Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 10 of 203
Found at i:3441520 original size:3 final size:3
Alignment explanation
Indices: 3441512--3441546 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3441502 AGCCCGACTT
3441512 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3441547 GGAAAGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3443443 original size:42 final size:43
Alignment explanation
Indices: 3443347--3443443 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
3443337 ATAAACACTG
* * *
3443347 CTAAAGGTCATGACCTTTAGCGGCGCTTTACTCACAAACGCCG
1 CTAAAGGTCATGACCTTTAGCGGCGCTTTAATCAAAAACGCCA
* * *
3443390 CTAAAGATCATGACCTTTAGTGGCG-TTTAGAT-AAAAACGTCA
1 CTAAAGGTCATGACCTTTAGCGGCGCTTTA-ATCAAAAACGCCA
3443432 CTAAAGGTCATG
1 CTAAAGGTCATG
3443444 TCACAAACGC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 22 0.48
43 24 0.52
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
CTAAAGGTCATGACCTTTAGCGGCGCTTTAATCAAAAACGCCA
Found at i:3443532 original size:7 final size:7
Alignment explanation
Indices: 3443520--3443577 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
3443510 AAACATTTAA
3443520 AAATATT
1 AAATATT
3443527 AAATATT
1 AAATATT
3443534 AAATATT
1 AAATATT
3443541 AAA-ATT
1 AAATATT
*
3443547 AAACATT
1 AAATATT
*
3443554 ATTAATATC
1 A--AATATT
*
3443563 AAAAATT
1 AAATATT
*
3443570 AATTATT
1 AAATATT
3443577 A
1 A
3443578 TTAAATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.14
7 31 0.74
9 5 0.12
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:3443549 original size:20 final size:22
Alignment explanation
Indices: 3443519--3443578 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
3443509 AAAACATTTA
3443519 AAAATATTAAATATTA-AATAT-
1 AAAA-ATTAAATATTATAATATC
* *
3443540 TAAAATTAAACATTATTAATATC
1 AAAAATTAAATATTA-TAATATC
*
3443563 AAAAATTAATTATTAT
1 AAAAATTAAATATTAT
3443579 TAAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.32
21 3 0.10
22 6 0.19
23 12 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTAAATATTATAATATC
Found at i:3443556 original size:23 final size:24
Alignment explanation
Indices: 3443530--3443585 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3443520 AAATATTAAA
*
3443530 TATTAAATAT-TAAAATTAAACAT
1 TATTAAATATCAAAAATTAAACAT
**
3443553 TATT-AATATCAAAAATTAATTAT
1 TATTAAATATCAAAAATTAAACAT
3443576 TATTAAATAT
1 TATTAAATAT
3443586 ATACTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 18 0.64
24 5 0.18
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAATATCAAAAATTAAACAT
Found at i:3449001 original size:15 final size:15
Alignment explanation
Indices: 3448972--3449006 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3448962 AACTCTAATT
3448972 TAATT-ATATTAAGA
1 TAATTAATATTAAGA
*
3448986 TAATTAATATTGAGA
1 TAATTAATATTAAGA
3449001 TAATTA
1 TAATTA
3449007 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:3451029 original size:6 final size:6
Alignment explanation
Indices: 3451018--3451042 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3451008 TCACGAATTC
3451018 CATCGG CATCGG CATCGG CATCGG C
1 CATCGG CATCGG CATCGG CATCGG C
3451043 CTCATCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CATCGG
Found at i:3451420 original size:20 final size:20
