Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 134 of 433
Found at i:41305688 original size:15 final size:14
Alignment explanation
Indices: 41305668--41305699 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
41305658 GGATTGTAAT
41305668 TTTTTTAATTTTTTA
1 TTTTTTAA-TTTTTA
41305683 TTTTTTAATTTTTA
1 TTTTTTAATTTTTA
41305697 TTT
1 TTT
41305700 CTTGAGGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTAATTTTTA
Found at i:41308884 original size:43 final size:43
Alignment explanation
Indices: 41308803--41308941 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 43
41308793 GAGATTACAA
** *
41308803 GTAAGACCATGTCTGGGACATTGGCATTATATTGTGATTACGT
1 GTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTACGT
**
41308846 GTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTTTGT
1 GTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTACGT
* * * * * *
41308889 GTAAGACCTTATTTGGGACAGTGGCATCG-ATATATGATAACAT
1 GTAAGACCATGTCTGGGACATTGGCATCGTAT-TATGATTACGT
*
41308932 GTAATACCAT
1 GTAAGACCAT
41308942 ATCTAGGATA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
42 2 0.03
43 78 0.98
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACATTGGCATCGTATTATGATTACGT
Found at i:41335227 original size:40 final size:40
Alignment explanation
Indices: 41335161--41335327 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41335151 AAATTGAATG
* * *
41335161 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41335200 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41335240 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41335280 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41335320 ATATCCGG
1 ATATCCGG
41335328 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41343288 original size:37 final size:37
Alignment explanation
Indices: 41343201--41343306 Score: 151
Period size: 37 Copynumber: 2.8 Consensus size: 37
41343191 CTGGAAATTA
* *
41343201 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGGC
*
41343239 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGT-TC
1 TATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGGC
41343276 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCA-TTGTGC
41343307 ACGTGATTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
37 32 0.51
38 31 0.49
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (37 bp):
TATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGGC
Found at i:41348410 original size:40 final size:40
Alignment explanation
Indices: 41348351--41348492 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
41348341 AAATTGAATG
* * *
41348351 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
41348391 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
41348431 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
41348471 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
41348493 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:41348493 original size:40 final size:39
Alignment explanation
Indices: 41348390--41348518 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
41348380 TGCTGGAAAT
* * *
41348390 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
41348430 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
41348470 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
41348510 TATATCCGG
1 TATATCCGG
41348519 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:41352661 original size:10 final size:10
Alignment explanation
Indices: 41352642--41352670 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41352632 CATTCATATG
41352642 GCCC-ATCAC
1 GCCCAATCAC
41352651 GCCCAATCAC
1 GCCCAATCAC
41352661 GCCCAATCAC
1 GCCCAATCAC
41352671 ATTCATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.28, C:0.52, G:0.10, T:0.10
Consensus pattern (10 bp):
GCCCAATCAC
Found at i:41352788 original size:17 final size:18
Alignment explanation
Indices: 41352766--41352799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41352756 TGCCTATTAT
41352766 GGGCCC-TATAGCCCATC
1 GGGCCCATATAGCCCATC
*
41352783 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
41352800 TTTGGCCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.21
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:41359530 original size:25 final size:25
Alignment explanation
Indices: 41359496--41359546 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41359486 TTCGAGGCTA
41359496 AGATGTGTAGAAGATTTAAAGATGG
1 AGATGTGTAGAAGATTTAAAGATGG
41359521 AGATGTGTAGAAGATTTAAAGATGG
1 AGATGTGTAGAAGATTTAAAGATGG
41359546 A
1 A
41359547 CTTAATGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (25 bp):
AGATGTGTAGAAGATTTAAAGATGG
Found at i:41366180 original size:20 final size:22
Alignment explanation
Indices: 41366146--41366185 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
41366136 ATTTACTCTT
41366146 AATTATAATTAAAATTATTTAA
1 AATTATAATTAAAATTATTTAA
41366168 AATTA-AATT-AAATTATTT
1 AATTATAATTAAAATTATTT
41366186 TGTATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTATAATTAAAATTATTTAA
Found at i:41368014 original size:25 final size:25
Alignment explanation
Indices: 41367965--41368017 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41367955 GTAAGCTTAG
*
41367965 AAAGTTTAGTAAGCCATAAGCAAAT
1 AAAGCTTAGTAAGCCATAAGCAAAT
41367990 AAAGCTTAGTAAGCCATAAGCAAAT
1 AAAGCTTAGTAAGCCATAAGCAAAT
41368015 AAA
1 AAA
41368018 TCATCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (25 bp):
AAAGCTTAGTAAGCCATAAGCAAAT
Found at i:41369114 original size:34 final size:34
Alignment explanation
Indices: 41369069--41369157 Score: 153
Period size: 34 Copynumber: 2.6 Consensus size: 34
41369059 TTTCAAAGCT
*
41369069 CAACTCAATTCAGCAACATATATATATTTCTTTA
1 CAACTCAATTCAGCAACATATATATATTTCTGTA
*
41369103 CAATTCAATTCAGCAACATATATATATTTCTGTA
1 CAACTCAATTCAGCAACATATATATATTTCTGTA
41369137 CAACTCAATTCAGC-ACATATA
1 CAACTCAATTCAGCAACATATA
41369158 ATGCACATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 7 0.13
34 45 0.87
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (34 bp):
CAACTCAATTCAGCAACATATATATATTTCTGTA
Found at i:41373236 original size:45 final size:46
Alignment explanation
Indices: 41373183--41373271 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
41373173 CCTGAGCTGA
* *
41373183 TGAACAGTAAGCTC-TATTGAGCTGA-AATAGTAAGCTCTGACGAAC
1 TGAACAGTAAGCTCATA-CGAGCTAAGAATAGTAAGCTCTGACGAAC
*
41373228 TGAACAGTAAGCTCATACGAGCTAAGAATAGTAAGCTCTTACGA
1 TGAACAGTAAGCTCATACGAGCTAAGAATAGTAAGCTCTGACGA
41373272 GTTGATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (46 bp):
TGAACAGTAAGCTCATACGAGCTAAGAATAGTAAGCTCTGACGAAC
Found at i:41373239 original size:22 final size:22
Alignment explanation
Indices: 41373183--41373241 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
41373173 CCTGAGCTGA
* *
41373183 TGAACAGTAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATCGAAC
*
41373205 TGAAATAGTAAGCTCTGA-CGAAC
1 TG-AACAGTAAGCTCT-ATCGAAC
41373228 TGAACAGTAAGCTC
1 TGAACAGTAAGCTC
41373242 ATACGAGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.42
23 17 0.55
24 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCGAAC
Found at i:41373263 original size:24 final size:21
Alignment explanation
Indices: 41373183--41373272 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 21
41373173 CCTGAGCTGA
* *
41373183 TGAACAGTAAGCTCTATTGAGC
1 TGAATAGTAAGCTCTA-CGAGC
*
41373205 TGAAATAGTAAGCTCTGACGAAC
1 TG-AATAGTAAGCTCT-ACGAGC
*
41373228 TGAACAGTAAGCTCATACGAGC
1 TGAATAGTAAGCTC-TACGAGC
41373250 TAAGAATAGTAAGCTCTTACGAG
1 T--GAATAGTAAGCTC-TACGAG
41373273 TTGATATATC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
22 19 0.34
23 18 0.32
24 19 0.34
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TGAATAGTAAGCTCTACGAGC
Found at i:41378071 original size:16 final size:16
Alignment explanation
Indices: 41378046--41378079 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41378036 ATGAATATAT
*
41378046 ATGTGTAAATGTAATA
1 ATGTGCAAATGTAATA
*
41378062 ATGTGCAAATGTGATA
1 ATGTGCAAATGTAATA
41378078 AT
1 AT
41378080 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATGTAATA
Found at i:41384593 original size:14 final size:14
Alignment explanation
Indices: 41384574--41384600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41384564 GATTATCAGT
41384574 TACCAGATACCAGG
1 TACCAGATACCAGG
41384588 TACCAGATACCAG
1 TACCAGATACCAG
41384601 AATTATAATA
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:0.37, C:0.30, G:0.19, T:0.15
Consensus pattern (14 bp):
TACCAGATACCAGG
Found at i:41390523 original size:129 final size:129
Alignment explanation
Indices: 41390293--41390550 Score: 408
Period size: 129 Copynumber: 2.0 Consensus size: 129
41390283 TAATCCTTCA
* * *
41390293 ACATAGGCGGTCGGTACCACGAGAGCTCGATTACAGCAAACTTGTTTCATTTGATTTATTTAAAT
1 ACATAGACGGTCGGTACCACGAGAGCTCGATTACAACAAACTTGTTTCATTTGACTTATTTAAAT
* * *
41390358 TTGGGTTTAAGCATTTTGTAATATTTGGATTGTTTTGGTTTTGCGATTTTATTTTCTATTTTTG
66 TTAGGTTTAAGCATTTTGTAATATCTGAATTGTTTTGGTTTTGCGATTTTATTTTCTATTTTTG
* * * * *
41390422 ACATAGACGGTCGGTACCACGGGAGCTCGGTTACAATAAATTTGTTTCGTTTGACTTATTTAAAT
1 ACATAGACGGTCGGTACCACGAGAGCTCGATTACAACAAACTTGTTTCATTTGACTTATTTAAAT
*
41390487 TTAGGTTTAAGCATTTTGTAATATCTGAATTGTTTTGGTTTTGGGATTTTATTTTCTATTTTTG
66 TTAGGTTTAAGCATTTTGTAATATCTGAATTGTTTTGGTTTTGCGATTTTATTTTCTATTTTTG
41390551 CATGATACTA
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (129 bp):
ACATAGACGGTCGGTACCACGAGAGCTCGATTACAACAAACTTGTTTCATTTGACTTATTTAAAT
TTAGGTTTAAGCATTTTGTAATATCTGAATTGTTTTGGTTTTGCGATTTTATTTTCTATTTTTG
Found at i:41392401 original size:2 final size:2
Alignment explanation
Indices: 41392396--41392425 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41392386 GAATTTTTTA
41392396 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
41392426 TTCCATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41399899 original size:14 final size:14
Alignment explanation
Indices: 41399882--41399908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41399872 TTTAGTGATG
