Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008639.1 Hibiscus syriacus cultivar Beakdansim tig00111614_pilon, whole genome shotgun sequence
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: 1076872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:65 original size:12 final size:12
Alignment explanation
Indices: 48--72 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38 ATATAATCCT
48 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60 GAAGAAGAAAAA
1 GAAGAAGAAAAA
72 G
1 G
73 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2386 original size:14 final size:14
Alignment explanation
Indices: 2367--2402 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2357 GCGAAATGAA
2367 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2381 AATCGCAACGAGGG
1 AATCGCAACGAGAG
2395 AATCGCAA
1 AATCGCAA
2403 TGCGAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.22, G:0.28, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2445 original size:19 final size:20
Alignment explanation
Indices: 2423--2465 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2413 AAATCGCAAC
2423 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2442 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2462 GCGA
1 GCGA
2466 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2450 original size:14 final size:14
Alignment explanation
Indices: 2451--2484 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2441 TGCGATTTTC
2451 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2465 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2479 ATTTTC
1 ATTTTC
2485 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2624 original size:14 final size:14
Alignment explanation
Indices: 2605--2641 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2595 CATCAATTAA
2605 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2619 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2633 ACAAATCAA
1 ACAAATCAA
2642 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6197 original size:33 final size:33
Alignment explanation
Indices: 6140--6238 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
6130 ACGAGATAAT
*
6140 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
6174 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
6207 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
6239 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:6232 original size:19 final size:19
Alignment explanation
Indices: 6115--6299 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
6105 TCTTTTGGTT
*
6115 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
6134 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
6154 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
6172 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
6188 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
6206 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
6221 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* * *
6241 GAAATTAAAATCCCAACTC
1 GAAATGAAAATCGCAACGC
6260 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
6279 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
6298 GA
1 GA
6300 TTTTGGTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 59 0.44
20 44 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:6263 original size:39 final size:38
Alignment explanation
Indices: 6115--6299 Score: 129
Period size: 33 Copynumber: 5.1 Consensus size: 38
6105 TCTTTTGGTT
* * *
6115 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCCCAACGC
** * *
6154 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCCCAACGC
** * * *
6188 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCCCAACGC
* *
6221 GAAATGAAAATCGCAACCGCGAAATTAAAATCCCAACTC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCCCAACGC
* *
6260 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCCCAACGC
6298 GA
1 GA
6300 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
33 42 0.34
34 16 0.13
35 2 0.02
38 22 0.18
39 26 0.21
40 14 0.11
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCCCAACGC
Found at i:6328 original size:19 final size:19
Alignment explanation
Indices: 6295--6339 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
6285 AAAATCGCAA
*
6295 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
6314 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
6333 TGCGATT
1 TGCGATT
6340 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:6976 original size:20 final size:20
Alignment explanation
Indices: 6891--6984 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
6881 CGCTAAGTAA
*
6891 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
6911 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
6931 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
6952 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
6972 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
6985 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:7003 original size:41 final size:41
Alignment explanation
Indices: 6973--7068 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
6963 ATAGTCAGTA
* * *
6973 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
7014 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
7055 TCGCATTGCGAATT
1 TCGCATTGCGAATT
7069 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:7017 original size:20 final size:20
Alignment explanation
Indices: 6973--7065 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
6963 ATAGTCAGTA
* **
6973 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
6994 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
7014 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
7035 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
7055 TCGCATTGCGA
1 TCGCATTGCGA
7066 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:11072 original size:28 final size:28
Alignment explanation
Indices: 11007--11115 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 28
10997 CTTATATCAT
* *
11007 AAATAAATACTTATAGTATATTTTATTTTTT
1 AAATAAATACTTA-A-AATATTTT-TTTTTC
**
11038 ATTTAAATACTTAAAATATTTTTTTTTC
1 AAATAAATACTTAAAATATTTTTTTTTC
* **
11066 AAATAAATACTTAAAATTATCTTTTAGTC
1 AAATAAATACTTAAAA-TATTTTTTTTTC
* *
11095 AAAATAGATACCTAAAATATT
1 -AAATAAATACTTAAAATATT
11116 CTATATCAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
28 19 0.30
29 19 0.30
30 15 0.23
31 11 0.17
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (28 bp):
AAATAAATACTTAAAATATTTTTTTTTC
Found at i:11111 original size:30 final size:29
Alignment explanation
Indices: 11066--11143 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
11056 TTTTTTTTTC
* * *
11066 AAATAAATACTTAAAATTA-TCTTTTAGTCA
1 AAATAGATACCTAAAATTATTC-TATA-TCA
11096 AAATAGATACCTAAAA-TATTCTATATCA
1 AAATAGATACCTAAAATTATTCTATATCA
11124 AAATAGATACCT-AAATTATT
1 AAATAGATACCTAAAATTATT
11144 TAAACTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
27 3 0.07
28 19 0.44
29 5 0.12
30 16 0.37
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATAGATACCTAAAATTATTCTATATCA
Found at i:11285 original size:30 final size:29
Alignment explanation
Indices: 11226--11316 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 29
11216 GAAAAAATTG
* *
11226 AATATTTTAGATTTCTATTTTGAGAAAAAA
1 AATATTTTA-ATTACTATTTTGACAAAAAA
*
11256 AATATTTTAATTACCTATTTTGACCAAAAA
1 AATATTTTAATTA-CTATTTTGACAAAAAA
* * *
11286 GATAATTTTAAGTACTCATTTTGATAAAAAA
1 AAT-ATTTTAATTACT-ATTTTGACAAAAAA
11317 TTACTTTAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.06
30 27 0.53
31 21 0.41
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
AATATTTTAATTACTATTTTGACAAAAAA
Found at i:11507 original size:11 final size:11
Alignment explanation
Indices: 11491--11517 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11481 GTAGTGATGA
11491 ATAACTAAATT
1 ATAACTAAATT
11502 ATAACTAAATT
1 ATAACTAAATT
11513 ATAAC
1 ATAAC
