Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5117.1
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: 32863
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 2344 characters in sequence are not A, C, G, or T
Found at i:41 original size:18 final size:18
Alignment explanation
Indices: 8--156 Score: 115
Period size: 18 Copynumber: 8.3 Consensus size: 18
1 TGTATAA
* *
8 AATAACTGATTATTACTG
1 AATAATTGACTATTACTG
* *
26 AATAATTGACTGTTACCG
1 AATAATTGACTATTACTG
* *
44 GATAATTGACTGTTACTG
1 AATAATTGACTATTACTG
62 AAT-ATTAGACTATTACTG
1 AATAATT-GACTATTACTG
* *
80 AATAACTGAATATTACTG
1 AATAATTGACTATTACTG
* *
98 GATAATTGA-TCATTATTG
1 AATAATTGACT-ATTACTG
* * * * *
116 AATAACTGATTGTCATTG
1 AATAATTGACTATTACTG
134 AATGAA-TGACTATTACTG
1 AAT-AATTGACTATTACTG
152 AATAA
1 AATAA
157 CTTAATTGTT
Statistics
Matches: 105, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
17 6 0.06
18 94 0.90
19 5 0.05
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAATTGACTATTACTG
Found at i:96 original size:36 final size:36
Alignment explanation
Indices: 8--158 Score: 146
Period size: 36 Copynumber: 4.2 Consensus size: 36
1 TGTATAA
* *
8 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGATTATTACTGAATAATTGACTATTACTG
* * * *
44 GATAATTGACTGTTACTGAAT-ATTAGACTATTACTG
1 AATAACTGATTATTACTGAATAATT-GACTATTACTG
* * *
80 AATAACTGAATATTACTGGATAATTGA-TCATTATTG
1 AATAACTGATTATTACTGAATAATTGACT-ATTACTG
* * *
116 AATAACTGATTGTCATTGAATGAA-TGACTATTACTG
1 AATAACTGATTATTACTGAAT-AATTGACTATTACTG
152 AATAACT
1 AATAACT
159 TAATTGTTAT
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
35 4 0.04
36 82 0.89
37 6 0.07
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAATTGACTATTACTG
Found at i:199 original size:14 final size:14
Alignment explanation
Indices: 180--207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
170 TTTGTTATTA
180 AATAAATATTTAAT
1 AATAAATATTTAAT
194 AATAAATATTTAAT
1 AATAAATATTTAAT
208 TGATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAATATTTAAT
Found at i:360 original size:21 final size:20
Alignment explanation
Indices: 323--364 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
313 ATTTATTTAC
323 TTATTATTTAAGAAATAATAA
1 TTATTATTTAAGAAAT-ATAA
*
344 TTATTA-TTAAGTTAATATAA
1 TTATTATTTAAG-AAATATAA
364 T
1 T
365 AATATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
TTATTATTTAAGAAATATAA
Found at i:1192 original size:39 final size:40
Alignment explanation
Indices: 1149--1224 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 40
1139 AATTGAGATT
* * * *
1149 AATACTGAACTGAATTATGGAA-TATTGAATATTGTTTTG
1 AATACCGAACTGAACTATGAAATTACTGAATATTGTTTTG
* *
1188 AATACCGAATTGAACTGTGAAATTACTGAATATTGTT
1 AATACCGAACTGAACTATGAAATTACTGAATATTGTT
1225 ACGTATACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
39 17 0.57
40 13 0.43
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (40 bp):
AATACCGAACTGAACTATGAAATTACTGAATATTGTTTTG
Found at i:1220 original size:40 final size:40
Alignment explanation
Indices: 1174--1251 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
1164 TATGGAATAT
** *
1174 TGAATATTGTTTTGAATACCGAATTGAACTGTGAAATTAC
1 TGAATATTGTTACGAATACCGAATTGAACTGTAAAATTAC
* * *
1214 TGAATATTGTTACGTATACTGCATTGAACTGTAAAATT
1 TGAATATTGTTACGAATACCGAATTGAACTGTAAAATT
1252 TTTGATGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (40 bp):
TGAATATTGTTACGAATACCGAATTGAACTGTAAAATTAC
Found at i:3411 original size:25 final size:23
Alignment explanation
Indices: 3359--3413 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
3349 TATAAATAGT
3359 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
3382 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
3407 AATAGTG
1 AATAGTG
3414 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:3485 original size:26 final size:26
Alignment explanation
Indices: 3454--3505 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
3444 TAATATATAC
3454 ATATGT-ATAAAATAGATATAAAAAAA
1 ATATGTAATAAAATAG-TATAAAAAAA
*
3480 ATATGTACATAATATAGTATAAAAAA
1 ATATGTA-ATAAAATAGTATAAAAAA
3506 TACATACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (26 bp):
ATATGTAATAAAATAGTATAAAAAAA
Found at i:3495 original size:22 final size:22
Alignment explanation
Indices: 3469--3543 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
3459 TATAAAATAG
*
3469 ATATAAAAAAAATATGTACATA
1 ATATAAAAAAAATATATACATA
*
