Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2440
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: 80513
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6285 original size:21 final size:22
Alignment explanation
Indices: 6261--6311 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6251 CGTCCTTTAC
6261 ACAAAAAAAA-AAAAAAAAAAA
1 ACAAAAAAAACAAAAAAAAAAA
* *
6282 ACAAAAAAAACAAGAAAAAAAT
1 ACAAAAAAAACAAAAAAAAAAA
*
6304 AGAAAAAA
1 ACAAAAAA
6312 TAGAAGGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.88, C:0.06, G:0.04, T:0.02
Consensus pattern (22 bp):
ACAAAAAAAACAAAAAAAAAAA
Found at i:6307 original size:10 final size:10
Alignment explanation
Indices: 6264--6311 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
6254 CCTTTACACA
*
6264 AAAAAAAAAA
1 AAAAAAAAAG
*
6274 AAAAAAAAACA
1 AAAAAAAAA-G
6285 AAAAAAACAAG
1 AAAAAAA-AAG
*
6296 AAAAAAATAG
1 AAAAAAAAAG
6306 AAAAAA
1 AAAAAA
6312 TAGAAGGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 17 0.50
11 15 0.44
12 2 0.06
ACGTcount: A:0.90, C:0.04, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:6311 original size:1 final size:1
Alignment explanation
Indices: 6263--6302 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
6253 TCCTTTACAC
* * *
6263 AAAAAAAAAAAAAAAAAAAACAAAAAAAACAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6303 TAGAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.93, C:0.05, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:7622 original size:29 final size:29
Alignment explanation
Indices: 7503--8514 Score: 1017
Period size: 28 Copynumber: 35.9 Consensus size: 29
7493 ATGTTATCCC
*
7503 TTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
7532 TTCGAAGTCCACGAGTAAGTGGCAC-C-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
7559 TTCAAAGGCCCACAAGTC-GT-GCACT-GT
1 TTCAAA-GCCCACAAGTCAGTGGCACTCTT
* *
7586 TTCCAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
7615 TTCAAAGCCCACAAGTCAGTGGAAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* **
7643 TTCAAAGCCCACAAATCAGTAACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
7672 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
7701 TTCACAAGCCCACAAATCAGTGGCACTCTT
1 TTCA-AAGCCCACAAGTCAGTGGCACTCTT
* *
7731 TTCAAAG-CCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
7758 TTCAAAGCCCACAAATCAGTGACACT-TT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
7786 TTCGAAGCCC-CACAGTTAGTGGTACCCTT
1 TTCAAAGCCCACA-AGTCAGTGGCACTCTT
* *
7815 TT-TAAGCCCACAATTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
**
7843 TTCAAAGCCCACAAGTCAGTGATACTCTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-TT
* * * * * *
7873 TTCAAAGGCCACAAATTAGTGACATTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
7902 TTCAAAACCCACAAGTTAGTGGCAC-C-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
7929 TTCAAAGCCCAC-AGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
7957 TTC-AAGCCCACAAGTTAGTGGC-CTC--
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
7982 TTC-AAGCCCAC-AGTTAGT-GCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
8007 TTCAAAACCCACAATGTTAATGGCCCTC-T
1 TTCAAAGCCCACAA-GTCAGTGGCACTCTT
8036 TTCAAAAGCCCACAAGTCAGTGGCACTCTT
1 TTC-AAAGCCCACAAGTCAGTGGCACTCTT
*
8066 TT-AAAG-CCACAACATCAGTGG-ACTCTT
1 TTCAAAGCCCACAA-GTCAGTGGCACTCTT
* *
8093 TTCAAAGCCTACAAGTCAGT-GCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
8120 TTCAAAGCCCGCAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
8149 TTCAAAACCCAC-AGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
8176 TTCAAAGCCCACAAATCAGTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
8205 TTCAAAG-CCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
8233 TTCAAAGCCCACAACTCAGTGGCACTC--
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
8260 TTCAAAGCCCATAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
8288 TTCAAAGCCCACAAGTCAGTGGCA--CTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
8315 TTCAATGCCCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
8343 TTCAAAACCCAACAAGTCAGTGGCACCCTT
1 TTCAAAGCCC-ACAAGTCAGTGGCACTCTT
*
8373 TTCAAAGCCCACACGTCAGTGGCAC-CTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
8401 TTCAAAACCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
8429 TTCAAAG-CCACAAGTCAGTGGCACT-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT-T
* **
8457 TTCAAAGCCCCCACGAGTTGGTGGCAACTCTT
1 TTCAAAG--CCCACAAGTCAGTGGC-ACTCTT
**
8489 TTCAAAGCCACACAAGTTGGTGGCAC
1 TTCAAAGCC-CACAAGTCAGTGGCAC
8515 AAATTTTTTT