41399882 TATATTTATAAAAC
1 TATATTTATAAAAC
41399896 TATATTTATAAAA
1 TATATTTATAAAA
41399909 GGAATTTTGA
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATTTATAAAAC
Found at i:41401684 original size:11 final size:11
Alignment explanation
Indices: 41401657--41401690 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41401647 GACTTTTAAA
41401657 TTATTTTGGTT
1 TTATTTTGGTT
*
41401668 TT-TTTTTGTT
1 TTATTTTGGTT
41401678 TTATTTTGGTT
1 TTATTTTGGTT
41401689 TT
1 TT
41401691 GGTGTAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (11 bp):
TTATTTTGGTT
Found at i:41407559 original size:24 final size:24
Alignment explanation
Indices: 41407531--41407580 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
41407521 TTAACTTTAC
41407531 TATAGACATTGATTAAAGATTATT
1 TATAGACATTGATTAAAGATTATT
*
41407555 TATAGACATTGATTAAAGATTGTT
1 TATAGACATTGATTAAAGATTATT
41407579 TA
1 TA
41407581 ATTGTCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (24 bp):
TATAGACATTGATTAAAGATTATT
Found at i:41409630 original size:3 final size:3
Alignment explanation
Indices: 41409622--41410055 Score: 337
Period size: 3 Copynumber: 147.3 Consensus size: 3
41409612 AACATATATA
*
41409622 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
41409670 AA- AAT ACT AA- ATT AATT AAT AAT AA- AAG AAT CAAT AA- AA- AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* ***
41409712 AAT AAT AGT GGC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
41409760 AAT AAGT AAA AAC AA- AA- AAA AAT AA- AA- AAT AA- AAA AAT ATAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * * * *
41409802 AAT -AT AAT AAT AGT -AT AAA AATT AATT AGT -TT AAT ACT -AT GAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT AAT AAT
* * * * * *
41409845 AAT AAT AAC AGT AAT AA- AAC AAC AAT AAT AAT AA- AGT ACAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
41409889 AAT AAT AAT -AT ATT AAT AAG GAT AAA AAT AAT -AT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
41409935 AAT AGAA AAT AAT AAT AAT AAT AAT AAT TAT ACATT AAT AAG GAT AAC
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
*
41409983 AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41410031 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
41410056 GGAACATTAA
Statistics
Matches: 350, Mismatches: 57, Indels: 48
0.77 0.13 0.11
Matches are distributed among these distances:
2 31 0.09
3 295 0.84
4 22 0.06
5 2 0.01
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41411699 original size:45 final size:45
Alignment explanation
Indices: 41411631--41411883 Score: 205
Period size: 45 Copynumber: 5.7 Consensus size: 45
41411621 GTAGCTTTAA
*
41411631 TCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAG
1 TCTGCTCCGCTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAG
* ** * * *
41411676 TCTGCTCCGCTG-TAACTTTAGGGAGATAAG-GCTGGTGGCTTCAA
1 TCTGCTCCGCTGCT-ACTTCAGGGAGATAAGATTTGCTGTCTTCAG
* *
41411720 TCTGCTCCGTTGCTACTTCAGGGAGATGAGATTTGCTGTCTTCAG
1 TCTGCTCCGCTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAG
* ** * *
41411765 TCTGCTCCGCTG-TAACTTCAGGAAGATAAG-GCTGGTGT-TTCAA
1 TCTGCTCCGCTGCT-ACTTCAGGGAGATAAGATTTGCTGTCTTCAG
* * * * * * *
41411808 TCTGCTCCCCTACTAC-CCCGAGAAGATAAGATTTGCTGTCTTTAA
1 TCTGCTCCGCTGCTACTTCAG-GGAGATAAGATTTGCTGTCTTCAG
* * * *
41411853 TCTACTCCACTACTGC-TCAGGGAGATAAGAT
1 TCTGCTCCGCTGCTACTTCAGGGAGATAAGAT
41411884 CTACAATCTT
Statistics
Matches: 164, Mismatches: 36, Indels: 17
0.76 0.17 0.08
Matches are distributed among these distances:
42 2 0.01
43 25 0.15
44 57 0.35
45 80 0.49
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (45 bp):
TCTGCTCCGCTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAG
Found at i:41411742 original size:89 final size:88
Alignment explanation
Indices: 41411624--41411849 Score: 319
Period size: 89 Copynumber: 2.6 Consensus size: 88
41411614 GCAACTTGTA
*
41411624 GCTTTAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAGTCTGCTCCGCTGT
1 GCTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAGTCTGCTCCGCTGT
* *
41411689 AACTTTAGGGAGATAAGGCTGGT
66 AACTTCAGGAAGATAAGGCTGGT
** *
41411712 GGCTTCAATCTGCTCCGTTGCTACTTCAGGGAGATGAGATTTGCTGTCTTCAGTCTGCTCCGCTG
1 -GCTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAGTCTGCTCCGCTG
41411777 TAACTTCAGGAAGATAAGGCTGGT
65 TAACTTCAGGAAGATAAGGCTGGT
* * * * * *
41411801 GTTTCAATCTGCTCCCCTACTAC-CCCGAGAAGATAAGATTTGCTGTCTT
1 GCTTCAATCTGCTCCACTGCTACTTCAG-GGAGATAAGATTTGCTGTCTT
41411850 TAATCTACTC
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
87 2 0.02
88 38 0.31
89 82 0.67
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (88 bp):
GCTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAGTCTGCTCCGCTGT
AACTTCAGGAAGATAAGGCTGGT
Found at i:41411970 original size:44 final size:44
Alignment explanation
Indices: 41411858--41411970 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 44
41411848 TTTAATCTAC
* * * *
41411858 TCCACTACTGCTCAGGGAGATAAGATCTACAATCTTCAGCCTGT
1 TCCACTGCTGCTCAGGGAGACAAGGTCTAAAATCTTCAGCCTGT
*
41411902 TCCACTGTTGCTCAGGGAGACAAGGTCTAAAATCTTCAGCCTGT
1 TCCACTGCTGCTCAGGGAGACAAGGTCTAAAATCTTCAGCCTGT
*
41411946 TCCACTGCTGCTCAGAGAGACAAGG
1 TCCACTGCTGCTCAGGGAGACAAGG
41411971 CTAGTGGCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (44 bp):
TCCACTGCTGCTCAGGGAGACAAGGTCTAAAATCTTCAGCCTGT
Found at i:41412289 original size:88 final size:88
Alignment explanation
Indices: 41412164--41412623 Score: 259
Period size: 88 Copynumber: 5.2 Consensus size: 88
41412154 TATTCAATCC
* * * ** ** * *
41412164 GCTCCACTACTGCTTAAGAAGATAAGATCCGTGATCTTCAACCTACTCTACTGCTACTCAGAGAG
1 GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCAACCTACTCCACTACTACTCAGAGAG
* * * * * *
41412229 ATAAGATTTTCCATCTTC-GATCT
66 ACAACATCTACAATCTTCAG-CCT
* * * * * *
41412252 GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCAACCTACTCCACTACTACTCAGAGAG
41412317 ACAACATCTACAATCTTCAGCCT
66 ACAACATCTACAATCTTCAGCCT
* * * * * * *
41412340 ACTCCATTACTGCTTAGGGAGACAAGATTTGCCATTTTCAATCTATTCCACTACTGCTTA-AGGA
1 GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCAACCTACTCCACTACTACTCAGA-GA
*
41412404 GACAAGATCTACAATCTTCAGCCT
65 GACAACATCTACAATCTTCAGCCT
* * * * * * * * * * * * *
41412428 ACTTCACTACTACTTAGGGAGATAGGATGGTG---GCTTAAATCTGCTCCACTACTGCTTAGGGA
1 GCTCCACTACTGCTTAGGGAGACAAGAT-TTGCCATCTTCAACCTACTCCACTACTACTCAGAGA
* * * * * *
41412490 GACAAGATTTTCCATCTT-TGATCT
65 GACAACATCTACAATCTTCAG-CCT
* * * * ** * ** * * *
41412514 GCTCTACTACTACTTAGGGAGAGAAGATCTGTTATCTTCGATATGCTCCACTACTGCTTATGA-A
1 GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCAACCTACTCCACTACTACTCA-GAGA
*
41412578 GACAAGATCTACAATCTTCAGCCT
65 GACAACATCTACAATCTTCAGCCT
* *
41412602 ACTCCACTACTGCTTATGGAGA
1 GCTCCACTACTGCTTAGGGAGA
41412624 TAGGATGGTG
Statistics
Matches: 296, Mismatches: 66, Indels: 20
0.77 0.17 0.05
Matches are distributed among these distances:
85 3 0.01
86 63 0.21
88 225 0.76
89 5 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (88 bp):
GCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCAACCTACTCCACTACTACTCAGAGAG
ACAACATCTACAATCTTCAGCCT
Found at i:41412491 original size:174 final size:174
Alignment explanation
Indices: 41412292--41412753 Score: 629
Period size: 174 Copynumber: 2.7 Consensus size: 174
41412282 GCCATCTTCG
* * * * * * * *
41412292 ATCTGCTCCACTACTGCTTAGGGAGACAACATCTACAATCTTC-AGCCTACTCCATTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGA-TCTGCTCTACTACTACTTA
* * *
41412356 GGGAGACAAGATTTGCCATTTTCAATCTATTCCACTACTGCTTAAGGAGACAAGATCTACAATCT
65 GGGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCTACAATCT
*
41412421 TCAGCCTACTTCACTACTACTTAGGGAGATAGGATGGTGGCTTAA
130 TCAGCCTACTCCACTACTACTTAGGGAGATAGGATGGTGGCTTAA
* *
41412466 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTTCCATCTTTGATCTGCTCTACTACTACTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
* ** * * * * * *
41412531 GGAGAGAAGATCTGTTATCTTCGATATGCTCCACTACTGCTTATGAAGACAAGATCTACAATCTT
66 GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCTACAATCTT
* *
41412596 CAGCCTACTCCACTACTGCTTATGGAGATAGGATGGTGGCTTAA
131 CAGCCTACTCCACTACTACTTAGGGAGATAGGATGGTGGCTTAA
* * *
41412640 ATCTGCTCCACTACTGCTTAGGGAGACAGGATTTACCATCTTCGATCTGTTCTACTACTTCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
* * *
41412705 GGAGACAAGATCTACAATTTTCAACCTACTCCACTATTGCTTAAGGAGA
66 GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGA
41412754 TAGGATGGTG
Statistics
Matches: 246, Mismatches: 41, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
174 245 1.00
175 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (174 bp):
ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCTACAATCTT
CAGCCTACTCCACTACTACTTAGGGAGATAGGATGGTGGCTTAA
Found at i:41412644 original size:130 final size:128
Alignment explanation
Indices: 41412248--41412835 Score: 475
Period size: 130 Copynumber: 4.5 Consensus size: 128
41412238 TCCATCTTCG
* *
41412248 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTACTTAGGGAGACAAGATTT--TATCTTCGATCTGCTCCACTACTGCTTAG
* * * * * * * * *
41412313 GGAGACAACATCTACAATCTTCAGCCTACTCCATTACTGCTTAGGGAGACAAGAT-TTGCCATTT
64 GAAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGC---T
*
41412377 TCA
126 TAA
** * * ** * * * *
41412380 ATCTATTCCACTACTGCTTAAGGAGACAAGATCTACAATCTTC-AGCCTACTTCACTACTACTTA
1 ATCTGCTCCACTACTACTTAGGGAGACAAGAT-T-TTATCTTCGA-TCTGCTCCACTACTGCTTA
* * * * ** * * * * * * ** **
41412444 GGGAGATAGGATGGT---GGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGATTTTCCATC
63 GGAAGACAAGAT-CTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAGGATGGT--GGC
**
41412506 TTTG
125 TTAA
* * * *
41412510 ATCTGCTCTACTACTACTTAGGGAGAGAAGATCTGTTATCTTCGATATGCTCCACTACTGCTTAT
1 ATCTGCTCCACTACTACTTAGGGAGACAAGAT-T-TTATCTTCGATCTGCTCCACTACTGCTTAG
* *
41412575 GAAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTATGGAGATAGGATGGTGGCTTAA
64 GAAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAA
* * * * * *