11518 AATAAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAACTAAATT
Found at i:13417 original size:16 final size:16
Alignment explanation
Indices: 13382--13442 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
13372 AGATCCAACT
* *
13382 GAAAATAATCCGAATT
1 GAAAATAATCCAAATC
*
13398 GAAAGTAATCCAAATC
1 GAAAATAATCCAAATC
13414 GAAAATAA-CACAAATC
1 GAAAATAATC-CAAATC
13430 -AAAAGTAATCCAA
1 GAAAA-TAATCCAA
13443 TTCAAATTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 32 0.84
17 1 0.03
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.18
Consensus pattern (16 bp):
GAAAATAATCCAAATC
Found at i:13447 original size:16 final size:16
Alignment explanation
Indices: 13399--13448 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
13389 ATCCGAATTG
13399 AAAGTAATCCAAATCGA
1 AAAGTAATCCAAATC-A
13416 AAA-TAA-CACAAATCA
1 AAAGTAATC-CAAATCA
*
13431 AAAGTAATCCAATTCA
1 AAAGTAATCCAAATCA
13447 AA
1 AA
13449 TTGACACCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAGTAATCCAAATCA
Found at i:20965 original size:2 final size:2
Alignment explanation
Indices: 20958--20998 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20948 TTAACTGACA
20958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20999 GATGCAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23263 original size:13 final size:13
Alignment explanation
Indices: 23245--23271 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23235 CATAATTGAA
23245 CAGTCTTCATATG
1 CAGTCTTCATATG
23258 CAGTCTTCATATG
1 CAGTCTTCATATG
23271 C
1 C
23272 GCGTCTGTAC
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:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:24196 original size:29 final size:30
Alignment explanation
Indices: 24163--24225 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
24153 AAATTTTGGC
*
24163 TAGTGACTAAAATATAAGCTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
24192 TAGTGGCTAAAGTATAAACTTTGTAAAAGTT
1 TAGTGACTAAAATATAAACTTTG-AAAAGTT
24223 TAG
1 TAG
24226 GGATCAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
31 9 0.31
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:29100 original size:59 final size:59
Alignment explanation
Indices: 29024--29165 Score: 178
Period size: 59 Copynumber: 2.4 Consensus size: 59
29014 ATATGGATAA
* * ** ***
29024 TCAGGTGACCATGTTGTATCTTTTAATAGTCGAGGGACTCAACAAAGTAATGTCCTATAG
1 TCAGG-GACCATTTTGTATCTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAG
*
29084 TCAGGGACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAG
1 TCAGGGACCATTTTGTATCTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAG
29143 TCAAGGGACCA-TTTGTATACTTT
1 TC-AGGGACCATTTTGTAT-CTTT
29166 GCCCTAAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
59 54 0.76
60 17 0.24
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (59 bp):
TCAGGGACCATTTTGTATCTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAG
Found at i:31847 original size:31 final size:30
Alignment explanation
Indices: 31812--31870 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
31802 AAACTATCAA
** *
31812 TTTTGGTTTGCTTTAGTACTTAAACTTTTAG
1 TTTTGGTCCGCTTTAGTACCTAAA-TTTTAG
31843 TTTTGGTCCGCTTTAGTACCTAAATTTT
1 TTTTGGTCCGCTTTAGTACCTAAATTTT
31871 CATTCTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.53
Consensus pattern (30 bp):
TTTTGGTCCGCTTTAGTACCTAAATTTTAG
Found at i:32160 original size:13 final size:12
Alignment explanation
Indices: 32137--32179 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 12
32127 CATACGATTT
32137 TTATAATATAAAA
1 TTAT-ATATAAAA
32150 TTCATATATAAAA
1 TT-ATATATAAAA
32163 TTATATTATAAATA
1 TTATA-TATAAA-A
32177 TTA
1 TTA
32180 CAAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.11
13 18 0.67
14 6 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATATATAAAA
Found at i:34806 original size:2 final size:2
Alignment explanation
Indices: 34799--34832 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34789 AAATAATAAT
34799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34833 TAATAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35419 original size:14 final size:16
Alignment explanation
Indices: 35389--35421 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
35379 TTAGGTGATT
35389 TTAAAAATTATTAAAA
1 TTAAAAATTATTAAAA
35405 TTAAAAA-TA-TAAAA
1 TTAAAAATTATTAAAA
35419 TTA
1 TTA
35422 TACATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAAAATTATTAAAA
Found at i:35560 original size:19 final size:19
Alignment explanation
Indices: 35536--35573 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35526 CCATTTTTGT
35536 TGCCACTACCGTCGAACCA
1 TGCCACTACCGTCGAACCA
35555 TGCCACTACCGTCGAACCA
1 TGCCACTACCGTCGAACCA
35574 CCGACCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.16, T:0.16
Consensus pattern (19 bp):
TGCCACTACCGTCGAACCA
Found at i:43614 original size:36 final size:33
Alignment explanation
Indices: 43574--43644 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
43564 AACTTTAAGT
43574 ATTAAAACGAAACAAAAGTAATAAATTAGATACTAA
1 ATTAAAACGAAACAAAAG---TAAATTAGATACTAA
* *
43610 ATTAAAATGGAACAAAAGTAAATTAGATACTAA
1 ATTAAAACGAAACAAAAGTAAATTAGATACTAA
43643 AT
1 AT
43645 ATTTTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.52
36 16 0.48
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (33 bp):
ATTAAAACGAAACAAAAGTAAATTAGATACTAA
Found at i:44467 original size:16 final size:16
Alignment explanation
Indices: 44448--44488 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
44438 AAATTTTTTA
44448 TATTTTAAAAT-TAAAT
1 TATTTTAAAATAT-AAT
*
44464 TATTTT-ATATATAAT
1 TATTTTAAAATATAAT
44479 TATTTTAAAA
1 TATTTTAAAA
44489 AGTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTTAAAATATAAT
Found at i:44485 original size:31 final size:34
Alignment explanation
Indices: 44448--44511 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
44438 AAATTTTTTA
*
44448 TATTTT-AAAA-TTAAATTAT-TTTATATATAAT
1 TATTTTAAAAAGTTAAATTATATATATATATAAT
44479 TATTTTAAAAAGTTTAAATTATATATATATATA
1 TATTTTAAAAAG-TTAAATTATATATATATATA
44512 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 4 0.14
34 9 0.32
35 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
TATTTTAAAAAGTTAAATTATATATATATATAAT
Found at i:44505 original size:2 final size:2
Alignment explanation
Indices: 44498--44536 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44488 AAGTTTAAAT
44498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44537 CTTTCTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44655 original size:62 final size:61
Alignment explanation
Indices: 44536--44659 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 61
44526 TATATATATA
* * * *
44536 TCTTTCTTACTATGTTTGTTATTCATCTATTTTTAAAAAAGTTTAAATTGCATATTATTTTT
1 TCTTTCTTACAATGTTTGTTATTCATCTATATTTAAAAAAATTTAAAAT-CATATTATTTTT
*
44598 TCTTTCTTACAATGTTTGTTATTCATTTATCATTTAAAAATAATTATAAAAT-A-ATTATTTTT
1 TCTTTCTTACAATGTTTGTTATTCATCTAT-ATTTAAAAA-AATT-TAAAATCATATTATTTTT
44660 AAATAAGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 37 0.69
63 9 0.17
64 3 0.06
65 5 0.09
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (61 bp):
TCTTTCTTACAATGTTTGTTATTCATCTATATTTAAAAAAATTTAAAATCATATTATTTTT
Found at i:44657 original size:25 final size:25
Alignment explanation
Indices: 44629--44695 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
44619 TTCATTTATC
44629 ATTTAAAAATAATTATAAAATAAT-T
1 ATTTAAAAATAATTAT-AAATAATAT
** *
44654 ATTTTTAAATAAGTT-TAAATTATAT
1 ATTTAAAAATAA-TTATAAATAATAT
44679 ATTATAAAAATAATTAT
1 ATT-TAAAAATAATTAT
44696 TTTTAAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 6 0.18
25 17 0.52
26 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
ATTTAAAAATAATTATAAATAATAT
Found at i:44693 original size:40 final size:39
Alignment explanation
Indices: 44640--44721 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
44630 TTTAAAAATA
* *
44640 ATTATAAAATAATTATTTTTAAATAAGTTTAAATTATAT
