Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 139 of 335
Found at i:40818426 original size:19 final size:19
Alignment explanation
Indices: 40818388--40818438 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
40818378 AGTATAAACT
40818388 AAATAACATAAAAT--TTTA
1 AAATAA-ATAAAATAGTTTA
*
40818406 AAATAGATAAAATAGTTTA
1 AAATAAATAAAATAGTTTA
40818425 AAATAAATAAAATA
1 AAATAAATAAAATA
40818439 TGTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 17 0.59
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AAATAAATAAAATAGTTTA
Found at i:40818444 original size:28 final size:28
Alignment explanation
Indices: 40818404--40818483 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
40818394 CATAAAATTT
40818404 TAAAATA-GATAAAATAGTTTAAAATAAA
1 TAAAATATG-TAAAATAGTTTAAAATAAA
40818432 TAAAATATGTAAAAATA-TTTAAAATAAA
1 TAAAATATGT-AAAATAGTTTAAAATAAA
* * *
40818460 TAATATATAATAAAACAGTTTAAA
1 TAAAATAT-GTAAAATAGTTTAAA
40818484 GTATACGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 31 0.69
29 14 0.31
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (28 bp):
TAAAATATGTAAAATAGTTTAAAATAAA
Found at i:40818446 original size:19 final size:19
Alignment explanation
Indices: 40818388--40818448 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
40818378 AGTATAAACT
40818388 AAATAACATAAAAT-T-TTA
1 AAATAA-ATAAAATATGTTA
*
40818406 AAATAGATAAAATA-GTTTA
1 AAATAAATAAAATATG-TTA
*
40818425 AAATAAATAAAATATGTAA
1 AAATAAATAAAATATGTTA
40818444 AAATA
1 AAATA
40818449 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
19 23 0.64
20 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATAAATAAAATATGTTA
Found at i:40819353 original size:16 final size:17
Alignment explanation
Indices: 40819317--40819353 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
40819307 ATTCATTCCA
40819317 AAATAAGAAATAAAAAT
1 AAATAAGAAATAAAAAT
*
40819334 -AATAA-AAATAAAATT
1 AAATAAGAAATAAAAAT
40819349 AAATA
1 AAATA
40819354 GATCTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAGAAATAAAAAT
Found at i:40827457 original size:47 final size:47
Alignment explanation
Indices: 40827403--40827498 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
40827393 CATAGGTACC
40827403 ATCATTAATATTAGTCACAAGCAATTATAATTCATATTTAATCCATG
1 ATCATTAATATTAGTCACAAGCAATTATAATTCATATTTAATCCATG
40827450 ATCATTAATATTAGTCACAAGCAATTATAATTCATATTTAATCCATG
1 ATCATTAATATTAGTCACAAGCAATTATAATTCATATTTAATCCATG
40827497 AT
1 AT
40827499 TCAATTCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (47 bp):
ATCATTAATATTAGTCACAAGCAATTATAATTCATATTTAATCCATG
Found at i:40828772 original size:2 final size:2
Alignment explanation
Indices: 40828760--40828789 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40828750 AAAATAGTTC
*
40828760 AT AT GT 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
40828790 TAGAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40831405 original size:26 final size:26
Alignment explanation
Indices: 40831369--40831478 Score: 186
Period size: 26 Copynumber: 4.2 Consensus size: 26
40831359 TGATACAAAT
40831369 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
40831395 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40831421 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
40831447 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
40831473 TGATAA
1 TGATAA
40831479 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 1 0.01
26 79 0.99
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40833519 original size:137 final size:136
Alignment explanation
Indices: 40833250--40833534 Score: 527
Period size: 137 Copynumber: 2.1 Consensus size: 136
40833240 GAGTAGTCTC
*
40833250 CCCAAAT-GGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
40833314 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
40833379 CTGTTA
131 CTGTTA
40833385 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
40833450 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
40833515 ACTGTTA
130 ACTGTTA
**
40833522 CCTGAATGGGCTT
1 CCCAAATGGGCTT
40833535 AGGCCCAATG
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 7 0.05
136 12 0.08
137 126 0.87
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:40837355 original size:51 final size:50
Alignment explanation
Indices: 40837300--40837406 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 50
40837290 TGATACAAAT
40837300 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAAT-GGTTAGGTAAATGTTTCA
40837351 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTTCA
40837401 TGATAA
1 TGATAA
40837407 GAATTTCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
49 13 0.24
50 19 0.35
51 23 0.42
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (50 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTTCA
Found at i:40837358 original size:25 final size:25
Alignment explanation
Indices: 40837300--40837406 Score: 189
Period size: 25 Copynumber: 4.2 Consensus size: 25
40837290 TGATACAAAT
40837300 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
40837326 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
40837351 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
40837376 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
40837401 TGATAA
1 TGATAA
40837407 GAATTTCATG
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.16
25 44 0.55
26 23 0.29
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:40838940 original size:25 final size:25
Alignment explanation
Indices: 40838892--40838940 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40838882 ACAGTTTTAC
40838892 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
40838917 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
40838941 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:40839432 original size:136 final size:136
Alignment explanation
Indices: 40839188--40839473 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 136
40839178 GAGTAGTCTC
*
40839188 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
40839253 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
40839318 CTGTTA
131 CTGTTA
40839324 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCC-TAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
40839388 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
40839453 ACTGTTA
130 ACTGTTA
**
40839460 CCTGAATGGGCTTG
1 CCCAAATGGGCTTG
40839474 AGCTGACTTG
Statistics
Matches: 146, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
136 107 0.73
137 39 0.27
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:40839626 original size:7 final size:7
Alignment explanation
Indices: 40839614--40839640 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40839604 CCCGTTCTGA
40839614 AAGTTTG
1 AAGTTTG
40839621 AAGTTTG
1 AAGTTTG
40839628 AAGTTTG
1 AAGTTTG
40839635 AAGTTT
1 AAGTTT
40839641 TGGGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
AAGTTTG
Found at i:40841516 original size:25 final size:25
Alignment explanation
Indices: 40841486--40841657 Score: 125
Period size: 22 Copynumber: 7.4 Consensus size: 25
40841476 GACTTCAGCA
*
40841486 TGCTCTTTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
40841511 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
40841533 TGCTCTCTGATATTTAACACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* * **
40841558 AGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
* *
40841580 TGATCTCTAATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
40841605 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
40841627 TGCTCTCTG-TA--TAGCACTTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
40841649 TGCTCTCTG
1 TGCTCTCTG
40841658 TTCATTAGTG
Statistics
Matches: 113, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
22 67 0.59
23 4 0.04
24 2 0.02
25 40 0.35
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (25 bp):
TGCTCTCTGATATTTAGCACGTCAG
Found at i:40841555 original size:47 final size:47
Alignment explanation
Indices: 40841486--40841657 Score: 269
Period size: 47 Copynumber: 3.7 Consensus size: 47
40841476 GACTTCAGCA
*
40841486 TGCTCTTTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
40841533 TGCTCTCTGATATTTAACACGTCAGAGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
40841580 TGATCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
*
40841627 TGCTCTCTG-TA--TAGCACTTCAGTGCTCTCTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG
