Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2166
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: 40247
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1295 original size:1 final size:1
Alignment explanation
Indices: 1284--1403 Score: 96
Period size: 1 Copynumber: 120.0 Consensus size: 1
1274 GGCGTCCTCC
* ** ** ** * **
1284 AAAACAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAACAAAAAAAAAAAAAAACGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * *
1349 AAAAATTAAAAAAAAAAAAAAAAAAAAAAACAATAAAAAAACAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1404 GGGGTCCGGA
Statistics
Matches: 94, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:1324 original size:36 final size:35
Alignment explanation
Indices: 1284--1403 Score: 158
Period size: 33 Copynumber: 3.4 Consensus size: 35
1274 GGCGTCCTCC
1284 AAAACAAAAAAAAAAAAAAAAAAACGAAAAAAATGA
1 AAAACAAAAAAAAAAAAAAAAAAACGAAAAAAAT-A
*
1320 AAAACCAAAACAAAAAAAAAAAAAAACG-AAAAAATT
1 AAAA-CAAAA-AAAAAAAAAAAAAAACGAAAAAAATA
1356 AAAA-AAAAAAAAAAAAAAAAAAAC-AATAAAAA-A
1 AAAACAAAAAAAAAAAAAAAAAAACGAA-AAAAATA
1389 ACAAACAAAAAAAAA
1 A-AAACAAAAAAAAA
1404 GGGGTCCGGA
Statistics
Matches: 76, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
33 18 0.24
34 12 0.16
35 9 0.12
36 8 0.11
37 12 0.16
38 17 0.22
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (35 bp):
AAAACAAAAAAAAAAAAAAAAAAACGAAAAAAATA
Found at i:2897 original size:30 final size:29
Alignment explanation
Indices: 2842--3309 Score: 360
Period size: 30 Copynumber: 15.9 Consensus size: 29
2832 TCACCCTTCA
* *
2842 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
2871 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
2900 GAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2928 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
2958 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2987 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
3017 TTTTGTAAGCTCACAACTCTA-TAGCA-CTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCATCT-TTTTC
* * *
3051 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
3078 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
3108 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
3137 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
3166 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * **
3196 AAAAGCCCACAAGTCAGTGGCAACCTTTAA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3226 AAAGCCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
3253 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
3283 GAAGCCCACAAATCGGTGGCACCTTTT
1 AAAGCCCACAAGTCAGTGGCATCTTTT
3310 CCATCTTTAA
Statistics
Matches: 359, Mismatches: 58, Indels: 44
0.78 0.13 0.10
Matches are distributed among these distances:
26 1 0.00
27 59 0.16
28 27 0.08
29 86 0.24
30 164 0.46
33 2 0.01
34 5 0.01
35 15 0.04
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:3167 original size:58 final size:59
Alignment explanation
Indices: 2838--3308 Score: 353
Period size: 57 Copynumber: 8.0 Consensus size: 59
2828 TTCATCACCC
* *** ***
2838 TTCAAAAGTCCACAAGTCAGTGGCATTTTTTTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* * * *