41412640 ATCTGCTCCACTACTGCTTAGGGAGACAGGATTTACCATCTTCGATCTGTTCTACTACTTCTTAG
1 ATCTGCTCCACTACTACTTAGGGAGACAAGATTT--TATCTTCGATCTGCTCCACTACTGCTTAG
* * *
41412705 GGAGACAAGATCTACAATTTTCAACCTACTCCACTATTGCTTAAGGAGATAGGATGGTGGCTTAA
64 GAAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAA
* *
41412770 ATCTGCTCCACTACTACTTAGGGAGATAAGATTTTCCATCTTCGATCTGCTCCACTGCTGCTTAG
1 ATCTGCTCCACTACTACTTAGGGAGACAAGATTTT--ATCTTCGATCTGCTCCACTACTGCTTAG
41412835 G
64 G
41412836 GAGATAGGAT
Statistics
Matches: 360, Mismatches: 81, Indels: 32
0.76 0.17 0.07
Matches are distributed among these distances:
128 1 0.00
129 2 0.01
130 260 0.72
131 4 0.01
132 90 0.25
133 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (128 bp):
ATCTGCTCCACTACTACTTAGGGAGACAAGATTTTATCTTCGATCTGCTCCACTACTGCTTAGGA
AGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAAGGAGATAGGATGGTGGCTTAA
Found at i:41412820 original size:174 final size:172
Alignment explanation
Indices: 41412292--41412839 Score: 551
Period size: 174 Copynumber: 3.2 Consensus size: 172
41412282 GCCATCTTCG
* * * * * * * *
41412292 ATCTGCTCCACTACTGCTTAGGGAGACAACATCTACAATCTTC-AGCCTACTCCATTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGA-TCTGCTCTACTACTACTTA
* * *
41412356 GGGAGACAAGATTTGCCATTTTCAATCTATTCCACTACTGCTTAAGGAGACAAGATCTACAATCT
65 GGGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCT--AATCT
* * * *
41412421 TCAGCCTACTTCACTACTACTTAGGGAGATAGGATGGTGGCTTAA
128 TCAACCTACTCCACTACTACTTAGGGAGATAAGATGGTAGCTTAA
* *
41412466 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTTCCATCTTTGATCTGCTCTACTACTACTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
* ** * * * * * *
41412531 GGAGAGAAGATCTGTTATCTTCGATATGCTCCACTACTGCTTATGAAGACAAGATCTACAATCTT
66 GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCT--AATCTT
* * * * *
41412596 CAGCCTACTCCACTACTGCTTATGGAGATAGGATGGTGGCTTAA
129 CAACCTACTCCACTACTACTTAGGGAGATAAGATGGTAGCTTAA
* * *
41412640 ATCTGCTCCACTACTGCTTAGGGAGACAGGATTTACCATCTTCGATCTGTTCTACTACTTCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
* * * * * * ** *
41412705 GGAGACAAGATCTACAATTTTCAACCTACTCCACTATTGCTTAAGGAGATAGGATGGT-GGCTTA
66 GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGAT-CTAATCTTC
* * ** * **
41412769 AATCTGCTCCACTACTACTTAGGGAGATAAGATTTTCCATCTTCG
130 AACCTACTCCACTACTACTTAGGGAGATAAGATGGT--AGCTTAA
*
41412814 ATCTGCTCCACTGCTGCTTAGGGAGA
1 ATCTGCTCCACTACTGCTTAGGGAGA
41412840 TAGGATCTGT
Statistics
Matches: 310, Mismatches: 60, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
172 31 0.10
174 277 0.89
175 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (172 bp):
ATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCTACTACTACTTAG
GGAGACAAGATCTGCAATTTTCAATCTACTCCACTACTGCTTAAGGAGACAAGATCTAATCTTCA
ACCTACTCCACTACTACTTAGGGAGATAAGATGGTAGCTTAA
Found at i:41412841 original size:44 final size:44
Alignment explanation
Indices: 41412226--41412839 Score: 422
Period size: 44 Copynumber: 14.1 Consensus size: 44
41412216 GCTACTCAGA
*
41412226 GAGATAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
*
41412270 GAGACAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * * * * *
41412314 GAGACAACATCTACAATCTTC-AGCCTACTCCATTACTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGA-TCTGCTCCACTACTGCTTAGG
* * * ** *
41412358 GAGACAAGATTTGCCATTTTCAATCTATTCCACTACTGCTTAAG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * * * * *
41412402 GAGACAAGATCTACAATCTTC-AGCCTACTTCACTACTACTTAGG
1 GAGACAAGATTTTCCATCTTCGA-TCTGCTCCACTACTGCTTAGG
* * ** ** **
41412446 GAGATAGGATGGT--GGCTTAAATCTGCTCCACTACTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * *
41412488 GAGACAAGATTTTCCATCTTTGATCTGCTCTACTACTACTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * *
41412532 GAGAGAAGATCTGTT--ATCTTCGATATGCTCCACTACTGCTTATG
1 GAGACAAGAT-T-TTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * * * * *
41412576 AAGACAAGATCTACAATCTTC-AGCCTACTCCACTACTGCTTATG
1 GAGACAAGATTTTCCATCTTCGA-TCTGCTCCACTACTGCTTAGG
* * ** ** **
41412620 GAGATAGGATGGT--GGCTTAAATCTGCTCCACTACTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * * *
41412662 GAGACAGGATTTACCATCTTCGATCTGTTCTACTACTTCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * * * * * * *
41412706 GAGACAAGATCTACAATTTTCAACCTACTCCACTATTGCTTAAG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* * ** ** ** *
41412750 GAGATAGGATGGT--GGCTTAAATCTGCTCCACTACTACTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
* *
41412792 GAGATAAGATTTTCCATCTTCGATCTGCTCCACTGCTGCTTAGG
1 GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
41412836 GAGA
1 GAGA
41412840 TAGGATCTGT
Statistics
Matches: 434, Mismatches: 120, Indels: 32
0.74 0.20 0.05
Matches are distributed among these distances:
42 90 0.21
43 5 0.01
44 335 0.77
45 2 0.00
46 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
GAGACAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGG
Found at i:41412847 original size:130 final size:130
Alignment explanation
Indices: 41411851--41412839 Score: 617
Period size: 132 Copynumber: 7.5 Consensus size: 130
41411841 TGCTGTCTTT
* * * * * * * ** *
41411851 AATCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTC-AGCCTGTTCCACTGTTGCTC
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGA-TCTGCTCCACTACTGCTT
* * * ** * * * * *
41411915 AGGGAGACAAGGTCTAAAATCTTCAGCCTGTTCCACTGCTGCTCAGAGAGACAAGGCTAGTGGCT
65 AGGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAA-GATGGTGGCT
41411980 TA
129 TA
* * * * * * * * * *
41411982 AATTTACTTCC-CTACTACCTCGGGAAGATAAGATTTACCGTCTTTGATCTGTTCCACTACTCCT
1 AATCTGC-TCCACTACTGCTTAGGG-AGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCT
* * * ** * ** * * * *
41412046 AAGGGAGATAAGATCTACAATCTTTAACCTGTTCCACTGCTATTTAGGAAGACAATGCTAGTAGC
64 TAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAA-GATGGTGGC
41412111 TTA
128 TTA
* * * * * ** * * * *
41412114 AATTTGCTTCC-CTACTACCTCGGGAAGATAAGATTCGCCGTATTCAATCCGCTCCACTACTGCT
1 AATCTGC-TCCACTACTGCTTAGGG-AGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCT
* * * **** * * * * * * ** **
41412178 TAAGAAGATAAGATCCGTGATCTTCAACCTACTCTACTGCTACTCAGAGAGATAAGATTTTCCAT
64 TAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGT--GG
*
41412243 CTTC
127 CTTA
* *
41412247 GATCTGCTCCACTACTGCTTAGGGAGACAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTA
* * * * *
41412312 GGGAGACAACATCTACAATCTTCAGCCTACTCCATTACTGCTTAGGGAGACAAGAT-TTGCCATT
66 GGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGTGGC---
*
41412376 TTC
128 TTA
** * * * * * * *
41412379 AATCTATTCCACTACTGCTTAAGGAGACAAGATCTACAATCTTC-AGCCTACTTCACTACTACTT
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGA-TCTGCTCCACTACTGCTT
* * * ** * * * ** **
41412443 AGGGAGATAGGATGGT---GGCTTAAATCTGCTCCACTACTGCTTAGGGAGACAAGATTTTCCAT
65 AGGGAGACAAGAT-CTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGT--GG
*
41412505 CTTT
127 CTTA
* * * * * *** *
41412509 GATCTGCTCTACTACTACTTAGGGAGAGAAGATCTGTTATCTTCGATATGCTCCACTACTGCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTA
* * * * * *
41412574 TGAAGACAAGATCTACAATCTTCAGCCTACTCCACTACTGCTTATGGAGATAGGATGGTGGCTTA
66 GGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGTGGCTTA
* * * *
41412639 AATCTGCTCCACTACTGCTTAGGGAGACAGGATTTACCATCTTCGATCTGTTCTACTACTTCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTA
* * * * *
41412704 GGGAGACAAGATCTACAATTTTCAACCTACTCCACTATTGCTTAAGGAGATAGGATGGTGGCTTA
66 GGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGTGGCTTA
* * * *
41412769 AATCTGCTCCACTACTACTTAGGGAGATAAGATTTTCCATCTTCGATCTGCTCCACTGCTGCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTA
41412834 GGGAGA
66 GGGAGA
41412840 TAGGATCTGT
Statistics
Matches: 669, Mismatches: 171, Indels: 37
0.76 0.19 0.04
Matches are distributed among these distances:
129 2 0.00
130 267 0.40
131 24 0.04
132 354 0.53
133 22 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (130 bp):
AATCTGCTCCACTACTGCTTAGGGAGACAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTA
GGGAGACAAGATCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGACAAGATGGTGGCTTA
Found at i:41418852 original size:76 final size:76
Alignment explanation
Indices: 41418726--41418869 Score: 288
Period size: 76 Copynumber: 1.9 Consensus size: 76
41418716 CAGTTACATA
41418726 CGAGGAAGGATTAGCACCCTAGTAACGCCTAAAATTGGTACCTAGTTCATTAATTAGTGTCTTAA
1 CGAGGAAGGATTAGCACCCTAGTAACGCCTAAAATTGGTACCTAGTTCATTAATTAGTGTCTTAA
41418791 TGTTGAAAGTT
66 TGTTGAAAGTT
41418802 CGAGGAAGGATTAGCACCCTAGTAACGCCTAAAATTGGTACCTAGTTCATTAATTAGTGTCTTAA
1 CGAGGAAGGATTAGCACCCTAGTAACGCCTAAAATTGGTACCTAGTTCATTAATTAGTGTCTTAA
41418867 TGT
66 TGT
41418870 CAAAAGTTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (76 bp):
CGAGGAAGGATTAGCACCCTAGTAACGCCTAAAATTGGTACCTAGTTCATTAATTAGTGTCTTAA
TGTTGAAAGTT
Found at i:41419585 original size:3 final size:3
Alignment explanation
Indices: 41419577--41419898 Score: 113
Period size: 3 Copynumber: 109.0 Consensus size: 3
41419567 TAATAAAACA
* * * * *
41419577 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAC AA- AAT ACT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * ***
41419623 ATT AATT AAT AAT AA- AAT AAT CAAT AA- AAA AAT AAT AAT AGT GGC
1 AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
41419668 AAT AAT AAT AAT AGT AAT AAT AGT AAGT AAA AAC ACA- AAA AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT
* *
41419713 AA- AAT AA- AA- AAA AAT ATAT AAT -AT AAT AAT AAT AGCAT AAA AATT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A--AT AAT AA-T
* * * * * * * *
41419758 AATT AGT -TT AAT ACT -AT GAT AAT AAT AAC AGT AAT AA- AAC AAC
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
41419801 AAT AAT AAT AA- AGT ACAA AAT AAT AAT AAT -AT ATT AAT -AT GGAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
41419845 AAT AAT AAT -AT ATT AAT AAT AAT AAT AAT CGAA- AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT
41419890 AAT AAT AAT
1 AAT AAT AAT
41419899 TATACATTAA
Statistics
Matches: 247, Mismatches: 44, Indels: 56
