.07
43 90 0.92
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATATAATCACATATCG
Found at i:39723735 original size:40 final size:40
Alignment explanation
Indices: 39723687--39723878 Score: 235
Period size: 40 Copynumber: 4.8 Consensus size: 40
39723677 ATAACAACTC
*
39723687 GCACAAATGCCTTCGGGTCTTAGCCCGAATATAGTCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
* * * * *
39723727 GCATAAATGCCTCCGGGACTTAGCTCGGATATAGTCGCTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
* *
39723767 GCACAAATGCCTTCGGGTCTTAACCCAGATATAG-CAACTCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC-ACT-A
* * *
39723808 -CACAAATGCCTTCGGATCTTAGTCCGGATATAGTTACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
* *
39723847 GCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
39723879 CATTCGAATA
Statistics
Matches: 126, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.02
40 123 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTA
Found at i:39726602 original size:30 final size:31
Alignment explanation
Indices: 39726557--39726616 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
39726547 TCCCGAGCCT
39726557 AGGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 AGGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * * *
39726588 AGGGG-AAAATTGTAATTTTGCTAAAGTTT
1 AGGGGCAAAAGTGTAAATATGCAAAAGTTT
39726617 GAGTTAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (31 bp):
AGGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:39727399 original size:68 final size:68
Alignment explanation
Indices: 39727327--39727474 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 68
39727317 CATCATGTGT
* * * *
39727327 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-CGTACACCA
1 ACAAGAGAGCTACAAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
39727390 TGTAG
64 TGTAG
* ** * *
39727395 ACAAGAGAGCT--ATGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCAT
1 ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCAT
39727458 GTAG
65 GTAG
39727462 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
39727475 GAGATAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
64 24 0.36
65 3 0.05
66 5 0.08
67 23 0.35
68 11 0.17
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATG
TAG
Found at i:39733401 original size:47 final size:47
Alignment explanation
Indices: 39733347--39733540 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
39733337 TTAGGATTTT
** * *
39733347 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
39733394 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
39733441 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
39733488 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
39733535 ATGTGA
1 ATGTGA
39733541 AATATATATG
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:39733447 original size:22 final size:22
Alignment explanation
Indices: 39733376--39733447 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
39733366 GTATATATGA
39733376 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
39733398 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
39733423 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
39733445 GAT
1 GAT
39733448 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:39733496 original size:25 final size:25
Alignment explanation
Indices: 39733421--39733496 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
39733411 ATGCATATAT
39733421 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
39733446 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
39733468 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
39733493 GTGA
1 GTGA
39733497 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:39733792 original size:37 final size:37
Alignment explanation
Indices: 39733742--39733813 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
39733732 GGAAATATAT
* *
39733742 TCCGGGTACGACCCGATGAC-TACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACAT-CGTGTGGAGATTTTG
39733779 TCCGGGTAAGACCCGATAACATCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACATCGTGTGGAGATTT
39733814 CGTCTGAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACATCGTGTGGAGATTTTG
Found at i:39743407 original size:46 final size:46
Alignment explanation
Indices: 39743341--39743468 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
39743331 TGTAACCTGC
* *
39743341 CCATAAGCGAA-TCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
39743386 CCATAAGTGAACTCAGACTCAAATCAACAAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
*
39743432 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA
39743469 TGCCCAAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 10 0.13
46 65 0.87