1 ATTATAAAATAATTATTTTTAAACAAATTTAAATTATAT
*
44679 ATTATAAAAATAATTATTTTTAAACAAATTTAAATTCTAT
1 ATTAT-AAAATAATTATTTTTAAACAAATTTAAATTATAT
44719 ATT
1 ATT
44722 GTTTTGTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 5 0.13
40 34 0.87
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (39 bp):
ATTATAAAATAATTATTTTTAAACAAATTTAAATTATAT
Found at i:44751 original size:131 final size:130
Alignment explanation
Indices: 44563--44812 Score: 405
Period size: 131 Copynumber: 1.9 Consensus size: 130
44553 GTTATTCATC
44563 TATTTTTAAAAAAGTTTAAATTGCATATTATTTTTTCTTTCTTACAATGTTTGTTATTCATTTAT
1 TATTTTTAAAAAAGTTTAAATTGCATATTATTTTTTCTTTCTTACAATGTTTGTTATTCATTTAT
44628 CATTTAAAAATAATTATAAAATAATTATTTTTAAATAAGTTTAAATTATATATTATAAAAATAAT
66 CATTTAAAAATAATTATAAAATAATTATTTTTAAATAAGTTTAAATTATATATTATAAAAATAAT
* *
44693 TATTTTTAAACAAA-TTTAAATT-CTATATTGTTTTGTTCTTTCTTGCAATGTTTGTTATTCATT
1 TATTTTTAAA-AAAGTTTAAATTGC-ATATTATTTT-TTCTTTCTTACAATGTTTGTTATTCATT
* * * *
44756 TATCATTTAAACATAATTGTAAAATGATTATTTTTAAATAATTTTAAATTATATATT
63 TATCATTTAAAAATAATTATAAAATAATTATTTTTAAATAAGTTTAAATTATATATT
44813 GTTGAACTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
129 1 0.01
130 27 0.24
131 83 0.75
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (130 bp):
TATTTTTAAAAAAGTTTAAATTGCATATTATTTTTTCTTTCTTACAATGTTTGTTATTCATTTAT
CATTTAAAAATAATTATAAAATAATTATTTTTAAATAAGTTTAAATTATATATTATAAAAATAAT
Found at i:46530 original size:17 final size:15
Alignment explanation
Indices: 46508--46545 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
46498 AAAGAATAAG
46508 GAAAAAGAAGAAGAGAA
1 GAAAAAGAA-AA-AGAA
46525 GAAAAAGAAAAAGAA
1 GAAAAAGAAAAAGAA
46540 -AAAAAG
1 GAAAAAG
46546 GAGTTGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 4 0.19
16 2 0.10
17 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAAGAA
Found at i:47131 original size:21 final size:23
Alignment explanation
Indices: 47090--47132 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
47080 TTGAAGTTTC
47090 AAAAATCAAAATCAATGATTTAG
1 AAAAATCAAAATCAATGATTTAG
*
47113 AAAAAT-AAAATC-TTGATTTA
1 AAAAATCAAAATCAATGATTTA
47133 AAAGTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAATCAAAATCAATGATTTAG
Found at i:50174 original size:18 final size:18
Alignment explanation
Indices: 50139--50185 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
50129 TCCAAAATAC
* *
50139 ATTATCTTTAAAATTTTA
1 ATTATATTTAAAAGTTTA
*
50157 TATTAT-TTTAGAAGTTTA
1 -ATTATATTTAAAAGTTTA
50175 ATTATATTTAA
1 ATTATATTTAA
50186 TAATCCGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTATATTTAAAAGTTTA
Found at i:50222 original size:26 final size:24
Alignment explanation
Indices: 50193--50240 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
50183 TAATAATCCG
50193 TTTTAAGTGAAATATCAAACATATTT
1 TTTTAAGTGAAA-ATCAAA-ATATTT
* *
50219 TTTTAATTTAAAATCAAAATAT
1 TTTTAAGTGAAAATCAAAATAT
50241 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 6 0.30
26 10 0.50
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTAAGTGAAAATCAAAATATTT
Found at i:51661 original size:40 final size:40
Alignment explanation
Indices: 51586--51661 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
51576 TTTTAAGAGT
* ** *
51586 TACAACTGAAAATGTTATACAAATTCATAATATTTTCGAC
1 TACAACTGAAAATCTTATACAAAAACATAACATTTTCGAC
*
51626 TACAACTGAAAATCTTATA-AATAAAGATAACATTTT
1 TACAACTGAAAATCTTATACAA-AAACATAACATTTT
51662 TAGTTCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.07
40 28 0.93
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (40 bp):
TACAACTGAAAATCTTATACAAAAACATAACATTTTCGAC
Found at i:52418 original size:9 final size:9
Alignment explanation
Indices: 52406--52431 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52396 ATTATGGTTC
52406 GTGATTACG
1 GTGATTACG
52415 GTGATTACG
1 GTGATTACG
52424 GTGATTAC
1 GTGATTAC
52432 AATAATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (9 bp):
GTGATTACG
Found at i:57578 original size:13 final size:13
Alignment explanation
Indices: 57560--57613 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
57550 GTCATAAATC
*
57560 TATGACGCACATT
1 TATGACGCTCATT
**
57573 TATGACATTCATT
1 TATGACGCTCATT
57586 TATGACGCTCATT
1 TATGACGCTCATT
*
57599 TATGATGCTCATT
1 TATGACGCTCATT
57612 TA
1 TA
57614 GCGTCATTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (13 bp):
TATGACGCTCATT
Found at i:64303 original size:21 final size:21
Alignment explanation
Indices: 64277--64323 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
64267 ATCCAGGCGA
64277 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
64298 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
64319 CATAC
1 CATAC
64324 AAGCCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (21 bp):
CATACGGGGTGACATACGAGC
Found at i:64322 original size:9 final size:9
Alignment explanation
Indices: 64310--64349 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
64300 TACGGGGTGA
64310 CATACGAGC
1 CATACGAGC
*
64319 CATACAAGC
1 CATACGAGC
64328 CATATACGAGC
1 C--ATACGAGC
64339 CATACGAGC
1 CATACGAGC
64348 CA
1 CA
64350 ATGGAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:64336 original size:20 final size:20
Alignment explanation
Indices: 64311--64349 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
64301 ACGGGGTGAC
64311 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
64331 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
64350 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:64392 original size:28 final size:28
Alignment explanation
Indices: 64352--64408 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
64342 ACGAGCCAAT
*
64352 GGAGAGGTCGCCATGCAGTCTTATACGA
1 GGAGAGGTCGCCATGCAGTCTTAGACGA
64380 GGAGAGGTCGCCATGCAGTCTTAGACGA
1 GGAGAGGTCGCCATGCAGTCTTAGACGA
64408 G
1 G
64409 TCATACGAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.35, T:0.19
Consensus pattern (28 bp):
GGAGAGGTCGCCATGCAGTCTTAGACGA
Found at i:64477 original size:29 final size:29
Alignment explanation
Indices: 64445--64531 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
64435 ATGCCGCCTG
64445 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
64474 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
**
64503 GGCGACCAAGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
64532 ATGTAGTCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (29 bp):
GGCGACCTTGTAGGTCGCCATGTAGTCCC
Found at i:64892 original size:25 final size:26
Alignment explanation
Indices: 64842--64892 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
64832 CTTGGTCGCC
**
64842 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
64868 GAGATTGCAGCCG-AGAAAGAAAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
64893 AGGGAGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.08
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:65093 original size:41 final size:41
Alignment explanation
Indices: 65048--65136 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
65038 TATATGATTG
* *
65048 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
65089 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
65130 TTAGTTT
1 TTAGTTT
65137 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:65179 original size:44 final size:46
Alignment explanation
Indices: 65116--65206 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
65106 GTTATATAGT
*
65116 TAAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
*
65159 TAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
65206 T
1 T
65207 TTGTTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.17
44 15 0.36
45 5 0.12
46 7 0.17
47 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (46 bp):
TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
Found at i:65283 original size:32 final size:33
Alignment explanation
Indices: 65247--65323 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
65237 TTAGTTAGTA