0.71 0.13 0.16
Matches are distributed among these distances:
2 31 0.13
3 190 0.77
4 21 0.09
5 5 0.02
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:41419585 original size:15 final size:14
Alignment explanation
Indices: 41419567--41419662 Score: 59
Period size: 15 Copynumber: 6.4 Consensus size: 14
41419557 GCACAATTTG
41419567 TAATAAAACAAATAA
1 TAATAAAA-AAATAA
*
41419582 TAATAATAATAATAA
1 TAATAA-AAAAATAA
41419597 TAATAACAACAACA-ACA
1 TAATAA-AA-AA-ATA-A
* ** *
41419614 AAATACTAAATTAA
1 TAATAAAAAAATAA
*
41419628 TTAATAATAAAATAA
1 -TAATAAAAAAATAA
41419643 TCAATAAAAAAATAA
1 T-AATAAAAAAATAA
41419658 TAATA
1 TAATA
41419663 GTGGCAATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.10
15 46 0.73
16 5 0.08
17 6 0.10
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (14 bp):
TAATAAAAAAATAA
Found at i:41419849 original size:23 final size:23
Alignment explanation
Indices: 41419819--41419920 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
41419809 TAAAGTACAA
*
41419819 AATAATAATAATATATTAATATG
1 AATAATAATAATATATTAATAAG
* *
41419842 GATAATAATAATATATTAATAAT
1 AATAATAATAATATATTAATAAG
* * *
41419865 AATAATAATCGAAAATAATAATAAA
1 AATAATAAT--AATATATTAATAAG
* *
41419890 AATAATAATTATACATTAATAAG
1 AATAATAATAATATATTAATAAG
*
41419913 GATAATAA
1 AATAATAA
41419921 CAACAACAAC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 44 0.69
25 20 0.31
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (23 bp):
AATAATAATAATATATTAATAAG
Found at i:41419925 original size:3 final size:3
Alignment explanation
Indices: 41419919--41420007 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
41419909 TAAGGATAAT
41419919 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
41419967 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
41420008 TAATAATAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41420377 original size:31 final size:31
Alignment explanation
Indices: 41420334--41420409 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
41420324 ATTTATAAAA
*
41420334 AACACGCGGATCCTCCTTGGAAGGTCGGGTC
1 AACACGCGGATCCTCCCTGGAAGGTCGGGTC
* **
41420365 AACATGCGGATCCTCCCTGGCGGGTCGGGTC
1 AACACGCGGATCCTCCCTGGAAGGTCGGGTC
*
41420396 AACACGCGAATCCT
1 AACACGCGGATCCT
41420410 AGGGCCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (31 bp):
AACACGCGGATCCTCCCTGGAAGGTCGGGTC
Found at i:41422967 original size:15 final size:17
Alignment explanation
Indices: 41422947--41422979 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41422937 TAATGTTATA
41422947 ATAATTT-T-TTATTTG
1 ATAATTTATGTTATTTG
41422962 ATAATTTATGTTATTTG
1 ATAATTTATGTTATTTG
41422979 A
1 A
41422980 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
ATAATTTATGTTATTTG
Found at i:41426086 original size:30 final size:30
Alignment explanation
Indices: 41426052--41426117 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
41426042 GTCACATGGT
41426052 CGTGTGCCACACATGGTCACACTACACGGC
1 CGTGTGCCACACATGGTCACACTACACGGC
* *
41426082 CGTGTGCCACACATGGTCATACTACATGGC
1 CGTGTGCCACACATGGTCACACTACACGGC
*
41426112 TGTGTG
1 CGTGTG
41426118 TCATTATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (30 bp):
CGTGTGCCACACATGGTCACACTACACGGC
Found at i:41442534 original size:34 final size:34
Alignment explanation
Indices: 41442496--41442583 Score: 158
Period size: 34 Copynumber: 2.6 Consensus size: 34
41442486 TGCATTATGG
41442496 ATTTAGCCTGGACGGTAATCCAATTAGGGTCTGA
1 ATTTAGCCTGGACGGTAATCCAATTAGGGTCTGA
*
41442530 ATTTAGCCTGGACGGTAATCCGATTAGGGTCTGA
1 ATTTAGCCTGGACGGTAATCCAATTAGGGTCTGA
41442564 ATTTAGCCTGGACTGGTAAT
1 ATTTAGCCTGGAC-GGTAAT
41442584 TCAGATCCGA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 46 0.88
35 6 0.12
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (34 bp):
ATTTAGCCTGGACGGTAATCCAATTAGGGTCTGA
Found at i:41445332 original size:6 final size:6
Alignment explanation
Indices: 41445304--41445360 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
41445294 AATTAAACAG
*
41445304 AAAAAT AAGAAA- ACAAAACT AAAAAT AAAAAT -AAAAG AAAAAT -AAAAT
1 AAAAAT AA-AAAT A-AAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
41445352 -AAAAT AAAA
1 AAAAAT AAAA
41445361 TAAGTGGACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 14 0.33
6 20 0.47
7 8 0.19
8 1 0.02
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:41445333 original size:5 final size:5
Alignment explanation
Indices: 41445325--41445363 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
41445315 AACAAAACTA
*
41445325 AAAAT AAAAAT AAAAGA AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT -AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AA
41445364 GTGGACTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:41445339 original size:11 final size:11
Alignment explanation
Indices: 41445325--41445363 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
41445315 AACAAAACTA
41445325 AAAATAAAAAT
1 AAAATAAAAAT
*
41445336 AAAAGAAAAAT
1 AAAATAAAAAT
41445347 AAAAT-AAAAT
1 AAAATAAAAAT
41445357 AAAATAA
1 AAAATAA
41445364 GTGGACTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:41446951 original size:3 final size:3
Alignment explanation
Indices: 41446943--41447079 Score: 171
Period size: 3 Copynumber: 46.3 Consensus size: 3
41446933 TCAATAAAGC
*
41446943 AAT AAT AATT AGT AA- AACT AAT AA- AACT AAT AA- AAT AA- AGA- AAT
1 AAT AAT AA-T AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT A-AT AAT
41446987 AAT AA- AGA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41447031 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41447079 A
1 A
41447080 CAAGGGTAAA
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
2 10 0.08
3 106 0.87
4 6 0.05
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41446992 original size:11 final size:11
Alignment explanation
Indices: 41446976--41447002 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41446966 AAACTAATAA
41446976 AATAAAGAAAT
1 AATAAAGAAAT
41446987 AATAAAGAAAT
1 AATAAAGAAAT
41446998 AATAA
1 AATAA
41447003 TAATAATAAT
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:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (11 bp):
AATAAAGAAAT
Found at i:41448152 original size:29 final size:29
Alignment explanation
Indices: 41448110--41448175 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
41448100 TGTGTCCAGG
41448110 CCGTGTGTGTCACACGGCCAAGGACACGC
1 CCGTGTGTGTCACACGGCCAAGGACACGC
*
41448139 CCGTGTGTGTCACACGGCCAAGTACACGC
1 CCGTGTGTGTCACACGGCCAAGGACACGC
41448168 CCGTGTGT
1 CCGTGTGT
41448176 CCAGGCTGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (29 bp):
CCGTGTGTGTCACACGGCCAAGGACACGC
Found at i:41472492 original size:42 final size:42
Alignment explanation
Indices: 41472431--41472581 Score: 196
Period size: 42 Copynumber: 3.6 Consensus size: 42
41472421 GATTATGTGC
* * *
41472431 AAGACCATATCTGGTATATGGCATCTATATAAGACTTCGTGT
1 AAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTGT
*
41472473 AAGACCATATCTGGGATATGGCATCGATATGAGACTTCGCGT
1 AAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTGT
* * * * *
41472515 AAGACCATAGCTGGGCTATTGGAATCGATACGAGA-TTACATGT
1 AAGACCATATCTGGGATA-TGGCATCGATATGAGACTT-CGTGT
41472558 AAGACCATATCTGGGATATGGCAT
1 AAGACCATATCTGGGATATGGCAT
41472582 TGGTTTGGTG
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
42 61 0.65
43 33 0.35
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
AAGACCATATCTGGGATATGGCATCGATATGAGACTTCGTGT
Found at i:41476599 original size:45 final size:45
Alignment explanation
Indices: 41476535--41476625 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
41476525 CCGAAACATG
* *
41476535 TGTCATATACATCATGAACTCATACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
*
41476580 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
41476625 T
1 T
41476626 TTCATAGTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
Found at i:41480262 original size:25 final size:24
Alignment explanation
Indices: 41480234--41480284 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
41480224 AAAAACTTGA
41480234 AAAAAATTGAG-ATATAAAAAGTCTC
1 AAAAAATTGAGCA-A-AAAAAGTCTC
*
41480259 AAAATATTGAGCAAAAAAAGTCTC
1 AAAAAATTGAGCAAAAAAAGTCTC
41480283 AA
1 AA
41480285 TCCAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 12 0.50
25 11 0.46
26 1 0.04
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAAAAATTGAGCAAAAAAAGTCTC
Found at i:41481954 original size:46 final size:46
Alignment explanation
Indices: 41481898--41482067 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
41481888 TGGTTGAGCA
41481898 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
41481944 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* *
41481989 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
41482037 -CCCAAGCTCATTGAGTTGAGTCCGAGTTCAC
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCAC
41482068 TTAGGGGCGG
Statistics
Matches: 104, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 5 0.05
46 52 0.50
47 28 0.27
48 1 0.01
50 4 0.04
51 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:41482054 original size:93 final size:93
Alignment explanation
Indices: 41481895--41482065 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
41481885 GGATGGTTGA
* * *
41481895 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCATTGAGT
41481960 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41481988 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCATTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCATTGAG
41482052 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
41482066 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41489629 original size:93 final size:93
Alignment explanation
Indices: 41489470--41489640 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
41489460 GGATGGTTGA
* *
41489470 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
41489535 TGAGTCCGAGTTCGTCAGATGTAACTAG
66 TGAGTCCGAGTTCGTCAGATGTAACTAG
* *
41489563 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
