Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1672
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: 67475
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3029 original size:8 final size:8
Alignment explanation
Indices: 3016--3066 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
3006 CCTTAGTACA
3016 AAAAAAAC
1 AAAAAAAC
3024 AAAAAAAAAC
1 --AAAAAAAC
3034 AAAAACAAAC
1 -AAAA-AAAC
3044 AAAAAAAC
1 AAAAAAAC
*
3052 AAACAAAC
1 AAAAAAAC
3060 AAAAAAA
1 AAAAAAA
3067 GGGTCCAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 17 0.45
9 9 0.24
10 12 0.32
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:3030 original size:10 final size:10
Alignment explanation
Indices: 3015--3065 Score: 66
Period size: 10 Copynumber: 4.8 Consensus size: 10
3005 TCCTTAGTAC
3015 AAAAAAAACA
1 AAAAAAAACA
3025 AAAAAAAACA
1 AAAAAAAACA
*
3035 AAAACAAACAA
1 AAAAAAAAC-A
3046 AAAAACAAACA
1 AAAAA-AAACA
3057 AACAAAAAA
1 AA-AAAAAA
3066 AGGGTCCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 18 0.50
11 11 0.31
12 7 0.19
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:3039 original size:16 final size:16
Alignment explanation
Indices: 3015--3066 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
3005 TCCTTAGTAC
3015 AAAAAAAACAAA-AAA
1 AAAAAAAACAAACAAA
3030 AAACAAAAACAAACAAA
1 AAA-AAAAACAAACAAA
*
3047 AAAACAAACAAACAAA
1 AAAAAAAACAAACAAA
3063 AAAA
1 AAAA
3067 GGGTCCAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 3 0.09
16 25 0.74
17 6 0.18
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAACAAA
Found at i:4103 original size:26 final size:26
Alignment explanation
Indices: 4074--4123 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4064 ATAGCATTCT
*
4074 GCATCATATATTCATAATATCATCTC
1 GCATCATACATTCATAATATCATCTC
4100 GCATCATACATTCATAATATCATC
1 GCATCATACATTCATAATATCATC
4124 ATACATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (26 bp):
GCATCATACATTCATAATATCATCTC
Found at i:4130 original size:26 final size:26
Alignment explanation
Indices: 4075--4132 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
4065 TAGCATTCTG
* *
4075 CATCATATATTCATAATATCATCTCG
1 CATCATACATTCATAATATCATCTCA
4101 CATCATACATTCATAATATCATCAT-A
1 CATCATACATTCATAATATCATC-TCA
4127 CATCAT
1 CATCAT
4133 TTTTTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (26 bp):
CATCATACATTCATAATATCATCTCA
Found at i:4324 original size:13 final size:14
Alignment explanation
Indices: 4293--4325 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4283 TAATTTGCCA
4293 TTTGTCAAGAAACT
1 TTTGTCAAGAAACT
*
4307 ATTGTCAA-AAACT
1 TTTGTCAAGAAACT
4320 TTTGTC
1 TTTGTC
4326 TATAACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (14 bp):
TTTGTCAAGAAACT
Found at i:4372 original size:28 final size:28
Alignment explanation
Indices: 4341--4915 Score: 633
Period size: 28 Copynumber: 20.5 Consensus size: 28
4331 CATTCATCTC
* *
4341 TTCAAAGCCCATAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4369 TTCAAAGCCCACAAGTTAGT-GCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
4396 TTCAAAGCCCACAAGTTTGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4424 TTCAAAGCCCATAAGTCAGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
4452 TTCAAAAACCATAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4479 CTTCAAAAGACCACAAGTCAATGGCA-CCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* * *
4508 TTTAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4536 TTCAAAGCCCACAAGTCAGT-GCTACCCC
1 TTCAAAGCCCACAAGTCAGTGGC-ATCCT
* * *
4564 TTCAAAGCCCACAAGTTAGTGGCACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
4592 TTCAAAATCCACAAGTTAGTGGCATAACCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
4622 TTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
4650 TTCAAAGGCCATAAATCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4678 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
4706 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4734 TTCAAAGCCCAC-A-T-AGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * **
4759 TTCAAAGCCCACAAGTTAGTGGCTTTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
4787 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
4815 TTCAAAGCCCACAAGTTGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
4843 TTCAAAGCCCACACAGGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA-A-GTCAGTGGC-A-TCCT
*
4875 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
4903 TTCAAAGCCCACA
1 TTCAAAGCCCACA
4916 TAACTTAGTG
Statistics
Matches: 478, Mismatches: 53, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
25 22 0.05
26 2 0.00
27 51 0.11
28 324 0.68
29 24 0.05
30 38 0.08
31 2 0.00
32 15 0.03
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:4865 original size:223 final size:224
Alignment explanation
Indices: 4340--4915 Score: 723
Period size: 223 Copynumber: 2.6 Consensus size: 224
4330 ACATTCATCT
* * * * *
4340 CTTCAAAGCCCATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGT-GCATCTTTTCAAAGC
1 CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGC
** * * ** *
4404 CCACAAGTTTGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGTATCCTTTCAAAAACCATAAGTC
66 CCACAAGTCGGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC
*
4469 AGTGGCATCTCTTCAAAAGACCACAAGTCAATGGCACCTTTTAAAGCCCACAAGTCAATGGCACC
131 AGTGGCATCTCTTCAAAAGACCACAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAATGGCACC
4534 CTTTCAAAGCCCACAAGTCAGTGCTACCC
196 CTTTCAAAGCCCACAAGTCAGTGCTACCC
* * **
4563 CTTCAAAGCCCACAAGTTAGTGGCACCCCTTCAAAATCCACAAGTTAGTGGCATAACCTTTCAAA
1 CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC--AACCTTTCAAA
* * *
4628 GCCCACAAGTCGGTGGCACCCTTTCAAAGGCCATAAATCAGTGGCATCCTTTCAAAGCCCACAAG