Statistics
Matches: 821, Mismatches: 112, Indels: 99
0.80 0.11 0.10
Matches are distributed among these distances:
23 3 0.00
24 8 0.01
25 14 0.02
26 33 0.04
27 163 0.20
28 268 0.33
29 215 0.26
30 80 0.10
31 25 0.03
32 11 0.01
33 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTT
Found at i:8489 original size:31 final size:32
Alignment explanation
Indices: 8428--8513 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
8418 AGTGGCACCC
**
8428 TTTCAAAG-C-CACAAGTCAGTGGC-ACTTC-
1 TTTCAAAGCCACACAAGTTGGTGGCAACTTCT
* *
8456 TTTCAAAGCCCCCACGAGTTGGTGGCAAC-TCT
1 TTTCAAAG-CCACACAAGTTGGTGGCAACTTCT
8488 TTTCAAAGCCACACAAGTTGGTGGCA
1 TTTCAAAGCCACACAAGTTGGTGGCA
8514 CAAATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 8 0.17
30 1 0.02
31 29 0.60
32 10 0.21
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (32 bp):
TTTCAAAGCCACACAAGTTGGTGGCAACTTCT
Found at i:9364 original size:20 final size:19
Alignment explanation
Indices: 9335--9409 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
9325 AAAAAGACAT
9335 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
9354 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
9375 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
9395 AATGTATCGATACAT
1 AATGTATCGATACAT
9410 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:9392 original size:40 final size:39
Alignment explanation
Indices: 9332--9409 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
9322 GGTAAAAAGA
*
9332 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
9371 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
9410 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:10069 original size:28 final size:29
Alignment explanation
Indices: 9972--10998 Score: 1289
Period size: 29 Copynumber: 35.9 Consensus size: 29
9962 AAAAAAATTT
**
9972 GTGCCACCAACTTGTGTGGCTTTGAAAAGA
1 GTGCCACTGACTTGTG-GGCTTTGAAAAGA
**
10002 GTTGCCACCAACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
*
10034 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10062 GTGCCACTGACTTGTGGGTTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10090 GTGCCACTGACGTGTGGGCTTTGAAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10119 GTGCCACTGACTTGTGGGTTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10147 GTGCCACTAACTTGTGGGCATTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10176 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10204 GTGCCACTGACTTATGGGCTTTG--AAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10231 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
10260 GTGCCACTGACTTGT-GGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10288 GTGCTACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10316 GTGCCACTAACTTGTGGGTTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10345 GTGCCACTGATTTGCGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10373 GTGCCACTGACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10402 GT-CCACTGATTTGTGGGCTTT-AAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10429 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
10458 GTGCCATTAACTTGTGGGTTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10486 GTGCCACTAACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10515 -TGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10543 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10571 GTGCCACTAACTTGTGGGTTTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
10600 ATGTCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
**
10629 GTATCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10658 GTGCCACTGAATTGTGGGCTTT-AAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10686 GTACCACTAACTTGTGGGCTTCGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10715 GTGTCACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10743 GTGCCACTAACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10772 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
10801 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
** * *
10830 GTGTTACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10858 GTTCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10887 GTGCCACTGATTTGTGGGCTTTGAAAACA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10916 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
10944 GTGCCACTTACTCGTGGACTTCGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10973 GTGCCACTGACTTGTGAGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
10999 GGGATAAACA
Statistics