2897 TTCGAAAGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * * * * *
2954 TTCCGAAGCCCACAAGTCGGTGGCA-TCTTTTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * * * * *
3014 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTC---AGCCCACAAGTTAGTGGCACCCTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
***
3075 TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * **
3134 TT-AAAAGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
* *
3193 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTTAAAAAGCCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * * *
3250 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTTC-GAAGCCCACAAATCGGTGGC-ACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCC-TTTTCAAAAGCCCACAAGTCAGTGGCAACCT
3307 TT
1 TT
3309 TCCATCTTTA
Statistics
Matches: 333, Mismatches: 57, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
56 27 0.08
57 88 0.26
58 55 0.17
59 72 0.22
60 48 0.14
61 5 0.02
62 15 0.05
63 1 0.00
64 15 0.05
65 7 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:3382 original size:43 final size:43
Alignment explanation
Indices: 3314--3403 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
3304 CCTTTTCCAT
*
3314 CTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
* * *
3357 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
3400 CTTT
1 CTTT
3404 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
Found at i:3435 original size:52 final size:53
Alignment explanation
Indices: 3357--3494 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 53
3347 ACATTGGCAC
* *
3357 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
* * *
3409 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC-TTTTC-CAT
* * * * *
3464 CTTTAAGCCCCATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
3495 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 38 0.54
53 2 0.03
54 5 0.07
55 26 0.37
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
Found at i:4360 original size:13 final size:13
Alignment explanation
Indices: 4342--4366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4332 CATAAAGTGT
4342 TGTATCGATACAA
1 TGTATCGATACAA
4355 TGTATCGATACA
1 TGTATCGATACA
4367 TGTTTTTTTG
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:4447 original size:13 final size:13
Alignment explanation
Indices: 4429--4453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4419 ATCACTTAAA
4429 TGTATCGATACAT
1 TGTATCGATACAT
4442 TGTATCGATACA
1 TGTATCGATACA
4454 CTGATCTTTG
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:4506 original size:52 final size:51
Alignment explanation
Indices: 4442--4590 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
4432 ATCGATACAT
**
4442 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
4494 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
4546 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
4591 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:9187 original size:79 final size:79
Alignment explanation
Indices: 9045--9337 Score: 320
Period size: 79 Copynumber: 3.7 Consensus size: 79
9035 AAAGTATCGA
* * * * * ** * *
9045 TTTTTCACCATCGGGGATACTCCAACCCCATTATCTCCGAGGAGATATTATAACCCCGCTTTTAT