64 GCCCACAAGTCGGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
4693 TCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC-A-T-AGTGGC
129 TCAGTGGCATCTCTTCAAAAGACCACAAGTCAATGGCA-CCTTTCAAAGCCCACAAGTCAATGGC
* * * ***
4754 ATCTTTTCAAAGCCCACAAGTTAGTGGCT-TTT
193 ACCCTTTCAAAGCCCACAAGTCAGT-GCTACCC
* * *
4786 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTGGTGGCACCCTTTCAAAGC
1 CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGC
* *
4851 CCACACAGGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACA
66 CCACA-A-GTCGGTGGC-AC-CTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACA
4916 TAACTTAGTG
Statistics
Matches: 302, Mismatches: 42, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
221 17 0.06
222 1 0.00
223 124 0.41
224 8 0.03
225 59 0.20
226 93 0.31
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (224 bp):
CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGC
CCACAAGTCGGTGGCACCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC
AGTGGCATCTCTTCAAAAGACCACAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAATGGCACC
CTTTCAAAGCCCACAAGTCAGTGCTACCC
Found at i:5087 original size:46 final size:46
Alignment explanation
Indices: 5015--5127 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 46
5005 CCTGGTATTA
* * * * *
5015 AATCAGCATATTG-GCACCTTTATTAGCTCAATGCCGCTGGCCTTG
1 AATCAGCACATTGTCCACCTTTTTTAGCTCAATGCCACTGGCCCTG
*
5060 AATCAGCACATTGTCCACCTTTTTTAGCTCAATGTCACTGGCCCTG
1 AATCAGCACATTGTCCACCTTTTTTAGCTCAATGCCACTGGCCCTG
*
5106 AATTAGCACATTGTCCA-CTTTT
1 AATCAGCACATTGTCCACCTTTT
5128 CCCTTAGCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 17 0.28
46 43 0.72
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (46 bp):
AATCAGCACATTGTCCACCTTTTTTAGCTCAATGCCACTGGCCCTG
Found at i:5163 original size:48 final size:46
Alignment explanation
Indices: 5029--5166 Score: 143
Period size: 46 Copynumber: 3.0 Consensus size: 46
5019 AGCATATTGG
* * * * *
5029 CACCTTTATTAGCTCAATGCCGCTGGCCTTGAATCAGCACATTGTC
1 CACCTTTTTTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTC
* *
5075 CACCTTTTTTAGCTCAATGTCACTGGCCCTGAATTAGCACATTGTC
1 CACCTTTTTTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTC
* ** *
5121 CA-CTTTTCCCTTAGCTCGATGTTGCTAGCCTTGAATTGGCACATTG
1 CACCTTTT---TTAGCTCAATGTCACTAGCCTTGAATTAGCACATTG
5167 GCACTCCTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 5 0.06
46 43 0.55
48 30 0.38
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (46 bp):
CACCTTTTTTAGCTCAATGTCACTAGCCTTGAATTAGCACATTGTC
Found at i:5959 original size:20 final size:20
Alignment explanation
Indices: 5934--6098 Score: 102
Period size: 20 Copynumber: 7.8 Consensus size: 20
5924 TTTTACCTAG
*
5934 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* * * *
5954 ATGTATCAATACATGCATGA
1 ATGTATCGATACATTCTTCA
*
5974 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCTTCA
5994 ATGTATCGATACATTCTGTCTTTTTTCCCAA
1 ATGTATCGATACA---T-TC----TT--C-A
* **
6025 ATGTATCAATACA---TAAA
1 ATGTATCGATACATTCTTCA
* * *
6042 ATGTATCGATACATGCATGA
1 ATGTATCGATACATTCTTCA
6062 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
6082 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
6099 GTTTTTTCTC
Statistics
Matches: 110, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
17 13 0.12
20 78 0.71
23 1 0.01
24 2 0.02
28 2 0.02
30 1 0.01
31 13 0.12
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:6045 original size:17 final size:17
Alignment explanation
Indices: 6023--6055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6013 CTTTTTTCCC
6023 AAATGTATCAATACATA
1 AAATGTATCAATACATA
*
6040 AAATGTATCGATACAT
1 AAATGTATCAATACAT
6056 GCATGAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
AAATGTATCAATACATA
Found at i:6079 original size:88 final size:87
Alignment explanation
Indices: 5903--6124 Score: 320
Period size: 88 Copynumber: 2.5 Consensus size: 87
5893 TTTTACTCAG
* * **
5903 ATGTATCGATACATTCTGTTTTTTTACCTAGATGTATCGATACATTTTTCAATGTATCAATACAT
1 ATGTATCGATACATTCTGTTTTTTT-CCCAGATGTATCAATACA---TAAAATGTATCAATACAT
*
5968 GCATGAATGTATCGATATATTCTTCA
62 GCATGAATGTATCGATACATTCTTCA
* *
5994 ATGTATCGATACATTCTGTCTTTTTTCCCAAATGTATCAATACATAAAATGTATCGATACATGCA
1 ATGTATCGATACATTCTGT-TTTTTTCCCAGATGTATCAATACATAAAATGTATCAATACATGCA
6059 TGAATGTATCGATACATTCTTCA
65 TGAATGTATCGATACATTCTTCA
*
6082 ATGTATCGATACATTCTG-TTTTTTCTCAGATGTATCAATACAT
1 ATGTATCGATACATTCTGTTTTTTTCCCAGATGTATCAATACAT
6125 TTTTTTATGT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
86 23 0.19
88 58 0.48
91 34 0.28
92 6 0.05
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (87 bp):
ATGTATCGATACATTCTGTTTTTTTCCCAGATGTATCAATACATAAAATGTATCAATACATGCAT
GAATGTATCGATACATTCTTCA
Found at i:8357 original size:26 final size:27
Alignment explanation
Indices: 8298--8364 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
8288 TATCAGGGCC
8298 ACTCCAACCCCATTCCTCCAAAGGGAT
1 ACTCCAACCCCATTCCTCCAAAGGGAT
8325 ACTCCAACCCCATTCCTCCAAA-GGAT
1 ACTCCAACCCCATTCCTCCAAAGGGAT
8351 ACTCCAACCCCATT
1 ACTCCAACCCCATT
8365 TTTCAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 18 0.45
27 22 0.55
ACGTcount: A:0.30, C:0.43, G:0.07, T:0.19
Consensus pattern (27 bp):
ACTCCAACCCCATTCCTCCAAAGGGAT
Found at i:11597 original size:10 final size:10
Alignment explanation
Indices: 11584--11608 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11574 TTTTGATGCA
11584 TTTTCTACCT
1 TTTTCTACCT
11594 TTTTCTACCT
1 TTTTCTACCT
11604 TTTTC
1 TTTTC
11609 ATATATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTCTACCT
Found at i:15284 original size:409 final size:409
Alignment explanation
Indices: 14525--15342 Score: 1573
Period size: 409 Copynumber: 2.0 Consensus size: 409
14515 ATGTAAAGCC