40841658 TTCATTAGTG
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 19 0.17
46 2 0.02
47 94 0.82
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (47 bp):
TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
Found at i:40844336 original size:48 final size:50
Alignment explanation
Indices: 40844259--40844362 Score: 169
Period size: 48 Copynumber: 2.1 Consensus size: 50
40844249 TGATACAAAT
*
40844259 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGT-AGT-TTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTTCA
40844307 TGATAAT-GGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAATGGTTAGGTAAATGTTTCA
40844357 TGATAA
1 TGATAA
40844363 GAATTTCATG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
47 15 0.29
48 24 0.46
49 2 0.04
50 11 0.21
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (50 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTTCA
Found at i:40844339 original size:25 final size:25
Alignment explanation
Indices: 40844259--40844362 Score: 160
Period size: 25 Copynumber: 4.2 Consensus size: 25
40844249 TGATACAAAT
40844259 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAAT-GGTTAGGTAAATGTTTCA
*
40844284 TGATAATGGTTAGGT-AGT-TTTCA
1 TGATAATGGTTAGGTAAATGTTTCA
*
40844307 TGATAATGGTTAGGTAAATGTTCCA
1 TGATAATGGTTAGGTAAATGTTTCA
40844332 TGATAATGGTTAGGTAAATGTTTCA
1 TGATAATGGTTAGGTAAATGTTTCA
40844357 TGATAA
1 TGATAA
40844363 GAATTTCATG
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 21 0.29
24 10 0.14
25 41 0.57
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTTCA
Found at i:40846382 original size:137 final size:135
Alignment explanation
Indices: 40846138--40846422 Score: 534
Period size: 137 Copynumber: 2.1 Consensus size: 135
40846128 GAGTAGTCTC
40846138 CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
1 CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
40846203 TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
66 TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
40846268 TGTTA
131 TGTTA
40846273 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTA-TGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
40846338 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
64 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
40846403 ACTGTTA
129 ACTGTTA
**
40846410 CCTGAATGGGCTT
1 CCCAAATGGGCTT
40846423 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
135 20 0.14
136 3 0.02
137 123 0.84
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (135 bp):
CCCAAATGGGCTTGCATATGTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTG
TTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCAC
TGTTA
Found at i:40850243 original size:51 final size:51
Alignment explanation
Indices: 40850188--40850295 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 51
40850178 TGATACAAAT
40850188 TGATAATAGGTTAGGTAAATGTTCCATGATAAT-AGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAATGA-GTTAGGTAAATGTTTCA
40850239 TGATAATAGGTTAGGTAAATGTTCATGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGAGTTAGGTAAATGTTTCA
40850290 TGATAA
1 TGATAA
40850296 GAATTTCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
50 21 0.38
51 34 0.62
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGAGTTAGGTAAATGTTTCA
Found at i:40850246 original size:25 final size:25
Alignment explanation
Indices: 40850188--40850295 Score: 182
Period size: 25 Copynumber: 4.2 Consensus size: 25
40850178 TGATACAAAT
40850188 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
40850214 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
40850239 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
40850264 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATG-TTCA
40850290 TGATAA
1 TGATAA
40850296 GAATTTCATG
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
24 1 0.01
25 46 0.57
26 33 0.41
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:40852319 original size:137 final size:136
Alignment explanation
Indices: 40852074--40852360 Score: 529
Period size: 137 Copynumber: 2.1 Consensus size: 136
40852064 GAGTAGTCTC
*
40852074 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
40852139 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
40852204 CTGTTA
131 CTGTTA
*
40852210 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCCTAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
40852275 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
40852340 ACTGTTA
130 ACTGTTA
**
40852347 CCTGAATGGGCTTG
1 CCCAAATGGGCTTG
40852361 AGCTGACTTG
Statistics
Matches: 146, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 20 0.14
137 126 0.86
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:40852506 original size:7 final size:7
Alignment explanation
Indices: 40852494--40852526 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
40852484 AGTGGCCACC
40852494 AGTTTGA
1 AGTTTGA
40852501 AGTTTGA
1 AGTTTGA
40852508 AGTTTGA
1 AGTTTGA
40852515 AGTTTGA
1 AGTTTGA
40852522 AGTTT
1 AGTTT
40852527 TGGGTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (7 bp):
AGTTTGA
Found at i:40854411 original size:25 final size:25
Alignment explanation
Indices: 40854381--40854552 Score: 125
Period size: 22 Copynumber: 7.4 Consensus size: 25
40854371 GACTTCAGCA
*
40854381 TGCTCTTTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
40854406 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
40854428 TGCTCTCTGATATTTAACACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* * **
40854453 AGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
* *
40854475 TGATCTCTAATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
40854500 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
40854522 TGCTCTCTG-TA--TAGCACTTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
40854544 TGCTCTCTG
1 TGCTCTCTG
40854553 TTCATTAGTG
Statistics
Matches: 113, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
22 67 0.59
23 4 0.04
24 2 0.02
25 40 0.35
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (25 bp):
TGCTCTCTGATATTTAGCACGTCAG
Found at i:40854450 original size:47 final size:47
Alignment explanation
Indices: 40854381--40854552 Score: 269
Period size: 47 Copynumber: 3.7 Consensus size: 47
40854371 GACTTCAGCA
*
40854381 TGCTCTTTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
40854428 TGCTCTCTGATATTTAACACGTCAGAGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
40854475 TGATCTCTAATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
*
40854522 TGCTCTCTG-TA--TAGCACTTCAGTGCTCTCTG
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG
40854553 TTCATTAGTG
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 19 0.17
46 2 0.02
47 94 0.82
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (47 bp):
TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
Found at i:40857104 original size:13 final size:13
Alignment explanation
Indices: 40857086--40857112 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40857076 AGCAGGGGAG
40857086 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
40857099 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
40857112 G
1 G
40857113 GGAGAAAAGG
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAGAAA
Found at i:40862130 original size:3 final size:3
Alignment explanation
Indices: 40862117--40862206 Score: 171
Period size: 3 Copynumber: 29.7 Consensus size: 3
40862107 GTAAAATATA
40862117 ATT ACTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40862163 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40862207 GTCATATTAT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40863403 original size:37 final size:38
Alignment explanation
Indices: 40863361--40863455 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 38
40863351 GATAGATTCA
*
40863361 ATGAGGTGTTGGTCGCCAC-TTTGCTTCG-GCTTAGCCG
1 ATGAGGTGTTGGTCGCCACTTTTGCTTCGAAC-TAGCCG
* * *
40863398 ATGAGGCGTTGGTCGTCACTTATTTGCTTCGAACTATCCG
1 ATGAGGTGTTGGTCGCCAC-T-TTTGCTTCGAACTAGCCG
*
40863438 ATGAGGTGTTAGTCGCCA
1 ATGAGGTGTTGGTCGCCA
40863456 TCCTGGTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 17 0.36
40 29 0.62
41 1 0.02
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (38 bp):
ATGAGGTGTTGGTCGCCACTTTTGCTTCGAACTAGCCG
Found at i:40869779 original size:3 final size:3
Alignment explanation
Indices: 40869771--40869829 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