1 TTTTTCACCATCGAGGATACTCCAACCCCATCATTTCCAAGG-GATACTCCAACCTCGTTTTTAT
9110 TTCCAAAATATTAAT
65 TTCCAAAATATTAAT
*
9125 TTTTTTACCATCG-GGATACTCCAACCCCATCATTTCCAAGGGAATACTCCAACCTCGTTTTTAT
1 TTTTTCACCATCGAGGATACTCCAACCCCATCATTTCCAAGGG-ATACTCCAACCTCGTTTTTAT
*
9189 TGCCAAAATATTAA-
65 TTCCAAAATATTAAT
*** * * * *
9203 TTTTTCATTGTCGAGGATGCTCCAACTCCATCATATCCAAAGGGATACTCCAACCTCGTTTTTAC
1 TTTTTCACCATCGAGGATACTCCAACCCCATCATTTCC-AAGGGATACTCCAACCTCGTTTTTAT
* *
9268 TTCTAAAATATTGAT
65 TTCCAAAATATTAAT
* * * *
9283 TTTTTTACCATCGAGGATACTCTAACCCCATAATTTTCGAAGGGATACTCCAACC
1 TTTTTCACCATCGAGGATACTCCAACCCCATCA-TTTCCAAGGGATACTCCAACC
9338 CCATTTTTTC
Statistics
Matches: 177, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
78 10 0.06
79 106 0.60
80 58 0.33
81 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (79 bp):
TTTTTCACCATCGAGGATACTCCAACCCCATCATTTCCAAGGGATACTCCAACCTCGTTTTTATT
TCCAAAATATTAAT
Found at i:9673 original size:23 final size:22
Alignment explanation
Indices: 9642--9690 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
9632 CTTCCCTCCT
**
9642 TTTTATGTATTTTTGTGCGTTTA
1 TTTTATGTAAATTTGTGCG-TTA
* *
9665 TTTTGTGTAAATTTGTTCGTTA
1 TTTTATGTAAATTTGTGCGTTA
9687 TTTT
1 TTTT
9691 CTTTTTCGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.14, C:0.04, G:0.16, T:0.65
Consensus pattern (22 bp):
TTTTATGTAAATTTGTGCGTTA
Found at i:15608 original size:31 final size:31
Alignment explanation
Indices: 15563--15633 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
15553 ATCCTCCAAG
* *
15563 CCTTTTTCCAAAAGTCCACAACTTTGTGGCA
1 CCTTTTTCCAAAAGTCCACAACTCTGTGGAA
* * *
15594 CCTTTTTTCTAAAGTCCACGACTCTGTGGAA
1 CCTTTTTCCAAAAGTCCACAACTCTGTGGAA
*
15625 ACTTTTTCC
1 CCTTTTTCC
15634 TTTTTTTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (31 bp):
CCTTTTTCCAAAAGTCCACAACTCTGTGGAA
Found at i:15710 original size:63 final size:63
Alignment explanation
Indices: 15636--15872 Score: 252
Period size: 63 Copynumber: 3.8 Consensus size: 63
15626 CTTTTTCCTT
*
15636 TTTTTTAAAGCCTACACAAGTTGGTGGCAACTTTTAGTCCTTAAAGAGCAAGATGCCTTTTTC
1 TTTTTTAAAGCCCACACAAGTTGGTGGCAACTTTTAGTCCTTAAAGAGCAAGATGCCTTTTTC
* * * * ***
15699 TTTTTTAAAGCCCATACAAGTTGGTGGCACCTTTTAGT-CTTCAAAGAGTAGGATGCTGCGCCTT
1 TTTTTTAAAGCCCACACAAGTTGGTGGCAACTTTTAGTCCTT-AAAGAGCAAGATGC--CTTTTT
15763 -
63 C
* * *
15763 GTTTTTAAAGCTCACACAAGTTGGT-G-ATACTTTTTAGTCCTCAAAGAGC-AGAATGCCTTTTT
1 TTTTTTAAAGCCCACACAAGTTGGTGGCA-AC-TTTTAGTCCTTAAAGAGCAAG-ATGCCTTTTT
15825 C
63 C
* * *
15826 -TTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCTTTAAAGAG
1 TTTTTTAAAGCCCACACAAGTTGGTGGCAACTTTTAGTCCTTAAAGAG
15873 TGGTGTAGAC
Statistics
Matches: 141, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
62 44 0.31
63 52 0.37
64 40 0.28
65 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (63 bp):
TTTTTTAAAGCCCACACAAGTTGGTGGCAACTTTTAGTCCTTAAAGAGCAAGATGCCTTTTTC
Found at i:15798 original size:64 final size:62
Alignment explanation
Indices: 15632--15873 Score: 236
Period size: 62 Copynumber: 3.9 Consensus size: 62
15622 GAAACTTTTT
* * * * *
15632 CCTTTTTTTTAAAGCCTACACAAGTTGGTGGCAACTTTTAGTCCTT-AAAGAGCA-AGATGCCT
1 CCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGT-CTTCAAAGAGTAGA-ATGCCG