*
14525 TTAGACCGAATTTGAGATAATTTATACAACTATCTAATGAAACAAATCAAACTCTTTTCGAAACG
1 TTAGACCGAATTTGAGATAATCTATACAACTATCTAATGAAACAAATCAAACTCTTTTCGAAACG
14590 TTCAAATATCTTTAAAAACGTAACAAAATTATGAATAGTAAACTCGTCCTTTTATGCCTGGAATT
66 TTCAAATATCTTTAAAAACGTAACAAAATTATGAATAGTAAACTCGTCCTTTTATGCCTGGAATT
14655 CTAATCTACCGATTAGTCCAGATAACATAATTGCTTGCCCTTGGATGTCTGCTACGATAAATAGT
131 CTAATCTACCGATTAGTCCAGATAACATAATTGCTTGCCCTTGGATGTCTGCTACGATAAATAGT
14720 GAAATGGTGCTACAGGTACTGGAGTTGTCCTGCCTAGAGATGTCATCCTTGTCAAGCGTCCTTTA
196 GAAATGGTGCTACAGGTACTGGAGTTGTCCTGCCTAGAGATGTCATCCTTGTCAAGCGTCCTTTA
14785 TCATTCTCCTGGGTGTACCTAAGCAGTGGTCCCATGATAAAAGTCCGTTACGCGTGCTTAGTGTT
261 TCATTCTCCTGGGTGTACCTAAGCAGTGGTCCCATGATAAAAGTCCGTTACGCGTGCTTAGTGTT
* * *
14850 GGTTGTCGGGACCTAGACTAGTCGCACTCGAGTGTGACAAGCTGCTGAATATTAAGAAAAGACTA
326 AGTTATCGGGACCTAGACTAGTCGCACGCGAGTGTGACAAGCTGCTGAATATTAAGAAAAGACTA
14915 AGAAACAAGCAAAAATGAT
391 AGAAACAAGCAAAAATGAT
14934 TTAGACCGAATTTGAGATAATCTATACAACTATCTAATGAAACAAATCAAACTCTTTTCGAAACG
1 TTAGACCGAATTTGAGATAATCTATACAACTATCTAATGAAACAAATCAAACTCTTTTCGAAACG
*
14999 TTCAAATATCTTTAAAAACGTAACAAAATTATGAATAGTAAACTCGTCCTTTTATGCCTGGGATT
66 TTCAAATATCTTTAAAAACGTAACAAAATTATGAATAGTAAACTCGTCCTTTTATGCCTGGAATT
15064 CTAATCTACCGATTAGTCCAGATAACATAATTGCTTGCCCTTGGATGTCTGCTACGATAAATAGT
131 CTAATCTACCGATTAGTCCAGATAACATAATTGCTTGCCCTTGGATGTCTGCTACGATAAATAGT
15129 GAAATGGTGCTACAGGTACTGGAGTTGTCCTGCCTAGAGATGTCATCCTTGTCAAGCGTCCTTTA
196 GAAATGGTGCTACAGGTACTGGAGTTGTCCTGCCTAGAGATGTCATCCTTGTCAAGCGTCCTTTA
* *
15194 TCATTCTCTTGGGTGTACCTAAGCAGTGGTCCCATGATAAAAGTCCTTTACGCGTGCTTAGTGTT
261 TCATTCTCCTGGGTGTACCTAAGCAGTGGTCCCATGATAAAAGTCCGTTACGCGTGCTTAGTGTT
15259 AGTTATCGGGACCTAGACTAGTCGCACGCGAGTGTGACAAGCTGCTGAATATTAAGAAAAGACTA
326 AGTTATCGGGACCTAGACTAGTCGCACGCGAGTGTGACAAGCTGCTGAATATTAAGAAAAGACTA
15324 AGAAACAAGCAAAAATGAT
391 AGAAACAAGCAAAAATGAT
15343 AAATTACAAA
Statistics
Matches: 402, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
409 402 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (409 bp):
TTAGACCGAATTTGAGATAATCTATACAACTATCTAATGAAACAAATCAAACTCTTTTCGAAACG
TTCAAATATCTTTAAAAACGTAACAAAATTATGAATAGTAAACTCGTCCTTTTATGCCTGGAATT
CTAATCTACCGATTAGTCCAGATAACATAATTGCTTGCCCTTGGATGTCTGCTACGATAAATAGT
GAAATGGTGCTACAGGTACTGGAGTTGTCCTGCCTAGAGATGTCATCCTTGTCAAGCGTCCTTTA
TCATTCTCCTGGGTGTACCTAAGCAGTGGTCCCATGATAAAAGTCCGTTACGCGTGCTTAGTGTT
AGTTATCGGGACCTAGACTAGTCGCACGCGAGTGTGACAAGCTGCTGAATATTAAGAAAAGACTA
AGAAACAAGCAAAAATGAT
Found at i:15711 original size:14 final size:15
Alignment explanation
Indices: 15694--15722 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
15684 TTTAATATAT
15694 AATTTAAA-AAATAA
1 AATTTAAATAAATAA
15708 AATTTAAATAAATAA
1 AATTTAAATAAATAA
15723 GGCATATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTTAAATAAATAA
Found at i:15842 original size:13 final size:13
Alignment explanation
Indices: 15826--15852 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15816 AATAAATATA
15826 AAAATAATATAAT
1 AAAATAATATAAT
15839 AAAATAATATAAT
1 AAAATAATATAAT
15852 A
1 A
15853 TTTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:15866 original size:33 final size:33
Alignment explanation
Indices: 15824--15888 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
15814 TTAATAAATA
15824 TAAAAATAATATAATAAAATA-ATATAATATTTT
1 TAAAAATAAT-TAATAAAATATATATAATATTTT
* * *
15857 TAAATATAATTAATATAATATATATCATATTT
1 TAAAAATAATTAATAAAATATATATAATATTT
15889 ATATTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAAAATAATTAATAAAATATATATAATATTTT
Found at i:15907 original size:44 final size:42
Alignment explanation
Indices: 15854--15936 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 42
15844 AATATAATAT
15854 TTTTAAATATAATTAATATAATATATATCATATTTATATTTAAAA
1 TTTTAAATAT-ATTAA-ATAATATATATCAT-TTTATATTTAAAA
* * *
15899 TTTT-AATATATTTAATAATTTATATTATTTTATATTTA
1 TTTTAAATATATTAAATAATATATATCATTTTATATTTA
15937 TAAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 10 0.29
42 12 0.34
43 4 0.11
44 5 0.14
45 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (42 bp):
TTTTAAATATATTAAATAATATATATCATTTTATATTTAAAA
Found at i:15927 original size:17 final size:18
Alignment explanation
Indices: 15888--15938 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
15878 ATATCATATT
15888 TATATTTAA-AATTT-TAA
1 TATATTTAATAATTTAT-A
15905 TATATTTAATAATTTATA
1 TATATTTAATAATTTATA
*
15923 T-TATTTTAT-ATTTATA
1 TATATTTAATAATTTATA
15939 AAAATATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 7 0.23
17 16 0.52
18 7 0.23
19 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTAATAATTTATA
Found at i:16390 original size:23 final size:26
Alignment explanation
Indices: 16345--16395 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
16335 TATTTTTTGA
16345 TATTAAAAATTATAATATATTAATAT
1 TATTAAAAATTATAATATATTAATAT
16371 TATTAAAAATT-TAAT-T-TTAATAT
1 TATTAAAAATTATAATATATTAATAT
16394 TA
1 TA
16396 AACATAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.36
24 1 0.04
25 4 0.16
26 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTAAAAATTATAATATATTAATAT
Found at i:24255 original size:22 final size:25
Alignment explanation
Indices: 24210--24258 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 25
24200 TTAATTCAGT
24210 TATATATATATTAATTTTGATATTAA
1 TATATATATATTAATTTT-ATATTAA
24236 TATAT-TATATT-ATTTT-TATTAA
1 TATATATATATTAATTTTATATTAA
24258 T
1 T
24259 TAATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.30
24 5 0.22
25 6 0.26
26 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TATATATATATTAATTTTATATTAA
Found at i:33354 original size:52 final size:52
Alignment explanation
Indices: 33276--33406 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