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:39748651 original size:79 final size:80
Alignment explanation
Indices: 39748520--39748679 Score: 270
Period size: 79 Copynumber: 2.0 Consensus size: 80
39748510 TACCAGTGAT
* *
39748520 AACATCTAGCGCTGAAGCTTCCCCTCTAGCACGGATCGCATAAGCTCTAGCAGACACTCGTG-C-
1 AACATCTAGCGATGAAGCTTCCCCTCTAGCACAGATCGCATAAGCTCTAGCAGACACTCGTGACT
39748583 CAAGATCTCACAGTAG
66 C-AGATCTCACAGTAG
*
39748599 AACATCTAGTGATGAAGCTTCCCCTCTAGCACAGATCGCATAAGCTCTAGCAGACACTCGTGACT
1 AACATCTAGCGATGAAGCTTCCCCTCTAGCACAGATCGCATAAGCTCTAGCAGACACTCGTGACT
39748664 CAGATCTCACAGTAG
66 CAGATCTCACAGTAG
39748679 A
1 A
39748680 GTATTTCATC
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
79 59 0.78
80 16 0.21
81 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (80 bp):
AACATCTAGCGATGAAGCTTCCCCTCTAGCACAGATCGCATAAGCTCTAGCAGACACTCGTGACT
CAGATCTCACAGTAG
Found at i:39754946 original size:20 final size:20
Alignment explanation
Indices: 39754923--39755024 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 20
39754913 TGTAACCAGA
39754923 GGCACAAATGTACATTCAGG
1 GGCACAAATGTACATTCAGG
** ** *
39754943 GGCAC-CGTAGTACAAACAAG
1 GGCACAAAT-GTACATTCAGG
* * *
39754963 GGCATAGATGTGCATTCAGG
1 GGCACAAATGTACATTCAGG
* **
39754983 GGTACTAAA-GTACAAACAGG
1 GGCAC-AAATGTACATTCAGG
*
39755003 GGCACAAATGTGCATTCAGG
1 GGCACAAATGTACATTCAGG
39755023 GG
1 GG
39755025 TACCGAAGTA
Statistics
Matches: 56, Mismatches: 22, Indels: 8
0.65 0.26 0.09
Matches are distributed among these distances:
19 4 0.07
20 49 0.88
21 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (20 bp):
GGCACAAATGTACATTCAGG
Found at i:39754979 original size:40 final size:40
Alignment explanation
Indices: 39754923--39755126 Score: 239
Period size: 40 Copynumber: 5.1 Consensus size: 40
39754913 TGTAACCAGA
* * * * *
39754923 GGCACAAATGTACATTCAGGGGCACCGTAGTACAAACAAG
1 GGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAGG
* **
39754963 GGCATAGATGTGCATTCAGGGGTACTAAAGTACAAACAGG
1 GGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAGG
*
39755003 GGCACAAATGTGCATTCAGGGGTACCGAAGTACAAACAGG
1 GGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAGG
* * *
39755043 GGCACAGACGTGAATTCAGGGGTACCGGAGTACAAACAGG
1 GGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAGG
* ** * *
39755083 GGAACAGACATGCATTTAGGGGTA-CGAAAGTACAAATAGG
1 GGCACAGATGTGCATTCAGGGGTACCG-AAGTACAAACAGG
39755123 GGCA
1 GGCA
39755127 GTTCTTCATT
Statistics
Matches: 140, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 2 0.01
40 138 0.99
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (40 bp):
GGCACAGATGTGCATTCAGGGGTACCGAAGTACAAACAGG
Found at i:39755042 original size:20 final size:20
Alignment explanation
Indices: 39754979--39755084 Score: 63
Period size: 20 Copynumber: 5.3 Consensus size: 20
39754969 GATGTGCATT
**
39754979 CAGGGGTACTAAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * **
39754999 CAGGGGCA-CAAATGTGCATT
1 CAGGGGTACCGAA-GTACAAA
39755019 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * **
39755039 CAGGGGCACAGACGTGA-ATT
1 CAGGGGTACCGAAGT-ACAAA
*
39755059 CAGGGGTACCGGAGTACAAA
1 CAGGGGTACCGAAGTACAAA
39755079 CAGGGG
1 CAGGGG
39755085 AACAGACATG
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
19 4 0.07
20 53 0.87
21 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.13
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:39756962 original size:43 final size:43
Alignment explanation
Indices: 39756915--39757019 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
39756905 TCCCGGACAG
* * *
39756915 GGTCTTACAGGAAATCATAATACGATGCCAATGTTCC-AAACAT
1 GGTCTTACACGAAATCACAATACAATGCCAATG-TCCTAAACAT
* * * *
39756958 GGTCTTATACGTAATCACAATATAATGCCAATGTCCTAGACAT
1 GGTCTTACACGAAATCACAATACAATGCCAATGTCCTAAACAT
* *
39757001 GGTCTTACATGTAATCACA
1 GGTCTTACACGAAATCACA
39757020 TCTCGATAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.06
43 49 0.94
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGAAATCACAATACAATGCCAATGTCCTAAACAT
Found at i:39772719 original size:31 final size:31
Alignment explanation
Indices: 39772681--39772744 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
39772671 TTCAGTAATA
* *
39772681 TAGGCCCACACACCCATGTGGGTTGCTCGTG
1 TAGGCCCACACACCCATGTGGGTTACCCGTG
* * *
39772712 TAGGCCCAGACGCCCGTGTGGGTTACCCGTG
1 TAGGCCCACACACCCATGTGGGTTACCCGTG
39772743 TA
1 TA
39772745 ACACCCCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (31 bp):
TAGGCCCACACACCCATGTGGGTTACCCGTG
Found at i:39773974 original size:16 final size:16
Alignment explanation
Indices: 39773955--39773985 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39773945 CTTCTTCACT
39773955 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39773971 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39773986 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:39773991 original size:20 final size:20