65247 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
65279 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
65313 ATTTTATTAGT
1 AGTTTATTAGT
65324 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:65401 original size:16 final size:16
Alignment explanation
Indices: 65369--65415 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
65359 TTTAAAAAGT
*
65369 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
65385 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
65401 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
65416 AAGTTTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:65410 original size:15 final size:14
Alignment explanation
Indices: 65390--65420 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
65380 GTTTATTAGT
65390 TTATTATATTATAAG
1 TTATTATATTA-AAG
65405 TTATTATATTAAAG
1 TTATTATATTAAAG
65419 TT
1 TT
65421 TAGTATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:67579 original size:17 final size:17
Alignment explanation
Indices: 67557--67589 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
67547 CAATGATTTT
*
67557 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
67574 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
67590 AATATTTAGT
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:67606 original size:24 final size:22
Alignment explanation
Indices: 67574--67642 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
67564 AAATCATTAC
67574 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
67596 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
*
67621 TAGTATGAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
67643 AACAATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.30
23 6 0.16
24 7 0.19
25 11 0.30
26 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:67862 original size:35 final size:37
Alignment explanation
Indices: 67781--67867 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
67771 TTAGTATTCT
* * *
67781 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
67819 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
67854 ATAATTATTATAAA
1 ATAATTATTATAAA
67868 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:67888 original size:12 final size:13
Alignment explanation
Indices: 67797--68148 Score: 171
Period size: 14 Copynumber: 26.1 Consensus size: 13
67787 ATTAGTAATA
67797 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
67811 AGTATTAAATCATT
1 ATTA-TAAATCATT
67825 ATTATAAAT-A--
1 ATTATAAATCATT
67835 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
67846 ATAACTAAATAATT
1 ATTA-TAAATCATT
67860 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
67874 ATTAT-AATGATT
1 ATTATAAATCATT
67886 ATTATCAAATCATT
1 ATTAT-AAATCATT
67900 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
67919 AAATATTTAAATCATT
1 --AT-TATAAATCATT
67935 A-T-TAAATCATT
1 ATTATAAATCATT
* *
67946 TTTAT-AATGATT
1 ATTATAAATCATT
67958 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
67972 ATTAT-AATGATT
1 ATTATAAATCATT
67984 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
67998 ACTAT-AATGATT
1 ATTATAAATCATT
68010 ATTATCAAATCATT
1 ATTAT-AAATCATT
68024 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
68043 AAATATTTAAATCATT
1 --AT-TATAAATCATT
68059 A-T-TAAATCATT
1 ATTATAAATCATT
* *
68070 TTTAT-AATGATT
1 ATTATAAATCATT
68082 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
68096 ATTAT-AATGATT
1 ATTATAAATCATT
68108 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
68122 ACTAT-AATGATT
1 ATTATAAATCATT
68134 ATTATCAAATCATT
1 ATTAT-AAATCATT
68148 A
1 A
68149 CTAAATCATC
Statistics
Matches: 272, Mismatches: 29, Indels: 74
0.73 0.08 0.20
Matches are distributed among these distances:
10 4 0.01
11 33 0.12
12 77 0.28
13 12 0.04
14 94 0.35
15 2 0.01
16 16 0.06
17 2 0.01
18 6 0.02
19 22 0.08
20 2 0.01
21 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:67895 original size:26 final size:26
Alignment explanation
Indices: 67797--68148 Score: 265
Period size: 26 Copynumber: 14.2 Consensus size: 26
67787 ATTAGTAATA
* * *
67797 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
67822 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
67846 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
67871 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
67897 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
67920 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
67943 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
67969 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
67995 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
68021 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
68044 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
68067 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
68093 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
68119 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
68145 ATTA
1 ATTA
68149 CTAAATCATC
Statistics
Matches: 257, Mismatches: 48, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.03
22 4 0.02
23 30 0.12
24 26 0.10
25 34 0.13
26 153 0.60
27 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:68021 original size:124 final size:124
Alignment explanation
Indices: 67813--68206 Score: 695
Period size: 124 Copynumber: 3.2 Consensus size: 124
67803 AAATCATTAG
* * * * * * *
67813 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
67875 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
67934 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
67999 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
68058 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
68123 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
68182 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
68207 ATAAATACAT
Statistics
Matches: 262, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.07
123 17 0.06
124 227 0.87
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:70754 original size:16 final size:16
Alignment explanation
Indices: 70733--70793 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
70723 AATGTAAATT
70733 AAACAAAATATTTTTA
1 AAACAAAATATTTTTA
*
70749 AAACAACACTAAATATTTT-
1 AAACAA-A--ATAT-TTTTA
*
70768 AAACACAATATTTTTA
1 AAACAAAATATTTTTA
70784 AAACGAAAAT
1 AAAC-AAAAT
70794 TATCTCGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
15 4 0.11
16 13 0.37
17 5 0.14
18 1 0.03
19 8 0.23
20 4 0.11
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (16 bp):
AAACAAAATATTTTTA
Found at i:71309 original size:28 final size:28
Alignment explanation
Indices: 71278--71345 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
71268 TTATATAATA
*
71278 TAATAATATATAACTTAAACTAATAAAC
1 TAATAATATATAACTTAAACTAACAAAC
71306 TAAT-ATAATATAACTTAAACTAACAAAC
1 TAATAAT-ATATAACTTAAACTAACAAAC
*
71334 TAATAATTTATA
1 TAATAATATATA
71346 CTAACAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 32 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATAATATATAACTTAAACTAACAAAC
Found at i:71348 original size:21 final size:21
Alignment explanation
Indices: 71315--71363 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
71305 CTAATATAAT
71315 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
71336 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
71357 ATTAACT
1 A-TAACT
71364 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:71941 original size:20 final size:20
Alignment explanation
Indices: 71916--71988 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
71906 CCATGCACAA
71916 CATGCATCCCACAACTCCCC
1 CATGCATCCCACAACTCCCC
**
71936 CATGCATTCCCACGTC-CCATGCAC
1 CATGCA-TCCCACAACTCC---C-C
71960 AACATGCATCCCACAACTCCCC
1 --CATGCATCCCACAACTCCCC
71982 CATGCAT
1 CATGCAT
71989 GCTCCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 15 0.37
21 7 0.17
22 1 0.02
23 2 0.05
24 1 0.02
25 7 0.17
26 8 0.20
ACGTcount: A:0.26, C:0.48, G:0.08, T:0.18
Consensus pattern (20 bp):