Matches: 862, Mismatches: 115, Indels: 41
0.85 0.11 0.04
Matches are distributed among these distances:
27 32 0.04
28 378 0.44
29 413 0.48
30 1 0.00
31 20 0.02
32 14 0.02
33 4 0.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:11001 original size:57 final size:58
Alignment explanation
Indices: 9972--10998 Score: 1289
Period size: 57 Copynumber: 17.9 Consensus size: 58
9962 AAAAAAATTT
** **
9972 GTGCCACCAACTTGTGTGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTG-GGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
10034 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGTTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
10090 GTGCCACTGACGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGTTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10147 GTGCCACTAACTTGTGGGCATTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10204 GTGCCACTGACTTATGGGCTTTG--AAGAGTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10260 GTGCCACTGACTTGT-GGCTTTGAAAAGAGTGCTACTGATTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
10316 GTGCCACTAACTTGTGGGTTTTGAAAAGAGTGCCACTGATTTGCGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
10373 GTGCCACTGACTTGTAGGCTTTGAAAAGAGT-CCACTGATTTGTGGGCTTT-AAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
10429 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTAACTTGTGGGTTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10486 GTGCCACTAACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
10543 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGTTTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * **
10600 ATGTCACTAATTTGTGGGCTTTGAAAAGAGTATCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
10658 GTGCCACTGAATTGTGGGCTTT-AAAAGGGTACCACTAACTTGTGGGCTTCGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
10715 GTGTCACTGATTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
10772 GTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
** * * *
10830 GTGTTACTGATTTGTGGGCTTTG-AAAGGGTTCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
10887 GTGCCACTGATTTGTGGGCTTTGAAAACAGTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * * *
10944 GTGCCACTTACTCGTGGACTTCGAAAAGAGTGCCACTGACTTGTGAGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
10999 GGGATAAACA
Statistics
Matches: 860, Mismatches: 89, Indels: 36
0.87 0.09 0.04
Matches are distributed among these distances:
55 33 0.04
56 136 0.16
57 531 0.62
58 125 0.15
59 9 0.01
60 5 0.01
61 7 0.01
62 14 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (58 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:12196 original size:21 final size:20
Alignment explanation
Indices: 12170--12223 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
12160 ATCTAGACCC
12170 TTTTCTCTTTTTTTTGCTATT
1 TTTTCT-TTTTTTTTGCTATT
12191 TTTTCTTGGTTTTTTTG-T-TT
1 TTTTCTT--TTTTTTTGCTATT
12211 TTTT-TTTTTTTTT
1 TTTTCTTTTTTTTT
12224 TTTTGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.23
19 2 0.06
20 7 0.23
21 7 0.23
22 8 0.26
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTTTTTGCTATT
Found at i:26182 original size:20 final size:20
Alignment explanation
Indices: 26135--26209 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
26125 AAAAAGACAT
*
26135 AATGTATCGATACATTGA-A
1 AATGTATCGATACATTCATA
*
26154 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * * *
26175 CATGTATCAATATATTGAAA
1 AATGTATCGATACATTCATA
26195 AATGTATCGATACAT
1 AATGTATCGATACAT
26210 CTGGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:26192 original size:40 final size:39
Alignment explanation
Indices: 26132--26209 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
26122 GGTAAAAAGA
* *
26132 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* *
26171 CATACATGTATCAATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
26210 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:27238 original size:42 final size:39
Alignment explanation
Indices: 27191--27305 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 39
27181 TTAGTAAACA
27191 CCACTAAATTTGAATATTTAGTGGTGTTTATACCCAAAAATG
1 CCACTAAATTT-AATATTTAGTGGT-TTTATA-CCAAAAATG
* ***
27233 CCACTAAATTTATGTATTTAGTAGCGTTTTATATGGAAAATG
1 CCACTAAATTTA-ATATTTAGT-G-GTTTTATACCAAAAATG
27275 CCACTAAAATTTAAATATTTAGTGGTATTTA
1 CCACT-AAATTT-AATATTTAGTGGT-TTTA
27306 AAGTTATAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
41 3 0.05
42 35 0.56
43 21 0.34
44 3 0.05
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (39 bp):