Alignment explanation
Indices: 39773952--39773991 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39773942 AAACTTCTTC
* *
39773952 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
39773972 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
39773992 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:39774310 original size:53 final size:54
Alignment explanation
Indices: 39774188--39774432 Score: 184
Period size: 55 Copynumber: 4.6 Consensus size: 54
39774178 CTTACCATTT
* * * * * *
39774188 CCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAACTTACCATTG
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTCATCAATG
* * * *
39774237 TCATGTCTTGACATGGTCTTACATGGTATACATGCCTTATG-AACTCATCAATG
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTCATCAATG
* * * *
39774290 CCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATG
1 CCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTCATCAATG
* * * * * * *
39774345 CCATGTCTTGACATGATCTTAGATGATTTCCTTGCCTTA-GAAAC-CTTGCCAATTT
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTCAT--CAA-TG
*
39774400 CCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCATGCCTTGACATGGTCTTACATGGTATCCTT
39774433 AAACCCTAAT
Statistics
Matches: 152, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
49 26 0.17
50 1 0.01
52 2 0.01
53 47 0.31
54 6 0.04
55 68 0.45
56 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
CCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTCATCAATG
Found at i:39781387 original size:40 final size:40
Alignment explanation
Indices: 39781317--39781530 Score: 326
Period size: 40 Copynumber: 5.4 Consensus size: 40
39781307 AAACCAAGTA
* *
39781317 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39781356 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39781396 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39781436 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
39781476 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39781516 CCTTCGGGACTTAGC
1 CCTTCGGGACTTAGC
39781531 TCGGTTATCA
Statistics
Matches: 162, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 15 0.09
40 147 0.91
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39789420 original size:40 final size:40
Alignment explanation
Indices: 39789350--39789567 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
39789340 AAACCAAGTA
* *
39789350 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
39789389 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
39789429 CCTTCGGGACTTAGCCCGGATATAGTAACTCACAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39789469 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
39789509 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39789549 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39789568 TTATCATCCG
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.91
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39795747 original size:102 final size:101
Alignment explanation
Indices: 39795633--39795823 Score: 253
Period size: 101 Copynumber: 1.9 Consensus size: 101
39795623 CAAAAAAAAT
* **
39795633 TAAATTCAGAGTGTGTTGGGTTGAGTAACCGATGAG-AGGTG-TTGTGGTTGTCATTCCACTTTG
1 TAAATTCAGAGTGTGTTGGGCTGAGTAA-CGA-GAGTAGGTGATTG-GGTTGTCATTCCACTACG
39795696 AATCAAAAGGGCCAATACATTCTTAAAAAATAATAATAA
63 AATCAAAAGGGCCAATACATTCTTAAAAAATAATAATAA
** * * *
39795735 TAAATT-AGGAGTGTGTTGGGCTGAGTAATTAGGGTGGGTGATTGGGTTGTCATTCCACTACGCA
1 TAAATTCA-GAGTGTGTTGGGCTGAGTAACGAGAGTAGGTGATTGGGTTGTCATTCCACTACGAA
39795799 TCAAAAGGGCCAATACATTCTTAAA
65 TCAAAAGGGCCAATACATTCTTAAA
39795824 TAGAAATATA
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
100 2 0.03
101 48 0.62
102 28 0.36
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (101 bp):
TAAATTCAGAGTGTGTTGGGCTGAGTAACGAGAGTAGGTGATTGGGTTGTCATTCCACTACGAAT
CAAAAGGGCCAATACATTCTTAAAAAATAATAATAA
Found at i:39799158 original size:31 final size:32
Alignment explanation
Indices: 39799120--39799183 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
39799110 CTCGCTGCAA
* *
39799120 TCTGGTGGCTTCGCCAC-ATATATATATCTGG
1 TCTGGTGGCCTAGCCACAATATATATATCTGG
* *
39799151 TCTGGTGGCCTAGCCACAATATCTGTATCTGG
1 TCTGGTGGCCTAGCCACAATATATATATCTGG
39799183 T
1 T
39799184 GACTTCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGG
Found at i:39805210 original size:33 final size:32
Alignment explanation
Indices: 39805161--39805224 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
39805151 CTCGCTGCAA
* *
39805161 TCTGGTGGCTTCGCCACACATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
39805194 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