Alignment explanation
Indices: 3451350--3451420 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
3451340 TAATTTTAAA
* *
3451350 TAAATTATTTTTGAAA-ATT
1 TAAATAATTTTTAAAATATT
* *
3451369 TAAATAATATTTAAAATAAT
1 TAAATAATTTTTAAAATATT
* * *
3451389 TAGATAAATTTTAAAATTTT
1 TAAATAATTTTTAAAATATT
*
3451409 TATATAATTTTT
1 TAAATAATTTTT
3451421 TATGTAACAA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAAATAATTTTTAAAATATT
Found at i:3452892 original size:22 final size:21
Alignment explanation
Indices: 3452861--3452907 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
3452851 CTTTAAATCA
*
3452861 TAAACCATAAAT-CATAACCCT
1 TAAACCAT-AATCCATAAACCT
3452882 TAAACCCATAATCCATAAACCT
1 TAAA-CCATAATCCATAAACCT
3452904 TAAA
1 TAAA
3452908 ATAGTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCATAATCCATAAACCT
Found at i:3453319 original size:41 final size:40
Alignment explanation
Indices: 3453274--3453551 Score: 254
Period size: 41 Copynumber: 6.8 Consensus size: 40
3453264 TTTTTTGCGG
* *
3453274 CGCTTTTCTAAAAATACCGCTAAAACCCCGAGCATTAACGA
1 CGCTTTT-TAAAAACACCGCTAAAACCCCGAGCATTAGCGA
* *
3453315 CGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCATTAGCGG
1 CGCTTTTT-AAAAACACCGCTAAAACCCCGAGCATTAGCGA
* * * *
3453356 CACTTCTTCAAAAACACCGCTAAAACCTTCGAGCATTAGCGG
1 CGCTT-TTTAAAAACACCGCTAAAACC-CCGAGCATTAGCGA
* * * * *
3453398 TGCTTTTTCAAAATCGCCGCTAAAGCCCC-ATGCATTAGCAA
1 CGCTTTTT-AAAAACACCGCTAAAACCCCGA-GCATTAGCGA
* *
3453439 CGCTTTTTTAAAAACACCACTAAAACCCCGAGCATTAGCGG
1 CGC-TTTTTAAAAACACCGCTAAAACCCCGAGCATTAGCGA
* * * * *
3453480 CGCTTCTTCAAAAACGCCGTTAAAGCCCC-ATACATTAGCGA
1 CGCTT-TTTAAAAACACCGCTAAAACCCCGA-GCATTAGCGA
* *
3453521 CGCTTTTTCAAAAACGCTGCTAAAACCCCGA
1 CGCTTTTT-AAAAACACCGCTAAAACCCCGA
3453552 AAACACGTTG
Statistics
Matches: 191, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
40 7 0.04
41 144 0.75
42 40 0.21
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (40 bp):
CGCTTTTTAAAAACACCGCTAAAACCCCGAGCATTAGCGA
Found at i:3453504 original size:82 final size:82
Alignment explanation
Indices: 3453277--3453551 Score: 354
Period size: 82 Copynumber: 3.3 Consensus size: 82
3453267 TTTGCGGCGC
* * * *
3453277 TTTTCTAAAAATACCGCTAAAACCCCGAGCATTAACGACGCTTTTTCAAAAACGCCGCTAAAACC
1 TTTTC-AAAAACACCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCC
* *
3453342 CCGA-GCATTAGCGGCACT
65 CC-ATGCATTAGCGACGCT
* * * *
3453360 TCTTCAAAAACACCGCTAAAACCTTCGAGCATTAGCGGTGCTTTTTCAAAATCGCCGCTAAAGCC
1 TTTTCAAAAACACCGCTAAAACC-CCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCC
*
3453425 CCATGCATTAGCAACGCT
65 CCATGCATTAGCGACGCT
* * * *
3453443 TTTTTAAAAACACCACTAAAACCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGTTAAAGCCC
1 TTTTCAAAAACACCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
*
3453508 CATACATTAGCGACGCT
66 CATGCATTAGCGACGCT
* *
3453525 TTTTCAAAAACGCTGCTAAAACCCCGA
1 TTTTCAAAAACACCGCTAAAACCCCGA
3453552 AAACACGTTG
Statistics
Matches: 165, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
82 93 0.56
83 72 0.44
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (82 bp):
TTTTCAAAAACACCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
CATGCATTAGCGACGCT
Found at i:3458215 original size:26 final size:26