CCACTAAATTTAATATTTAGTGGTTTTATACCAAAAATG
Found at i:31163 original size:2 final size:2
Alignment explanation
Indices: 31156--31197 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31146 AACTAAAATA
31156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31198 GAAAGACTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31691 original size:12 final size:12
Alignment explanation
Indices: 31670--31709 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
31660 CATTATATTA
31670 TTAA-ATGTTAT
1 TTAATATGTTAT
31681 TTAATATGTTA-
1 TTAATATGTTAT
31692 TTAATA--TTAT
1 TTAATATGTTAT
31702 TTAATATG
1 TTAATATG
31710 ATTAACTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 3 0.12
10 6 0.24
11 10 0.40
12 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (12 bp):
TTAATATGTTAT
Found at i:31703 original size:21 final size:22
Alignment explanation
Indices: 31666--31740 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
31656 AAATCATTAT
*
31666 ATTATTAAATGTTATTTAATATG
1 ATTATT-AATATTATTTAATATG
31689 -TTATTAATATTATTTAATATG
1 ATTATTAATATTATTTAATATG
* * *
31710 ATTAACTAATATT-TTTAAAATA
1 ATT-ATTAATATTATTTAATATG
31732 ATT-TTAATA
1 ATTATTAATA
31741 CACTATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.11
21 15 0.33
22 17 0.38
23 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTATTAATATTATTTAATATG
Found at i:31788 original size:12 final size:11
Alignment explanation
Indices: 31744--31826 Score: 55
Period size: 12 Copynumber: 7.5 Consensus size: 11
31734 TTTAATACAC
31744 TATTAAATATTA
1 TATTAAATA-TA
*
31756 TCTTAAA-ATA
1 TATTAAATATA
* *
31766 TGTTTAATATA
1 TATTAAATATA
31777 CTATTAAATATA
1 -TATTAAATATA
*
31789 TCATTAAATGT-
1 T-ATTAAATATA
* *
31800 TATCAAAATAAA
1 TAT-TAAATATA
31812 TATTAAA-ATA
1 TATTAAATATA
31822 TATTA
1 TATTA
31827 TATCCACTAG
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
10 16 0.29
11 13 0.24
12 26 0.47
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:32923 original size:10 final size:10
Alignment explanation
Indices: 32908--32932 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32898 AGCTATGAAA
32908 AGAAAAGAAG
1 AGAAAAGAAG
32918 AGAAAAGAAG
1 AGAAAAGAAG
32928 AGAAA
1 AGAAA
32933 CATAGATGGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAAAAGAAG
Found at i:34141 original size:120 final size:114
Alignment explanation
Indices: 34034--34388 Score: 290
Period size: 120 Copynumber: 3.0 Consensus size: 114
34024 TAATTAAATG
*
34034 TTATATTTTATTTTATTAAAAATAATAATGAAAATA-TTTTTTATTTTTTTAAAAATATAATAAT
1 TTATATTTTATTTTATTAAAAATAATAAT-AAAATACTTTTTTTTTTTTTTAAAAA-ATAATAAT
34098 TAATATTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAA--TATTA-
64 TAATATTTTAATTTGTTAAT-TAAATTTTTTAAACTTAATTAAATTTATTAT
* * * *
34147 -T-T-TTTTATTTGATTAAAAATTATAATAAATTTTTTTATTTTTAAATTTTTATTTTATAAAAA
1 TTATATTTTATTTTATTAAAAATAATAATAAA-----ATACTTTT---TTTTT-TTTT-TAAAAA
* *
34209 CATAATAATTAATATTTTAATTTATTAATTTAA-TTTTTAAACTTAATTAAATATTATT-T
56 -ATAATAATTAATATTTTAATTTGTTAATTAAATTTTTTAAACTTAATTAAAT-TTATTAT
* * *
34268 TTA-ATTTTA--TTA-AAACAAATAATAATAAAAAAACCTTTTTATTTTTTATTTGAAAAA-AAT
1 TTATATTTTATTTTATTAA-AAATAATAAT-AAAATA-CTTTTT-TTTTTT-TTTAAAAAATAAT
*
34328 AATTAATATTTCAATTTGTTAATATAAATTTTTTTTAAACTTAATTAAATATTATT-T
61 AATTAATATTTTAATTTGTTAAT-TAAA--TTTTTTAAACTTAATTAAAT-TTATTAT
34385 TTAT
1 TTAT
34389 TAAAAAAATA
Statistics
Matches: 197, Mismatches: 17, Indels: 51
0.74 0.06 0.19
Matches are distributed among these distances:
109 3 0.02
110 22 0.11
111 1 0.01
112 1 0.01
113 24 0.12
114 6 0.03
115 12 0.06
116 6 0.03
117 30 0.15
118 26 0.13
119 7 0.04
120 35 0.18
121 15 0.08
122 4 0.02
123 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (114 bp):
TTATATTTTATTTTATTAAAAATAATAATAAAATACTTTTTTTTTTTTTTAAAAAATAATAATTA
ATATTTTAATTTGTTAATTAAATTTTTTAAACTTAATTAAATTTATTAT
Found at i:34195 original size:45 final size:46
Alignment explanation
Indices: 34148--34236 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
34138 TAAATATTAT
* * * *
34148 TTTTTATTTGATTAAAA-ATTATAATAAATTTTTTTATTT-TTAAA
1 TTTTTATTTGATAAAAACATAATAATAAATATTTTAATTTATTAAA
* *
34192 TTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAA
1 TTTTTATTTGATAAAAACATAATAATAAATATTTTAATTTATTAA
34237 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 15 0.41
45 18 0.49
46 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (46 bp):
TTTTTATTTGATAAAAACATAATAATAAATATTTTAATTTATTAAA
Found at i:34197 original size:14 final size:15
Alignment explanation