33266 CTCGAAATAT
* * * *
33276 GAAAATTTACTTGCATGTATCGATACATTTAATAGTTTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
*
33328 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
*
33380 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
33407 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
Found at i:33419 original size:52 final size:51
Alignment explanation
Indices: 33276--33426 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 51
33266 CTCGAAATAT
* * *
33276 GAAAATTTACTTGCATGTATCGATACATTTAATAGTTTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
* *
33328 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
* *
33380 GCAAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
33427 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (51 bp):
GAAAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGG
Found at i:33433 original size:13 final size:13
Alignment explanation
Indices: 33415--33439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33405 CAAAGATCAG
33415 TGTATCGATACAA
1 TGTATCGATACAA
33428 TGTATCGATACA
1 TGTATCGATACA
33440 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:33520 original size:13 final size:13
Alignment explanation
Indices: 33502--33526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33492 CAAAAAAATA
33502 TGTATCGATACAT
1 TGTATCGATACAT
33515 TGTATCGATACA
1 TGTATCGATACA
33527 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:34781 original size:33 final size:33
Alignment explanation
Indices: 34725--34789 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
34715 TACAAGCCAA
* *
34725 TGTATCGATACAATTTTTTGTGTATCAATACAT
1 TGTATCGATACAATCTTTGGTGTATCAATACAT
*
34758 TGTATCGATAC-ATACTTTGGTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCAATACA
34790 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCAATACAT
Found at i:36899 original size:21 final size:20
Alignment explanation
Indices: 36870--36912 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
36860 GGCTAGTATG
*
36870 GGGACTGCCCCGTTGCGACCT
1 GGGACTG-CCCGTCGCGACCT
* *
36891 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCCGTCGCGACCT
36911 GG
1 GG
36913 TGGTGCTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.33, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCCGTCGCGACCT
Found at i:43554 original size:20 final size:20
Alignment explanation
Indices: 43529--43593 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
43519 TACAAGCCAA
43529 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
43549 TGTATCGATAC-A-----T-
1 TGTATCGATACAATTTTTTG
43562 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
43582 TGTATCGATACA
1 TGTATCGATACA
43594 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 2 0.05
19 2 0.05
20 23 0.61
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATTTTTTG
Found at i:43567 original size:13 final size:13
Alignment explanation
Indices: 43549--43607 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
43539 CAATTTTTTG
43549 TGTATCGATACAT
1 TGTATCGATACAT
43562 TGTATCGATACAATTTTTT
1 TGTATCGATAC-A-----T
43581 GTGTATCGATACAT
1 -TGTATCGATACAT
43595 TGTATCGATACAT
1 TGTATCGATACAT
43608 ACTTTGGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 24 0.62
14 2 0.05
19 2 0.05
20 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43571 original size:33 final size:33
Alignment explanation
Indices: 43529--43626 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
43519 TACAAGCCAA
43529 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
43562 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
* *
43595 TGTATCGATAC-ATACTTTGGTGTATCGATACA
1 TGTATCGATACAAT-TTTTTGTGTATCGATACA
43627 AGTTTGGCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 2 0.03
33 60 0.97
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACAATTTTTTGTGTATCGATACAT
Found at i:44424 original size:49 final size:49
Alignment explanation
Indices: 44257--44961 Score: 762
Period size: 49 Copynumber: 14.8 Consensus size: 49
44247 CAAAAAATGA
* * ** * * **
44257 CAATGTGCTGATTCATGGCCAGCGACATTTAAACTTGAAGA-AAAAATGC
1 CAATGTGCTGATTCAAGGCCAGCTACA-TTGGACTTAAAGATGAAGGTGC
** * * **
44306 CAATGTGCTGAGGCAAGGCCAGCAACATCGGGTTTTAAAAATGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACAT-TGGACTT--AAA-GATGAAGGTGC
* * **
44359 CAATATGCTGATTCAAGGCCAGCGATGTTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
44408 CAATGTGCTAAATCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
44457 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
44500 CAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
44548 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
44597 CAATGTGCTAAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
44646 CAATATGCTGATTCAAGGCTAGTTATATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
44689 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
44732 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
44780 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
44829 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
44872 CAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGAAGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
44921 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA-AAGA
44962 GTTGCCACCG
Statistics
Matches: 560, Mismatches: 70, Indels: 51
0.82 0.10 0.07
Matches are distributed among these distances:
43 154 0.28
44 1 0.00
45 3 0.01
47 1 0.00
48 92 0.16
49 267 0.48
50 7 0.01
51 2 0.00
52 6 0.01
53 27 0.05
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:44628 original size:189 final size:187
Alignment explanation
Indices: 44353--44961 Score: 938
Period size: 189 Copynumber: 3.2 Consensus size: 187