40869761 AGATATTTAC
40869771 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40869819 TTA TTA TTA TT
1 TTA TTA TTA TT
40869830 TTCAAATGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40871043 original size:40 final size:37
Alignment explanation
Indices: 40870965--40871052 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 37
40870955 GATAGATTCA
*
40870965 ATGAGGCGTTGGTCGCCACTTTGCTTCGGCTTAGCCG
1 ATGAGGCGTTGGTCGCCACTTTGCTTCGACTTAGCCG
* *
40871002 ATGAGACGTTGGTCGCCACTTATTTGCTTCGAAC-TATCCG
1 ATGAGGCGTTGGTCGCCAC---TTTGCTTCG-ACTTAGCCG
40871042 ATGAGGCGTTG
1 ATGAGGCGTTG
40871053 ATCTCTATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
37 18 0.42
40 24 0.56
41 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.31
Consensus pattern (37 bp):
ATGAGGCGTTGGTCGCCACTTTGCTTCGACTTAGCCG
Found at i:40876284 original size:25 final size:25
Alignment explanation
Indices: 40876255--40876339 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
40876245 CTCACCACAA
*
40876255 CTCGTATGAGCTTACTGATTATCAG
1 CTCGTAAGAGCTTACTGATTATCAG
40876280 CTCGTAAGAGCTTACTGTATT-TCAG
1 CTCGTAAGAGCTTACTG-ATTATCAG
* * * *
40876305 CTCGGAGGAGCTTACTAATTAT-GG
1 CTCGTAAGAGCTTACTGATTATCAG
40876329 CTCGTAAGAGC
1 CTCGTAAGAGC
40876340 ATACATGTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
24 13 0.25
25 35 0.69
26 3 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (25 bp):
CTCGTAAGAGCTTACTGATTATCAG
Found at i:40880484 original size:17 final size:17
Alignment explanation
Indices: 40880459--40880503 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
40880449 ATGACCCAAA
*
40880459 TCGAAATTGACATGAAC
1 TCGAAATTGACACGAAC
*
40880476 TCTAAATTGACACGAAC
1 TCGAAATTGACACGAAC
40880493 TCGAAATTGAC
1 TCGAAATTGAC
40880504 TTAAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (17 bp):
TCGAAATTGACACGAAC
Found at i:40881935 original size:26 final size:26
Alignment explanation
Indices: 40881882--40881944 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
40881872 AAAAGAAATC
* * *
40881882 TAAAGTAAATAATATATATGAAATTT
1 TAAAGTAAATAACATATATAAAAGTT
40881908 TAAAGTAAATAACATATA-AAACAGTT
1 TAAAGTAAATAACATATATAAA-AGTT
*
40881934 TAAATTAAATA
1 TAAAGTAAATA
40881945 TTATACGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (26 bp):
TAAAGTAAATAACATATATAAAAGTT
Found at i:40882317 original size:2 final size:2
Alignment explanation
Indices: 40882310--40882334 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40882300 AATAAATGGC
40882310 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 A
40882335 ATAGGTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40883608 original size:12 final size:13
Alignment explanation
Indices: 40883593--40883631 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40883583 AACCGATTTT
40883593 AGAAAAT-TAAAA
1 AGAAAATATAAAA
*
40883605 AGAAAATAAAAAA
1 AGAAAATATAAAA
*
40883618 AGAAGATATAAAA
1 AGAAAATATAAAA
40883631 A
1 A
40883632 CAAAGAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (13 bp):
AGAAAATATAAAA
Found at i:40884454 original size:44 final size:43
Alignment explanation
Indices: 40884352--40884498 Score: 154
Period size: 44 Copynumber: 3.4 Consensus size: 43
40884342 CCCACTCCAG
* *
40884352 TCTGCTCCACTGCAACTTCAGAGAGATGAGACT--TGTCTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATGAGATTAATGGCTTAA
* * * * *
40884393 TCTGCTCTACCGTAACTTCAGAGAGATAAGGTTAATGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGAGAGATGAGATTAATGGCTT-AA
* * * *
40884437 TCTGCTCCACTGAAACTTCAAAAAGATGAGATCAATGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATGAGATTAATGGC-TTAA
*
40884481 TCTGCTTCACTGCAACTT
1 TCTGCTCCACTGCAACTT
40884499 TAGGAATATA
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
41 27 0.32
43 5 0.06
44 51 0.60
45 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGAGAGATGAGATTAATGGCTTAA
Found at i:40898685 original size:26 final size:26
Alignment explanation
Indices: 40898647--40898756 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40898637 CATGATATTC
40898647 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40898673 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40898699 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40898725 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40898751 TTATCA
1 TTATCA
40898757 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:40898725 original size:52 final size:52
Alignment explanation
Indices: 40898647--40898756 Score: 220
Period size: 52 Copynumber: 2.1 Consensus size: 52
40898637 CATGATATTC
40898647 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTA
40898699 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTA
40898751 TTATCA
1 TTATCA
40898757 ATTTGTATCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTA
Found at i:40899483 original size:106 final size:106
Alignment explanation
Indices: 40899367--40899580 Score: 401
Period size: 106 Copynumber: 2.0 Consensus size: 106
40899357 AAAATATCAA
40899367 ATTTAAAAAGCAAAAATAGATATAAAAAGTTAAAAATTTGAAATTCACAGATACCCTTAAATATA
1 ATTTAAAAAGCAAAAATAGATATAAAAAGTTAAAAATTTGAAATTCACAGATACCCTTAAATATA
40899432 ATTAAAGAGAATGATAGGATTTATAATATATATATATATAT
66 ATTAAAGAGAATGATAGGATTTATAATATATATATATATAT
* * *
40899473 ATTTAAAAAGCAAAAATATATATAAAAAGTTAAAATTTTGAAATTCACATATACCCTTAAATATA
1 ATTTAAAAAGCAAAAATAGATATAAAAAGTTAAAAATTTGAAATTCACAGATACCCTTAAATATA
40899538 ATTAAAGAGAATGATAGGATTTATAATATATATATATATAT
66 ATTAAAGAGAATGATAGGATTTATAATATATATATATATAT
40899579 AT
1 AT
40899581 ATATCAACAA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (106 bp):
ATTTAAAAAGCAAAAATAGATATAAAAAGTTAAAAATTTGAAATTCACAGATACCCTTAAATATA
ATTAAAGAGAATGATAGGATTTATAATATATATATATATAT
Found at i:40904034 original size:47 final size:47
Alignment explanation
Indices: 40903976--40904070 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
40903966 AACAATCAAT
40903976 TGATCTTTATTGTTTAGTAACAATCAGTCATCAGTAATAATCAGTTA
1 TGATCTTTATTGTTTAGTAACAATCAGTCATCAGTAATAATCAGTTA
40904023 TGATCTTTATTGTTTAGTAACAATCAGTCATCAGTAATAATCAGTTA
1 TGATCTTTATTGTTTAGTAACAATCAGTCATCAGTAATAATCAGTTA
40904070 T
1 T
40904071 TCAGTAACGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (47 bp):
TGATCTTTATTGTTTAGTAACAATCAGTCATCAGTAATAATCAGTTA
Found at i:40904064 original size:17 final size:18
Alignment explanation
Indices: 40904038--40904078 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
40904028 TTTATTGTTT
40904038 AGTAACAATCAGTCA-TC
1 AGTAACAATCAGTCATTC
* *
40904055 AGTAATAATCAGTTATTC
1 AGTAACAATCAGTCATTC
40904073 AGTAAC
1 AGTAAC
40904079 GGTCGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (18 bp):
AGTAACAATCAGTCATTC
Found at i:40904076 original size:18 final size:18
Alignment explanation
Indices: 40904038--40904131 Score: 68
Period size: 18 Copynumber: 5.3 Consensus size: 18
40904028 TTTATTGTTT
* *
40904038 AGTAACAATCAGTCA-TC
1 AGTAATAATCAGTTATTC
40904055 AGTAATAATCAGTTATTC
1 AGTAATAATCAGTTATTC
***
40904073 AGTAACGGTC-GTTTATTC
1 AGTAATAATCAG-TTATTC
* *
40904091 AAT-ATCAATCAATTATTC
1 AGTAAT-AATCAGTTATTC
* *
40904109 AGTAGTAGTCAGTTATTC
1 AGTAATAATCAGTTATTC
40904127 AGTAA
1 AGTAA
40904132 CAGTTATTGA
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
17 15 0.26
18 41 0.72
19 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (18 bp):
AGTAATAATCAGTTATTC
Found at i:40904145 original size:54 final size:54
Alignment explanation
Indices: 40904040--40904163 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
40904030 TATTGTTTAG
* * * * *
40904040 TAACAATCAGTCA-TCAGTAATAATCAGTTATTCAGTAACGGTCGTTTATTCAA
1 TAACAATCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTGATTCAA
* * * * *
40904093 TATCAATCAATTATTCAGTAGTAGTCAGTTATTCAGTAACAGTTATTGATTCAG
1 TAACAATCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTGATTCAA
* *
40904147 TAACAGTCGATTATTCA
1 TAACAATCAATTATTCA
40904164 ATAACGGTCA
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
53 10 0.18
54 47 0.82
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (54 bp):
TAACAATCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTGATTCAA
Found at i:40904161 original size:36 final size:36
Alignment explanation
Indices: 40904061--40904183 Score: 108
Period size: 36 Copynumber: 3.4 Consensus size: 36
40904051 CATCAGTAAT
* * * *
40904061 AATCAGTTATTCAGTAACGGTCGTTTATTCAATATC
1 AATCAATTATTCAGTAACAGTCGATTATTCAATAAC
** *
40904097 AATCAATTATTCAGTAGTAGTC-AGTTATTCAGTAAC