3491 ATATAGTATAAAAAATACATACATA
1 ATATA--A-AAAAAATATATACATA
**
3516 ATATAATTAAAATATATACATA
1 ATATAAAAAAAATATATACATA
*
3538 AGATAA
1 ATATAA
3544 CATGTAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 23 0.52
23 1 0.02
24 1 0.02
25 19 0.43
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.29
Consensus pattern (22 bp):
ATATAAAAAAAATATATACATA
Found at i:3513 original size:25 final size:25
Alignment explanation
Indices: 3475--3684 Score: 128
Period size: 25 Copynumber: 8.4 Consensus size: 25
3465 ATAGATATAA
*
3475 AAAAAATATGTACATAATATAGTAT
1 AAAAAATATATACATAATATAGTAT
*
3500 AAAAAATACATACATAATATA--AT
1 AAAAAATATATACATAATATAGTAT
* * *
3523 -TAAAATATATACATAAGATAACATGTAGA
1 AAAAAATATATACAT-A-AT-ATA-GTA-T
* *
3552 AAAAAAAATATAAATAATATAGTAT
1 AAAAAATATATACATAATATAGTAT
* * *
3577 TAAAGATATATACATAAAATAGTAT
1 AAAAAATATATACATAATATAGTAT
* * * *
3602 AATATATATATACGTAATATAGAAT
1 AAAAAATATATACATAATATAGTAT
** * *
3627 -TTAGA-ATATACCTAATATA-T-T
1 AAAAAATATATACATAATATAGTAT
*
3648 AAAAGAATATATACATAATATAATATT
1 AAAA-AATATATACATAATATAGTA-T
*
3675 AAGAAATATA
1 AAAAAATATA
3685 ATAATAACAA
Statistics
Matches: 140, Mismatches: 31, Indels: 27
0.71 0.16 0.14
Matches are distributed among these distances:
21 1 0.01
22 13 0.09
23 17 0.12
24 18 0.13
25 61 0.44
26 9 0.06
27 6 0.04
28 3 0.02
29 1 0.01
30 11 0.08
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (25 bp):
AAAAAATATATACATAATATAGTAT
Found at i:3590 original size:77 final size:82
Alignment explanation
Indices: 3439--3611 Score: 203
Period size: 77 Copynumber: 2.2 Consensus size: 82
3429 ATGTTAAGAT
* * * * *
3439 ATATATAATATATACATATGTATAAAATAGATATAAAAAAAATATGTACATAATATAGTATAAAA
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATATATAAATAATATAGTATAAAA
*
3504 AATACATACATAATATA
66 AATACATACATAAAATA
* *
3521 AT-TAAAATATATACATAAG-ATAACAT-G-TAGAAAAAAAA-ATATAAATAATATAGTATTAAA
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATATATAAATAATATAGTATAAAA
* *
3581 GATATATACATAAAATA
66 AATACATACATAAAATA
* *
3598 GTATAATATATATA
1 ATATAAAATATATA
3612 TACGTAATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
77 34 0.44
78 20 0.26
79 1 0.01
80 6 0.08
81 15 0.19
82 2 0.03
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (82 bp):
ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATATATAAATAATATAGTATAAAA
AATACATACATAAAATA
Found at i:3690 original size:47 final size:49
Alignment explanation
Indices: 3485--3690 Score: 131
Period size: 47 Copynumber: 4.2 Consensus size: 49
3475 AAAAAATATG
* *
3485 TACATAATATAGTATAAA-AAATACATACATAATAT-A-ATTAA-AATATA
1 TACATAATATAGTA-AAAGATATATATACATAATATAATATTAAGAA-ATA
* * * * * * *
3532 TACATAAGATAACATGTAGAAAAAAAAATATAAATAATATAGTATTAAAGATATA
1 TACAT-A-AT-ATA-GTA-AAAGATATATATACATAATATAATATT-AAGAAATA
* * * * *
3587 TACATAAAATAGTATAATATATATATACGTAATATAGA-ATTTAG-AATA
1 TACATAATATAGTAAAAGATATATATACATAATATA-ATATTAAGAAATA
* *
3635 TACCTAATATATTAAAAGA-ATATATACATAATATAATATTAAGAAATA
1 TACATAATATAGTAAAAGATATATATACATAATATAATATTAAGAAATA
3683 TA-ATAATA
1 TACATAATA
3691 ACAAAAAAAA
Statistics
Matches: 121, Mismatches: 26, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
46 1 0.01
47 30 0.25
48 24 0.20
49 4 0.03
50 21 0.17
51 9 0.07
52 16 0.13
53 1 0.01
54 4 0.03
55 10 0.08
56 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (49 bp):
TACATAATATAGTAAAAGATATATATACATAATATAATATTAAGAAATA
Found at i:4207 original size:30 final size:30
Alignment explanation
Indices: 4171--4238 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
4161 AGGTACAAGT
4171 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
* *
4201 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
4231 GGTGGTGG
1 GGTGGTGG
4239 CAAAGGCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.25
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
Found at i:5889 original size:45 final size:46
Alignment explanation
Indices: 5822--5945 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
5812 CATATGACCT
*
5822 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
5865 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
5911 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
5946 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:5928 original size:46 final size:45
Alignment explanation
Indices: 5822--6056 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
5812 CATATGACCT
*