Alignment explanation
Indices: 3458130--3458229 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
3458120 CTTAAGAGTG
* * * *
3458130 CGCCACAAAGGCGTTCCTTACAGATTT
1 CGCCACAAAGGC-TTTCTTTCATATTA
* * *
3458157 TGCCACAAAGG-TATTCCTTCCATATTC
1 CGCCACAAAGGCT-TT-CTTTCATATTA
*
3458184 CACCACAAAGGCTTTCTTTCATATTA
1 CGCCACAAAGGCTTTCTTTCATATTA
3458210 CGCCACAAAGGCTTTCTTTC
1 CGCCACAAAGGCTTTCTTTC
3458230 CTGATGTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.02
26 29 0.48
27 29 0.48
28 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (26 bp):
CGCCACAAAGGCTTTCTTTCATATTA
Found at i:3460417 original size:24 final size:24
Alignment explanation
Indices: 3460385--3460433 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3460375 GACTTTTAAT
3460385 GGGATGAGAGTGTGGGGAGTTATA
1 GGGATGAGAGTGTGGGGAGTTATA
3460409 GGGATGAGAGTGTGGGGAGTTATA
1 GGGATGAGAGTGTGGGGAGTTATA
3460433 G
1 G
3460434 TTGGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.51, T:0.24
Consensus pattern (24 bp):
GGGATGAGAGTGTGGGGAGTTATA
Found at i:3461376 original size:17 final size:17
Alignment explanation
Indices: 3461343--3461381 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3461333 ATAAAATAAT
*
3461343 TTTTCTGAAAATGACAA
1 TTTTCTGAAAATAACAA
3461360 CTTTTCTG-AAATAACAA
1 -TTTTCTGAAAATAACAA
3461377 TTTTC
1 TTTTC
3461382 AAGAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (17 bp):
TTTTCTGAAAATAACAA
Found at i:3469317 original size:31 final size:31
Alignment explanation
Indices: 3469282--3469341 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
3469272 TGGGATGGGA
*
3469282 TGGGAGGAGAGCAAAAGTTATGGG-GGAAAAG
1 TGGGAGG-GAACAAAAGTTATGGGAGGAAAAG
* *
3469313 TGGGAGGGAATAAAAGTTTTGGGAGGAAA
1 TGGGAGGGAACAAAAGTTATGGGAGGAAA
3469342 GTGAAGAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.38, C:0.02, G:0.43, T:0.17
Consensus pattern (31 bp):
TGGGAGGGAACAAAAGTTATGGGAGGAAAAG
Found at i:3469728 original size:22 final size:21
Alignment explanation
Indices: 3469661--3469733 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
3469651 CAAAAAAATT
* * *
3469661 AAAAATTTTAATCAAACCTTTC
1 AAAAATTTTAAT-GAATCTCTC
*
3469683 AAAAATTTT-A-GAATCCTCTT
1 AAAAATTTTAATGAAT-CTCTC
3469703 AAAAATTTTAATTGAATCTCTC
1 AAAAATTTTAA-TGAATCTCTC
*
3469725 AAAATTTTT
1 AAAAATTTT
3469734 GAAATTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 2 0.05
22 21 0.51
23 4 0.10
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAAATTTTAATGAATCTCTC
Found at i:3489372 original size:19 final size:19
Alignment explanation
Indices: 3489340--3489389 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
3489330 GTTCCTATTA
3489340 AAAAAAGGAA-AAAGGAAAA-
1 AAAAAA-GAAGAAA-GAAAAG
*
3489359 ATAAAAGAAGAAAGAAAAG
1 AAAAAAGAAGAAAGAAAAG
3489378 AAAAAAGAAGAA
1 AAAAAAGAAGAA
3489390 TCAATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAGAAAGAAAAG
Found at i:3492087 original size:307 final size:307
Alignment explanation
Indices: 3491507--3492105 Score: 765
Period size: 307 Copynumber: 2.0 Consensus size: 307
3491497 GCTAGGTTTA
* *
3491507 TTGTCATATGCCAATATCATAGACCCCAATTATACGATTGCGTCCACTAATCGAAGGGTATGTTG
1 TTGTCATATGCCAATATCATAGACCCCAATCATACGATTGCGTCCACTAATCAAAGGGTATGTTG
* * ***