1 AATCAATTATTCAGTAACAGTCGA-TTATTCAATAAC
* *
40904133 AGT-TATTGATTCAGTAACAGTCGATTATTCAATAAC
1 AATCAATT-ATTCAGTAACAGTCGATTATTCAATAAC
**
40904169 GGTCAATT-TTCAGTA
1 AATCAATTATTCAGTA
40904184 CCTTTATTTA
Statistics
Matches: 69, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
35 10 0.14
36 55 0.80
37 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (36 bp):
AATCAATTATTCAGTAACAGTCGATTATTCAATAAC
Found at i:40904162 original size:18 final size:18
Alignment explanation
Indices: 40904053--40904183 Score: 95
Period size: 18 Copynumber: 7.3 Consensus size: 18
40904043 CAATCAGTCA
* * *
40904053 TCAGTAATAATCAGTTAT
1 TCAGTAACAGTCAATTAT
* **
40904071 TCAGTAACGGTCGTTTAT
1 TCAGTAACAGTCAATTAT
* * *
40904089 TCAATATCAATCAATTAT
1 TCAGTAACAGTCAATTAT
** *
40904107 TCAGTAGTAGTCAGTTAT
1 TCAGTAACAGTCAATTAT
*
40904125 TCAGTAACAGT-TATTGAT
1 TCAGTAACAGTCAATT-AT
*
40904143 TCAGTAACAGTCGATTAT
1 TCAGTAACAGTCAATTAT
* *
40904161 TCAATAACGGTCAATT-T
1 TCAGTAACAGTCAATTAT
40904178 TCAGTA
1 TCAGTA
40904184 CCTTTATTTA
Statistics
Matches: 86, Mismatches: 25, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
17 8 0.09
18 75 0.87
19 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (18 bp):
TCAGTAACAGTCAATTAT
Found at i:40916036 original size:39 final size:39
Alignment explanation
Indices: 40915969--40916057 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
40915959 ATGCAACTTT
* *
40915969 TAATACACCGGCACACAGCCTACTAGGCACATAGCCCGAA
1 TAAT-CACCGGCACACAACCTACCAGGCACATAGCCCGAA
* * *
40916009 TAATCACCGGCACACAACTTGCCAGGCACATAGCTCGAA
1 TAATCACCGGCACACAACCTACCAGGCACATAGCCCGAA
*
40916048 AAATCACCGG
1 TAATCACCGG
40916058 ATTTCTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 39 0.91
40 4 0.09
ACGTcount: A:0.35, C:0.34, G:0.18, T:0.13
Consensus pattern (39 bp):
TAATCACCGGCACACAACCTACCAGGCACATAGCCCGAA
Found at i:40918482 original size:27 final size:27
Alignment explanation
Indices: 40918446--40918500 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40918436 GATTATAATA
40918446 ATATTAATAAACTAAATAAATTGAAAT
1 ATATTAATAAACTAAATAAATTGAAAT
40918473 ATATTAATAAACTAAATAAATTGAAAT
1 ATATTAATAAACTAAATAAATTGAAAT
40918500 A
1 A
40918501 AACTTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (27 bp):
ATATTAATAAACTAAATAAATTGAAAT
Found at i:40918501 original size:10 final size:9
Alignment explanation
Indices: 40918437--40918509 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
40918427 TGGAAGGAAG
40918437 ATTATAATAA
1 ATTA-AATAA
40918447 TATT-AATAA
1 -ATTAAATAA
*
40918456 ACTAAATAA
1 ATTAAATAA
*
40918465 ATTGAAATAT
1 ATT-AAATAA
40918475 ATT-AATAA
1 ATTAAATAA
*
40918483 ACTAAATAA
1 ATTAAATAA
40918492 ATTGAAATAA
1 ATT-AAATAA
40918502 ACTTAAAT
1 A-TTAAAT
40918510 CTACTCCTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.16
9 19 0.37
10 19 0.37
11 5 0.10
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (9 bp):
ATTAAATAA
Found at i:40921303 original size:29 final size:29
Alignment explanation
Indices: 40921271--40921372 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
40921261 CTTCGAGCTC
* * *
40921271 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
*
40921300 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
40921329 GCACACCTAGTGCCATATATTTTCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
*
40921358 GCACACTTAGTGCCA
1 GCACACCTAGTGCCA
40921373 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACCTAGTGCCATATATTTTCAGCAT
Found at i:40921304 original size:58 final size:58
Alignment explanation
Indices: 40921242--40921372 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
40921232 ATTTAAGCCC
* * *
40921242 GCACACATAGTGCCATA-CCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACTTAGTGCCATATACCTTC-AGCAT-GCACACCCAGTGCCATATATTTCCAGCAT
** * *
40921300 GCACACTTAGTGCCATATATTTTCAGCATGCACACCTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATACCTTCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
40921358 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
40921373 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
58 60 0.94
59 4 0.06
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (58 bp):
GCACACTTAGTGCCATATACCTTCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:40929047 original size:29 final size:29
Alignment explanation
Indices: 40929015--40929116 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
40929005 CTTCGAGCTC
* * *
40929015 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
*
40929044 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
40929073 GCACACCTAGTGCCATATATTTTCAGCAT
1 GCACACCTAGTGCCATATATTTTCAGCAT
*
40929102 GCACACTTAGTGCCA
1 GCACACCTAGTGCCA
40929117 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACCTAGTGCCATATATTTTCAGCAT
Found at i:40929048 original size:58 final size:58
Alignment explanation
Indices: 40928986--40929116 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
40928976 ATTTAAGCCC
* * *
40928986 GCACACATAGTGCCATA-CCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACTTAGTGCCATATACCTTC-AGCAT-GCACACCCAGTGCCATATATTTCCAGCAT
** * *
40929044 GCACACTTAGTGCCATATATTTTCAGCATGCACACCTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATACCTTCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
40929102 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
40929117 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
58 60 0.94
59 4 0.06
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (58 bp):
GCACACTTAGTGCCATATACCTTCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:40931395 original size:2 final size:2
Alignment explanation
Indices: 40931388--40931418 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40931378 TTGTTATGAT
40931388 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40931419 AGTTAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40931619 original size:16 final size:16
Alignment explanation
Indices: 40931600--40931634 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40931590 CAAAAATATC
*
40931600 CAAATTCAAAATAATT
1 CAAATTCAAAATAACT
*
40931616 CAAATTTAAAATAACT
1 CAAATTCAAAATAACT
40931632 CAA
1 CAA
40931635 TAAAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (16 bp):
CAAATTCAAAATAACT
Found at i:40932809 original size:2 final size:2
Alignment explanation
Indices: 40932802--40932835 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40932792 ATGCACCTGC
40932802 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
40932836 TGTAGTAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40934195 original size:15 final size:15
Alignment explanation
Indices: 40934175--40934204 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40934165 TTTTACTTAT
40934175 AAATTTATTTATTTA
1 AAATTTATTTATTTA
40934190 AAATTTATTTATTTA
1 AAATTTATTTATTTA
40934205 TTTAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATTTATTTATTTA
Found at i:40934201 original size:19 final size:19
Alignment explanation
Indices: 40934177--40934236 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 19
40934167 TTACTTATAA
40934177 ATTTATTTATTTAAAATTT
1 ATTTATTTATTTAAAATTT
40934196 ATTTATTTATTTAATATATATT
1 ATTTATTTATTTAA-A-AT-TT
40934218 A-TTATTTTATATTAAAATT
1 ATTTA-TTTAT-TTAAAATT
40934237 GCATGTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 14 0.39
20 2 0.06
21 7 0.19
22 9 0.25
23 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTTATTTAAAATTT
Found at i:40937109 original size:9 final size:9
Alignment explanation
Indices: 40937079--40937119 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
40937069 TTATTTATAC
40937079 TATTATATTT
1 TATTAT-TTT
* *
40937089 TATTACTGT
1 TATTATTTT
40937098 TATTATTTT
1 TATTATTTT
40937107 TATTATTTT
1 TATTATTTT
40937116 TATT
1 TATT
40937120 TATTAGCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
9 22 0.81
10 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TATTATTTT
Found at i:40937162 original size:2 final size:2
Alignment explanation
Indices: 40937157--40937181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40937147 ACTTAATACT
40937157 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 T
40937182 TAGATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40937332 original size:23 final size:20
Alignment explanation
Indices: 40937306--40937357 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
40937296 AACATTATAT
40937306 TATGTATATTTTTAAATATTATG