Indices: 34178--34206 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34168 ATAATAAATT
34178 TTTTTATTTT-TAAA
1 TTTTTATTTTATAAA
34192 TTTTTATTTTATAAA
1 TTTTTATTTTATAAA
34207 AACATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATTTTATAAA
Found at i:34314 original size:118 final size:116
Alignment explanation
Indices: 34016--34387 Score: 358
Period size: 118 Copynumber: 3.2 Consensus size: 116
34006 AAATTTTTTA
* * * * *
34016 TTTAAATTTAATTAAATGTTATATTTT-ATTTTATT--AAA-AATAAT-AATGAAA-ATATTT-T
1 TTTAAACTTAATTAAATATTAT-TTTTAATTTGATTAAAAATAATAATAAATAAAACATTTTTAT
* *
34074 TTATT-TTTTTAAAAATATAATAATTAATATTTTAATTTGTTAATGTAAATTT
65 TTTTTATTTTTAAAAA-ATAATAATTAATATTTTAATTTGTTAATATAAATTT
* * *****
34126 TTTAAACTTAATTAAATATTATTTTTTATTTGATTAAAAATTATAATAAATTTTTTTATTTTTAA
1 TTTAAACTTAATTAAATATTATTTTTAATTTGATTAAAAATAATAATAAA-TAAAACATTTTT-A
* * *
34191 ATTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAAT-TTAA-TT
64 TTTTTTATTTT-TAAAAA-ATAATAATTAATATTTTAATTTGTTAATATAAATTT
* *
34244 TTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAACAAATAATAATAAA-AAAACCTTTTT
1 TTTAAACTTAATTAAATATTATTTTTAATTTGATT--AA-AAATAATAATAAATAAAACATTTTT
* *
34308 ATTTTTTA--TTTGAAAAA-AATAATTAATATTTCAATTTGTTAATATAAATTTTT
63 ATTTTTTATTTTTAAAAAATAATAATTAATATTTTAATTTGTTAATATAAA--TTT
34361 TTTAAACTTAATTAAATATTATTTTTA
1 TTTAAACTTAATTAAATATTATTTTTA
34388 TTAAAAAAAT
Statistics
Matches: 216, Mismatches: 28, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
109 4 0.02
110 27 0.12
112 3 0.01
113 29 0.13
114 6 0.03
115 6 0.03
116 7 0.03
117 29 0.13
118 46 0.21
119 12 0.06
120 35 0.16
121 12 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (116 bp):
TTTAAACTTAATTAAATATTATTTTTAATTTGATTAAAAATAATAATAAATAAAACATTTTTATT
TTTTATTTTTAAAAAATAATAATTAATATTTTAATTTGTTAATATAAATTT
Found at i:34387 original size:117 final size:111
Alignment explanation
Indices: 34016--34387 Score: 396
Period size: 110 Copynumber: 3.2 Consensus size: 111
34006 AAATTTTTTA
* * * *
34016 TTTAAATTTAATTAAATGTTATATTTT-ATTTTATTAAAAATAATAATGAAAATATTTTT-TATT
1 TTTAAACTTAATTAAATATTAT-TTTTAATTTTATTAAAAATAATAATAAAAATATTTTTATTTT
* *
34079 TTTTTAAAAATATAATAATTAATATTTTAATTTGTTAATGTAAATTT
65 TTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATTT
* * * **
34126 TTTAAACTTAATTAAATATTATTTTTTATTTGATTAAAAATTATAATAAATTTTTTTATTTTTAA
1 TTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAA----AATATTTTT--
* *
34191 ATTTTTATTTTATAAAAACATAATAATTAATATTTTAATTTATTAAT-TTAA-TT
60 A-TTTT-TTTT-TAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATTT
*
34244 TTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAACAAATAATAATAAAAAAACCTTTTTA
1 TTTAAACTTAATTAAATATTATTTTTAATTTTATT--AA-AAATAATAATAAAAATA--TTTTTA
* *
34309 TTTTTTATTTGAAAA-A-AATAATTAATATTTCAATTTGTTAATATAAATTTTT
61 TTTTTT-TTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAA--TTT
34361 TTTAAACTTAATTAAATATTATTTTTA
1 TTTAAACTTAATTAAATATTATTTTTA
34388 TTAAAAAAAT
Statistics
Matches: 220, Mismatches: 21, Indels: 35
0.80 0.08 0.13
Matches are distributed among these distances:
109 4 0.02
110 40 0.18
113 24 0.11
114 11 0.05
115 7 0.03
116 6 0.03
117 31 0.14
118 38 0.17
119 12 0.05
120 35 0.16
121 12 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (111 bp):
TTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAAAATATTTTTATTTTT
TTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATTT
Found at i:35437 original size:155 final size:153
Alignment explanation
Indices: 35119--35435 Score: 381
Period size: 155 Copynumber: 2.1 Consensus size: 153
35109 ATTAAAAACT
* * *
35119 CTACATTTATAAAATACATCAAATTAAAAAGAAAATGGGCTAAAGCCCAAAAAAAAATTATAGAG
1 CTACATATATAAAATACATCAAAGTAAAAAGAAAATGGGCTAAAGCACAAAAAAAAATTATAGAG
* * * * *
35184 GAAGATGGTGTAAATGTCTACAATTAAAGTCTTGGTCTTGGCCAAGGTCAAATAATAATTAAGAC
66 GAAGATGGTGTAAATGTCTACAATTAAAGCCTTGGCCTTCGCCAAGATCAAATAATAATTAACAC
35249 AATTATTCCTCTTTACCCGTCAA
131 AATTATTCCTCTTTACCCGTCAA
** * *
35272 CTACATATATAAAATA-ATCAAAGTGGAAAGAAGAA-GTGCTAAAGCACAAAGAAAAATTATAGA
1 CTACATATATAAAATACATCAAAGTAAAAAGAA-AATGGGCTAAAGCACAAAAAAAAATTATAGA
* * ** * * *
35335 GGAAGATGGTGCTGTAAATGTCTCCATTTAAAGCCTTGGCCTTCGTTAAGATTAGATCATAATTA
65 GGAAGAT-G-G-TGTAAATGTCTACAATTAAAGCCTTGGCCTTCGCCAAGATCAAATAATAATTA
* *
35400 ACACAATTATTTCTCTTTACCCTTCAA
127 ACACAATTATTCCTCTTTACCCGTCAA
35427 --ACATATATA
1 CTACATATATA
35436 TATTAAAGAC
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
152 45 0.32
153 27 0.19
154 1 0.01
155 66 0.47
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (153 bp):