44343 AAAATGATGA
* **
44353 AGGTGCCAATATGCTGATTCAAGGCCAGCGATGTTGGACTTAAAGATGAAGGTGCCAATGTGCTA
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTA
*
44418 AATCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
66 AATCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
*
44483 ATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTG
131 ATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA-G-G
*
44542 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTA
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTA
* * *
44607 AGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCTAGTTAT
66 AATCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
*
44672 ATTAGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA--
131 ATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGG
* * * * *
44726 AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATATGCTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTA
* *
44790 ATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
66 AATCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
* * *
44855 ATTGGACTTAGAGGTGCCAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGAAG
131 ATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG--G
* *
44914 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGA
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA-AAGA
44962 GTTGCCACCG
Statistics
Matches: 386, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
183 123 0.32
184 48 0.12
188 2 0.01
189 210 0.54
190 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (187 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTA
AATCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTAT
ATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGG
Found at i:44756 original size:232 final size:234
Alignment explanation
Indices: 44303--44956 Score: 874
Period size: 232 Copynumber: 2.8 Consensus size: 234
44293 GAAGAAAAAA
** * * **
44303 TGCCAATGTGCTGAGGCAAGGCCAGCAACATCGGGTTTTAAAAATGATGAAGGTGCCAATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACAT-TGGACTT--AAA-GATGAAGGTGCCAATATGCT
* * *
44368 GATTCAAGGCCAGCGATGTTGGACTTAAAGATGAAGGTGCCAATGTGCTAAATCAAGGCCAGCTA
62 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
* * *
44433 CATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
127 CATTAGACTT----ATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGT
44498 GCCAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTGAGG
188 GCCAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTGAGG
* * *
44545 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTAAGT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * * * *
44610 CAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCTAGTTATATT
66 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
*
44675 AGAC-T-TAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGT
131 AGACTTATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGT
*
44738 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGG
196 GCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTGAGG
*
44777 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
*
44842 CAAGGCCAGCGATATTGGACTT----A-G-AGGTGCCAATGTGCTGATTCAAGGCCAACTACATT
66 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
* * * * *
44901 GGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
131 AGACTT--A-TA-AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTA
44957 GAAGAGTTGC
Statistics
Matches: 366, Mismatches: 40, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
226 33 0.09
227 2 0.01
228 1 0.00
231 1 0.00
232 213 0.58
237 1 0.00
238 80 0.22
239 3 0.01
241 4 0.01
242 28 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (234 bp):
TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
AGACTTATAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGT
GCTGAGTCAAGGCCAGCTACATTAGACTTAAAGGTGAGG
Found at i:45001 original size:33 final size:33
Alignment explanation
Indices: 44956--45124 Score: 265
Period size: 33 Copynumber: 5.2 Consensus size: 33
44946 TATTGGGCTT
*
44956 AGAAGAGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
44989 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
45022 AG-AGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
45054 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
45087 -GAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
45118 GGAAGGG
1 AGAAGGG
45125 AGAAAGATGC
Statistics
Matches: 127, Mismatches: 5, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
31 4 0.03
32 60 0.47
33 62 0.49
34 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:45038 original size:65 final size:65
Alignment explanation
Indices: 44949--45116 Score: 272
Period size: 65 Copynumber: 2.6 Consensus size: 65
44939 CCAGCTATAT
*
44949 TGGGC-TTAGA-AGAGTTGCCACCGACTTGTGTGGGCTTTAG-AGAATGGTTGCCACCAACTTGT
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAA-GGTTGCCACCAACTTGT
45011 G
65 G
*
45012 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
45077 TGGGCTTTAG-GAAGGGTTGCCACCGACTTGTGTGGGCTTT
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTGTGGGCTTT
45117 GGGAAGGGAG
Statistics
Matches: 99, Mismatches: 2, Indels: 6
0.93 0.02 0.06
Matches are distributed among these distances:
63 5 0.05
64 6 0.06
65 84 0.85
66 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (65 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
Found at i:45124 original size:32 final size:31
Alignment explanation
Indices: 44949--45116 Score: 248
Period size: 32 Copynumber: 5.3 Consensus size: 31
44939 CCAGCTATAT
*
44949 TGGGC-TTAGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
* *
44979 TGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTT--AGAAGGGTTGCCACCGACTTGTG