41489628 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41489641 ACTTAGGGCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTCAGATGTAACTAG
Found at i:41489643 original size:46 final size:46
Alignment explanation
Indices: 41489474--41489645 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
41489464 GGTTGAGCAT
* * *
41489474 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
41489520 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTCA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
41489565 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
41489613 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41489646 GGGCCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 60 0.56
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:41493603 original size:15 final size:15
Alignment explanation
Indices: 41493572--41493630 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
41493562 AAAAACAGAA
*
41493572 TTTTCCTCGAA-TTT
1 TTTTCCACGAATTTT
*
41493586 TTTTCTCA-TAATTTT
1 TTTTC-CACGAATTTT
41493601 TTTTCCACGAATTTT
1 TTTTCCACGAATTTT
41493616 TTTT--A-GAATTTT
1 TTTTCCACGAATTTT
41493628 TTT
1 TTT
41493631 AGAATCTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
14 9 0.23
15 19 0.49
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTTCCACGAATTTT
Found at i:41493611 original size:29 final size:27
Alignment explanation
Indices: 41493572--41493630 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
41493562 AAAAACAGAA
* *
41493572 TTTTCCTCGAATTTTTTTCTCATAATTTT
1 TTTTCCACGAATTTTTTT-T-AGAATTTT
41493601 TTTTCCACGAATTTTTTTTAGAATTTT
1 TTTTCCACGAATTTTTTTTAGAATTTT
41493628 TTT
1 TTT
41493631 AGAATCTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.36
28 1 0.04
29 17 0.61
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (27 bp):
TTTTCCACGAATTTTTTTTAGAATTTT
Found at i:41493615 original size:14 final size:13
Alignment explanation
Indices: 41493580--41493630 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
41493570 AATTTTCCTC
41493580 GAATTTTTTTCTCA
1 GAATTTTTTTC-CA
*
41493594 TAATTTTTTTTCCA
1 GAA-TTTTTTTCCA
*
41493608 CGAATTTTTTT-TA
1 -GAATTTTTTTCCA
41493621 GAATTTTTTT
1 GAATTTTTTT
41493631 AGAATCTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 10 0.31
13 1 0.03
14 11 0.34
15 10 0.31
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.63
Consensus pattern (13 bp):
GAATTTTTTTCCA
Found at i:41498866 original size:12 final size:12
Alignment explanation
Indices: 41498849--41498875 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41498839 TTTATCAAGA
41498849 TAAATATTATAT
1 TAAATATTATAT
41498861 TAAATATTATAT
1 TAAATATTATAT
41498873 TAA
1 TAA
41498876 TCAATCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:41501870 original size:13 final size:14
Alignment explanation
Indices: 41501846--41501883 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
41501836 ATCAAACTTC
*
41501846 ACATTAATTTTTCA
1 ACATTAATTTTCCA
41501860 ACATTAATTTTCCA
1 ACATTAATTTTCCA
41501874 A-ATTAATTTT
1 ACATTAATTTT
41501884 GCAAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (14 bp):
ACATTAATTTTCCA
Found at i:41505006 original size:80 final size:80
Alignment explanation
Indices: 41504922--41505070 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
41504912 TATGGTAACC
* * * *
41504922 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
41504986 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
41505002 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
41505067 CCGG
66 CCGG
41505071 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:41505012 original size:40 final size:38
Alignment explanation
Indices: 41504963--41505070 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
41504953 ATCACGATTT
*
41504963 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
41505003 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
41505043 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
41505071 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:41513121 original size:80 final size:80
Alignment explanation
Indices: 41513037--41513185 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
41513027 TATGGTAACC
* * * *
41513037 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
41513101 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
41513117 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
41513182 CCGG
66 CCGG
41513186 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:41513127 original size:40 final size:38
Alignment explanation
Indices: 41513078--41513185 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
41513068 ATCACGATTT
*
41513078 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
41513118 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
41513158 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
41513186 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:41524839 original size:49 final size:48
Alignment explanation
Indices: 41524694--41524953 Score: 400
Period size: 49 Copynumber: 5.4 Consensus size: 48
41524684 TACATATATG
* * * *
41524694 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGCA-TATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATTATA
*
41524741 TGTGATAAGGCCGT-ATGGCCAATGTGATGAATGTGAAAGTGTA-TATA
1 TGTGATAAGGCC-TAATGGCCGATGTGATGAATGTGAAAGTGTATTATA
41524788 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
*
41524837 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
*
41524886 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-TATA
41524935 TGTGATAAGGCCTAATGGC
1 TGTGATAAGGCCTAATGGC
41524954 TAATGTAAAA
Statistics
Matches: 203, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 83 0.41
49 119 0.59
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (48 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATTATA
Found at i:41525105 original size:37 final size:37
Alignment explanation
Indices: 41525055--41525139 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
41525045 GGAATATGTT
*
41525055 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
41525092 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
41525129 CCGGGTAAGAC
1 CCGGGTAAGAC
41525140 TTCGTAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:41527260 original size:29 final size:29
Alignment explanation
Indices: 41527228--41527388 Score: 304
Period size: 29 Copynumber: 5.6 Consensus size: 29
41527218 CGTTAACCGA
41527228 GCACTATGTGTGCGAGATCAGTAATCGAG
1 GCACTATGTGTGCGAGATCAGTAATCGAG
41527257 GCACTATGTGTGCGAGATCAGTAATCGAG
1 GCACTATGTGTGCGAGATCAGTAATCGAG
41527286 GCACTATGTGTGCGAGATCAGTAATCGAG
1 GCACTATGTGTGCGAGATCAGTAATCGAG
41527315 GCACTATGTGTGCGAGATCAGTAATCGAG
1 GCACTATGTGTGCGAGATCAGTAATCGAG
*
41527344 GCACTATGTGTGCGAGATCAGTAATTGAG
1 GCACTATGTGTGCGAGATCAGTAATCGAG
*
41527373 GCACTGTGTGTGCGAG
1 GCACTATGTGTGCGAG
41527389 TTTTTCAACA
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 130 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
GCACTATGTGTGCGAGATCAGTAATCGAG
Found at i:41527388 original size:87 final size:88
Alignment explanation
Indices: 41527196--41527388 Score: 311
Period size: 87 Copynumber: 2.2 Consensus size: 88
41527186 CGAATGATTA
* *
41527196 GAGGCACTGTGTGTGC-AAATTCCGTTAACCGAGCACTATGTGTGCGAGATCAGTAATCGAGGCA
1 GAGGCACTGTGTGTGCGAGATTCAGTTAACCGAGCACTATGTGTGCGAGATCAGTAATCGAGGCA
41527260 CTATGTGTGCGAGATCAGTAATC
66 CTATGTGTGCGAGATCAGTAATC
* *
41527283 GAGGCACTATGTGTGCGAGA-TCAG-TAATCGAGGCACTATGTGTGCGAGATCAGTAATCGAGGC
1 GAGGCACTGTGTGTGCGAGATTCAGTTAACCGA-GCACTATGTGTGCGAGATCAGTAATCGAGGC
*
41527346 ACTATGTGTGCGAGATCAGTAATT
65 ACTATGTGTGCGAGATCAGTAATC
41527370 GAGGCACTGTGTGTGCGAG
1 GAGGCACTGTGTGTGCGAG
41527389 TTTTTCAACA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
86 6 0.06
87 90 0.92
88 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (88 bp):
GAGGCACTGTGTGTGCGAGATTCAGTTAACCGAGCACTATGTGTGCGAGATCAGTAATCGAGGCA
CTATGTGTGCGAGATCAGTAATC
Found at i:41531045 original size:49 final size:49
Alignment explanation
Indices: 41530932--41531192 Score: 436
Period size: 49 Copynumber: 5.4 Consensus size: 49
41530922 TACATATATG
* * * * * *
41530932 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGCA--TATG
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
41530979 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
41531028 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
41531077 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
41531126 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
41531175 TGTGATAAGGCCTAATGG
1 TGTGATAAGGCCTAATGG
41531193 TTAATGTAAA
Statistics
Matches: 205, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 39 0.19
49 166 0.81
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:41531346 original size:37 final size:37
Alignment explanation
Indices: 41531296--41531379 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
41531286 GAATATGTTT
*
41531296 CGGGTGAGACCCGATGACTACGTGTGGAGATTATGAC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGAC
*
41531333 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGAC
41531370 CGGGTAAGAC
1 CGGGTAAGAC
41531380 TTCGTAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGAC
Found at i:41539191 original size:9 final size:9
Alignment explanation
Indices: 41539173--41539292 Score: 75
Period size: 9 Copynumber: 13.0 Consensus size: 9
41539163 AAAAATATAA
*
41539173 TTTATTATT
1 TTTATAATT
41539182 TTTATAA-T
1 TTTATAATT
*
41539190 TTTATTATT
1 TTTATAATT
41539199 TATTATGACATT
1 T-TTAT-A-ATT
** *
41539211 AAT-TAACT
1 TTTATAATT
41539219 TTTAT-ATT
1 TTTATAATT
*
41539227 TTTATAAAT
1 TTTATAATT
41539236 TTTATAATT
1 TTTATAATT
*
41539245 TTAATTAATT
1 TTTA-TAATT
*
41539255 TTTAATGATT
1 TTT-ATAATT
41539265 TTTATAATT
1 TTTATAATT
* *
41539274 TTTTTATGTT
1 TTTATA-ATT
41539284 TTTATAATT
1 TTTATAATT
41539293 CTAGGATGAA
Statistics
Matches: 83, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
8 17 0.20