3491572 GATTGGTAGATCGCACCCGCATCGTTAATGGCCCATAAGTTTTCCAACATTTCACAAAAAAGGTG
66 GATAGGTAGATCCCACCCGCATCGTTAACAACCCATAAGTTTTCCAACATTTCACAAAAAAGGTG
*** ** * *
3491637 TCGGGCAAGCTCATACCCTGTCGAGGAAAGTAAATAGGTTATCCACTAATCAGAACATTTTCTGA
131 TCGAAAAAGCTCATACCCTCCCGAGAAAAGTAAATAGGTTATCCACTAATCAGAACATTGTCTGA
* *
3491702 CCGATTAAATATCAAACAATTGATATAGTGACGAATATAAACCCATGTTGATCACTTGTGTGCAC
196 CCGATTAAATATCAAACAATTGATATAGTGACGAATACAAACCCATGTTGATCACTTGTGCGCAC
* *
3491767 TGAGTTGTAGAATTGTACTATCAGTGGTAGTTCGACCGCCAGGTCTG
261 TGAGCTATAGAATTGTACTATCAGTGGTAGTTCGACCGCCAGGTCTG
* * * * * * *
3491814 TTGTCA-AGTGCCCATATCGTAGACCCCCATCATATGATTGTGTCCACTGATCAAAGGTTATGTT
1 TTGTCATA-TGCCAATATCATAGACCCCAATCATACGATTGCGTCCACTAATCAAAGGGTATGTT
* ** ** **
3491878 GGATAGGTAGCTCCCACTTGCATCGTTAACAACCCATAAGTTTTCCAACATTTCACGGAACTGGT
65 GGATAGGTAGATCCCACCCGCATCGTTAACAACCCATAAGTTTTCCAACATTTCACAAAAAAGGT
* * * * *
3491943 GTCGAAAAAGTTCGTACCCTCCCTAGAAAA-TGAAATAGGTTATCCATTAATCAGTACATCTGT-
130 GTCGAAAAAGCTCATACCCTCCCGAGAAAAGT-AAATAGGTTATCCACTAATCAGAACAT-TGTC
*
3492006 TGACCCG-TTAAATATCAAACAATTGATATAGTGGCGAATACAAACCCATGTTGATCACTTGTGC
193 TGA-CCGATTAAATATCAAACAATTGATATAGTGACGAATACAAACCCATGTTGATCACTTGTGC
* * *
3492070 GCCCTGAGCTATAGAATTGTATTGTCAGTGGTAGTT
257 GCACTGAGCTATAGAATTGTACTATCAGTGGTAGTT
3492106 TGACGCAACA
Statistics
Matches: 247, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
306 2 0.01
307 240 0.97
308 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (307 bp):
TTGTCATATGCCAATATCATAGACCCCAATCATACGATTGCGTCCACTAATCAAAGGGTATGTTG
GATAGGTAGATCCCACCCGCATCGTTAACAACCCATAAGTTTTCCAACATTTCACAAAAAAGGTG
TCGAAAAAGCTCATACCCTCCCGAGAAAAGTAAATAGGTTATCCACTAATCAGAACATTGTCTGA
CCGATTAAATATCAAACAATTGATATAGTGACGAATACAAACCCATGTTGATCACTTGTGCGCAC
TGAGCTATAGAATTGTACTATCAGTGGTAGTTCGACCGCCAGGTCTG
Found at i:3494084 original size:15 final size:15
Alignment explanation
Indices: 3494064--3494120 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 15
3494054 ATAAAAATGT
3494064 TAAAAAATTAATATA
1 TAAAAAATTAATATA
3494079 TAAAAAAATATAA-ATTA
1 T-AAAAAAT-TAATA-TA
3494096 TAAAAAATTAATATA
1 TAAAAAATTAATATA
3494111 T-AAAAATTAA
1 TAAAAAATTAA
3494121 AAAAACTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.24
15 7 0.18
16 16 0.42
17 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAATTAATATA
Found at i:3494132 original size:25 final size:25
Alignment explanation
Indices: 3494086--3494143 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
3494076 ATATAAAAAA
3494086 ATAT-AAATTATAAAAAATTAATAT
1 ATATAAAATTATAAAAAATTAATAT
*
3494110 ATA-AAAATTA-AAAAAACTATAATTT
1 ATATAAAATTATAAAAAA-T-TAATAT
3494135 ATATAAAAT
1 ATATAAAAT
3494144 AAACTCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 6 0.21
24 10 0.34
25 8 0.28
26 5 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATAAAATTATAAAAAATTAATAT
Found at i:3499266 original size:26 final size:27
Alignment explanation
Indices: 3499209--3499266 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
3499199 CTCATTAACA
**
3499209 GATTTATTAATTTTTAACCTATCTATT
1 GATTTATTAATTTGCAACCTATCTATT
* * *
3499236 AATTTATTAA-TTGCAACCTATTTGTT
1 GATTTATTAATTTGCAACCTATCTATT
3499262 GATTT
1 GATTT
3499267 TTTTTCATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.53
Consensus pattern (27 bp):