45012 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
45044 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTG
45077 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
45109 TGGGCTTT
1 TGGGCTTT
45117 GGGAAGGGAG
Statistics
Matches: 126, Mismatches: 5, Indels: 12
0.88 0.03 0.08
Matches are distributed among these distances:
30 5 0.04
31 7 0.06
32 55 0.44
33 55 0.44
34 4 0.03
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:45165 original size:34 final size:34
Alignment explanation
Indices: 45127--45405 Score: 321
Period size: 34 Copynumber: 8.1 Consensus size: 34
45117 GGGAAGGGAG
* *
45127 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAA
* *
45161 AAAGAGTGCCACGGAGTTGTGGGTTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
45196 ACAGGCGCCACGGAGTTGTGGGCTTTGAAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT--AAAAGGAA
*
45232 AAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
45267 AAAGGTGCCACAGAGTTGTGGGCTTTGAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * * * * *
45301 TAAGGTGCCATGGGGTCGTGGAC-TTAAAAAG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
45333 AAAGGTGCCACGGAGTGGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
45367 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
45403 AAA
1 AAA
45406 AAGTGCCCGT
Statistics
Matches: 207, Mismatches: 29, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
32 19 0.09
33 14 0.07
34 95 0.46
35 36 0.17
36 21 0.10
37 22 0.11
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.19
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:45241 original size:71 final size:68
Alignment explanation
Indices: 45127--45398 Score: 345
Period size: 71 Copynumber: 4.0 Consensus size: 68
45117 GGGAAGGGAG
* * * *
45127 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGTTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
45191 AAGA
65 AAGA
*
45195 AACAGGCGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTA
1 AA-AGGTGCCACGGAGTTGTGGGCTTT-AAAAAGGAAAAA-GGTGCCACGGAGTTGTGGGCTTTA
45260 AAAAGAA
63 AAAAG-A
* * * * * * *
45267 AAAGGTGCCACAGAGTTGTGGGCTTT-GAAAGGAATAAGGTGCCATGGGGTCGTGGAC-TTAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
45330 AGA
66 AGA
* *
45333 AAAGGTGCCACGGAGTGGTGGGCTTTAAAAA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
45397 AG
66 AG
45399 GGAAAAAAAG
Statistics
Matches: 175, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
66 46 0.26
67 18 0.10
68 18 0.10
69 27 0.15
70 2 0.01
71 60 0.34
72 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (68 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
AGA
Found at i:45354 original size:100 final size:104
Alignment explanation
Indices: 45127--45398 Score: 349
Period size: 100 Copynumber: 2.6 Consensus size: 104
45117 GGGAAGGGAG
* * * * *
45127 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGTTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
* *
45191 AAGAAACAGGCGCCACGGAGTTGTGGGCTTTGAAAAAGGAA
64 AAGAAACAGGCGCCACGGAGTCGTGGACTTTGAAAAAGGAA
*
45232 AAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
* * * *
45297 GGAATA-AGGTGCCATGGGGTCGTGGAC-TT-AAAAA-G-A
65 AGAA-ACAGGCGCCACGGAGTCGTGGACTTTGAAAAAGGAA
*
45333 AAAGGTGCCACGGAGTGGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
45398 G
66 G
45399 GGAAAAAAAG
Statistics
Matches: 149, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
100 60 0.40
101 4 0.03
102 1 0.01
103 5 0.03
104 2 0.01
105 45 0.30
106 26 0.17
107 6 0.04
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (104 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
GAAACAGGCGCCACGGAGTCGTGGACTTTGAAAAAGGAA
Found at i:49110 original size:79 final size:76
Alignment explanation
Indices: 49022--49194 Score: 265
Period size: 76 Copynumber: 2.2 Consensus size: 76
49012 GTAAAAAAGT
*
49022 CGGGGTTGGAGTATTCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGT
49087 TTTAGAAATAAAAC
63 TTTAGAAATAAAAC
* **
49101 TGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTT
1 CGGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTT
49166 AGAAATAAAAC
66 AGAAATAAAAC
* *
49177 CGAGATTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
49195 GAGATGAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
76 44 0.51
79 43 0.49
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (76 bp):
CGGGGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTT
AGAAATAAAAC
Found at i:51389 original size:20 final size:20
Alignment explanation
Indices: 51364--51470 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
51354 AAAATGCCTG
*
51364 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
51384 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
51404 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAGA
*
51420 -A--TATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
*
51437 AATATATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
51457 AATGTATCGATACA
1 AATGTATCGATACA
51471 TCTGGGTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 12 0.16
15 1 0.01
18 1 0.01
19 1 0.01
20 58 0.78
21 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:51419 original size:13 final size:13
Alignment explanation
Indices: 51403--51433 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51393 ATACAATGAG
51403 CAATGTATCGATA
1 CAATGTATCGATA
*
51416 CAATATATCGATA
1 CAATGTATCGATA
51429 CAATG
1 CAATG
51434 AGCAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:51430 original size:33 final size:33
Alignment explanation
Indices: 51388--51452 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
51378 TTGTAAAATG
*
51388 TATCGATACAATGAGCAATGTATCGATACAATA
1 TATCGATACAATGAGCAATATATCGATACAATA