CTACATATATAAAATACATCAAAGTAAAAAGAAAATGGGCTAAAGCACAAAAAAAAATTATAGAG
GAAGATGGTGTAAATGTCTACAATTAAAGCCTTGGCCTTCGCCAAGATCAAATAATAATTAACAC
AATTATTCCTCTTTACCCGTCAA
Found at i:35531 original size:14 final size:14
Alignment explanation
Indices: 35512--35541 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35502 TAACAGAAAT
*
35512 TAAGTTTTCATGTA
1 TAAGTTTTCATATA
35526 TAAGTTTTCATATA
1 TAAGTTTTCATATA
35540 TA
1 TA
35542 TAATACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (14 bp):
TAAGTTTTCATATA
Found at i:35645 original size:18 final size:18
Alignment explanation
Indices: 35620--35662 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35610 GAACAAGTTC
*
35620 TTTATATATGACTTAT-T
1 TTTATATATAACTTATAT
35637 TTGTATATATAACTTATAT
1 TT-TATATATAACTTATAT
35656 TTTATAT
1 TTTATAT
35663 TTTATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 18 0.78
19 3 0.13
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTATATATAACTTATAT
Found at i:35767 original size:22 final size:22
Alignment explanation
Indices: 35739--35780 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35729 ATTTAATAAA
*
35739 ATTAAT-ATAAATGATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
35761 ATTAATAATAAAAATTTAAT
1 ATTAATAATAAAAATTTAAT
35781 AAATGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:37818 original size:2 final size:2
Alignment explanation
Indices: 37811--37855 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
37801 ATTTCCAGTC
37811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37853 AT A
1 AT A
37856 ACTTTGTAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39144 original size:25 final size:26
Alignment explanation
Indices: 39094--39147 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
39084 AATTATTTAA
* *
39094 AATCTCAGATAAAGTTAAATTTTATC
1 AATCTCAGATAAAATTAAACTTTATC
39120 AATCTCAG-TAAAATTAAACTTTATC
1 AATCTCAGATAAAATTAAACTTTATC
39145 AAT
1 AAT
39148 TCTATCTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (26 bp):
AATCTCAGATAAAATTAAACTTTATC
Found at i:47154 original size:26 final size:26
Alignment explanation
Indices: 47117--47173 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
47107 ACTTATCTAG
* *
47117 AATCCCAAATAAAATTAAACTTTATC
1 AATCCCAAATAAAAGTAAACTTAATC
* *
47143 AATCCCAGATAAAAGTGAACTTAATC
1 AATCCCAAATAAAAGTAAACTTAATC
47169 AATCC
1 AATCC
47174 TATCTCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (26 bp):
AATCCCAAATAAAAGTAAACTTAATC
Found at i:47355 original size:3 final size:3
Alignment explanation
Indices: 47347--47393 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
47337 TAAGCCATAT
47347 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
47394 CAAAGTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:47533 original size:2 final size:2
Alignment explanation
Indices: 47526--47565 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47516 TTTAGCTGTC
47526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47566 TAGATACTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50171 original size:13 final size:14
Alignment explanation
Indices: 50144--50173 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
50134 AAAAGGAATG
50144 AATTAAAATAATAA
1 AATTAAAATAATAA
50158 AATTAAAA-AATAA
1 AATTAAAATAATAA
50171 AAT
1 AAT
50174 ACATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATTAAAATAATAA
Found at i:50179 original size:22 final size:22
Alignment explanation
Indices: 50147--50203 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
50137 AGGAATGAAT
*
50147 TAAAATAATAAAATTAA-AAAA
1 TAAAATAATAAAATAAACAAAA
50168 TAAAATACAT-AAATAAACAAAA
1 TAAAATA-ATAAAATAAACAAAA
50190 TAAAATAAATAAAA
1 TAAAAT-AATAAAA
50204 AATAATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAATAATAAAATAAACAAAA
Found at i:50190 original size:9 final size:9
Alignment explanation
Indices: 50147--50241 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 9
50137 AGGAATGAAT
50147 TAAAAT-AA
1 TAAAATAAA
*
50155 TAAAATTAA
1 TAAAATAAA
50164 -AAAATAAA
1 TAAAATAAA
*
50172 -ATACATAAA
1 TA-AAATAAA
50181 TAAACA-AAA
1 TAAA-ATAAA
50190 TAAAATAAA
1 TAAAATAAA
*
50199 TAAAAAATAA
1 TAAAATA-AA
* *
50209 TTAGATAAA
1 TAAAATAAA
*
50218 TATAAATTAAT
1 TA-AAA-TAAA
*
50229 TAAAATGAA
1 TAAAATAAA
50238 TAAA
1 TAAA
50242 TCAAAAAAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
8 15 0.22
9 34 0.51
10 13 0.19
11 5 0.07
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (9 bp):
TAAAATAAA
Found at i:50218 original size:19 final size:19
Alignment explanation