CATGCATCCCACAACTCCCC
Found at i:71955 original size:46 final size:46
Alignment explanation
Indices: 71896--71988 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
71886 CCATGCACAG
71896 TTCCAACGTCCCATGCACAACATGCATCCCACAACTCCCCCATGCA
1 TTCCAACGTCCCATGCACAACATGCATCCCACAACTCCCCCATGCA
*
71942 TTCCCACGTCCCATGCACAACATGCATCCCACAACTCCCCCATGCA
1 TTCCAACGTCCCATGCACAACATGCATCCCACAACTCCCCCATGCA
71988 T
1 T
71989 GCTCCAATAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.27, C:0.46, G:0.09, T:0.18
Consensus pattern (46 bp):
TTCCAACGTCCCATGCACAACATGCATCCCACAACTCCCCCATGCA
Found at i:76839 original size:28 final size:25
Alignment explanation
Indices: 76808--76859 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
76798 ATTTCAAAAT
76808 TATAATTATGAAAAAAAAATAATTTATA
1 TATAATTAT--AAAAAAAAT-ATTTATA
* *
76836 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
76860 TTATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
28 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:76866 original size:23 final size:26
Alignment explanation
Indices: 76823--76872 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
76813 TTATGAAAAA
*
76823 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
76849 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
76872 A
1 A
76873 TCAGAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:78456 original size:2 final size:2
Alignment explanation
Indices: 78449--78513 Score: 95
Period size: 2 Copynumber: 35.0 Consensus size: 2
78439 TGTTTGTAAT
78449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78490 -A TA -A TA -A TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78514 ATAATTTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 5 0.09
2 53 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:78526 original size:33 final size:33
Alignment explanation
Indices: 78464--78550 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 33
78454 ATATATATAT
78464 ATATATATATATATATATATATATTAATAATAA-TA
1 ATATATATATATATA-ATA-ATATTAATAA-AATTA
78499 ATATATATATATATAATAAT-TTAAATAAAATTA
1 ATATATATATATATAATAATATT-AATAAAATTA
78532 AT-TATA-ATAATTATAATAA
1 ATATATATAT-A-TATAATAA
78551 AAAAAATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
31 2 0.04
32 9 0.19
33 19 0.40
34 3 0.06
35 15 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATATATATATATAATAATATTAATAAAATTA
Found at i:78558 original size:24 final size:24
Alignment explanation
Indices: 78510--78558 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
78500 TATATATATA
**
78510 TATAATAATTTAAATAAAATTAAT
1 TATAATAATTTAAATAAAAAAAAT
78534 TATAATAA-TTATAATAAAAAAAAT
1 TATAATAATTTA-AATAAAAAAAAT
78558 T
1 T
78559 TAGTATCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAATTTAAATAAAAAAAAT
Found at i:81768 original size:27 final size:28
Alignment explanation
Indices: 81738--81800 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
81728 TCTCTATTAA
*
81738 TTTAATATTA-GT-TAAATAAATATAAAT
1 TTTAATATTATGTAT-AATAAAAATAAAT
* *
81765 TTTAA-ATTATGTATGATAAAAATAATT
1 TTTAATATTATGTATAATAAAAATAAAT
81792 TTTAATATT
1 TTTAATATT
81801 TATATTATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.13
27 22 0.73
28 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTAATATTATGTATAATAAAAATAAAT
Found at i:81987 original size:15 final size:15
Alignment explanation
Indices: 81967--81996 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
81957 ATTTTTAAGC
81967 AATTTAGTCTTTAAT
1 AATTTAGTCTTTAAT
*
81982 AATTTAGTTTTTAAT
1 AATTTAGTCTTTAAT
81997 TAAAATTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (15 bp):
AATTTAGTCTTTAAT
Found at i:84115 original size:35 final size:36
Alignment explanation
Indices: 84062--84131 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
84052 AATTCATGTT
84062 CAAAATTCTAAAACACTTTAATTACATTCTAAACCC
1 CAAAATTCTAAAACACTTTAATTACATTCTAAACCC
* *
84098 CAAATTTC-AAAATACTTTAATTACATTCTAAACC
1 CAAAATTCTAAAACACTTTAATTACATTCTAAACC
84132 TTAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (36 bp):
CAAAATTCTAAAACACTTTAATTACATTCTAAACCC
Found at i:84190 original size:35 final size:35
Alignment explanation
Indices: 84134--84210 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
84124 TCTAAACCTT
* *
84134 AAATTAAAGTATTTTAGAATTTAAGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
* * *
84169 TAATTGAATTATTTT-GAAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTAG-AATTTAAGGTTTAAAATA
84204 AAATTGA
1 AAATTGA
84211 GGAATGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
Found at i:85381 original size:13 final size:13
Alignment explanation
Indices: 85363--85387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85353 TGTGTTCGTA
85363 TTCGTATTAATTT
1 TTCGTATTAATTT
85376 TTCGTATTAATT
1 TTCGTATTAATT
85388 GCGTGACCAC
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (13 bp):
TTCGTATTAATTT
Found at i:88977 original size:7 final size:7
Alignment explanation
Indices: 88958--88989 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
88948 ATTTCAATAT
88958 TAATAAA
1 TAATAAA
88965 -AATAAA
1 TAATAAA
88971 TAATAAA
1 TAATAAA
88978 TAATAAA
1 TAATAAA
88985 TAATA
1 TAATA
88990 TCATTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAATAAA
Found at i:90706 original size:29 final size:29
Alignment explanation
Indices: 90666--90742 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
90656 TGTTAGAGGG
* * **
90666 TAAACTTAAATTTTTAAAACTCTAGGGGA
1 TAAACTTGAATTTTTAAAAATCTAAAGGA
* *
90695 TAAATTTGAATTTATAAAAATCTAAAGGA
1 TAAACTTGAATTTTTAAAAATCTAAAGGA
* *
90724 TGAACTTGAACTTTTAAAA
1 TAAACTTGAATTTTTAAAA
90743 TTTCAGACGA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (29 bp):
TAAACTTGAATTTTTAAAAATCTAAAGGA
Found at i:90760 original size:26 final size:26
Alignment explanation
Indices: 90725--90774 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
90715 TCTAAAGGAT
*
90725 GAACTTGAACTTTTAAAATTTCAGAC
1 GAACTTGAACTTATAAAATTTCAGAC
90751 GAACTTGAACTTATAAAATTTCAG
1 GAACTTGAACTTATAAAATTTCAG
90775 GGGCGGAAAC
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:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (26 bp):
GAACTTGAACTTATAAAATTTCAGAC
Found at i:92351 original size:20 final size:21
Alignment explanation
Indices: 92316--92361 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
92306 ATTAAACATG
92316 ATTAAAACTAATAATTTAAAT
1 ATTAAAACTAATAATTTAAAT
*
92337 ATTAAAAGT-ATAATTT-AAT
1 ATTAAAACTAATAATTTAAAT
92356 -TTAAAA
1 ATTAAAA
92362 AATTCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 7 0.29
21 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTAAAACTAATAATTTAAAT
Found at i:93862 original size:48 final size:48
Alignment explanation
Indices: 93803--93896 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
93793 TGGAAAATAG
93803 AATGCCACTTCTAAGGACTGCAATGTATGCAAAAGGTTGGATTTTTGA
1 AATGCCACTTCTAAGGACTGCAATGTATGCAAAAGGTTGGATTTTTGA
93851 AATGCCACTTCTAAGGACTGCAATGTATGCAAAAGGTTGGATTTTT
1 AATGCCACTTCTAAGGACTGCAATGTATGCAAAAGGTTGGATTTTT
93897 TAACCTTCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (48 bp):
AATGCCACTTCTAAGGACTGCAATGTATGCAAAAGGTTGGATTTTTGA
Found at i:97157 original size:9 final size:9
Alignment explanation
Indices: 97135--97184 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
97125 CCGTTTATTT
*
97135 TTATTATTA
1 TTATAATTA
97144 TTATAATTA
1 TTATAATTA
*
97153 TTATAATTG
1 TTATAATTA
*
97162 TTATAATAAA
1 TTATAAT-TA
*
97172 TAATAATTA
1 TTATAATTA
97181 TTAT
1 TTAT
97185 TACTAAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTATAATTA
Found at i:97179 original size:19 final size:20
Alignment explanation
Indices: 97137--97195 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
97127 GTTTATTTTT
*
97137 ATTATTATT-ATAATTATTATA
1 ATTATTATTAATAA--ATAATA
*
97158 ATTGTTA-TAATAAATAATA
1 ATTATTATTAATAAATAATA
*
97177 ATTATTATTACTAAATAAT
1 ATTATTATTAATAAATAAT