51421 TATCGATACAATGAGCAATATATCGATACAAT
1 TATCGATACAATGAGCAATATATCGATACAAT
51453 GCAAAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
TATCGATACAATGAGCAATATATCGATACAATA
Found at i:55643 original size:52 final size:52
Alignment explanation
Indices: 55565--55693 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
55555 GAAGAAATGA
55565 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
55617 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
55669 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
55694 AAGATCAATA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:55713 original size:52 final size:51
Alignment explanation
Indices: 55565--55713 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 51
55555 GAAGAAATGA
*
55565 AAATTTGCCTGCATGTATCGATAC-ATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATATCA-A-TGTATCGATACATCTGGGC
* *
55617 AAATTTGCCTGCATGTATCGATACATTTTAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ATATCAATGTATCGATACATCTGGGC
* * *
55669 AAATTTGCCTGCATGTATCGATACAAAGATCAATATATCAATACA
1 AAATTTGCCTGCATGTATCGATAC-AATATCAATGTATCGATACA
55714 ATGTATTGAT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
51 2 0.02
52 78 0.93
53 1 0.01
54 1 0.01
55 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAATATCAATGTATCGATACATCTGGGC
Found at i:55793 original size:19 final size:18
Alignment explanation
Indices: 55769--55866 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
55759 TAGCTTACAT
55769 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
55788 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
55801 TGTATCGATATAACACTTA
1 TGTATCGATACAA-ACTTA
55820 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
55833 TGTATCGATATAACACTTTA
1 TGTATCGATACAA-AC-TTA
55853 TGTATCGATACAAA
1 TGTATCGATACAAA
55867 TCGTTGAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 26
0.67 0.04 0.28
Matches are distributed among these distances:
13 20 0.32
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.37
20 12 0.19
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:55805 original size:32 final size:32
Alignment explanation
Indices: 55764--55864 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
55754 GGTAGTAGCT
* *
55764 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATATAACACTTATGTATCGA
55796 TACATTGTATCGATATAACACTTATGTATCGA
1 TACATTGTATCGATATAACACTTATGTATCGA
55828 TACATTGTATCGATATAACACTTTATGTATCGA
1 TACATTGTATCGATATAACAC-TTATGTATCGA
55861 TACA
1 TACA
55865 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATATAACACTTATGTATCGA
Found at i:55806 original size:13 final size:13
Alignment explanation
Indices: 55788--55842 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
55778 ACAAAACTTA
55788 TGTATCGATACAT
1 TGTATCGATACAT
55801 TGTATCGATATAACACTT
1 TGTATCG--AT-ACA--T
55819 ATGTATCGATACAT
1 -TGTATCGATACAT
55833 TGTATCGATA
1 TGTATCGATA
55843 TAACACTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 17 0.47
14 1 0.03
15 2 0.06
16 6 0.17
17 2 0.06
18 1 0.03
19 7 0.19
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:56400 original size:60 final size:61
Alignment explanation
Indices: 56166--56399 Score: 298
Period size: 61 Copynumber: 3.9 Consensus size: 61
56156 AGGAAGTGTG
* * *
56166 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAGGCA
* * * *
56227 TCCTGCCCTTTGAGGA-TTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAA-AGAAAGCA
1 TCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAGAGAAGGCA
*
56288 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAGAAGGCA
* * * *
56349 TACTGCTCTTTGAGGACTGAAGA-TGCCACCAGCTTGTGAGGGCTTT-AAAAG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG
56400 GCATCCTACT
Statistics
Matches: 151, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
59 5 0.03
60 27 0.18
61 113 0.75
62 6 0.04
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAGGCA
Found at i:56609 original size:215 final size:214
Alignment explanation
Indices: 56224--56631 Score: 561
Period size: 215 Copynumber: 1.9 Consensus size: 214
56214 AAAAGAAAAG
*
56224 GCGTCCTGCCCTTTGAGGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAGCAT
1 GCGTCCTGCCCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-CAAAAAGAAAGCAT
* * *
56289 CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATACTG
65 CCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCATACTG
* **
56354 CTCTTTGAGGACTGAAGATGCCACCAGCTTGTGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGA
130 CTCTTTGAGGACTGAAGATGCCACCAACTCATGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGA
56419 CAAAAAGGCAAAAGGAGAGA
195 CAAAAAGGCAAAAGGAGAGA
* *
56439 GCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGC
1 GCGTCCTGCCCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTCAAAA--AGAAAGC
* * * * * * *
56502 GTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTTATGTGGTCTTTAAAAGAAAAAGGCGTCC
63 ATCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCATAC
* * * * *
56566 TGCTCTTTGAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
128 TGCTCTTTGAGGACT-GAAGATGCCACCAACTCATGAGGGCTTTAAAAGGCATCCTACTCTTTGA
56631 G
192 G
56632 AACTGAAAGG
Statistics
Matches: 168, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
213 4 0.02
214 52 0.31
215 109 0.65
216 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (214 bp):
GCGTCCTGCCCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAAGAAAGCATC
CTACTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCATACTGC
TCTTTGAGGACTGAAGATGCCACCAACTCATGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGAC
AAAAAGGCAAAAGGAGAGA
Found at i:56647 original size:55 final size:56
Alignment explanation
Indices: 56439--56695 Score: 272