1 TATGTATATTTTT---TATTATG
40937329 TATGTAT-TTTTTTATTATG
1 TATGTATATTTTTTATTATG
*
40937348 TATATATATT
1 TATGTATATT
40937358 ATGTACATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
22 5 0.19
23 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TATGTATATTTTTTATTATG
Found at i:40937853 original size:3 final size:3
Alignment explanation
Indices: 40937799--40937837 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
40937789 TTGTTACTTA
40937799 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40937838 CATTTTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40940808 original size:35 final size:34
Alignment explanation
Indices: 40940767--40940843 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
40940757 ATTAAATATC
*
40940767 TGCATCTGT-ATCTG-AGATGGGCTTGGGCCTGAATA
1 TGCATCTGTGA-CTGTA-ATGGGCTTAGGCC-GAATA
*
40940802 TGCATCTGTGACTGTAATGGGCTTAGGCCGAATC
1 TGCATCTGTGACTGTAATGGGCTTAGGCCGAATA
*
40940836 TGTATCTG
1 TGCATCTG
40940844 ACTGATTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 11 0.30
35 24 0.65
36 2 0.05
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.32
Consensus pattern (34 bp):
TGCATCTGTGACTGTAATGGGCTTAGGCCGAATA
Found at i:40948191 original size:20 final size:22
Alignment explanation
Indices: 40948149--40948194 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
40948139 TTACACCAAA
*
40948149 CCCAAAACCTATTTACTTACCT
1 CCCAAAACCTATTTACTCACCT
*
40948171 CCCAAAA-CT-TTTACTCCCCT
1 CCCAAAACCTATTTACTCACCT
40948191 CCCA
1 CCCA
40948195 TCCTACCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (22 bp):
CCCAAAACCTATTTACTCACCT
Found at i:40953761 original size:3 final size:3
Alignment explanation
Indices: 40953755--40953787 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40953745 AACGAACAAC
*
40953755 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40953788 GATGTAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40954354 original size:20 final size:17
Alignment explanation
Indices: 40954311--40954356 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 17
40954301 AAGACTAATG
40954311 AATTAAAATAATATAAA
1 AATTAAAATAATATAAA
40954328 AA-T-AAATAATATAACA
1 AATTAAAATAATATAA-A
40954344 AGATTTAAAATAA
1 A-A-TTAAAATAA
40954357 ATGATAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 3 0.12
19 1 0.04
20 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AATTAAAATAATATAAA
Found at i:40954429 original size:24 final size:25
Alignment explanation
Indices: 40954393--40954464 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
40954383 AAAATAAAAT
*
40954393 TTTAACATAAATAATATATAAAAGG
1 TTTAAAATAAATAATATATAAAAGG
*
40954418 TTTAAAAT-AATAATATATGAAACGG
1 TTTAAAATAAATAATATAT-AAAAGG
* * *
40954443 TTCAGAATAAACAATATATAAA
1 TTTAAAATAAATAATATATAAA
40954465 TTTTTAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 10 0.25
25 21 0.52
26 9 0.22
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (25 bp):
TTTAAAATAAATAATATATAAAAGG
Found at i:40954796 original size:11 final size:11
Alignment explanation
Indices: 40954782--40954808 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40954772 TTTTGCTACC
40954782 ATTTTACTATT
1 ATTTTACTATT
40954793 ATTTTACTATT
1 ATTTTACTATT
40954804 ATTTT
1 ATTTT
40954809 GTTGTTATTG
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:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTACTATT
Found at i:40955287 original size:27 final size:27
Alignment explanation
Indices: 40955257--40955349 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
40955247 AAATAATTTA
40955257 AAATAATAATACAAAACAAATTAAAAT
1 AAATAATAATACAAAACAAATTAAAAT
* * * *
40955284 AAATAAT-ATGATATAACAATTTAAAAC
1 AAATAATAAT-ACAAAACAAATTAAAAT
* ** *
40955311 AAATACTATATGGAAAA-AGACTTAAAAT
1 AAATAATA-ATACAAAACA-AATTAAAAT
40955339 AAATAATAATA
1 AAATAATAATA
40955350 AAATTGTTCA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
26 2 0.04
27 29 0.58
28 17 0.34
29 2 0.04
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAATAATAATACAAAACAAATTAAAAT
Found at i:40963019 original size:42 final size:42
Alignment explanation
Indices: 40962955--40963043 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
40962945 CTAGGAATAT
* *
40962955 TTTTATTTTATCTTTTTGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
* *
40962997 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTT
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
40963039 TTTTC
1 TTTTC
40963044 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.54
Consensus pattern (42 bp):
TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:40964194 original size:11 final size:11
Alignment explanation
Indices: 40964150--40964197 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
40964140 CAATGACAAT
*
40964150 AAAATAGTAGC
1 AAAATAATAGC
* *
40964161 AATATAATAGA
1 AAAATAATAGC
* *
40964172 AAAATGACAGC
1 AAAATAATAGC
40964183 AAAATAATAGC
1 AAAATAATAGC
40964194 AAAA
1 AAAA
40964198 CAACAACAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.17
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:40964207 original size:22 final size:22
Alignment explanation
Indices: 40964164--40964207 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40964154 TAGTAGCAAT
** *
40964164 ATAATAGAAAAATGACAGCAAA
1 ATAATAGAAAAACAACAACAAA
*
40964186 ATAATAGCAAAACAACAACAAA
1 ATAATAGAAAAACAACAACAAA
40964208 TGGCAACAGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (22 bp):
ATAATAGAAAAACAACAACAAA
Found at i:40965942 original size:49 final size:49
Alignment explanation
Indices: 40965654--40965947 Score: 338
Period size: 49 Copynumber: 5.9 Consensus size: 49
40965644 TCTATTGTGA
* *
40965654 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
* * * **
40965703 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAA-TT
** * * * **
40965753 CAATCACGTGTGTAGTACTAAATGCAGGCTACTACATGTA-TCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATAATT
* *
40965803 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
* * * *
40965853 GGTCACATGTGTAGTACCAAGTGCAGGGTACTACATGTACTGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
* * *
40965902 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATA
40965948 GCTTTGGCTA
Statistics
Matches: 205, Mismatches: 36, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
49 126 0.61
50 44 0.21
51 35 0.17
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAATT
Found at i:40970403 original size:19 final size:19
Alignment explanation
Indices: 40970381--40970417 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40970371 AAAATTTTTA
*
40970381 AAAATCATTAAAAACCAAC
1 AAAATCATAAAAAACCAAC
40970400 AAAATCATAAAAAACCAA
1 AAAATCATAAAAAACCAA
40970418 AAACAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAATCATAAAAAACCAAC
Found at i:40970665 original size:20 final size:20
Alignment explanation
Indices: 40970653--40970704 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40970643 TTTAAGATTT
* *
40970653 TTTTTGTATTTTTATGAAAA
1 TTTTTATATTTTTAAGAAAA
40970673 TTTTTATATTTTTAAG-AAA
1 TTTTTATATTTTTAAGAAAA
*
40970692 -TTTTAAATTTTTA
1 TTTTTATATTTTTA
40970705 CACTGACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.41
19 3 0.10
20 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTTATATTTTTAAGAAAA
Found at i:40970701 original size:18 final size:20
Alignment explanation
Indices: 40970660--40970704 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
40970650 TTTTTTTTGT
* *
40970660 ATTTTTATGAAAATTTTTAT
1 ATTTTTAAGAAAATTTTTAA
40970680 ATTTTTAAG-AAA-TTTTAA
1 ATTTTTAAGAAAATTTTTAA
40970698 ATTTTTA
1 ATTTTTA
40970705 CACTGACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 3 0.13
20 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTTAAGAAAATTTTTAA
Found at i:40970991 original size:13 final size:14
Alignment explanation
Indices: 40970964--40970990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40970954 TTCGCTTATG
40970964 TATTGATGAAAAAA
1 TATTGATGAAAAAA
40970978 TATTGATGAAAAA
1 TATTGATGAAAAA
40970991 TGGGGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TATTGATGAAAAAA
Found at i:40977216 original size:1 final size:1
Alignment explanation
Indices: 40977210--40977236 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
40977200 TCTTTTGGTG
40977210 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
40977237 AGTATGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40977368 original size:61 final size:61