GATTTATTAATTTGCAACCTATCTATT
Found at i:3501276 original size:43 final size:43
Alignment explanation
Indices: 3501180--3501413 Score: 236
Period size: 42 Copynumber: 5.6 Consensus size: 43
3501170 TTCGGTTACT
* **
3501180 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAAAGATA
* *
3501222 CGG-AGAATCAGCACATAGCAACC-CCTTTCACAA-TCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-A-AATTCAAAGATA
**
3501264 CGGTGGAATCAGCACTTAGCAACCACC-TTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAAAGATA
* *
3501306 CGG-AGAATCAGCACATAGCAACC-CCTTTCACAA-TCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-A-AATTCAAAGATA
* *
3501348 CGGTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAATA-ATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAA-AGATA
* *
3501391 CAG-GGAATCAACACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
3501414 CCTCGAGGAA
Statistics
Matches: 161, Mismatches: 18, Indels: 26
0.79 0.09 0.13
Matches are distributed among these distances:
40 4 0.02
41 41 0.25
42 57 0.35
43 51 0.32
44 8 0.05
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAAAGATA
Found at i:3501321 original size:84 final size:84
Alignment explanation
Indices: 3501180--3501416 Score: 386
Period size: 84 Copynumber: 2.8 Consensus size: 84
3501170 TTCGGTTACT
*
3501180 CGGTGGATTCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGAGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGAGAATCAGCACATAGCAACC
3501245 CCTTTCACAATCAAAGATA
66 CCTTTCACAATCAAAGATA
3501264 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGAGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGAGAATCAGCACATAGCAACC
3501329 CCTTTCACAATCAAAGATA
66 CCTTTCACAATCAAAGATA
* * * * * *
3501348 CGGTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAATAATTCAGG-GAATCAACACTTAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACC-TTAAATTCAGTGATAC-GGAGAATCAGCACATAGCAA
3501412 CCCCT
64 CCCCT
3501417 CGAGGAATCT
Statistics
Matches: 144, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
84 110 0.76
85 32 0.22
86 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGAGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGATA
Found at i:3501325 original size:41 final size:43
Alignment explanation
Indices: 3501188--3501376 Score: 214
Period size: 43 Copynumber: 4.5 Consensus size: 43
3501178 CTCGGTGGAT
**
3501188 TCAGCACTTAGCAACCACCTT-A-AATTCAGTGATACGG-AGAA
1 TCAGCACTTAGCAACCACCTTCACAA-TCAAAGATACGGTAGAA
* *
3501229 TCAGCACATAGCAACC-CCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACC-TTCACAATCAAAGATACGGTAGAA
**
3501272 TCAGCACTTAGCAACCACCTT-A-AATTCAGTGATACGG-AGAA
1 TCAGCACTTAGCAACCACCTTCACAA-TCAAAGATACGGTAGAA
* *
3501313 TCAGCACATAGCAACC-CCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACC-TTCACAATCAAAGATACGGTAGAA
3501356 TCAGCACTTAGCAACCACCTT
1 TCAGCACTTAGCAACCACCTT
3501377 TAAAGTCAAT
Statistics
Matches: 124, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
40 4 0.03
41 39 0.31
42 33 0.27
43 44 0.35
44 4 0.03
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (43 bp):
TCAGCACTTAGCAACCACCTTCACAATCAAAGATACGGTAGAA
Found at i:3503963 original size:13 final size:14
Alignment explanation