Indices: 50161--50232 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
50151 ATAATAAAAT
* *
50161 TAAAAAATAAAATACATAAA
1 TAAAAAAT-AATTAAATAAA
* *
50181 TAAACAA-AATAAAATAAA
1 TAAAAAATAATTAAATAAA
*
50199 TAAAAAATAATTAGATAAA
1 TAAAAAATAATTAAATAAA
* *
50218 TATAAATTAATTAAA
1 TAAAAAATAATTAAA
50233 ATGAATAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
18 14 0.34
19 21 0.51
20 6 0.15
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (19 bp):
TAAAAAATAATTAAATAAA
Found at i:50259 original size:10 final size:10
Alignment explanation
Indices: 50244--50281 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
50234 TGAATAAATC
50244 AAAAAAAGAA
1 AAAAAAAGAA
*
50254 AAAAAAATATA
1 AAAAAAAGA-A
50265 AAAAAAAGAA
1 AAAAAAAGAA
50275 AAAAAAA
1 AAAAAAA
50282 ACTAATGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.89, C:0.00, G:0.05, T:0.05
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:54138 original size:27 final size:27
Alignment explanation
Indices: 54106--54179 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
54096 AAACAACATG
*
54106 CCACCATTTTTGACAAATAAAAACAAA
1 CCACCATTTTTGACAAACAAAAACAAA
* * **
54133 CCACCATTTTTTACAAACACAAAGTAA
1 CCACCATTTTTGACAAACAAAAACAAA
* *
54160 TCACAATTTTTGACAAACAA
1 CCACCATTTTTGACAAACAA
54180 TGGGTGGTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAACAAA
Found at i:58709 original size:27 final size:27
Alignment explanation
Indices: 58675--58796 Score: 97
Period size: 27 Copynumber: 4.6 Consensus size: 27
58665 AAATAACATG
58675 TCACCATTTTTTACAAATAAAAAGAAA
1 TCACCATTTTTTACAAATAAAAAGAAA
* * *
58702 TCACCATTTTTTACAAACATAAAGTAA
1 TCACCATTTTTTACAAATAAAAAGAAA
* ** * * * * **
58729 CCATAAATTTTGAC-AA-ACAACG-TG
1 TCACCATTTTTTACAAATAAAAAGAAA
*
58753 TCACCATTTTTGACAAATAAAAAGAAA
1 TCACCATTTTTTACAAATAAAAAGAAA
*
58780 TCACTATTTTTTACAAA
1 TCACCATTTTTTACAAA
58797 CACAAAATAA
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
24 10 0.14
25 6 0.09
26 6 0.09
27 48 0.69
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (27 bp):
TCACCATTTTTTACAAATAAAAAGAAA
Found at i:58756 original size:78 final size:78
Alignment explanation
Indices: 58652--58819 Score: 264
Period size: 78 Copynumber: 2.2 Consensus size: 78
58642 AAAAATTAGT
* *
58652 CACAAATTTTGACAAATAACATGTCACCATTTTTTACAAATAAAAAGAAATCACCATTTTTTACA
1 CACAAATTTTGACAAACAACATGTCACCATTTTTGACAAATAAAAAGAAATCACCATTTTTTACA
* *
58717 AACATAAAGTAAC
66 AACACAAAATAAC
* * *
58730 CATAAATTTTGACAAACAACGTGTCACCATTTTTGACAAATAAAAAGAAATCACTATTTTTTACA
1 CACAAATTTTGACAAACAACATGTCACCATTTTTGACAAATAAAAAGAAATCACCATTTTTTACA
58795 AACACAAAATAAC
66 AACACAAAATAAC
*
58808 CACAATTTTTGA
1 CACAAATTTTGA
58820 TAAATAATGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (78 bp):
CACAAATTTTGACAAACAACATGTCACCATTTTTGACAAATAAAAAGAAATCACCATTTTTTACA
AACACAAAATAAC
Found at i:61744 original size:17 final size:16
Alignment explanation
Indices: 61714--61745 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
61704 TAATATCACA
61714 TTTATTTTTATTTTAT
1 TTTATTTTTATTTTAT
61730 TTTATTTTGTATTTTA
1 TTTATTTT-TATTTTA
61746 ATAAAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTATTTTTATTTTAT
Found at i:63906 original size:16 final size:14
Alignment explanation
Indices: 63889--63947 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 14
63879 TTTCTAAATG
63889 TATACATATTATATT
1 TATA-ATATTATATT
63904 GTATTTAA-ATTAT-TT
1 -TA--TAATATTATATT
63919 TATAATATTATATT
1 TATAATATTATATT
*
63933 TAT-ATATCATATT
1 TATAATATTATATT
63946 TA
1 TA
63948 ATATTATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 3 0.08
13 16 0.42
14 7 0.18
15 2 0.05
16 7 0.18
17 1 0.03
18 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (14 bp):
TATAATATTATATT
Found at i:63939 original size:13 final size:13
Alignment explanation
Indices: 63898--63954 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
63888 GTATACATAT
*
63898 TATATTGTATTTA
1 TATATTATATTTA
63911 -A-ATTAT-TTTA
1 TATATTATATTTA
63921 TAATATTATATTTA
1 T-ATATTATATTTA
*
63935 TATATCATATTTA
1 TATATTATATTTA
63948 -ATATTAT
1 TATATTAT
63955 CAAATAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.11
11 4 0.11
12 8 0.22
13 16 0.43
14 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:65276 original size:20 final size:20
Alignment explanation
Indices: 65251--65290 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65241 TAGTTTAATT
65251 CATCTGCTTTTCTATGGCAA
1 CATCTGCTTTTCTATGGCAA
65271 CATCTGCTTTTCTATGGCAA
1 CATCTGCTTTTCTATGGCAA