97196 TTTATTTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.34
20 11 0.34
21 10 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTATTATTAATAAATAATA
Found at i:97417 original size:16 final size:18
Alignment explanation
Indices: 97373--97417 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
97363 GGTTCACAGA
97373 AGGTTCATCATGAATCCCT
1 AGGTT-ATCATGAATCCCT
97392 AGGGTT-TCAT-AA-CCCT
1 A-GGTTATCATGAATCCCT
97408 AGGTTATCAT
1 AGGTTATCAT
97418 CATGCGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 2 0.08
18 4 0.17
19 1 0.04
20 4 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (18 bp):
AGGTTATCATGAATCCCT
Found at i:98609 original size:37 final size:36
Alignment explanation
Indices: 98542--98611 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
98532 TTAGATACAA
* *
98542 GTTTTATTATTTTTTACTATAGTTTGAATTTTAATT
1 GTTTTATTATTTTTAAATATAGTTTGAATTTTAATT
*
98578 GTTTTAGTTATTGTTTAAATATA-TTTTAATTTTA
1 GTTTTA-TTATT-TTTAAATATAGTTTGAATTTTA
98612 TATTTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 6 0.21
37 15 0.52
38 8 0.28
ACGTcount: A:0.27, C:0.01, G:0.09, T:0.63
Consensus pattern (36 bp):
GTTTTATTATTTTTAAATATAGTTTGAATTTTAATT
Found at i:98624 original size:21 final size:24
Alignment explanation
Indices: 98598--98642 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
98588 TTGTTTAAAT
98598 ATATTTT-AATT-TTA-TATTTTA
1 ATATTTTAAATTATTATTATTTTA
98619 ATATTTTAAATTATTATTATTTTA
1 ATATTTTAAATTATTATTATTTTA
98643 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 3 0.14
24 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATATTTTAAATTATTATTATTTTA
Found at i:98660 original size:27 final size:27
Alignment explanation
Indices: 98630--98756 Score: 95
Period size: 27 Copynumber: 4.6 Consensus size: 27
98620 TATTTTAAAT
98630 TATTATTATTTTATTTTTATTAATATA
1 TATTATTATTTTATTTTTATTAATATA
* * *
98657 TATTATT-TGATTAATTTTATAAAT-TAA
1 TATTATTAT-TTTATTTTTATTAATAT-A
*
98684 TAATATT-TGTTTATTTTTATT-A-ATA
1 TATTATTAT-TTTATTTTTATTAATATA
98709 TA-TATTATTTTATTTTTAATATATATATA
1 TATTATTATTTTATTTTT-AT-TA-ATATA
*
98738 TATATATATATATTATTTT
1 TAT-TAT-TATTTTATTTT
98757 AAACATGTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
24 13 0.16
25 6 0.08
26 5 0.06
27 37 0.46
28 1 0.01
29 5 0.06
31 3 0.04
32 10 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATTATTATTTTATTTTTATTAATATA
Found at i:98680 original size:51 final size:53
Alignment explanation
Indices: 98616--98718 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 53
98606 ATTTTATATT
98616 TTAATATTTTAAATT-AT-TATTAT-TTTATTTTTATTAATATATATTATTTGA
1 TTAATATTTTAAATTAATATATT-TGTTTATTTTTATTAATATATATTATTTGA
98667 TTAAT-TTTATAAATTAATAATATTTGTTTATTTTTATTAATATATATTATTT
1 TTAATATTT-TAAATTAAT-ATATTTGTTTATTTTTATTAATATATATTATTT
98719 TATTTTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
50 3 0.06
51 11 0.23
52 2 0.04
53 1 0.02
54 30 0.64
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (53 bp):
TTAATATTTTAAATTAATATATTTGTTTATTTTTATTAATATATATTATTTGA
Found at i:98706 original size:23 final size:24
Alignment explanation
Indices: 98633--98738 Score: 108
Period size: 24 Copynumber: 4.1 Consensus size: 24
98623 TTTAAATTAT
98633 TATTATTTTATTTTTATTAATATA
1 TATTATTTTATTTTTATTAATATA
98657 TATTATTTGATTAATTTTATAAATTAATA-A
1 TATTA-TT--TT-ATTTT-T--ATTAATATA
98687 TATT-TGTTTATTTTTATTAATATA
1 TATTAT-TTTATTTTTATTAATATA
*
98711 TATTATTTTATTTTTAATATATATA
1 TATTATTTTATTTTTATTA-ATATA
98736 TAT
1 TAT
98739 ATATATATAT
Statistics
Matches: 70, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
23 7 0.10
24 22 0.31
25 12 0.17
26 5 0.07
27 4 0.06
28 6 0.09
29 2 0.03
30 5 0.07
31 7 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTATTTTATTTTTATTAATATA
Found at i:104278 original size:7 final size:7
Alignment explanation
Indices: 104263--104343 Score: 94
Period size: 7 Copynumber: 11.1 Consensus size: 7
104253 CTCATTCATC
104263 AGAAAAA
1 AGAAAAA
104270 AGGAAAAA
1 A-GAAAAA
*
104278 GAGATAAA
1 -AGAAAAA
104286 A-AAAAA
1 AGAAAAA
104292 AGAAAAA
1 AGAAAAA
104299 AGAAAAA
1 AGAAAAA
104306 AGAAAAAAA
1 AG--AAAAA
104315 AGAAAAAA
1 AG-AAAAA
104323 AGAAAAA
1 AGAAAAA
104330 A-AAAAA
1 AGAAAAA
104336 AGAAAAA
1 AGAAAAA
104343 A
1 A
104344 ATTGAATCAA
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
6 11 0.17
7 28 0.42
8 19 0.29
9 8 0.12
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (7 bp):
AGAAAAA
Found at i:104287 original size:1 final size:1
Alignment explanation
Indices: 104283--104344 Score: 70
Period size: 1 Copynumber: 62.0 Consensus size: 1
104273 AAAAAGAGAT
* * * * * *
104283 AAAAAAAAAAGAAAAAAGAAAAAAGAAAAAAAAGAAAAAAAGAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
104345 TTGAATCAAG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:104341 original size:29 final size:29
Alignment explanation
Indices: 104263--104344 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
104253 CTCATTCATC
* * *
104263 AGAAAAAAGGAAAAAGAGATAAAAAAAAA
1 AGAAAAAAGAAAAAAGAAAAAAAAAAAAA
104292 AGAAAAAAGAAAAAAGAAAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAAG-AAAAAAA-AAAAAA
104323 AGAAAAAA-AAAAAAGAAAAAAA
1 AGAAAAAAGAAAAAAGAAAAAAA
104345 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
29 22 0.46
30 12 0.25
31 14 0.29
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.01
Consensus pattern (29 bp):
AGAAAAAAGAAAAAAGAAAAAAAAAAAAA
Found at i:104343 original size:21 final size:21
Alignment explanation
Indices: 104265--104344 Score: 106
Period size: 21 Copynumber: 3.7 Consensus size: 21
104255 CATTCATCAG
* * *
104265 AAAAAAGGAAAAAGAGATAAA
1 AAAAAAAGAAAAAAAGAAAAA
*
104286 AAAAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAA-AGAAAA-A
104309 AAAAAAAGAAAAAAAGAAAAA
1 AAAAAAAGAAAAAAAGAAAAA
104330 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
104345 TTGAATCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 28 0.54
22 9 0.17
23 15 0.29
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.01
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAGAAAAA
Found at i:104963 original size:32 final size:32
Alignment explanation
Indices: 104927--104991 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
104917 CCTGAGAGTC
*
104927 TGGAAAC-AAGAAGTATCTCTACGAGATGAGCA
1 TGGAAACGAA-AAGTATCTCTACAAGATGAGCA
104959 TGGAAACGAAAAGTATCTCTACAAGATGAGCA
1 TGGAAACGAAAAGTATCTCTACAAGATGAGCA
104991 T
1 T
104992 AACAACCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (32 bp):
TGGAAACGAAAAGTATCTCTACAAGATGAGCA
Found at i:107971 original size:75 final size:75
Alignment explanation
Indices: 107817--107955 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 75
107807 AAATACTGAA
** * * * ** *
107817 GCATGCTGGAAGCCCATTTCAATCAGAATCAGGAATGTTGATGTATTTTGAACGTTTGTATTAGC
1 GCATGCTAAAAGCCCATTTCAATCAGAATCAAGAATGTTGACGCATTTTGAACGTTCATATCAGC
107882 AAATTCTGGG
66 AAATTCTGGG
* *
107892 GCATGCTAAAAGCCCCTTTTAATCAGAAAT-AAGAATGTTGACGCATTTTGAACGTTCATATCAG
1 GCATGCTAAAAGCCCATTTCAATCAG-AATCAAGAATGTTGACGCATTTTGAACGTTCATATCAG
107956 TAATTGTTGG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 50 0.94
76 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (75 bp):
GCATGCTAAAAGCCCATTTCAATCAGAATCAAGAATGTTGACGCATTTTGAACGTTCATATCAGC
AAATTCTGGG
Found at i:109284 original size:20 final size:20
Alignment explanation
Indices: 109259--109390 Score: 120
Period size: 20 Copynumber: 6.4 Consensus size: 20
109249 TCTACATCTT
109259 TTCTCTTTAAAGATGATAAA
1 TTCTCTTTAAAGATGATAAA
**
109279 TTCTCTCTTCAAAGATGATATT
1 TTCTCT-TT-AAAGATGATAAA
* * *
109301 TTCTCTTCAAATATGATAGA
1 TTCTCTTTAAAGATGATAAA
*
109321 TTCTCTTCAAAGATGATAGATA
1 TTCTCTTTAAAGATGATA-A-A
* * **
109343 CTCTCTTTAAATATGATATT
1 TTCTCTTTAAAGATGATAAA
* *
109363 TTCTCTTCAAAGATGATAGA
1 TTCTCTTTAAAGATGATAAA
109383 TTCTCTTT
1 TTCTCTTT
109391 TCAAAGAAGA
Statistics
Matches: 89, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
20 54 0.61
21 3 0.03
22 32 0.36