** * *
15694 TTTTCTTTTTTAAAGCCCATACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGGATGCTGCG
1 CCTTC-TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGAATGC--CG
* * ** * * * *
15759 CCTTGTTTTTAAAGCTCACACAAGTTGGTGATACTTTTTAGTCCTCAAAGAGCAGAATGCCT
1 CCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGAATGCCG
** * *
15821 TTTTCTTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCTTTAAAGAGT
1 CCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGT
15874 GGTGTAGACA
Statistics
Matches: 143, Mismatches: 32, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
62 48 0.34
63 45 0.31
64 47 0.33
65 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (62 bp):
CCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGAATGCCG
Found at i:15798 original size:127 final size:126
Alignment explanation
Indices: 15632--15873 Score: 366
Period size: 127 Copynumber: 1.9 Consensus size: 126
15622 GAAACTTTTT
* *
15632 CCTTTTTTTTAAAGCCTACACAAGTTGGTGGCAACTTTTAGTCCTTAAAGAGCA-AGATGCCTTT
1 CCTTGTTTTTAAAGCCTACACAAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGA-ATGCCTTT
*
15696 TTCTTTTTTAAAGCCCATACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGGATGCTGCG
65 TTC-TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGGATGCTGCG
15759 CCTTGTTTTTAAAG-CTCACACAAGTTGGT-G-ATACTTTTTAGTCCTCAAAGAGCAGAATGCCT
1 CCTTGTTTTTAAAGCCT-ACACAAGTTGGTGGCA-AC-TTTTAGTCCTCAAAGAGCAGAATGCCT
* *
15821 TTTTCTTTTTAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCTTTAAAGAGT
63 TTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGT
15874 GGTGTAGACA
Statistics
Matches: 106, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
125 1 0.01
126 50 0.47
127 54 0.51
128 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (126 bp):
CCTTGTTTTTAAAGCCTACACAAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGAATGCCTTTT
TCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTCAAAGAGTAGGATGCTGCG
Found at i:16210 original size:21 final size:21
Alignment explanation
Indices: 16186--16239 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
16176 TTCTACAATT
*
16186 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATAAGTGAA
16207 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
16227 TGTATCGATACAA
1 TGTATCGATACAA
16240 GTCTTAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:29956 original size:13 final size:13
Alignment explanation
Indices: 29938--29962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29928 ATACAAAGAT
29938 CAATGTATCGATA
1 CAATGTATCGATA
29951 CAATGTATCGAT
1 CAATGTATCGAT
29963 TCATTTGAGT
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):
CAATGTATCGATA
Found at i:30034 original size:19 final size:19
Alignment explanation
Indices: 30010--30073 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
30000 AGCTTCATTA
30010 GTATCGATACAAAACTTAT
1 GTATCGATACAAAACTTAT
30029 GTATCGATAC---A--T-T
1 GTATCGATACAAAACTTAT
*
30042 GTATCGATACAACACTTAT
1 GTATCGATACAAAACTTAT
30061 GTATCGATACAAA
1 GTATCGATACAAA
30074 TCGTTGAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
GTATCGATACAAAACTTAT
Found at i:30046 original size:13 final size:13
Alignment explanation