65291 GACAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (20 bp):
CATCTGCTTTTCTATGGCAA
Found at i:68385 original size:16 final size:18
Alignment explanation
Indices: 68364--68399 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
68354 ATTTACATAA
68364 AAAAATTAT-T-AATATT
1 AAAAATTATATAAATATT
68380 AAAAATTATATAAATATT
1 AAAAATTATATAAATATT
68398 AA
1 AA
68400 TAACTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTATATAAATATT
Found at i:68674 original size:20 final size:19
Alignment explanation
Indices: 68610--68676 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
68600 ATAAAATAAA
68610 ATAAAAATAGTAT-TAATAT
1 ATAAAAATA-TATATAATAT
* *
68629 AATATAAATTTATA-AATAT
1 -ATAAAAATATATATAATAT
* *
68648 GTTAAAATATATATAATAAT
1 ATAAAAATATATATAAT-AT
68668 ATAAAAATA
1 ATAAAAATA
68677 ACACAAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 9 0.25
19 11 0.31
20 16 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
ATAAAAATATATATAATAT
Found at i:70780 original size:2 final size:2
Alignment explanation
Indices: 70767--70798 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
70757 AAAATCTCAA
*
70767 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70799 TAAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:71539 original size:19 final size:19
Alignment explanation
Indices: 71491--71539 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
71481 ATCATCAAAT
* *
71491 AATTTTATTTTATTTTTTA
1 AATTTTATTTTATTTATAA
71510 AATTATTATTTT-TTTATAA
1 AATT-TTATTTTATTTATAA
71529 AAGTTTTATTT
1 AA-TTTTATTT
71540 AAAAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
AATTTTATTTTATTTATAA
Found at i:71993 original size:103 final size:102
Alignment explanation
Indices: 71864--72067 Score: 306
Period size: 103 Copynumber: 2.0 Consensus size: 102
71854 TAATATCAAA
** *
71864 AAATAATATAGAGTATTTTGGGTTTTAATTTTTTATATAAATTTAAAAAATAAATTACTTATTTT
1 AAATAATATAGAACATTTTGGGTTTTAACTTTTTATATAAATTTAAAAAATAAATTACTTA--TT
71929 TAAAAAAAA-CTAT-TTTTAAAAAACTATCATAAAACTAT
64 TAAAAAAAATCTATGTTTT-AAAAACTATCATAAAACTAT
* *
71967 AAATAATATA-AACATTTTGGGTTTTTAACTTTTTATATAAATTTAGAAATTAAATTACTTATTT
1 AAATAATATAGAACATTTTGGG-TTTTAACTTTTTATATAAATTTAAAAAATAAATTACTTATTT
72031 AAAAAAAATCTATGTTTTAAAAACTATCATAAAACTA
65 AAAAAAAATCTATGTTTTAAAAACTATCATAAAACTA
72068 CATACTTCTT
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
101 11 0.12
102 32 0.34
103 50 0.54
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (102 bp):
AAATAATATAGAACATTTTGGGTTTTAACTTTTTATATAAATTTAAAAAATAAATTACTTATTTA
AAAAAAATCTATGTTTTAAAAACTATCATAAAACTAT
Found at i:73068 original size:10 final size:10
Alignment explanation
Indices: 73053--73077 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
73043 TGATAGAATG
73053 ATTAAAAATA
1 ATTAAAAATA
73063 ATTAAAAATA
1 ATTAAAAATA
73073 ATTAA
1 ATTAA
73078 TAAAACTAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:73804 original size:22 final size:22
Alignment explanation
Indices: 73762--73804 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
73752 TGATCTAATT
**
73762 TGAATAATTTAAATATTAAATC
1 TGAATAATTTAAATAAAAAATC
*
73784 TGAATTATTTAAATAAAAAAT
1 TGAATAATTTAAATAAAAAAT
73805 AAAGAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TGAATAATTTAAATAAAAAATC
Found at i:74733 original size:17 final size:16
Alignment explanation
Indices: 74705--74756 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
74695 TATTAAAAAT
* *
74705 ATATAAGTATTTTTTA
1 ATATAAATATTTTTAA
*
74721 ATATAAATAATTTATGAA
1 ATATAAAT-ATTT-TTAA
74739 ATATAAATATTTTTAA
1 ATATAAATATTTTTAA
74755 AT
1 AT
74757 TTTATCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 12 0.40
17 8 0.27
18 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
ATATAAATATTTTTAA
Found at i:74956 original size:13 final size:12
Alignment explanation
Indices: 74898--74955 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
74888 TATTAAAATA
74898 TTTATAATTATT
1 TTTATAATTATT
*
74910 TTTTTAA-TATT
1 TTTATAATTATT
* *
74921 TTTATAAATAAT
1 TTTATAATTATT
74933 TTTATTAATTTATT
1 TTTA-TAA-TTATT
74947 TTTATAATT
1 TTTATAATT
74956 TGTTATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.26
12 15 0.39
13 6 0.16
14 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATAATTATT
Found at i:75937 original size:3 final size:3
Alignment explanation
Indices: 75929--75959 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
75919 CTCTTTTCCT
75929 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
75960 GCTCTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.