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (20 bp):
TTCTCTTTAAAGATGATAAA
Found at i:109317 original size:42 final size:40
Alignment explanation
Indices: 109259--109390 Score: 158
Period size: 42 Copynumber: 3.2 Consensus size: 40
109249 TCTACATCTT
* *
109259 TTCTCTTTAAAGATGATAAATTCTCTCTTCAAAGATGATATT
1 TTCTCTTTAAATATGAT-AATT-TCTCTTCAAAGATGATATA
*
109301 TTCTCTTCAAATATGATAGA-TTCTCTTCAAAGATGATAGATA
1 TTCTCTTTAAATATGATA-ATTTCTCTTCAAAGATGAT--ATA
* * *
109343 CTCTCTTTAAATATGATATTTTCTCTTCAAAGATGATAGA
1 TTCTCTTTAAATATGATAATTTCTCTTCAAAGATGATATA
109383 TTCTCTTT
1 TTCTCTTT
109391 TCAAAGAAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
40 25 0.32
41 2 0.03
42 51 0.65
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (40 bp):
TTCTCTTTAAATATGATAATTTCTCTTCAAAGATGATATA
Found at i:109359 original size:62 final size:62
Alignment explanation
Indices: 109259--109389 Score: 208
Period size: 62 Copynumber: 2.1 Consensus size: 62
109249 TCTACATCTT
* * *
109259 TTCTCTTTAAAGATGATAAATTCTCTCTTCAAAGATGATATTTTCTCTTCAAATATGATAGA
1 TTCTCTTCAAAGATGATAAATACTCTCTTCAAAGATGATATTTTCTCTTCAAAGATGATAGA
* * *
109321 TTCTCTTCAAAGATGATAGATACTCTCTTTAAATATGATATTTTCTCTTCAAAGATGATAGA
1 TTCTCTTCAAAGATGATAAATACTCTCTTCAAAGATGATATTTTCTCTTCAAAGATGATAGA
109383 TTCTCTT
1 TTCTCTT
109390 TTCAAAGAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (62 bp):
TTCTCTTCAAAGATGATAAATACTCTCTTCAAAGATGATATTTTCTCTTCAAAGATGATAGA
Found at i:109967 original size:113 final size:113
Alignment explanation
Indices: 109779--110455 Score: 835
Period size: 113 Copynumber: 5.9 Consensus size: 113
109769 CATCACTCAA
* * *
109779 ATGGATCAATATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
109843 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
* * * *
109891 ATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATTTGAAAAAGGAAGAAAAAGT
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
109956 TTATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
* *
110004 ATGGATCAATATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGT
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
110069 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCAAT-ACTTG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCACTTG
* * *
110117 ATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * **
110182 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTAATTACCCG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
* * * *
110230 ATGGATTAACACTGCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * * *
110294 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG-ACTCTATCACAAAAGGAGATAG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCAC---------TTG
* * * * * * * *
110352 ACCAGGATAAACTTTTCTAGAG-AAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGA
1 A--TGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
110415 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
63 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAAT
110456 CTATCACAGA
Statistics
Matches: 500, Mismatches: 48, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
112 17 0.03
113 387 0.77
114 2 0.00
122 2 0.00
123 48 0.10
124 44 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTG
Found at i:110472 original size:123 final size:124
Alignment explanation
Indices: 110245--110516 Score: 460
Period size: 123 Copynumber: 2.2 Consensus size: 124
110235 TTAACACTGC
110245 CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
110310 TTTGTTCAACCTTTTGCTTGACTCTATCACAAAAGGAGATAGACCAGGATAAAC-TTTT
66 TTTGTTCAACCTTTTGCTTGAATCTATCACAAAAGGAGATAGACCAGCATAAACATTTT
*
110368 CTAGAGAAAGTTCGTAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGA
1 C-AGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* *
110432 ATTTGTTCAACCTTTTGCTTGAATCTATCACAGAAA-GAGATAGATCAGCATCAACATTTT
65 ATTTGTTCAACCTTTTGCTTGAATCTATCACA-AAAGGAGATAGACCAGCATAAACATTTT
110492 CAGAGAAAGTTCATAATGAGAAGAA
1 CAGAGAAAGTTCATAATGAGAAGAA
110517 TTTGTTCAAC
Statistics
Matches: 140, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
123 98 0.70
124 42 0.30
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (124 bp):
CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCTTGAATCTATCACAAAAGGAGATAGACCAGCATAAACATTTT
Found at i:110556 original size:84 final size:83
Alignment explanation
Indices: 110409--110596 Score: 297
Period size: 84 Copynumber: 2.2 Consensus size: 83
110399 CTGAAGAGGA
110409 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCTATCACAGAAAGAGATA
1 AGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCTATCACAGAAAGAGATA
*
110474 GATCAGCATCAACATTTTC
65 GATCAGCATCAACATTTCC
*
110493 AGAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TATGAATCTATCACAGAAGGAGAT
1 AGA-AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT-TGAATCTATCACAGAAAGAGAT
*
110557 AGATCAGTATCAACATTTCC
64 AGATCAGCATCAACATTTCC
**
110577 AGAAGTGTTCATAATGAGAA
1 AGAAAAGTTCATAATGAGAA
110597 TAACTCATCT
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
83 16 0.16
84 80 0.82
85 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (83 bp):
AGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATCTATCACAGAAAGAGATAG
ATCAGCATCAACATTTCC
Found at i:111007 original size:9 final size:9
Alignment explanation
Indices: 110995--111051 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
110985 CCGTTTATTT
*
110995 TTATTATTA
1 TTATAATTA
*
111004 TTATAATTG
1 TTATAATTA
111013 TTATAATTA
1 TTATAATTA
* *
111022 TTAAAATAA
1 TTATAATTA
*
111031 TAATAATTA
1 TTATAATTA
*
111040 TTATTATTA
1 TTATAATTA
111049 TTA
1 TTA
111052 AATAATTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTATAATTA
Found at i:111048 original size:27 final size:26
Alignment explanation
Indices: 111006--111057 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
110996 TATTATTATT
*
111006 ATAATTGTTATAATTATTAAAATAATA
1 ATAATTATTATAATTATT-AAATAATA
*
111033 ATAATTATTATTATTATTAAATAAT
1 ATAATTATTATAATTATTAAATAAT
111058 TTTATTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAATTATTATAATTATTAAATAATA
Found at i:111271 original size:16 final size:17
Alignment explanation
Indices: 111250--111287 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
111240 CATCATGAAT
111250 CCCTAGGGTT-TCACAA
1 CCCTAGGGTTATCACAA
111266 CCCTA-GGTTATCACAA
1 CCCTAGGGTTATCACAA
*
111282 ACCTAG
1 CCCTAG
111288 AGCCCAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CCCTAGGGTTATCACAA
Found at i:111405 original size:154 final size:154
Alignment explanation
Indices: 111125--111432 Score: 616
Period size: 154 Copynumber: 2.0 Consensus size: 154
111115 GGTCCAAACC
111125 CAAACCTAGAGCCCAACAGTAACCCTAAAACCCAACTAGGGTTTCATCATCTTAGCCTCAGCCAC
1 CAAACCTAGAGCCCAACAGTAACCCTAAAACCCAACTAGGGTTTCATCATCTTAGCCTCAGCCAC
111190 CAACATTCTCAGTCGTTGGATCTGAGAGATCCAACGGTCCACAGAAGGTTCATCATGAATCCCTA
66 CAACATTCTCAGTCGTTGGATCTGAGAGATCCAACGGTCCACAGAAGGTTCATCATGAATCCCTA
111255 GGGTTTCACAACCCTAGGTTATCA
131 GGGTTTCACAACCCTAGGTTATCA
111279 CAAACCTAGAGCCCAACAGTAACCCTAAAACCCAACTAGGGTTTCATCATCTTAGCCTCAGCCAC
1 CAAACCTAGAGCCCAACAGTAACCCTAAAACCCAACTAGGGTTTCATCATCTTAGCCTCAGCCAC
111344 CAACATTCTCAGTCGTTGGATCTGAGAGATCCAACGGTCCACAGAAGGTTCATCATGAATCCCTA
66 CAACATTCTCAGTCGTTGGATCTGAGAGATCCAACGGTCCACAGAAGGTTCATCATGAATCCCTA
111409 GGGTTTCACAACCCTAGGTTATCA
131 GGGTTTCACAACCCTAGGTTATCA
111433 TCACACAGCC
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (154 bp):
CAAACCTAGAGCCCAACAGTAACCCTAAAACCCAACTAGGGTTTCATCATCTTAGCCTCAGCCAC
CAACATTCTCAGTCGTTGGATCTGAGAGATCCAACGGTCCACAGAAGGTTCATCATGAATCCCTA
GGGTTTCACAACCCTAGGTTATCA
Found at i:112203 original size:23 final size:23
Alignment explanation
Indices: 112173--112235 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
112163 TCTCTGAATT
112173 TGTAATCTTTATGATTTATTCAC
1 TGTAATCTTTATGATTTATTCAC
112196 TGTAATCTTTATGATTTATTCAC
1 TGTAATCTTTATGATTTATTCAC
*
112219 TGAAATCATTTTATGAT
1 TGTAATC--TTTATGAT
112236 CATTTGAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 29 0.78