Alignment explanation
Indices: 40977273--40977395 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
40977263 ATATCATGTC
*
40977273 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGCAAAGTCAACCAACAT
1 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
40977334 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
1 CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
40977395 C
1 C
40977396 CTTGCTAACC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (61 bp):
CTTGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACAT
Found at i:40977569 original size:24 final size:24
Alignment explanation
Indices: 40977537--40977584 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
40977527 ATTGTTCAAC
40977537 GGAAAGAGAATCAATCAATGCCTT
1 GGAAAGAGAATCAATCAATGCCTT
40977561 GGAAAGAGAATCAATCAATGCCTT
1 GGAAAGAGAATCAATCAATGCCTT
40977585 ACTTTGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (24 bp):
GGAAAGAGAATCAATCAATGCCTT
Found at i:40979536 original size:27 final size:30
Alignment explanation
Indices: 40979478--40979539 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 30
40979468 TAGATTTTTA
* * *
40979478 ATTTTTATAATAACAAATTTAACTCTCGAC
1 ATTTATATAATAACAAATTTAACTCCCAAC
40979508 ATTTATATAA-AA-AAATTTAA-TCCCAAC
1 ATTTATATAATAACAAATTTAACTCCCAAC
40979535 ATTTA
1 ATTTA
40979540 CTCATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 8 0.28
29 2 0.07
30 9 0.31
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTATATAATAACAAATTTAACTCCCAAC
Found at i:40983070 original size:20 final size:20
Alignment explanation
Indices: 40983045--40983084 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40983035 AATCATTTTA
40983045 GTCCTTTGGATAATTACTAT
1 GTCCTTTGGATAATTACTAT
40983065 GTCCTTTGGATAATTACTAT
1 GTCCTTTGGATAATTACTAT
40983085 CTAGGCCCCT
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:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
GTCCTTTGGATAATTACTAT
Found at i:40985674 original size:17 final size:19
Alignment explanation
Indices: 40985632--40985676 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
40985622 CTCAAAGTAA
*
40985632 AGAAAATAAGCATAACAAT
1 AGAAAATAAGCACAACAAT
*
40985651 AGAAAATAAG-ACAACCAT
1 AGAAAATAAGCACAACAAT
40985669 -GAAAATAA
1 AGAAAATAA
40985677 AGCTTGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (19 bp):
AGAAAATAAGCACAACAAT
Found at i:40988531 original size:14 final size:15
Alignment explanation
Indices: 40988506--40988534 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40988496 AATATTTGTA
40988506 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
40988521 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
40988535 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:40990591 original size:21 final size:21
Alignment explanation
Indices: 40990547--40990597 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40990537 TTTAGCAAAA
*
40990547 AAAATTCTACAATTTCTCCCT
1 AAAATTCTACAATTTCTCACT
*
40990568 AAAATTCT-CAAATTTCTCATT
1 AAAATTCTAC-AATTTCTCACT
*
40990589 AAATTTCTA
1 AAAATTCTA
40990598 AAAACTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATTCTACAATTTCTCACT
Found at i:40990877 original size:54 final size:54
Alignment explanation
Indices: 40990758--40990876 Score: 170
Period size: 52 Copynumber: 2.2 Consensus size: 54
40990748 GTAAAGGTTT
* *
40990758 ATTTTAAATTTTGAATATTATTTAATATTTTTTTCATTTCTGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
**
40990812 ATTTTAATTTTTGAATATTATTT-A-ATTTTTTTCATTTATGTAATTTTCGTTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
*
40990864 ATTTGTATTTTTT
1 ATTT-TAATTTTT
40990877 TATTTTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
52 29 0.49
53 8 0.14
54 22 0.37
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (54 bp):
ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
Found at i:40991817 original size:7 final size:7
Alignment explanation
Indices: 40991807--40991831 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40991797 AGTCATTTCA
40991807 TATTTAG
1 TATTTAG
40991814 TATTTAG
1 TATTTAG
40991821 TATTTAG
1 TATTTAG
40991828 TATT
1 TATT
40991832 ATTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40992749 original size:21 final size:21
Alignment explanation
Indices: 40992725--40992770 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
40992715 TCCTCTCAAC
40992725 ACCACAACCCCCGCCA-GAGCA
1 ACCACAACCCCCG-CAGGAGCA
40992746 ACCACAACCCCCGCAGGAGCA
1 ACCACAACCCCCGCAGGAGCA
40992767 ACCA
1 ACCA
40992771 AGAAGGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (21 bp):
ACCACAACCCCCGCAGGAGCA
Found at i:40992968 original size:33 final size:31
Alignment explanation
Indices: 40992904--40992968 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
40992894 AAAAGAATTT
*
40992904 TTTTATATTTTAATAGTAAATTAATTTTTTTA
1 TTTTATATTTTAATAG-AAATTAATTCTTTTA
40992936 TTTTATAATTTTAATA-AAATATAAGTTCTTTTA
1 TTTTAT-ATTTTAATAGAAAT-TAA-TTCTTTTA
40992969 AATAAGGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.14
32 9 0.31
33 16 0.55
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTATATTTTAATAGAAATTAATTCTTTTA
Found at i:40996478 original size:24 final size:24
Alignment explanation
Indices: 40996446--40996500 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
40996436 GTTAGGACAT
* *
40996446 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAACTC
40996470 ATTAAATTCGTCAACCAGCAACTC
1 ATTAAATTCGTCAACCAGCAACTC
40996494 ATTAAAT
1 ATTAAAT
40996501 CTGTCCAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAACTC
Found at i:40996594 original size:17 final size:18
Alignment explanation
Indices: 40996574--40996608 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40996564 TGTACACACA
40996574 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
40996591 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
40996609 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:40996877 original size:9 final size:9
Alignment explanation
Indices: 40996863--40996887 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40996853 TAATTGTTAA
40996863 AACTAATTT
1 AACTAATTT
40996872 AACTAATTT
1 AACTAATTT
40996881 AACTAAT
1 AACTAAT
40996888 CAGCAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (9 bp):
AACTAATTT
Found at i:40998698 original size:25 final size:24
Alignment explanation
Indices: 40998657--40998704 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40998647 ACAATTGACC
*
40998657 AAACTAAGATATGGGAAGCTTTTAA
1 AAACTAAGATATCGGAA-CTTTTAA
40998682 AAACTAAG-TCATCGGAACTTTTA
1 AAACTAAGAT-ATCGGAACTTTTA
40998705 TCGACAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (24 bp):
AAACTAAGATATCGGAACTTTTAA
Found at i:40998977 original size:15 final size:15
Alignment explanation
Indices: 40998957--40998985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40998947 GTTCTGTTCA
40998957 CTCATTTCTTTTTCT
1 CTCATTTCTTTTTCT
40998972 CTCATTTCTTTTTC
1 CTCATTTCTTTTTC
40998986 AAACTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
CTCATTTCTTTTTCT
Found at i:41001436 original size:24 final size:24
Alignment explanation
Indices: 41001404--41001458 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
41001394 GTTGGGACAT
*
41001404 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
*
41001428 ATTAAATTCGTTAACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
41001452 ATTAAAT
1 ATTAAAT
41001459 CTGTCACGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:41001552 original size:17 final size:18
Alignment explanation
Indices: 41001532--41001566 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41001522 TGTACACACA
41001532 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
41001549 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
41001567 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:41002985 original size:126 final size:126
Alignment explanation
Indices: 41002760--41003082 Score: 468
Period size: 126 Copynumber: 2.6 Consensus size: 126
41002750 GGCTAAGTAT
* * * * *
41002760 GAACTACTGTAGAAAAAGAGCATCCATGTGAGAGCTTTTTTTAGAAATTTTGATAACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGATGACATTGCATC
* *
41002825 CTGCTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTTAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * *
41002886 GAACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTAATGACATTTCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGATGACATTGCATC
* * *
41002951 CTGCTTGAAGTGTTTTTGATACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * * * *
41003012 GAACTATTATAGCAAAAGAGTGTCCACGTGGGAGC-TTTTTCAAAAATTTTGATGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGATGACATTGCATC
*
41003076 CTACTTG
66 CTGCTTG
41003083 TTCAGAAGTG
Statistics
Matches: 176, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
125 32 0.18
126 144 0.82
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGATGACATTGCATC
CTGCTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
Found at i:41003228 original size:22 final size:22
Alignment explanation
Indices: 41003200--41003317 Score: 77
Period size: 22 Copynumber: 5.5 Consensus size: 22
41003190 ATTTTAACCC
41003200 AAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
**
41003222 AAAACCCTAGAACCCTAATTTA-CT
1 AAAACCCT--AA-TTTAATTTATCT
* * **
41003246 -TAA-TCT-ATTTAA-AAATCAT
1 AAAACCCTAATTTAATTTATC-T
* *
41003265 AA-ACCTTAATTTAATTTATTT
1 AAAACCCTAATTTAATTTATCT
*
41003286 TAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
41003308 AAAACCCTAA
1 AAAACCCTAA
41003318 AACCCTAATT
Statistics
Matches: 68, Mismatches: 18, Indels: 20
0.64 0.17 0.19
Matches are distributed among these distances:
17 1 0.01
18 4 0.06
19 3 0.04
20 1 0.01
21 8 0.12
22 38 0.56
23 2 0.03
24 4 0.06
25 7 0.10
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (22 bp):
AAAACCCTAATTTAATTTATCT
Found at i:41003238 original size:30 final size:30
Alignment explanation
Indices: 41003173--41003482 Score: 169
Period size: 30 Copynumber: 10.7 Consensus size: 30
41003163 TAAAAAAACT
* **
41003173 AAACCCTAATTTAATTAAT-TTTAACCC-A
1 AAACCCTAATTTAATTTATCTAAAACCCTA
41003201 AAACCCTAATTTAATTTATCTAAAACCCTA
1 AAACCCTAATTTAATTTATCTAAAACCCTA
* * * **
41003231 GAACCCTAATTTACTTAATCTATTTAAA-AATCA
1 AAACCCTAATTTAATTTATCTA---AAACCCT-A
* *
41003264 TAAACCTTAATTTAATTTAT-T-------TT
1 -AAACCCTAATTTAATTTATCTAAAACCCTA
41003287 AAACCCTAATTTAATTTATCTAAAACCCTA
1 AAACCCTAATTTAATTTATCTAAAACCCTA
* **
41003317 AAACCCTAATTTAATTAAT-TTTAACCC-A
1 AAACCCTAATTTAATTTATCTAAAACCCTA
*
41003345 AAACCCTAATTTAATTTATCTAAAATCCTA
1 AAACCCTAATTTAATTTATCTAAAACCCTA
* * * **
41003375 GAACCCTAATTTACTTAATCTATTTAAA-AATAAA
1 AAACCCTAATTTAATTTATCTA---AAACCCT--A
*
41003409 AAACCCTAATTTAATTTAT-T-------TT
1 AAACCCTAATTTAATTTATCTAAAACCCTA
*
41003431 AAACCCCAATTTAATTTATCTAAAACCCTA
1 AAACCCTAATTTAATTTATCTAAAACCCTA
* *
41003461 AAACCCTAATTTACTTAATCTA
1 AAACCCTAATTTAATTTATCTA
41003483 TTTAAAAATC
Statistics
Matches: 216, Mismatches: 36, Indels: 58
0.70 0.12 0.19
Matches are distributed among these distances:
22 36 0.17
23 2 0.01
24 2 0.01
28 37 0.17
29 17 0.08
30 79 0.37
32 2 0.01
33 9 0.04
34 32 0.15
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (30 bp):
AAACCCTAATTTAATTTATCTAAAACCCTA
Found at i:41003332 original size:144 final size:144
Alignment explanation
Indices: 41003173--41003479 Score: 560
Period size: 144 Copynumber: 2.1 Consensus size: 144
41003163 TAAAAAAACT
41003173 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
* * * *
41003238 AATTTACTTAATCTATTTAAAAATCATAAACCTTAATTTAATTTATTTTAAACCCTAATTTAATT
66 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
41003303 TATCTAAAACCCTA
131 TATCTAAAACCCTA
*
41003317 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAATCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
41003382 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
66 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
41003447 TATCTAAAACCCTA
131 TATCTAAAACCCTA
*
41003461 AAACCCTAATTTACTTAAT
1 AAACCCTAATTTAATTAAT
41003480 CTATTTAAAA
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 157 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (144 bp):
AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
TATCTAAAACCCTA
Found at i:41003441 original size:22 final size:22
Alignment explanation
Indices: 41003408--41003458 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
41003398 TTAAAAATAA
* *
41003408 AAAACCCTAATTTAATTTATTT
1 AAAACCCCAATTTAATTTATCT
*
41003430 TAAACCCCAATTTAATTTATCT
1 AAAACCCCAATTTAATTTATCT
41003452 AAAACCC
1 AAAACCC
41003459 TAAAACCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAACCCCAATTTAATTTATCT
Found at i:41003471 original size:86 final size:86
Alignment explanation
Indices: 41003345--41003508 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 86
41003335 TTTTAACCCA
* * *
41003345 AAACCCTAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
1 AAACCCCAATTTAATTTATCTAAAACCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
41003410 AACCCTAATTTAATTTATTTT
66 AACCCTAATTTAATTTATTTT
* *
41003431 AAACCCCAATTTAATTTATCTAAAACCCTAAAACCCTAATTTACTTAATCTATTTAAAAATCATA
1 AAACCCCAATTTAATTTATCTAAAACCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
41003496 AACCCTAATTTAA
66 AACCCTAATTTAA
41003509 ATAATTTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.37
Consensus pattern (86 bp):
AAACCCCAATTTAATTTATCTAAAACCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
AACCCTAATTTAATTTATTTT
Found at i:41003489 original size:34 final size:34
Alignment explanation
Indices: 41003441--41003507 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
41003431 AAACCCCAAT
* *
41003441 TTAATTTATCT-AAAACCCTAAAACCCTAATTTAC
1 TTAATCTATCTAAAAACCAT-AAACCCTAATTTAC
* *
41003475 TTAATCTATTTAAAAATCATAAACCCTAATTTA
1 TTAATCTATCTAAAAACCATAAACCCTAATTTA
41003508 AATAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.37
Consensus pattern (34 bp):
TTAATCTATCTAAAAACCATAAACCCTAATTTAC
Found at i:41004271 original size:19 final size:19
Alignment explanation
Indices: 41004243--41004294 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
41004233 ATTTGACTTC
41004243 TTCATATTTAATTTTT-AA
1 TTCATATTTAATTTTTCAA
41004261 TTCAGTATTTAATTTTTCAA
1 TTCA-TATTTAATTTTTCAA
*
41004281 TTTATCATTTAATT
1 TTCAT-ATTTAATT
41004295 AACGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (19 bp):
TTCATATTTAATTTTTCAA
Found at i:41009788 original size:93 final size:89
Alignment explanation
Indices: 41009659--41009853 Score: 207
Period size: 93 Copynumber: 2.1 Consensus size: 89
41009649 ATACAAAAAT
* * **
41009659 AATTTAATACAAATAAATTTTTTTCCATCATGCACATGTCAT-A-AACTTTAATACAAAGAAATC
1 AATTTAATACAAATAAATTTTTTTCCATCATACACATGAC-TGACAA-TAAAATACAAAGAAATC
* * * *
41009722 TATTTTTGTCATGTACAATAATAACCAAAC
64 CATTTCTATAATGT---ATAATAA-CAAAC
** *
41009752 AATTTAATACAAATAAATTTATTTT-TGTCCTACACATGACTGACAATAAAATACAAAGAAATCC
1 AATTTAATACAAATAAATTT-TTTTCCATCATACACATGACTGACAATAAAATACAAAGAAATCC
41009816 ATTTCTATAATGTATAATAACAAAC
65 ATTTCTATAATGTATAATAACAAAC
41009841 AATTTAATACAAA
1 AATTTAATACAAA
41009854 CAATTCAAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
89 18 0.20
90 7 0.08
92 1 0.01
93 56 0.64
94 6 0.07
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (89 bp):
AATTTAATACAAATAAATTTTTTTCCATCATACACATGACTGACAATAAAATACAAAGAAATCCA
TTTCTATAATGTATAATAACAAAC
Found at i:41009854 original size:14 final size:15
Alignment explanation
Indices: 41009830--41009858 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41009820 CTATAATGTA
41009830 TAATAACAAACAATT
1 TAATAACAAACAATT
41009845 TAAT-ACAAACAATT
1 TAATAACAAACAATT
41009859 CAAATATGAT
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:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAACAAACAATT
Found at i:41010480 original size:19 final size:21
Alignment explanation
Indices: 41010434--41010481 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
41010424 ATAATAAATT
41010434 AAATAAAT-TTAAAAACATAA
1 AAATAAATATTAAAAACATAA
*
41010454 AAACAAATATT-AAAACA-AA
1 AAATAAATATTAAAAACATAA
41010473 AAATAAATA
1 AAATAAATA
41010482 AAAAATGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 13 0.52
21 2 0.08
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (21 bp):
AAATAAATATTAAAAACATAA
Found at i:41013936 original size:2 final size:2
Alignment explanation
Indices: 41013923--41013970 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
41013913 GATGCCCTTT
* *
41013923 GA GA GA GT GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41013965 GA GA GA
1 GA GA GA
41013971 ACGGAATCTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.00, G:0.52, T:0.02
Consensus pattern (2 bp):
GA
Found at i:41016402 original size:2 final size:2
Alignment explanation
Indices: 41016395--41016430 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41016385 TTACTTTTTC