9 35 0.42
10 26 0.31
11 2 0.02
12 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:41539193 original size:17 final size:17
Alignment explanation
Indices: 41539168--41539258 Score: 69
Period size: 17 Copynumber: 5.1 Consensus size: 17
41539158 TAGAAAAAAA
41539168 TATAA-TTTATTATTTT
1 TATAATTTTATTATTTT
41539184 TATAATTTTATTATTTAT
1 TATAATTTTATTATTT-T
* *
41539202 TATGACA-TTAATTAACTTT
1 TAT-A-ATTTTATT-ATTTT
* * *
41539221 TATATTTTTATAAATTT
1 TATAATTTTATTATTTT
41539238 TATAATTTTAATTAATTTT
1 TATAATTTT-ATT-ATTTT
41539257 TA
1 TA
41539259 ATGATTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.09
17 22 0.38
18 11 0.19
19 16 0.28
20 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:41539272 original size:19 final size:18
Alignment explanation
Indices: 41539173--41539292 Score: 75
Period size: 19 Copynumber: 6.5 Consensus size: 18
41539163 AAAAATATAA
* *
41539173 TTTATTATTTTTAT-AAT
1 TTTATAATTTTTATGATT
* **
41539190 TTTATTATTTATTATGACA
1 TTTATAATTT-TTATGATT
* *
41539209 TTAATTAACTTTTAT-ATT
1 TTTA-TAATTTTTATGATT
* *
41539227 TTTATAAATTTTATAATT
1 TTTATAATTTTTATGATT
*
41539245 TTAATTAATTTTTAATGATT
1 TTTA-TAATTTTT-ATGATT
41539265 TTTATAATTTTTTTATG-TT
1 TTTATAA--TTTTTATGATT
41539284 TTTATAATT
1 TTTATAATT
41539293 CTAGGATGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
17 21 0.26
18 14 0.17
19 27 0.33
20 15 0.18
21 5 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATAATTTTTATGATT
Found at i:41539285 original size:29 final size:29
Alignment explanation
Indices: 41539218--41539287 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
41539208 ATTAATTAAC
41539218 TTTTATATTTTT-ATAAATTTTATAATTT
1 TTTTATATTTTTAATAAATTTTATAATTT
* * *
41539246 TAATTA-ATTTTTAATGATTTTTATAATTT
1 T-TTTATATTTTTAATAAATTTTATAATTT
*
41539275 TTTTATGTTTTTA
1 TTTTATATTTTTA
41539288 TAATTCTAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATATTTTTAATAAATTTTATAATTT
Found at i:41539358 original size:12 final size:12
Alignment explanation
Indices: 41539341--41539368 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41539331 CTAGACTTGC
41539341 TTTTAAAATTAA
1 TTTTAAAATTAA
41539353 TTTTAAAATTAA
1 TTTTAAAATTAA
41539365 TTTT
1 TTTT
41539369 TTGAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAAAATTAA
Found at i:41542799 original size:6 final size:6
Alignment explanation
Indices: 41542788--41542813 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41542778 CCTAACTATG
41542788 ACTGTT ACTGTT ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT AC
41542814 CCTACGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (6 bp):
ACTGTT
Found at i:41545988 original size:15 final size:16
Alignment explanation
Indices: 41545970--41545999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41545960 GAATTAAAAC
41545970 ATAA-TTTATTATTTT
1 ATAATTTTATTATTTT
41545985 ATAATTTTATTATTT
1 ATAATTTTATTATTT
41546000 ATTATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATAATTTTATTATTTT
Found at i:41546042 original size:27 final size:28
Alignment explanation
Indices: 41545989--41546051 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
41545979 TATTTTATAA
*
41545989 TTTTATTATTTATTATGAATTTAATCAAT
1 TTTTATTATTTATTATAAATTTAATC-AT
41546018 TTTTA-TATTT-TTATAAATGTT-ATCAT
1 TTTTATTATTTATTATAAAT-TTAATCAT
*
41546044 TTTAATTA
1 TTTTATTA
41546052 ATTTTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 7 0.23
29 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTATTATTTATTATAAATTTAATCAT
Found at i:41547508 original size:127 final size:127
Alignment explanation
Indices: 41547282--41547539 Score: 516
Period size: 127 Copynumber: 2.0 Consensus size: 127
41547272 GTAGTTGACA
41547282 AAATGATTTCATACCATATTGAAAAATGAGGGTAAAATTCAAGTAGCAGGCTATATATAACCATT
1 AAATGATTTCATACCATATTGAAAAATGAGGGTAAAATTCAAGTAGCAGGCTATATATAACCATT
41547347 TTTGTATCTGCTATGCAAAGATAAATTAGTAAGGCATGAACCTAAACATACTCTTCTGCTTC
66 TTTGTATCTGCTATGCAAAGATAAATTAGTAAGGCATGAACCTAAACATACTCTTCTGCTTC
41547409 AAATGATTTCATACCATATTGAAAAATGAGGGTAAAATTCAAGTAGCAGGCTATATATAACCATT
1 AAATGATTTCATACCATATTGAAAAATGAGGGTAAAATTCAAGTAGCAGGCTATATATAACCATT
41547474 TTTGTATCTGCTATGCAAAGATAAATTAGTAAGGCATGAACCTAAACATACTCTTCTGCTTC
66 TTTGTATCTGCTATGCAAAGATAAATTAGTAAGGCATGAACCTAAACATACTCTTCTGCTTC
41547536 AAAT
1 AAAT
41547540 TGGATTAATT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (127 bp):
AAATGATTTCATACCATATTGAAAAATGAGGGTAAAATTCAAGTAGCAGGCTATATATAACCATT
TTTGTATCTGCTATGCAAAGATAAATTAGTAAGGCATGAACCTAAACATACTCTTCTGCTTC
Found at i:41549198 original size:3 final size:3
Alignment explanation
Indices: 41549182--41549240 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
41549172 TATTGCTCTA
41549182 ATT A-T ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41549228 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
41549241 GATATTTTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41549282 original size:15 final size:15
Alignment explanation
Indices: 41549262--41549292 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41549252 ACTCAAATAC
*
41549262 TTTTATTTATCTATT
1 TTTTATCTATCTATT
41549277 TTTTATCTATCTATT
1 TTTTATCTATCTATT
41549292 T
1 T
41549293 ATATTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATCTATCTATT
Found at i:41549361 original size:26 final size:25
Alignment explanation
Indices: 41549300--41549364 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
41549290 TTTATATTTC
* *
41549300 TATCATTATTATATTTTTGTGTATTA
1 TATCATTATT-TATATTTATGTATTA
*
41549326 TAT-TTCTATTTATATTTATGTATTAA
1 TATCAT-TATTTATATTTATGTATT-A
41549352 TATCATTATTTAT
1 TATCATTATTTAT
41549365 TATTGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 13 0.41
26 18 0.56
27 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (25 bp):
TATCATTATTTATATTTATGTATTA
Found at i:41549387 original size:3 final size:3
Alignment explanation
Indices: 41549381--41549465 Score: 53
Period size: 3 Copynumber: 27.3 Consensus size: 3
41549371 TTTTATAAAC
* * * * *
41549381 TAT TAT TAT TAT CAT TAT TAT TACCT TTT TAC TAT TAT TAT TTT GTAC
1 TAT TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT -TAT
** * * *
41549429 CGT TAT TGT TAT TGT TAT TAT TAT TTT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41549466 TCTTCTTCTT
Statistics
Matches: 59, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
3 56 0.95
4 1 0.02
5 2 0.03
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:41549599 original size:12 final size:12
Alignment explanation
Indices: 41549584--41549619 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41549574 TATTCCTTAC
41549584 ATTATTGTTATT
1 ATTATTGTTATT
*
41549596 ATTATTTTTATT
1 ATTATTGTTATT
*
41549608 ATTTTTGTTATT
1 ATTATTGTTATT
41549620 GGTATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (12 bp):
ATTATTGTTATT
Found at i:41551404 original size:56 final size:56
Alignment explanation
Indices: 41551338--41551450 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
41551328 GGTCAGAGAA
41551338 AACGCAATTGGAAAAAAGAGATAGCTTGACAGCGAGGTATACGCCAGAGTTATGGG
1 AACGCAATTGGAAAAAAGAGATAGCTTGACAGCGAGGTATACGCCAGAGTTATGGG
** *
41551394 AACGCAATTGGAAAAGGGAGATAGCTTGACAGCGAGGTATACGTCAGAGTTATGGG
1 AACGCAATTGGAAAAAAGAGATAGCTTGACAGCGAGGTATACGCCAGAGTTATGGG
41551450 A
1 A
41551451 CTTCACTCGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (56 bp):
AACGCAATTGGAAAAAAGAGATAGCTTGACAGCGAGGTATACGCCAGAGTTATGGG
Found at i:41553175 original size:12 final size:12
Alignment explanation
Indices: 41553154--41553196 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
41553144 GTAAAACTGC
*
41553154 GAACTTCGAGTT
1 GAACTCCGAGTT
41553166 GAACTCCGAGTT
1 GAACTCCGAGTT
41553178 GAACTCCGAGTT
1 GAACTCCGAGTT
41553190 GAACTCC
1 GAACTCC
41553197 ATCGTTCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (12 bp):
GAACTCCGAGTT
Found at i:41558151 original size:53 final size:53
Alignment explanation
Indices: 41558063--41558213 Score: 187
Period size: 53 Copynumber: 2.8 Consensus size: 53
41558053 CTTACACGGT
* ** *
41558063 TCACATATCATACCGAAGCCATATTCCAGAC-ATGGTCTTATACGGAATCATATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
* *
41558118 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACAGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
41558171 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
41558214 GCACACTTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:41560003 original size:40 final size:40
Alignment explanation
Indices: 41559959--41560216 Score: 195
Period size: 40 Copynumber: 6.1 Consensus size: 40
41559949 CAGGATTTAA
* *
41559959 CCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGC
* *
41559999 CCGGATATAG-TAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGC
* *
41560039 ACGGATATAGCAACTCGCACAAATGCCTTCGGGAC-TATGC
1 CCGGATATAGCTACTCGCACAAATGCCTTCGGGACATA-GC
*
41560079 CTTCGGGACT-TAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 C--C-GGA-TATAG--C--------T-ACTCGCACAAATGCCTTCGGGACATAGC
*
41560133 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGC
* * *
41560173 CCGGA-ACTAG-TCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGCT-ACTCGCACAAATGCCTTCGGGACATAGC
41560213 CCGG
1 CCGG
41560217 TTATCATCCA
Statistics
Matches: 186, Mismatches: 11, Indels: 42
0.78 0.05 0.18
Matches are distributed among these distances:
39 4 0.02
40 137 0.74
42 1 0.01
43 6 0.03
44 1 0.01
45 1 0.01
50 1 0.01
51 6 0.03
52 1 0.01
54 26 0.14
55 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGC
Found at i:41560080 original size:14 final size:14
Alignment explanation
Indices: 41560061--41560088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41560051 ACTCGCACAA
41560061 ATGCCTTCGGGACT
1 ATGCCTTCGGGACT
41560075 ATGCCTTCGGGACT
1 ATGCCTTCGGGACT
41560089 TAGCCCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (14 bp):
ATGCCTTCGGGACT
Found at i:41560085 original size:54 final size:54
Alignment explanation
Indices: 41560021--41560128 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