5822 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
5865 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
5911 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
5948 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
5985 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
6022 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
6057 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:5949 original size:37 final size:37
Alignment explanation
Indices: 5907--6083 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
5897 AGCTGAAGCT
* **
5907 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
5944 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
5981 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
6018 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
6055 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
6084 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:9103 original size:117 final size:119
Alignment explanation
Indices: 8808--9601 Score: 1060
Period size: 117 Copynumber: 6.7 Consensus size: 119
8798 GGAAGAGAAT
* * * * * * *
8808 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* *
8873 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAGAAACGAAAACTACAAGCAGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
*
8928 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* *
8993 AAGATTACTAAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A-AGAT
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
9045 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
*
9110 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTAC-A-AGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
9162 GTTGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * ***
9227 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* * * *
9282 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGATGAAGGAGATAATCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
* * * * **
9347 AAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTAC-A-AGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
* * *
9399 GTTGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
** * * **
9464 AAGATTACTAGCAGGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAA-CAGAC
* * *
9519 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGACAATCCTCC
* *
9584 AGCAAGATTACTAGAAGA
63 AGAAAGATTACTAAAAGA
9602 AGAAGACGAC
Statistics
Matches: 602, Mismatches: 63, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
117 319 0.53
118 2 0.00
119 2 0.00
120 248 0.41
123 31 0.05
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.16
Consensus pattern (119 bp):
GTCGAGGAAGAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAACAGAC
Found at i:9291 original size:237 final size:237
Alignment explanation
Indices: 8808--9601 Score: 1146
Period size: 237 Copynumber: 3.3 Consensus size: 237
8798 GGAAGAGAAT
* * * *
8808 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATCCCCCAGA
*
8873 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAGAAACGAAAACTACAAG-CAGATGTCGAGGAA
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGAC-G-T-T-GAGGAA
*
8937 GAGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
127 GAGAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACT
* ** *
9002 AAAAGACATCGAGGTCATCGGTGAGAAACGAAAACTAC-A--AGAT
192 AAAAGACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
* * *
9045 GTTGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATCCCCCAGA
*
9110 AAGATTACTAAAAGACATTGAGGTCATCGGTAAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* *
9175 GTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
131 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* * *
9240 GACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGAC
196 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
*
9282 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGATGAAGGAGATAATCCCCCAGA
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATCCCCCAGA
* * * * **
9347 AAGATTATTAAAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGA
66 AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
* * **
9412 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCA
131 GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
* *
9477 GGCATTGGGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
196 GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