39805225 GTGACTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:39805238 original size:27 final size:26
Alignment explanation
Indices: 39805186--39805245 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39805176 ACACATATAT
*
39805186 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
39805212 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
39805239 ATATCTG
1 ATATCTG
39805246 GTAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:39809170 original size:51 final size:52
Alignment explanation
Indices: 39809098--39809204 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 52
39809088 GTCATTATAG
* * *
39809098 ATGTAAGCATTCGAGCTCGTTGAGTGGTCTGAGTTCATAATGGATGCGATAC
1 ATGTAAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGCGATAC
* *
39809150 ATGTAA-CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGTGATAC
1 ATGTAAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGCGATAC
39809201 ATGT
1 ATGT
39809205 TATAAGGTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 44 0.88
52 6 0.12
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (52 bp):
ATGTAAGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGATGCGATAC
Found at i:39811066 original size:20 final size:20
Alignment explanation
Indices: 39811038--39811078 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39811028 CTGAGGACAT
39811038 GGGCATGTCCCAAGCCACAC
1 GGGCATGTCCCAAGCCACAC
*
39811058 GGGCGTGTCCCAAGCCACAC
1 GGGCATGTCCCAAGCCACAC
39811078 G
1 G
39811079 ACCCAACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (20 bp):
GGGCATGTCCCAAGCCACAC
Found at i:39817234 original size:49 final size:50
Alignment explanation
Indices: 39817178--39817355 Score: 198
Period size: 50 Copynumber: 3.6 Consensus size: 50
39817168 ATCTGGTACG
* * **
39817178 CATAGTAGTCTGCACTTAGTACTACACATGCGACC-AATTATCCGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACA
** * *
39817227 TGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACA
* * * * * *
39817277 CATAGTAGCCTGCACTTAGTACTACACACGTC-ATCGAAGCTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACG-CGACCTAA-CCATCCGATACA
39817328 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
39817356 TGTGACCTCA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 30 0.28
50 43 0.39
51 36 0.33
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACA
Found at i:39817637 original size:27 final size:27
Alignment explanation
Indices: 39817607--39817660 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39817597 TCATAAAACC
* *
39817607 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
39817634 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
39817661 TCCCATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:39819219 original size:42 final size:43
Alignment explanation
Indices: 39819115--39819220 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 43
39819105 GAAATCCGAG
** *
39819115 TCGTTGAGTGGT-TCGAGTTCGTGATATATGTGAGAATCTGAAC
1 TCGTTGAGTGGTCT-GAGTTCACGATATATGAGAGAATCTGAAC
* ** * *
39819158 TTGTTGAGTGGTCCAAGTTCACGATATATGAG-GCATCTGAGC
1 TCGTTGAGTGGTCTGAGTTCACGATATATGAGAGAATCTGAAC
*
39819200 TCGTTAAGTGGTCTGAGTTCA
1 TCGTTGAGTGGTCTGAGTTCA
39819221 TTATGGATGC
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (43 bp):
TCGTTGAGTGGTCTGAGTTCACGATATATGAGAGAATCTGAAC
Found at i:39826080 original size:25 final size:25
Alignment explanation
Indices: 39826031--39826131 Score: 82
Period size: 25 Copynumber: 4.0 Consensus size: 25
39826021 TCATGTACAT
39826031 GTATGCTCA-TACGAGCTGT-GAATCG
1 GTATGCTCACT-CGAGCTGTAG-ATCG
*
39826056 GTATGCTCACTCCAGCTGTAGATCG
1 GTATGCTCACTCGAGCTGTAGATCG
* * ** * * *
39826081 ATTTGCTTTCACGAGCTATAAATCG
1 GTATGCTCACTCGAGCTGTAGATCG
39826106 GTATGCTCACAT-GAGCTGTAGATCG
1 GTATGCTCAC-TCGAGCTGTAGATCG
39826131 G
1 G
39826132 AATACTCTCA
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
25 55 0.96
26 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
GTATGCTCACTCGAGCTGTAGATCG
Found at i:39827733 original size:41 final size:40
Alignment explanation
Indices: 39827688--39827856 Score: 135
Period size: 41 Copynumber: 4.2 Consensus size: 40
39827678 GCACAAACAT
*
39827688 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATT-ATAGCACTGGCTCAAAAGC
* * * * * *
39827729 CCTTC-GAGACCAAGCTCGGATTAGACCACTGGCTCGAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATAGCACTGGCTCAAAAGC
* * * *
39827770 CCTTCGGAACTAAGTCCGGTTATAACACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATAGCACTGGCTCAAAAGC
** ** *
39827810 CCTTCTAAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTA-TAGCACTGGCTCAAAAGC
39827851 CCTTCG
1 CCTTCG
39827857 AGACCAAGCT
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
40 40 0.39
41 55 0.54
42 7 0.07