41560011 ACTCGCACCA
41560021 ATGCCTTCGGGACTTAGCACGGATATAGCAACTCGCACAAATGCCTTCGGGACT
1 ATGCCTTCGGGACTTAGCACGGATATAGCAACTCGCACAAATGCCTTCGGGACT
* *
41560075 ATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACT
1 ATGCCTTCGGGACTTAGCACGGATATAGCAACTCGCACAAATGCCTTCGGGACT
41560129 TAGCCCGGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (54 bp):
ATGCCTTCGGGACTTAGCACGGATATAGCAACTCGCACAAATGCCTTCGGGACT
Found at i:41560142 original size:94 final size:94
Alignment explanation
Indices: 41559981--41560168 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
41559971 ACTCGCTCGA
*
41559981 ATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCACGGATA
1 ATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCACGGATA
41560046 TAGCAACTCGCACAAATGCCTTCGGGACT
66 TAGCAACTCGCACAAATGCCTTCGGGACT
* *
41560075 ATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
1 ATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCACGGATA
*
41560140 TAGTAACTCGCACAAATGCCTTCGGGACT
66 TAGCAACTCGCACAAATGCCTTCGGGACT
41560169 TAGCCCGGAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (94 bp):
ATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCACGGATA
TAGCAACTCGCACAAATGCCTTCGGGACT
Found at i:41560199 original size:134 final size:134
Alignment explanation
Indices: 41559959--41560208 Score: 389
Period size: 134 Copynumber: 1.9 Consensus size: 134
41559949 CAGGATTTAA
* * *
41559959 CCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
*
41560024 CCTTCGGGACTTAGCACGGATATAGCAACTCGCACAAATGCCTTCGGGACTATGCCTTCGGGACT
66 CCTTCGGGACTTAGCACGGATATAGCAACTAGCACAAATGCCTTCGGGACTATGCCTTCGGGACT
41560089 TAGC
131 TAGC
*
41560093 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAAT
1 CCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAAT
* *
41560157 GCCTTCGGGACTTAGCCCGGA-ACTAGTC-ACTAGCGCAAATGCCTTCGGGACT
65 GCCTTCGGGACTTAGCACGGATA-TAG-CAACTAGCACAAATGCCTTCGGGACT
41560209 TAGCCCGGTT
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
133 2 0.02
134 103 0.97
135 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (134 bp):
CCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
CCTTCGGGACTTAGCACGGATATAGCAACTAGCACAAATGCCTTCGGGACTATGCCTTCGGGACT
TAGC
Found at i:41566511 original size:53 final size:53
Alignment explanation
Indices: 41566441--41566580 Score: 172
Period size: 53 Copynumber: 2.6 Consensus size: 53
41566431 CACATATCAT
* * ** *
41566441 ACCGAAGCCATATCCCAGAGATGGTCTTATACGGAATCACATTATCACATTAT
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC
* * ** * *
41566494 ATCGATGCCATAGCCCAGCTATGGTCTTATATAGAGTCACATTATCACATTGC
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC
*
41566547 ACCGATGCCATAACCCAGCTATGGTCTTAAACGG
1 ACCGATGCCATAACCCAGCTATGGTCTTATACGG
41566581 GCGCACTTAT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 72 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (53 bp):
ACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC
Found at i:41572779 original size:45 final size:44
Alignment explanation
Indices: 41572673--41573018 Score: 288
Period size: 45 Copynumber: 7.7 Consensus size: 44
41572663 TGATGAGTCC
* * * * * * * *
41572673 ACAAACCTTATCTCACTGAAGTTACAATGGAACAGATTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
* *
41572717 ACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
* * * *
41572761 AGCAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGTT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
* * *
41572806 ACAAGTCTTATCCCCCTGAAGTTGTAGTGGAGCAGACTAAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
41572850 AGCAAATCTTATCTCCCTGAAGTTGCAGTGGAATAG-ATCGAAGCTATAA-ATT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGG---AGCA--G-A-CTA-AAGA-T
* * * * * *
41572902 ACAGATCTTATCTCTCTGAAGTTGCAATAGAACAGA-TCAA-A-
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
* * *
41572943 ACAAACCCTATCTCCCTGAAGTTGAAGTGGAGCAGACTAAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
* * *
41572987 ATCGAATCTTATTTCCCTAAAGTTGCAGTGGA
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGA
41573019 ATAGATTGAA
Statistics
Matches: 239, Mismatches: 47, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
41 28 0.12
42 3 0.01
43 4 0.02
44 74 0.31
45 88 0.37
46 1 0.00
47 2 0.01
48 3 0.01
49 2 0.01
50 1 0.00
51 29 0.12
52 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT
Found at i:41572798 original size:89 final size:89
Alignment explanation
Indices: 41572674--41572892 Score: 366
Period size: 89 Copynumber: 2.5 Consensus size: 89
41572664 GATGAGTCCA
* * *
41572674 CAAACCTTATCTCACTGAAGTTACAATGGAACAGATTGAAGTTACAAGTCTTATCCCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGTTACAAGTCTTATCCCCCTGAAGT
41572739 TGCAGTGGAGCAGACTAAAGATAG
66 TGCAGTGGAGCAGACTAAAGATAG
*
41572763 CAAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGTTACAAGTCTTATCCCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGTTACAAGTCTTATCCCCCTGAAGT
*
41572828 TGTAGTGGAGCAGACTAAAGATAG
66 TGCAGTGGAGCAGACTAAAGATAG
* * *
41572852 CAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATCGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAG
41572893 CTATAAATTA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 121 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (89 bp):
CAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGTTACAAGTCTTATCCCCCTGAAGT
TGCAGTGGAGCAGACTAAAGATAG
Found at i:41574574 original size:3 final size:3
Alignment explanation
Indices: 41574556--41574606 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
41574546 TTATTTTTGC
41574556 TAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41574601 TAT TAT
1 TAT TAT
41574607 ATTTTCAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41574654 original size:14 final size:14
Alignment explanation
Indices: 41574635--41574670 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41574625 ACTCAAATAC
41574635 TTTTATTTATCTAT
1 TTTTATTTATCTAT
*
41574649 TTTTATCTATCTAT
1 TTTTATTTATCTAT
*
41574663 TTATATTT
1 TTTTATTT
41574671 CTATCATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTATCTAT
Found at i:41574698 original size:26 final size:25
Alignment explanation
Indices: 41574669--41574737 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
41574659 CTATTTATAT
41574669 TTCTATCATTATTATATTTTTATGTA
1 TTCTATCATTATT-TATTTTTATGTA
* *
41574695 TTCTATC-TCTATTTCTATTTATGTA
1 TTCTATCAT-TATTTATTTTTATGTA
*
41574720 TTAATATCATTATTTATT
1 TT-CTATCATTATTTATT
41574738 ATTGTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 13 0.37
26 21 0.60
27 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.61
Consensus pattern (25 bp):
TTCTATCATTATTTATTTTTATGTA
Found at i:41574835 original size:25 final size:25
Alignment explanation
Indices: 41574789--41574836 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41574779 CCTTTTTTAC
*
41574789 TATTATTATTTTGTACCGTTATTGT
1 TATTATTATTTTGTACCATTATTGT
* *
41574814 TATTATTATTTTTTACTATTATT
1 TATTATTATTTTGTACCATTATT
41574837 TCTTCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (25 bp):
TATTATTATTTTGTACCATTATTGT
Found at i:41574945 original size:3 final size:3
Alignment explanation
Indices: 41574910--41575031 Score: 112
Period size: 3 Copynumber: 41.7 Consensus size: 3
41574900 ACATTTTAAT
* * *
41574910 TTA TTA TT- TTA TTT TTA ATA TT- TT- TTA -TA TTA TTA TTA TTCC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
41574952 TTA -CA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
41574998 TTCG TTA TTG GTA TTTA TTA TTA TTA TTA TTA TT
1 TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
41575032 TCATTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
2 11 0.11
3 81 0.83
4 6 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41576315 original size:28 final size:28
Alignment explanation
Indices: 41576275--41576331 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41576265 ATTCCATGCC
41576275 ATCAATTTATTTATTAACAGCGACTCTT
1 ATCAATTTATTTATTAACAGCGACTCTT
*
41576303 ATCAATTTATTTATTAACAGTGACTCTT
1 ATCAATTTATTTATTAACAGCGACTCTT
41576331 A
1 A
41576332 ACCACCAATT
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:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (28 bp):
ATCAATTTATTTATTAACAGCGACTCTT
Found at i:41581465 original size:18 final size:19
Alignment explanation
Indices: 41581424--41581488 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
41581414 TTGATAATAC
41581424 GAAAAATGAAAAGAAACAGAA
1 GAAAAAT-AAAAGAAA-AGAA
41581445 GAAGAAA-AAAAGAAAAG-A
1 GAA-AAATAAAAGAAAAGAA
* *
41581463 GAAAAATAAATGAAAAAAA
1 GAAAAATAAAAGAAAAGAA
41581482 TGAAAAA
1 -GAAAAA
41581489 AGTAAGAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 3 0.08
20 14 0.37
21 3 0.08
22 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (19 bp):
GAAAAATAAAAGAAAAGAA
Found at i:41585401 original size:32 final size:33
Alignment explanation
Indices: 41585334--41585405 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
41585324 TGGAAAAGCT
* *
41585334 AATATTTTCTGGTGTTTGGATAAATTTGTGTAA
1 AATATTTTCTAGTGTTTGGATAAATTTCTGTAA
* *
41585367 AATATTTTCTATTGTTTGGCA-AATTTTCTG-AA
1 AATATTTTCTAGTGTTTGG-ATAAATTTCTGTAA
41585399 AATATTT
1 AATATTT
41585406 CATAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 9 0.26
33 24 0.71
34 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (33 bp):
AATATTTTCTAGTGTTTGGATAAATTTCTGTAA
Found at i:41587973 original size:18 final size:18
Alignment explanation
Indices: 41587952--41588014 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
41587942 ATGACTTATA
41587952 GGCTTCGCATGTACCTAG
1 GGCTTCGCATGTACCTAG
* * *
41587970 GGCTT-GCATG-GCATATA
1 GGCTTCGCATGTACCTA-G
*
41587987 GGCTTCACATGTACCTAG
1 GGCTTCGCATGTACCTAG
41588005 GG-TTCGCATG
1 GGCTTCGCATG
41588015 GCATATAGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
16 3 0.09
17 17 0.50
18 11 0.32
19 3 0.09
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (18 bp):
GGCTTCGCATGTACCTAG
Found at i:41587987 original size:35 final size:34