Indices: 30028--30052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30018 ACAAAACTTA
30028 TGTATCGATACAT
1 TGTATCGATACAT
30041 TGTATCGATACA
1 TGTATCGATACA
30053 ACACTTATGT
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:30051 original size:32 final size:33
Alignment explanation
Indices: 30005--30071 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
29995 GTAGTAGCTT
30005 CATTAGTATCGATACAAAACTTATGTATCGATA
1 CATTAGTATCGATACAAAACTTATGTATCGATA
*
30038 CATT-GTATCGATACAACACTTATGTATCGATA
1 CATTAGTATCGATACAAAACTTATGTATCGATA
30070 CA
1 CA
30072 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (33 bp):
CATTAGTATCGATACAAAACTTATGTATCGATA
Found at i:35765 original size:37 final size:37
Alignment explanation
Indices: 35715--35950 Score: 149
Period size: 37 Copynumber: 6.3 Consensus size: 37
35705 TTTATTCCTT
** *
35715 TTTTCCCTTTGTCCTTGAAGAGTAGGATGCCTACTCA
1 TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
* *
35752 TTTTCTCTTTGTCCTCAAAGAGCAGGATGCCTACTCC
1 TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
* * * * * *
35789 TTTTTCCTATATCCTCAAAGAGCAAGA--CCCATTTCA
1 TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTA-CTCA
* * * *
35825 TTATTCTTTTTCCTTTTTCCTAAAAGAGTAGGA--CATACTCA
1 TT-TTC-----CCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
* * * **
35866 TTTT-CCTTTGTCTTCAAAGAGAAAGACACCTACTCA
1 TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
* * * *
35902 TTTTCCCTTTGTCCTTAAAGAGTAGGACGCCTACTCT
1 TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
*
35939 TTTTTCCTTTGT
1 TTTTCCCTTTGT
35951 TTTCAAGAAG
Statistics
Matches: 154, Mismatches: 35, Indels: 20
0.74 0.17 0.10
Matches are distributed among these distances:
34 17 0.11
35 3 0.02
36 15 0.10
37 93 0.60
40 2 0.01
41 5 0.03
42 19 0.12
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (37 bp):
TTTTCCCTTTGTCCTCAAAGAGCAGGATGCCTACTCA
Found at i:35789 original size:116 final size:113
Alignment explanation
Indices: 35669--35923 Score: 296
Period size: 116 Copynumber: 2.2 Consensus size: 113
35659 CATTCCTTTT
* * * * **
35669 CTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTTATTCCTT-TTTTCCCTTTGTCCTTGA
1 CTCCTTTTTCCTTTGTCCTCAAAGAGCAAGACCCATTTCATT-ATTCTTTTCCCTTTGTCCTAAA
* * * **
35733 AGAGTAGGATGCCTACTCATTTTCTCTTTGTCCTCAAAGAGCAGGATGCCTA
65 AGAGTAGGA--CATACTCATTTTC-CTTTGTCCTCAAAGAGAAAGACACCTA
* * * *
35785 CTCCTTTTTCCTATATCCTCAAAGAGCAAGACCCATTTCATTATTCTTTTTCCTTTTTCCTAAAA
1 CTCCTTTTTCCTTTGTCCTCAAAGAGCAAGACCCATTTCATTATTCTTTTCCCTTTGTCCTAAAA
*
35850 GAGTAGGACATACTCATTTTCCTTTGTCTTCAAAGAGAAAGACACCTA
66 GAGTAGGACATACTCATTTTCCTTTGTCCTCAAAGAGAAAGACACCTA
* * *
35898 CTCATTTTCCCTTTGTCCTTAAAGAG
1 CTCCTTTTTCCTTTGTCCTCAAAGAG
35924 TAGGACGCCT
Statistics
Matches: 117, Mismatches: 21, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
113 43 0.37
114 12 0.10
115 2 0.02
116 60 0.51
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (113 bp):
CTCCTTTTTCCTTTGTCCTCAAAGAGCAAGACCCATTTCATTATTCTTTTCCCTTTGTCCTAAAA
GAGTAGGACATACTCATTTTCCTTTGTCCTCAAAGAGAAAGACACCTA
Found at i:35966 original size:37 final size:37
Alignment explanation
Indices: 35860--35966 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 37
35850 GAGTAGGACA