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGAACTAAGCCCGATTATAGCACTGGCTCAAAAGC
Found at i:39827812 original size:40 final size:40
Alignment explanation
Indices: 39827714--39827856 Score: 146
Period size: 41 Copynumber: 3.5 Consensus size: 40
39827704 CGATTCTTAG
* * *
39827714 CACTGGCTCAAAAGCCCTTC-GAGACCAAG-CTCGGATTAGAC
1 CACTGGCTCAAAAGCCCTTCGGA-ACTAAGTC-CGG-TTATAA
* *
39827755 CACTGGCTCGAAGGCCCTTCGGAACTAAGTCCGGTTATAA
1 CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTATAA
* ** * *
39827795 CACTGGCTCTAAAGCCCTTCTAAACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTA-TAA
39827836 CACTGGCTCAAAAGCCCTTCG
1 CACTGGCTCAAAAGCCCTTCG
39827857 AGACCAAGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 36 0.42
41 47 0.55
42 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTATAA
Found at i:39834818 original size:37 final size:37
Alignment explanation
Indices: 39834759--39834863 Score: 183
Period size: 37 Copynumber: 2.8 Consensus size: 37
39834749 AGCTCAGACG
* *
39834759 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
39834796 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
39834833 TAATCTCCACACGTAGTCATCGGGTCTTACC
1 AAATCTCCACACGTAGTCATCGGGTCTTACC
39834864 TGGAATATAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:39835148 original size:47 final size:47
Alignment explanation
Indices: 39835069--39835262 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
39835059 CATATATATT
* * * *
39835069 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
39835116 CCACATTGGCCATTCGACCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
39835163 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
39835210 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
39835257 TCACAT
1 TCACAT
39835263 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:39835189 original size:22 final size:22
Alignment explanation
Indices: 39835162--39835233 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
39835152 GCTCACATTC
39835162 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
39835184 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
39835208 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
39835231 ATC
1 ATC
39835234 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:39854805 original size:39 final size:39
Alignment explanation
Indices: 39854747--39854847 Score: 98
Period size: 40 Copynumber: 2.6 Consensus size: 39
39854737 ACCCAATTTT
*
39854747 CTTCGGGAT-TTAGCCGGATATAACCACCCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCGGATATAACCACCAGCACAAAGGC
*** * *
39854785 CTTCGGGTCTTAGTCCGGATATGGTCACTAGCACAAATGC
1 CTTCGGGTCTTAG-CCGGATATAACCACCAGCACAAAGGC
*
39854825 CTTCGGGACTTAGCCCGGATATA
1 CTTCGGGTCTTAG-CCGGATATA
39854848 GTAACTCGCA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 1 0.02
38 11 0.22
39 15 0.29
40 24 0.47
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (39 bp):
CTTCGGGTCTTAGCCGGATATAACCACCAGCACAAAGGC
Found at i:39854837 original size:40 final size:40
Alignment explanation
Indices: 39854775--39854996 Score: 279
Period size: 40 Copynumber: 5.6 Consensus size: 40
39854765 TATAACCACC
* * * * *
39854775 CGCAC-AAGGCCTTCGGGTCTTAGTCCGG-ATATGGTCACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACT
*
39854814 AGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACT
* *
39854854 CGCACAAATGCCTTTGGGGCTTAGCCCGGAATTAGTAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
39854894 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
* * *
39854934 CGCACAAATGCCTTCGAGACTTAGCCCGGAATTAATCACT
1 CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
* * *
39854974 AGCACAAATGTCTTTGGGACTTA
1 CGCACAAATGCCTTCGGGACTTA
39854997 ACCCCGTTAG
Statistics
Matches: 163, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
39 4 0.02
40 157 0.96
41 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACT
Found at i:39859100 original size:39 final size:40
Alignment explanation
Indices: 39859041--39859242 Score: 259
Period size: 40 Copynumber: 5.1 Consensus size: 40
39859031 CGGATGATAA
* *
39859041 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
39859081 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39859120 CCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39859160 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
39859199 CCGGGCTATGTCCAGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
39859239 CCGG
1 CCGG
39859243 TTAAATTCTG
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
39 70 0.49
40 72 0.51
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39859148 original size:40 final size:40
Alignment explanation
Indices: 39859037--39859230 Score: 259
Period size: 39 Copynumber: 4.9 Consensus size: 40
39859027 TATTCGGATG