* * * * *
9519 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGT---GACGAAGGAGATAATCCCCC
* *
9584 AGCAAGATTACTAGAAGA
63 AGAAAGATTACTAAAAGA
9602 AGAAGACGAC
Statistics
Matches: 500, Mismatches: 50, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
234 100 0.20
235 2 0.00
236 1 0.00
237 365 0.73
238 1 0.00
240 31 0.06
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.16
Consensus pattern (237 bp):
GTCGAGGAAGAAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGATAATCCCCCAGA
AAGATTACTAAAAGACATTGAGGTCATCGGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAGA
GTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTAAAA
GACATTGAGGTCATCGGTGAGAAACGATTACTACAAGCAGAC
Found at i:9461 original size:354 final size:356
Alignment explanation
Indices: 8808--9602 Score: 1171
Period size: 354 Copynumber: 2.2 Consensus size: 356
8798 GGAAGAGAAT
* * * * *
8808 GTCGAGGAAGAAAGTCCGTTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGATAAGCCCCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* *
8873 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAGAAACGAAAACTACAAGCAGATGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* * *
8938 AGAGTCCATTCGCCGGCGAGAAACCGCCTAGTGACGAAGGAGACAATCCTCCAGAAAGATTACTA
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCCCCAGAAAGATTACTA
* * *
9003 AAAGACATCGAGGTCATCGGTGAGAAACGAAAACTACAAGATGTTGAGGAAGAAAGTCCATTCGC
196 AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
9068 CGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
261 CGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
9133 TCATCGGTAAGAAACGAAAACTAC-A-AGAC
326 TCATCGGTAAGAAACGAAAACTACAACAGAC
* *
9162 GTTGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCTCCAGA
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
* * ***
9227 AAGATTACTAAAAGACATTGAGGTCGTCGGTGAAAAACGGTTACTACAAGCAGACGTCGAGGAAG
66 AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
* * *
9292 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGATGAAGGAGATAATCCCCCAGAAAGATTATTA
131 AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCCCCAGAAAGATTACTA
* * ** *
9357 AAAGACATTGAGCTCATCCGTGAGGAACGATTACTACAAGACGTTGAGGAAGAGAGTCCATTCGC
196 AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
* * ** * *
9422 CGGCGAGAAACCACCTAGTGACGAAGGAGATAGTCCTCCAGAAAGATTACTAGCAGGCATTGGGG
261 CGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
* **
9487 TCATCGGTGAGAAACGATTACTACAAGCAGAC
326 TCATCGGTAAGAAACGAAAACTACAA-CAGAC
* *
9519 GTCGAGGAAGAGAGTCCATTCGCCGGTGAGAAACCACCTAGTGACGACGAAGGAAACAATCCACC
1 GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGT---GACGAAGGAGACAATCCACC
* *
9584 AGCAAGATTACTAGAAGAA
63 AGAAAGATTACTAAAAGAA
9603 GAAGACGACG
Statistics
Matches: 392, Mismatches: 43, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
354 313 0.80
355 1 0.00
357 44 0.11
360 34 0.09
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.16
Consensus pattern (356 bp):
GTCGAGGAAGAGAGTCCATTTGCCGGTGAGAAACCACCTAGTGACGAAGGAGACAATCCACCAGA
AAGATTACTAAAAGAAATTGAGGTCATCGGTGAAAAACGAAAACTACAAGCAGACGTCGAGGAAG
AAAGTCCATTCGCCGGCGAGAAACCACCTAGTGACGAAGGAGACAATCCCCCAGAAAGATTACTA
AAAGACATCGAGCTCATCCGTGAGAAACGAAAACTACAAGACGTTGAGGAAGAAAGTCCATTCGC
CGGCGAGAAACCACCTAGTGACGAAGGAGAGAATCCTCCAGAAAGATTACTAAAAGACATTGAGG
TCATCGGTAAGAAACGAAAACTACAACAGAC
Found at i:15462 original size:11 final size:11
Alignment explanation
Indices: 15446--15476 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15436 ATACCCATAC
15446 CCCATACCTTG
1 CCCATACCTTG
*
15457 CCCATACCTTT
1 CCCATACCTTG
15468 CCCATACCT
1 CCCATACCT
15477 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:21845 original size:21 final size:21
Alignment explanation
Indices: 21819--21859 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21809 AGACGAGCAA
* *
21819 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
21840 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
21860 TTGAGTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:26532 original size:15 final size:14
Alignment explanation
Indices: 26495--26538 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
26485 ATTTAATAGT
26495 ATAATATATAAAAAA
1 ATAAT-TATAAAAAA
* *
26510 ATATTTATAAGAATA
1 ATAATTATAA-AAAA
26525 ATAATTATAAAAAA
1 ATAATTATAAAAAA
26539 TAAAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
ATAATTATAAAAAA
Done.