*
35860 TACTCA-TTTTCCTTTGTCTTCAA-AGAGAAAGACACC
1 TACTCATTTTTCCTTTGTCTTCAAGA-AGAAGGACACC
* * * *
35896 TACTCATTTTCCCTTTGTCCTTAAAG-AGTAGGACGCC
1 TACTCATTTTTCCTTTGT-CTTCAAGAAGAAGGACACC
* * *
35933 TACTCTTTTTTCCTTTGTTTTCAAGAAGCAGGAC
1 TACTCATTTTTCCTTTGTCTTCAAGAAGAAGGAC
35967 CCATTTTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
36 11 0.19
37 41 0.72
38 5 0.09
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (37 bp):
TACTCATTTTTCCTTTGTCTTCAAGAAGAAGGACACC
Found at i:36020 original size:150 final size:150
Alignment explanation
Indices: 35744--36024 Score: 343
Period size: 150 Copynumber: 1.9 Consensus size: 150
35734 GAGTAGGATG
* *
35744 CCTACTCATTTTCTCTTTGTCCTCAAAGAGCAGGATGCCTACTCCTTTTTCCTATATCCTCAAAG
1 CCTACTCATTTTCCCTTTGTCCTCAAAGAGCAGGACGCCTACTCCTTTTTCCTATATCCTCAAAG
* * *
35809 AGCAAGACCCATTTCATTATTCTTTTTCCTTTTTCCTAAAAGAGTAGGACATACTCATTTTCCTT
66 AGCAAGACCCATTTCATTATTCTTTTCCCTTTTACCTAAAAGAGTAGGACATACCCATTTTCCTT
35874 TGTCTTCAAAGAGAAAGACA
131 TGTCTTCAAAGAGAAAGACA
* * * * * **
35894 CCTACTCATTTTCCCTTTGTCCTTAAAGAGTAGGACGCCTACTCTTTTTTCCTTTGTTTTC-AAG
1 CCTACTCATTTTCCCTTTGTCCTCAAAGAGCAGGACGCCTACTCCTTTTTCCTATATCCTCAAAG
* * * *** *
35958 AAGCAGGACCCATTTTATTCA-TCTTTTCCCTTTGTACTTAAAA-AGTAGGGTGTACCCCTTTTC
66 -AGCAAGACCCATTTCATT-ATTCTTTTCCCTTT-TACCTAAAAGAGTAGGACATACCCATTTTC
36021 CTTT
128 CTTT
36025 ATCCTCAAGG
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
149 3 0.03
150 98 0.90
151 8 0.07
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.39
Consensus pattern (150 bp):
CCTACTCATTTTCCCTTTGTCCTCAAAGAGCAGGACGCCTACTCCTTTTTCCTATATCCTCAAAG
AGCAAGACCCATTTCATTATTCTTTTCCCTTTTACCTAAAAGAGTAGGACATACCCATTTTCCTT
TGTCTTCAAAGAGAAAGACA
Found at i:36313 original size:31 final size:31
Alignment explanation
Indices: 36275--36377 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
36265 TTAGAATGTT
36275 AAAGCCCACACGAGTTGGTGGCACCCTAGTC
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTC
* * *
36306 AAAGCCCACACAAGCTGGTGGCACCCGAGTC
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTC
* ** * * * *
36337 TAAGGTCGCACGAGTTGGCGGCA-CTTGAGTT
1 AAAGCCCACACGAGTTGGTGGCACCCT-AGTC
36368 AAAGCCCACA
1 AAAGCCCACA
36378 TAAGCTAGTG
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
AAAGCCCACACGAGTTGGTGGCACCCTAGTC
Found at i:36500 original size:180 final size:180
Alignment explanation
Indices: 36189--36586 Score: 526
Period size: 180 Copynumber: 2.2 Consensus size: 180
36179 CCACTTTTAT
* * *
36189 AAGCCCACACAAGCTAGTGGCATCTAAGTTTAAGTCAAGTCCAAATTAGTTGGCACCTGTCTAAG
1 AAGCCCACACAAGCTAGTGGCACCTAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTGTCTAAG
* * *
36254 GAGGTCAAGCCTTAGAATGTTAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAA
66 GAGGTCAAGCCTTAGAATATCAAAGCCCACACGAGTTAGTGGCACCCTAGTCAAAGCCCACACAA
*** * ** * ** *
36319 GCTGGTGGCACCCGAGTCTAAGGTCGCACGAGTTGGCGGCACTTGAGTTA
131 GCTGGCAACACCCAAGTCTAAGCCCGCACGAATTGGCAACACTTGAGTCA
* * *
36369 AAGCCCACATAAGCTAGTGGCACCTAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTGTTTGAG
1 AAGCCCACACAAGCTAGTGGCACCTAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTGTCTAAG
* * * **
36434 GAGGTCAAGCCTTAGAATATCAAAGCCTATACGAGTTAGTGGCACCCTAGTTAAAGCCTGCACAA