* *
39859037 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
39859077 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
39859116 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
39859156 ATATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
39859195 ATAACCGGGCTATGTCCAGAAGGCATTCGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
39859231 AGCTATATCC
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 69 0.51
40 66 0.49
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:39859168 original size:79 final size:79
Alignment explanation
Indices: 39859037--39859242 Score: 317
Period size: 79 Copynumber: 2.6 Consensus size: 79
39859027 TATTCGGATG
* * * *
39859037 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGCCCGAAGGCA
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATA-TCCGGGCTAAGCCCGAAGGCA
*
39859101 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACC
39859116 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCGAAGGCAT
39859181 TTGTGCGAGTTACC
66 TTGTGCGAGTTACC
* *
39859195 ATAACCGGGCTATGTCCAGAAGGCATTCGAGCGAG-TAGCTATATCCGG
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTA-CTATATCCGG
39859243 TTAAATTCTG
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
78 2 0.02
79 115 0.97
80 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (79 bp):
ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACC
Found at i:39867164 original size:40 final size:40
Alignment explanation
Indices: 39867109--39867312 Score: 250
Period size: 40 Copynumber: 5.1 Consensus size: 40
39867099 TAGATGATAA
* * *
39867109 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
39867149 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
39867189 CCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39867229 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACCATAA
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * * *
39867269 CCGGGCTATGTCCAGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTA-CTATAT
39867309 CCGG
1 CCGG
39867313 TTAAATTCTG
Statistics
Matches: 142, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
39 2 0.01
40 139 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39867238 original size:80 final size:80
Alignment explanation
Indices: 39867105--39867312 Score: 321
Period size: 80 Copynumber: 2.6 Consensus size: 80
39867095 TATTTAGATG
* * * *
39867105 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGCCCCGAAGGC
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATA-TCCGGGCTAAGCCCCGAAGGC
*
39867169 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACC
39867185 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
39867250 TTTGTGCGAGTTACC
66 TTTGTGCGAGTTACC
* *
39867265 ATAACCGGGCTATGTCCAGAAGGCATTCGAGCGAG-TAGCTATATCCGG
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTA-CTATATCCGG
39867313 TTAAATTCTG
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
79 2 0.02
80 116 0.97
81 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
TTTGTGCGAGTTACC
Found at i:39876498 original size:6 final size:6
Alignment explanation
Indices: 39876471--39876544 Score: 89
Period size: 6 Copynumber: 12.5 Consensus size: 6
39876461 TCCTCCTATT
* *
39876471 TTTTTA TTATTTA CTCTTA TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
39876518 TTTTTC TTTTGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
39876545 CAATTTTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
5 10 0.17
6 43 0.74
7 5 0.09
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:39876501 original size:5 final size:5
Alignment explanation
Indices: 39876491--39876564 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 5
39876481 TTACTCTTAT
*
39876491 TTTTA TTTTA TTTTA TTTTTA TTTTTA TTTTTC TTTTGA TTTTTA TTTTTA
1 TTTTA TTTTA TTTTA -TTTTA -TTTTA -TTTTA TTTT-A -TTTTA -TTTTA
*
39876542 TTTCAA TTTTA --TTA TTTTA TTTT
1 TTT-TA TTTTA TTTTA TTTTA TTTT
39876565 GAAAGACATA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
3 3 0.05
5 25 0.42
6 27 0.46
7 4 0.07
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:39876541 original size:41 final size:41
Alignment explanation
Indices: 39876470--39876564 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
39876460 ATCCTCCTAT
* *
39876470 TTTTTTATTATTTACTCTTATTTTTATTTTATTTTATTTTTA
1 TTTTTTATT-TTTACTCTTATTTTTATTTTATTTCAATTTTA
*
39876512 -TTTTTATTTTT-CTTTTGATTTTTATTTTTATTTCAATTTTA
1 TTTTTTATTTTTACTCTT-ATTTTTA-TTTTATTTCAATTTTA
39876553 TTATTTTATTTT
1 TT-TTTTATTTT
39876565 GAAAGACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
39 4 0.09
40 10 0.22
41 22 0.48
42 1 0.02
43 9 0.20
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (41 bp):
TTTTTTATTTTTACTCTTATTTTTATTTTATTTCAATTTTA
Done.