Alignment explanation
Indices: 41587938--41588061 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 34
41587928 ATATACAGGT
* *
41587938 TTGCATGACTTATAGGCTTCGCATGTACCTAGGG
1 TTGCATGGCATATAGGCTTCGCATGTACCTAGGG
*
41587972 CTTGCATGGCATATAGGCTTCACATGTACCTAGGG
1 -TTGCATGGCATATAGGCTTCGCATGTACCTAGGG
* * *
41588007 TTCGCATGGCATATAGGCTT-GTAGGTACTTAGGG
1 TT-GCATGGCATATAGGCTTCGCATGTACCTAGGG
*
41588041 TTTGCATGGTCATGTAGGCTT
1 -TTGCATGG-CATATAGGCTT
41588062 ACATTCCTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
34 18 0.23
35 60 0.77
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (34 bp):
TTGCATGGCATATAGGCTTCGCATGTACCTAGGG
Found at i:41587990 original size:17 final size:18
Alignment explanation
Indices: 41587948--41588026 Score: 56
Period size: 17 Copynumber: 4.5 Consensus size: 18
41587938 TTGCATGACT
* *
41587948 TATAGGCTTCGCATGTACC
1 TATAGGCTTCGCATG-GCA
*
41587967 TA-GGGCTT-GCATGGCA
1 TATAGGCTTCGCATGGCA
* *
41587983 TATAGGCTTCACAT-GTA
1 TATAGGCTTCGCATGGCA
** *
41588000 CCTAGGGTTCGCATGGCA
1 TATAGGCTTCGCATGGCA
41588018 TATAGGCTT
1 TATAGGCTT
41588027 GTAGGTACTT
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
16 3 0.07
17 22 0.51
18 16 0.37
19 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (18 bp):
TATAGGCTTCGCATGGCA
Found at i:41588225 original size:2 final size:2
Alignment explanation
Indices: 41588212--41588246 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
41588202 TGGGGTTCGC
*
41588212 AT AT AC 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 A
41588247 GTTCGCATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:41589644 original size:21 final size:21
Alignment explanation
Indices: 41589596--41589638 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41589586 TTTCAACCCT
41589596 AAATTTAGTAAGATTTATCCA
1 AAATTTAGTAAGATTTATCCA
*
41589617 AAATTTAGTAAGGTTTATCCA
1 AAATTTAGTAAGATTTATCCA
41589638 A
1 A
41589639 GTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATTTAGTAAGATTTATCCA
Found at i:41591311 original size:16 final size:17
Alignment explanation
Indices: 41591271--41591312 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
41591261 TTTATATATC
41591271 ATTTTTA-ATTTTTAGT
1 ATTTTTATATTTTTAGT
*
41591287 ATATTTTATA-TTTTATT
1 AT-TTTTATATTTTTAGT
41591304 ATTTTTATA
1 ATTTTTATA
41591313 AATTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 13 0.57
18 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTTATATTTTTAGT
Found at i:41591394 original size:19 final size:19
Alignment explanation
Indices: 41591337--41591399 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
41591327 TATTAAAAAG
* *
41591337 TTTATATGTTTTTATAATA
1 TTTATAAGTTTTTATAATT
* *
41591356 TTTATTAGTTTTTGTGAATT
1 TTTATAAGTTTTTAT-AATT
41591376 TTTATAAGTTTTTATAATT
1 TTTATAAGTTTTTATAATT
*
41591395 CTTAT
1 TTTAT
41591400 GATTTCTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTATAAGTTTTTATAATT
Found at i:41591399 original size:9 final size:9
Alignment explanation
Indices: 41591190--41591404 Score: 62
Period size: 10 Copynumber: 22.3 Consensus size: 9
41591180 ATATATGATT
41591190 TTTTTATAA
1 TTTTTATAA
*
41591199 CTTTTATAAAA
1 -TTTT-TATAA
* *
41591210 TTTTAATAG
1 TTTTTATAA
*
41591219 TTTATTAGAA
1 TTT-TTATAA
*
41591229 TTTTTTACAA
1 -TTTTTATAA
*
41591239 GTATTTATAA
1 -TTTTTATAA
41591249 TTTTTTTATAA
1 --TTTTTATAA
*
41591260 -ATTTATATA
1 TTTTTATA-A
41591269 TCATTTT-TAA
1 T--TTTTATAA
41591279 TTTTTAGT-A
1 TTTTTA-TAA
41591288 TATTTTAT-A
1 T-TTTTATAA
*
41591297 -TTTTATTA
1 TTTTTATAA
41591305 TTTTTATAAA
1 TTTTTAT-AA
*
41591315 TTATTTGTAA
1 TT-TTTATAA
*
41591325 TTTATTAAAA
1 TTT-TTATAA
** *
41591335 AGTTTATATG
1 TTTTTATA-A
41591345 TTTTTATAA
1 TTTTTATAA
* *
41591354 TATTTATTAG
1 TTTTTA-TAA
*
41591364 TTTTTGTGAA
1 TTTTTAT-AA
41591374 TTTTTATAA
1 TTTTTATAA
41591383 GTTTTTATAA
1 -TTTTTATAA
* *
41591393 TTCTTATGA
1 TTTTTATAA
41591402 TTT
1 TTT
41591405 CTTGATTTTT
Statistics
Matches: 150, Mismatches: 35, Indels: 41
0.66 0.15 0.18
Matches are distributed among these distances:
7 6 0.04
8 11 0.07
9 38 0.25
10 71 0.47
11 21 0.14
12 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41592307 original size:2 final size:2
Alignment explanation
Indices: 41592300--41592325 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41592290 ATGGATTAAA
41592300 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
41592326 TGTTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41592888 original size:30 final size:30
Alignment explanation
Indices: 41592854--41592913 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41592844 TTTATTTTGA
41592854 CTTTTTAAGTTAGCTTAGATCATATTAGGT
1 CTTTTTAAGTTAGCTTAGATCATATTAGGT
41592884 CTTTTTAAGTTAGCTTAGATCATATTAGGT
1 CTTTTTAAGTTAGCTTAGATCATATTAGGT
41592914 TCAATCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (30 bp):
CTTTTTAAGTTAGCTTAGATCATATTAGGT
Found at i:41593806 original size:153 final size:153
Alignment explanation
Indices: 41593528--41593835 Score: 580
Period size: 153 Copynumber: 2.0 Consensus size: 153
41593518 AAGAAAGCTT
* *
41593528 AGAACATCGAATTCGTCTCCAGGTAAGCATCAATTTTCATAGATAAGATTCAAGCTTTTTGAAAA
1 AGAACATCAAATTCGTCTCCAGGTAAGCATCAATTTTCATAGATAAGATTCAAGCTTCTTGAAAA
41593593 CTAAAAAATATAGGTCTTGAGTTTGATTTGAGTTTTTGAGTTTCTTTTTTCCTTAAACTGTTCAA
66 CTAAAAAATATAGGTCTTGAGTTTGATTTGAGTTTTTGAGTTTCTTTTTTCCTTAAACTGTTCAA
41593658 GAACTTGAAAATTGAAAATTATC
131 GAACTTGAAAATTGAAAATTATC
*
41593681 AGAACATCAAATTCGTCTCCAGGTAAGCATCAATTTTCATAGGTAAGATTCAAGCTTCTTGAAAA
1 AGAACATCAAATTCGTCTCCAGGTAAGCATCAATTTTCATAGATAAGATTCAAGCTTCTTGAAAA
*
41593746 CTAAACAATATAGGTCTTGAGTTTGATTTGAGTTTTTGAGTTTCTTTTTTCCTTAAACTGTTCAA
66 CTAAAAAATATAGGTCTTGAGTTTGATTTGAGTTTTTGAGTTTCTTTTTTCCTTAAACTGTTCAA
41593811 GAACTTGAAAATTGAAAATTATC
131 GAACTTGAAAATTGAAAATTATC
41593834 AG
1 AG
41593836 TCTTTGATGC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (153 bp):
AGAACATCAAATTCGTCTCCAGGTAAGCATCAATTTTCATAGATAAGATTCAAGCTTCTTGAAAA
CTAAAAAATATAGGTCTTGAGTTTGATTTGAGTTTTTGAGTTTCTTTTTTCCTTAAACTGTTCAA
GAACTTGAAAATTGAAAATTATC
Found at i:41597991 original size:35 final size:35
Alignment explanation
Indices: 41597945--41598014 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
41597935 AATCATAACC
41597945 ACCCACTACTTAGAATTCTAATTCCATCAGAACTT
1 ACCCACTACTTAGAATTCTAATTCCATCAGAACTT
41597980 ACCCACTACTTAGAATTCTAATTCCATCAGAACTT
1 ACCCACTACTTAGAATTCTAATTCCATCAGAACTT
41598015 TCTCACAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (35 bp):
ACCCACTACTTAGAATTCTAATTCCATCAGAACTT
Found at i:41606706 original size:7 final size:8
Alignment explanation
Indices: 41606687--41606714 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41606677 AGTTCTAATT
41606687 TTTTTCAA
1 TTTTTCAA
41606695 TTTTTCAA
1 TTTTTCAA
41606703 TTTTTCAA
1 TTTTTCAA
41606711 TTTT
1 TTTT
41606715 AATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTCAA
Found at i:41609979 original size:43 final size:43
Alignment explanation
Indices: 41609913--41610058 Score: 222
Period size: 43 Copynumber: 3.4 Consensus size: 43
41609903 CTATTCGAGC
* *
41609913 CTTCGAGCCTAGCATGCTATAATGCCGGTGAGTTAATATCGGG
1 CTTCAAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGG
41609956 CTTCAAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGG
1 CTTCAAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGG
* *
41609999 CTTCGAA-CCTAGCAGGCTATAATGCCAGTGAGTTAATATCAGG
1 CTTC-AAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGG
* *
41610042 CTTCGAGCCTAGTAGGC
1 CTTCAAGCCTAGCAGGC
41610059 GTAATTTGGG
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.01
43 92 0.97
44 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (43 bp):
CTTCAAGCCTAGCAGGCTATAATGCCGGTGAGTTAATATCGGG
Found at i:41610666 original size:16 final size:18
Alignment explanation
Indices: 41610635--41610667 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
41610625 AACTCGTCAC
41610635 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
41610653 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
41610668 AATTCGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:41611360 original size:58 final size:60
Alignment explanation
Indices: 41611293--41611423 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 60
41611283 TAATTCAGAT
* *
41611293 TTTAATAATAATTATGTTAAGA-ATG-TT-ATTAATTTATTTATTA-TTTTAATAAATTGTA
1 TTTAATAATAATTATGTTAAAATATGATTAATT-ATTTATTT-TTATTTTTAATAAATTATA
* *
41611351 TTTATTAATAATTATGTTAAAATATGATTAAATTATTTATTTTTATTTTTATTAAATTATA
1 TTTAATAATAATTATGTTAAAATATGATT-AATTATTTATTTTTATTTTTAATAAATTATA
41611412 TTTAATAATAAT
1 TTTAATAATAAT
41611424 CTTATTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 20 0.32
59 3 0.05
60 5 0.08
61 32 0.51
62 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (60 bp):
TTTAATAATAATTATGTTAAAATATGATTAATTATTTATTTTTATTTTTAATAAATTATA
Found at i:41613787 original size:10 final size:11
Alignment explanation
Indices: 41613707--41613807 Score: 69
Period size: 11 Copynumber: 9.2 Consensus size: 11
41613697 AAAGTAACAC
* *
41613707 CAAAACATCAC
1 CAAAACAGCAA
*
41613718 CAAAACAGCAT
1 CAAAACAGCAA
* * *
41613729 CAAGATAGCAC
1 CAAAACAGCAA
* *
41613740 CAAAATAGTAA
1 CAAAACAGCAA
* *
41613751 CAAAATAACAA
1 CAAAACAGCAA
41613762 CAAAACAGCAA
1 CAAAACAGCAA
41613773 CAAAACAGCACA
1 CAAAACAGCA-A
* *
41613785 AAAAATAGC-A
1 CAAAACAGCAA
*
41613795 CCAAACAGCAA
1 CAAAACAGCAA
41613806 CA
1 CA
41613808 GTGAAAACAT
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.10
11 55 0.79
12 8 0.11
ACGTcount: A:0.59, C:0.26, G:0.08, T:0.07
Consensus pattern (11 bp):
CAAAACAGCAA
Found at i:41617156 original size:22 final size:22
Alignment explanation
Indices: 41617131--41617174 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41617121 TTTGGGGAGC
**
41617131 ACCGAGATTGCAAATGAAGAAG
1 ACCGAGACCGCAAATGAAGAAG
41617153 ACCGAGACCGCAAATGAAGAAG
1 ACCGAGACCGCAAATGAAGAAG
41617175 CAAAAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.27, T:0.09
Consensus pattern (22 bp):
ACCGAGACCGCAAATGAAGAAG
Done.