Period size: 55 Copynumber: 4.5 Consensus size: 56
56429 AAAGGAGAGA
* *
56439 GCGTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTATGTGGGCTTT--AA--A-AAG
* *
56500 GCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAGCTTATGTGGTCTTTAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT-----AAAAAG
* * *
56560 GCGTCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTT-AAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG
* * * * *
56615 GCGTCCTGCTCTTTGAGAACTGAAAGGCGCCACCAACTTGTTTGGGCTTT-GAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG
56670 GCGTCCTGCTCTTTGAGGACT-AAAGG
1 GCGTCCTGCTCTTTGAGGACTGAAAGG
56696 GTGAAAGGAG
Statistics
Matches: 172, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
54 5 0.03
55 72 0.42
59 2 0.01
60 45 0.26
61 45 0.26
63 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (56 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAG
Found at i:56741 original size:270 final size:271
Alignment explanation
Indices: 56165--56790 Score: 814
Period size: 270 Copynumber: 2.3 Consensus size: 271
56155 AAGGAAGTGT
* *
56165 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAGGCGTC
1 GTCCTGCTCTTTGAGGACT-AGAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTC
* * * *
56229 CTGCCCTTTGAGGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAAAGAAAGCATCCTAC
64 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTT-CAAAAAAAAAGCATCCTAC
**
56294 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATACTGCTCTT
128 TCTTTGAGGACTGAAAAGTGCCACCAACTCATGTGGGCTTT--AA-GAGAAGGCATACTGCTCTT
* * *
56359 TGAGGACTGAAGATGCCACCAGCTTGTGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGACAAAA
190 TGAGAACTGAAGACGCCACCAACTTGTGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGACAAAA
56424 AGGCAAAAGGAGAGAGC
255 AGGCAAAAGGAGAGAGC
*
56441 GTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 GTCCTGCTCTTTGAGGACTA-GAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * *
56506 TGCTCTTTGAGGACTA-AAGGTGCCACCAGCTTATGTGGTCTTT-AAAAGAAAAAGGCGTCCTGC
65 TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTCAAAA-AAAAA-GCATCCTAC
* ** * *
56569 TCTTTGAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTT-A-A-AAGGCGTCCTGCTCTTTGA
128 TCTTTGAGGACTGAAAAGTGCCACCAACTCATGTGGGCTTTAAGAGAAGGCATACTGCTCTTTGA
* ** * * * * *
56631 GAACTGAAAGGCGCCACCAACTTGTTTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAGG
193 GAACTG-AAGACGCCACCAACTTGTGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGACAAAAAG
**
56696 GTGAAAGGAGAGAGC
257 GCAAAAGGAGAGAGC
* *
56711 GTCCTGCTCTTTGACGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
1 GTCCTGCTCTTTGAGGACTAGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
56776 TGCTCTTTGAGGACT
65 TGCTCTTTGAGGACT
56791 GAAAAGTGGA
Statistics
Matches: 310, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
269 25 0.08
270 135 0.44
272 1 0.00
273 4 0.01
274 4 0.01
275 72 0.23
276 69 0.22
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (271 bp):
GTCCTGCTCTTTGAGGACTAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
GCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTCAAAAAAAAAGCATCCTACTCT
TTGAGGACTGAAAAGTGCCACCAACTCATGTGGGCTTTAAGAGAAGGCATACTGCTCTTTGAGAA
CTGAAGACGCCACCAACTTGTGAGGGCTTTAAAAGGCATCCTACTCTTTGAGGACAAAAAGGCAA
AAGGAGAGAGC
Found at i:57787 original size:1 final size:1
Alignment explanation
Indices: 57767--57839 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
57757 CTTTTCTCTC
* * * * * * * * *
57767 TTTTTTCTTTGTTTTGTTTTTTGTTTTTGTTTTTTGTTTTTGTTTTTTTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
57832 TTTTTTTT
1 TTTTTTTT
57840 AGAAGAGAAA
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:57793 original size:6 final size:6
Alignment explanation
Indices: 57774--57836 Score: 85
Period size: 6 Copynumber: 10.5 Consensus size: 6
57764 CTCTTTTTTC
*
57774 TTTG-T TTTGTTT TTTGTT TTTGTTT TTTGTT TTTGTT TTTTTT TTTGTT
1 TTTGTT TTTG-TT TTTGTT TTTG-TT TTTGTT TTTGTT TTTGTT TTTGTT
57823 TTTGTT TTT-TT TTT
1 TTTGTT TTTGTT TTT
57837 TTTAGAAGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 9 0.17
6 33 0.62
7 11 0.21
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTGTT
Found at i:57812 original size:31 final size:31
Alignment explanation
Indices: 57774--57838 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
57764 CTCTTTTTTC
57774 TTTGTTTTGTTTTTTGTTTTTGTTTTTTGTT
1 TTTGTTTTGTTTTTTGTTTTTGTTTTTTGTT
* *
57805 TTTGTTTTTTTTTTTGTTTTTGTTTTTTTTT
1 TTTGTTTTGTTTTTTGTTTTTGTTTTTTGTT
57836 TTT
1 TTT
57839 TAGAAGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (31 bp):
TTTGTTTTGTTTTTTGTTTTTGTTTTTTGTT
Found at i:57837 original size:18 final size:18
Alignment explanation
Indices: 57778--57837 Score: 102
Period size: 18 Copynumber: 3.2 Consensus size: 18
57768 TTTTTCTTTG
57778 TTTTGTTTTTTGTTTTTGTT
1 TTTTG-TTTTTGTTTTT-TT
57798 TTTTGTTTTTGTTTTTTT
1 TTTTGTTTTTGTTTTTTT
57816 TTTTGTTTTTGTTTTTTT
1 TTTTGTTTTTGTTTTTTT
57834 TTTT
1 TTTT
57838 TTAGAAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 24 0.60
19 11 0.28
20 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTGTTTTTGTTTTTTT
Found at i:57838 original size:13 final size:13
Alignment explanation
Indices: 57768--57839 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
57758 TTTTCTCTCT
57768 TTTTTCTTTGTTTTG
1 TTTTT-TTT-TTTTG
*
57783 TTTTTTGTTTTTG
1 TTTTTTTTTTTTG
*
57796 TTTTTTGTTTTTG
1 TTTTTTTTTTTTG
57809 -TTTTTTTTTTTG
1 TTTTTTTTTTTTG
57821 TTTTTGTTTTTTT-
1 TTTTT-TTTTTTTG
57834 TTTTTT
1 TTTTTT
57840 AGAAGAGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
12 12 0.23
13 27 0.51
14 9 0.17
15 5 0.09
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Done.