25 8 0.22
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (23 bp):
TGTAATCTTTATGATTTATTCAC
Found at i:112607 original size:27 final size:27
Alignment explanation
Indices: 112577--112657 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
112567 TATTTTAAAT
112577 TATTATTATTTTATTTTTATTAATATA
1 TATTATTATTTTATTTTTATTAATATA
* *
112604 TATTATT-TGATTAATTTTA-TAA-AT-
1 TATTATTAT-TTTATTTTTATTAATATA
* *
112628 TAATAATATTTGT-TTTTTATTAATATA
1 TATTATTATTT-TATTTTTATTAATATA
112655 TAT
1 TAT
112658 ATATATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
24 11 0.27
25 7 0.17
26 6 0.15
27 17 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATTATTATTTTATTTTTATTAATATA
Found at i:112655 original size:2 final size:2
Alignment explanation
Indices: 112650--112685 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
112640 TTTTTTATTA
112650 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
112686 TATTTTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115890 original size:20 final size:20
Alignment explanation
Indices: 115861--115903 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
115851 ATTTTACCAC
*
115861 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
115881 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
115901 ATG
1 ATG
115904 AGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:127733 original size:20 final size:20
Alignment explanation
Indices: 127704--127746 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
127694 ATTTCATCAC
*
127704 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
127724 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
127744 ATG
1 ATG
127747 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:130201 original size:149 final size:149
Alignment explanation
Indices: 129931--130243 Score: 592
Period size: 149 Copynumber: 2.1 Consensus size: 149
129921 TATAATTGCA
*
129931 CCGAAGTG-CCGCGTAGAATTGCACCGTGGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
129995 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
130060 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
130080 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
130145 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
130210 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
*
130229 CCGAATGACCGCGTA
1 CCGAAGGACCGCGTA
130244 AACCCTCGAC
Statistics
Matches: 161, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:131152 original size:18 final size:18
Alignment explanation
Indices: 131131--131165 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
131121 TCCCATCTAG
131131 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
131149 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
131166 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:131770 original size:21 final size:21
Alignment explanation
Indices: 131746--131790 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
131736 TGTTGTTCGT
* *
131746 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
131767 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
131788 TTG
1 TTG
131791 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:136646 original size:23 final size:24
Alignment explanation
Indices: 136592--136646 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
136582 CTCAAGTAAA
* *
136592 AATTAAATAAAAACATTACAAACT
1 AATTAAATAAAAACAATAAAAACT
*
136616 AAAT-AATAAAAACAATAAAAAC-
1 AATTAAATAAAAACAATAAAAACT
136638 AATTAAATA
1 AATTAAATA
136647 CAAGCGTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (24 bp):
AATTAAATAAAAACAATAAAAACT
Found at i:136725 original size:43 final size:43
Alignment explanation
Indices: 136664--136792 Score: 204
Period size: 44 Copynumber: 2.9 Consensus size: 43
136654 TACAATTTAA
136664 ATAATTAAATAATAAAATATTAAGAAACAAAATAAATAAAAGTTC
1 ATAATTAAAT-A-AAAATATTAAGAAACAAAATAAATAAAAGTTC
136709 ATAATTAAATAAAAATATTAAGAAACAAAATAAATAAAAAGTTC
1 ATAATTAAATAAAAATATTAAGAAACAAAATAAAT-AAAAGTTC
* *
136753 ATAATTAAATAAAAACATTAAAAAAACAAAATAAATAAAA
1 ATAATTAAATAAAAATATT-AAGAAACAAAATAAATAAAA
136793 ACAAGTCTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
43 24 0.30
44 31 0.39
45 25 0.31
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (43 bp):
ATAATTAAATAAAAATATTAAGAAACAAAATAAATAAAAGTTC
Found at i:136764 original size:44 final size:44
Alignment explanation
Indices: 136664--136793 Score: 208
Period size: 45 Copynumber: 2.9 Consensus size: 44
136654 TACAATTTAA
136664 ATAATTAAATAATAAAATATTAAGAAACAAAATAAAT-AAAAGTTC
1 ATAATTAAAT-A-AAAATATTAAGAAACAAAATAAATAAAAAGTTC
136709 ATAATTAAATAAAAATATTAAGAAACAAAATAAATAAAAAGTTC
1 ATAATTAAATAAAAATATTAAGAAACAAAATAAATAAAAAGTTC
* *
136753 ATAATTAAATAAAAACATTAAAAAAACAAAATAAATAAAAA
1 ATAATTAAATAAAAATATT-AAGAAACAAAATAAATAAAAA
136794 CAAGTCTATC
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
43 24 0.30
44 27 0.33
45 30 0.37
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (44 bp):
ATAATTAAATAAAAATATTAAGAAACAAAATAAATAAAAAGTTC
Found at i:136794 original size:15 final size:15
Alignment explanation
Indices: 136731--136796 Score: 50
Period size: 19 Copynumber: 4.4 Consensus size: 15
136721 AAATATTAAG
136731 AAACAAAATAAATAA
1 AAACAAAATAAATAA
*
136746 AAAGTTCATAATTAAATAA
1 AAA---CA-AAATAAATAA
*
136765 AAAC---ATTAA-AA
1 AAACAAAATAAATAA
136776 AAACAAAATAAATAA
1 AAACAAAATAAATAA
136791 AAACAA
1 AAACAA
136797 GTCTATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
11 6 0.15
12 3 0.08
14 4 0.10
15 11 0.28
16 1 0.03
18 2 0.05
19 12 0.31
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.18
Consensus pattern (15 bp):
AAACAAAATAAATAA
Found at i:147517 original size:21 final size:21
Alignment explanation
Indices: 147493--147539 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
147483 GGCGGCATTG
*
147493 AAAATGGTTACGGTGCCATCT
1 AAAATGGCTACGGTGCCATCT
*
147514 AAAATGGCTACGGTGGCATCT
1 AAAATGGCTACGGTGCCATCT
*
147535 GAAAT
1 AAAAT
147540 AGTAACGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (21 bp):
AAAATGGCTACGGTGCCATCT
Found at i:150681 original size:16 final size:16
Alignment explanation
Indices: 150660--150692 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
150650 CATTAGAGAG
150660 CATGTATAATTGTAAA
1 CATGTATAATTGTAAA
150676 CATGTATAATTGTAAA
1 CATGTATAATTGTAAA
150692 C
1 C
150693 TCGATTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (16 bp):
CATGTATAATTGTAAA
Found at i:156203 original size:27 final size:30
Alignment explanation
Indices: 156145--156200 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
156135 CTCTGAATTA
** *
156145 TTTTATTATTATTTTTGTATAACATAACAT
1 TTTTATTATTATTTTAATATAAAATAACAT
156175 TTTTATTATTA-TTTAATATAAAATAA
1 TTTTATTATTATTTTAATATAAAATAA
156201 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (30 bp):
TTTTATTATTATTTTAATATAAAATAACAT
Found at i:157570 original size:28 final size:28
Alignment explanation
Indices: 157517--157570 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
157507 AAAATGAGGG
* *
157517 TCAAAATTTGAAGATAAAGTTGGAATAT
1 TCAAAATTTGAAGATAAACTTAGAATAT
*
157545 TCAAAAGTTTG-AGATTAACTTAGAAT
1 TCAAAA-TTTGAAGATAAACTTAGAAT
157571 GAGAGTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (28 bp):
TCAAAATTTGAAGATAAACTTAGAATAT
Found at i:158773 original size:22 final size:21
Alignment explanation
Indices: 158748--158836 Score: 92
Period size: 22 Copynumber: 4.2 Consensus size: 21
158738 AAAACATTAA
*
158748 AAAAATAACATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
158770 AAAAGTAAAATATTTA-TT-T
1 AAAAATAAAATATTAATTTAT
*
158789 AAAAATAATATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
158811 AAAAGTAAAATATTTATTTAT
1 AAAAATAAAATATTAATTTAT
158832 AAAAA
1 AAAAA
158837 AATATCAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
19 12 0.22
20 4 0.07
21 15 0.28
22 23 0.43
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAAAATATTAATTTAT
Done.