66 GAGGTCAAGCCTTAGAATATCAAAGCCCACACGAGTTAGTGGCACCCTAGTCAAAGCCCACACAA
* *
36499 GCTGGCAACACTCAAGTCTAAGCCCGCATGAATTGGCAACACTTGAGTCA
131 GCTGGCAACACCCAAGTCTAAGCCCGCACGAATTGGCAACACTTGAGTCA
* * * *
36549 AAGCCCACACAAACTGGTGGCACCAAAGTCTGAGTCAA
1 AAGCCCACACAAGCTAGTGGCACCTAAGTTTGAGTCAA
36587 AGCCTGCACA
Statistics
Matches: 187, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
180 187 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (180 bp):
AAGCCCACACAAGCTAGTGGCACCTAAGTTTGAGTCAAGTCCAAATTAGTTAGCACCTGTCTAAG
GAGGTCAAGCCTTAGAATATCAAAGCCCACACGAGTTAGTGGCACCCTAGTCAAAGCCCACACAA
GCTGGCAACACCCAAGTCTAAGCCCGCACGAATTGGCAACACTTGAGTCA
Found at i:37112 original size:20 final size:20
Alignment explanation
Indices: 37087--37125 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37077 CGATACAATT
*
37087 AGTGAATGTGTCAATACATA
1 AGTGAATGTATCAATACATA
*
37107 AGTGAATGTATCGATACAT
1 AGTGAATGTATCAATACAT
37126 GCCGTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGAATGTATCAATACATA
Found at i:38720 original size:21 final size:21
Alignment explanation
Indices: 38675--38720 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38665 TTTGGCATTA
*
38675 AAAAATAAAATATAATAAAAT
1 AAAAATAAAATATAATAAAAG
*
38696 AAAAATAAAATA-ATTAAATAG
1 AAAAATAAAATATAATAAA-AG
38717 AAAA
1 AAAA
38721 TATGTACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAATAAAATATAATAAAAG
Found at i:38915 original size:14 final size:14
Alignment explanation
Indices: 38896--38922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38886 TGCATATGTT
38896 CATTTCATGCATTA
1 CATTTCATGCATTA
38910 CATTTCATGCATT
1 CATTTCATGCATT
38923 CTTTCTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (14 bp):
CATTTCATGCATTA
Found at i:39323 original size:23 final size:23
Alignment explanation
Indices: 39295--39346 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
39285 AATAAAAAAA
39295 GCTGAAACAGCTGCAATTAAGCT
1 GCTGAAACAGCTGCAATTAAGCT
* *
39318 GCTGAAATAGCTGTAATTAAGCT
1 GCTGAAACAGCTGCAATTAAGCT
*
39341 ACTGAA
1 GCTGAA
39347 CTCAGAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (23 bp):
GCTGAAACAGCTGCAATTAAGCT
Found at i:40009 original size:7 final size:7
Alignment explanation
Indices: 39969--40019 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
39959 CAATAGTAGC
39969 AGCAAC-
1 AGCAACA
*
39975 AGTAAC-
1 AGCAACA
39981 AGCAACA
1 AGCAACA
39988 A-C-ACA
1 AGCAACA
39993 AGCGAACA
1 AGC-AACA
40001 AGCAACA
1 AGCAACA
40008 AGCAACA
1 AGCAACA
40015 AGCAA
1 AGCAA
40020 TGGCAGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.10
6 12 0.31
7 17 0.44
8 6 0.15
ACGTcount: A:0.55, C:0.27, G:0.16, T:0.02
Consensus pattern (7 bp):
AGCAACA
Found at i:40057 original size:23 final size:23
Alignment explanation
Indices: 40027--40111 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
40017 CAATGGCAGT
40027 AAAAATAGCAAGCAAATACCAAC
1 AAAAATAGCAAGCAAATACCAAC
40050 AAAAATAGCAAGCAAATACCAAC
1 AAAAATAGCAAGCAAATACCAAC
*
40073 AAAAATAACAAGCAAATACCAAC
1 AAAAATAGCAAGCAAATACCAAC
* *
40096 AAAAACATCAAGCAAA
1 AAAAATAGCAAGCAAA
40112 CATTAGCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.08
Consensus pattern (23 bp):
AAAAATAGCAAGCAAATACCAAC
Done.