41016395 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
41016431 GATTTTTACC
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:41016581 original size:15 final size:14
Alignment explanation
Indices: 41016537--41016603 Score: 107
Period size: 14 Copynumber: 4.7 Consensus size: 14
41016527 GTTTGCAGGT
* *
41016537 AAAATGTTTTCCGG
1 AAAATGATTTCTGG
41016551 AAAATGATTTCTGG
1 AAAATGATTTCTGG
41016565 AAAATGATTTCCTGG
1 AAAATGATTT-CTGG
41016580 AAAATGATTTCTGG
1 AAAATGATTTCTGG
41016594 AAAATGATTT
1 AAAATGATTT
41016604 ACTTTTCTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
14 36 0.72
15 14 0.28
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:41016588 original size:29 final size:28
Alignment explanation
Indices: 41016537--41016603 Score: 116
Period size: 29 Copynumber: 2.4 Consensus size: 28
41016527 GTTTGCAGGT
*
41016537 AAAATGTTTTCCGGAAAATGATTTCTGG
1 AAAATGATTTCCGGAAAATGATTTCTGG
41016565 AAAATGATTTCCTGGAAAATGATTTCTGG
1 AAAATGATTTCC-GGAAAATGATTTCTGG
41016594 AAAATGATTT
1 AAAATGATTT
41016604 ACTTTTCTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 11 0.30
29 26 0.70
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (28 bp):
AAAATGATTTCCGGAAAATGATTTCTGG
Found at i:41016715 original size:16 final size:16
Alignment explanation
Indices: 41016694--41016746 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
41016684 CTGTTTTTAC
41016694 ATATATTAATAAATTT
1 ATATATTAATAAATTT
*
41016710 ATATA-T-AT--ATAT
1 ATATATTAATAAATTT
41016722 ATATATTAATAAATTT
1 ATATATTAATAAATTT
*
41016738 ATATTTTAA
1 ATATATTAA
41016747 ATTGTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 4 0.13
15 1 0.03
16 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTAATAAATTT
Found at i:41018185 original size:21 final size:21
Alignment explanation
Indices: 41018161--41018202 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41018151 TCAATATCAT
41018161 TATCCAAC-TAAATAAATTCAA
1 TATCCAACAT-AATAAATTCAA
*
41018182 TATCTAACATAATAAATTCAA
1 TATCCAACATAATAAATTCAA
41018203 CAAGCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (21 bp):
TATCCAACATAATAAATTCAA
Found at i:41018236 original size:21 final size:21
Alignment explanation
Indices: 41018171--41018236 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
41018161 TATCCAACTA
41018171 AATAAATTCAATATCTAACAT
1 AATAAATTCAATATCTAACAT
* *
41018192 AATAAATTCAACAAGCTTAAAACAT
1 AATAAATTCAA-TATC-T--AACAT
41018217 AATAAATTCAATATCTAACA
1 AATAAATTCAATATCTAACA
41018237 AATTCAAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 15 0.41
22 2 0.05
23 2 0.05
24 2 0.05
25 16 0.43
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAAATTCAATATCTAACAT
Found at i:41018237 original size:32 final size:32
Alignment explanation
Indices: 41018210--41018270 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
41018200 CAACAAGCTT
* *
41018210 AAAACATAATAAATTCAATATCTAACAAATTC
1 AAAACATAATAAATTCAAAATCCAACAAATTC
* *
41018242 AAGACATAATAATTTCAAAATCCAACAAA
1 AAAACATAATAAATTCAAAATCCAACAAA
41018271 CTAAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (32 bp):
AAAACATAATAAATTCAAAATCCAACAAATTC
Found at i:41022574 original size:10 final size:10
Alignment explanation
Indices: 41022559--41022601 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
41022549 AATAATTTTA
41022559 AAATCAAATT
1 AAATCAAATT
41022569 AAATCAAATTTT
1 AAATCAAA--TT
*
41022581 AAAAACAAATT
1 -AAATCAAATT
41022592 AAATCAAATT
1 AAATCAAATT
41022602 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 2 0.07
13 7 0.25
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATCAAATT
Found at i:41022579 original size:23 final size:23
Alignment explanation
Indices: 41022552--41022608 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
41022542 CCAATTTAAT
*
41022552 AATTTTAAAATCAAATTAAATCA
1 AATTTTAAAAACAAATTAAATCA
41022575 AATTTTAAAAACAAATTAAATCA
1 AATTTTAAAAACAAATTAAATCA
41022598 AATTTTAAAAA
1 AATTTTAAAAA
41022609 ATTATTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTTTAAAAACAAATTAAATCA
Found at i:41023327 original size:20 final size:20
Alignment explanation
Indices: 41023302--41023367 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
41023292 TATTTTTTAG
41023302 TTAATTATTAAGTTATAATT
1 TTAATTATTAAGTTATAATT
*
41023322 TTAATTAGGTAA-TTATAATT
1 TTAATTA-TTAAGTTATAATT
* * * *
41023342 TTAA-AATTTAGATAAAATT
1 TTAATTATTAAGTTATAATT
41023361 TTAATTA
1 TTAATTA
41023368 AATAAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 20 0.56
21 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TTAATTATTAAGTTATAATT
Found at i:41029604 original size:354 final size:355
Alignment explanation
Indices: 41028936--41029644 Score: 1213
Period size: 354 Copynumber: 2.0 Consensus size: 355
41028926 TTCAAATTGT
* *
41028936 CCAAATCCTTTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTTTGGACATCGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
*
41029001 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTT
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
*
41029066 TTTCTCTCAAAATCTTGTTTAATGATCTCTAACTCAGATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTGTTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
* *
41029131 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTGACCCCACCATTAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTATCGCTGATCCTCTGACCCCACCATCAGT
* *
41029196 CATACTCAGGGGTAGTCATTGGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGGCA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
41029261 TTCGATATCTCACGAACTTTCTTTTTGTAA
326 TTCGATATCTCACGAACTTTCTTTTTGTAA
*
41029291 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTT-AGCTTCTAGTTTCTGGACATTGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
* * * ** * *
41029355 CATCTAGCCCCAGCTGTATTTTTTCTCCCTTTAATTGCTCGATCCTTTTTTCTATCTCCAAACTC
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
* *
41029420 TTTCTCTCGAAATCTTGTTTGATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTGTTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
*
41029485 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTATCGTTGATCCTCTGACCCCACCATCAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTATCGCTGATCCTCTGACCCCACCATCAGT
* * *
41029550 CATACTCAGGGGTGGTCATTAGATTAGCAGCAAACCTTTTCATTTTATGAGTTTGGTTCTAGACA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
41029615 TTCGATATCTCACGAACTTTCTTTTTGTAA
326 TTCGATATCTCACGAACTTTCTTTTTGTAA
41029645 TTATCTCCCT
Statistics
Matches: 332, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
354 292 0.88
355 40 0.12
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (355 bp):
CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
TTTCTCTCAAAATCTTGTTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTATCGCTGATCCTCTGACCCCACCATCAGT
CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
TTCGATATCTCACGAACTTTCTTTTTGTAA
Found at i:41032506 original size:3 final size:3
Alignment explanation
Indices: 41032500--41032540 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
41032490 TAATAGTAAG
41032500 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
41032541 TAATAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41033757 original size:21 final size:21
Alignment explanation
Indices: 41033733--41033779 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
41033723 TTGGGCTTTA
41033733 GGTTTAGGTTGGTTT-TTATTG
1 GGTTTAGGTTGGTTTGTT-TTG
** *
41033754 GGTTGGGGTTTGTTTGTTTTG
1 GGTTTAGGTTGGTTTGTTTTG
41033775 GGTTT
1 GGTTT
41033780 GATGGTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.04, C:0.00, G:0.38, T:0.57
Consensus pattern (21 bp):
GGTTTAGGTTGGTTTGTTTTG
Found at i:41035470 original size:40 final size:39
Alignment explanation
Indices: 41035423--41035559 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 39
41035413 AATACTGGCA
*
41035423 GCTTGTCTACAATACTGGCAGTTTATCTACATTACTGGTG
1 GCTTGTCTACAATA-TGGCAGTTTATCTGCATTACTGGTG
* * * *
41035463 GTTTGTCTACATTATTGGTA-TCTTGTCTGCATTACTGGTG
1 GCTTGTCTACAATA-TGGCAGT-TTATCTGCATTACTGGTG
* *
41035503 GCTTGT-TCACATTTATGGCAGTTTATCTGTATTACTGGTG
1 GCTTGTCT-ACA-ATATGGCAGTTTATCTGCATTACTGGTG
* *
41035543 GCTTGTCCACAAAATGG
1 GCTTGTCTACAATATGG
41035560 TGTGTTATTG
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
39 6 0.08
40 69 0.87
41 4 0.05
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (39 bp):
GCTTGTCTACAATATGGCAGTTTATCTGCATTACTGGTG
Done.