Indices: 3503945--3503979 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3503935 TGGTTCCACT
3503945 TGTTAAAATAAT-A
1 TGTTAAAATAATAA
3503958 TGTTAAAATAATAA
1 TGTTAAAATAATAA
3503972 T-TTAAAAT
1 TGTTAAAAT
3503980 TTAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (14 bp):
TGTTAAAATAATAA
Found at i:3505382 original size:18 final size:17
Alignment explanation
Indices: 3505359--3505397 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3505349 TTTTATAAAT
3505359 TGTGAATT-ATATGTGATA
1 TGTGAATTAATAT-TGA-A
3505377 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
3505394 TGTG
1 TGTG
3505398 GAAAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:3505640 original size:23 final size:24
Alignment explanation
Indices: 3505609--3505730 Score: 139
Period size: 23 Copynumber: 5.3 Consensus size: 24
3505599 AGTGTTATTG
3505609 ATCAGTGGTAGCTTCGGCTACAAT
1 ATCAGTGGTAGCTTCGGCTACAAT
* *
3505633 -TCAATGGTAGCTACGGCTAC-AT
1 ATCAGTGGTAGCTTCGGCTACAAT
*
3505655 ATCAGTGGTAGCCTCGGCTAC-AT
1 ATCAGTGGTAGCTTCGGCTACAAT
*
3505678 TTCAGTGGTAGCTAT-GGCTAC-AT
1 ATCAGTGGTAGCT-TCGGCTACAAT
*
3505701 ATCAGTGGTAGCTTTGGCTAC-AT
1 ATCAGTGGTAGCTTCGGCTACAAT
*
3505724 ATTAGTG
1 ATCAGTG
3505731 TGGCACTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
22 3 0.03
23 82 0.95
24 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (24 bp):
ATCAGTGGTAGCTTCGGCTACAAT
Found at i:3505723 original size:46 final size:46
Alignment explanation
Indices: 3505609--3505723 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
3505599 AGTGTTATTG
*
3505609 ATCAGTGGTAGCTTCGGCTACAATTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
* * *
3505655 ATCAGTGGTAGCCTCGGCTACATTTCAGTGGTAGCTATGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
*
3505701 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3505724 ATTAGTGTGG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
Found at i:3510440 original size:19 final size:18
Alignment explanation
Indices: 3510412--3510447 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3510402 AACTTAAATA
3510412 TTTAAGTTTTAAGTTTTTT
1 TTTAAGTTTTAA-TTTTTT
*
3510431 TTTAATTTTTAATTTTT
1 TTTAAGTTTTAATTTTT
3510448 CATAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTAAGTTTTAATTTTTT
Found at i:3510614 original size:8 final size:8
Alignment explanation
Indices: 3510601--3510626 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3510591 CTAAAGAGCT
3510601 TTTTAGAA
1 TTTTAGAA
3510609 TTTTAGAA
1 TTTTAGAA
3510617 TTTTAGAA
1 TTTTAGAA
3510625 TT
1 TT
3510627 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTTAGAA
Found at i:3518311 original size:23 final size:23
Alignment explanation
Indices: 3518285--3518331 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3518275 ACCACTCAAG
3518285 AAAGAGAGAAACCAATAACTAAT
1 AAAGAGAGAAACCAATAACTAAT
3518308 AAAGAGAGAAACCAATAACTAAT
1 AAAGAGAGAAACCAATAACTAAT
3518331 A
1 A
3518332 TATTGGCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAGAGAGAAACCAATAACTAAT
Found at i:3521804 original size:16 final size:16
Alignment explanation
Indices: 3521775--3521823 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
3521765 TACAATTTTA
*
3521775 AAAAATTATTTAAAAAT
1 AAAAA-TATATAAAAAT
3521792 AAAAATATATAAAAAT
1 AAAAATATATAAAAAT
*
3521808 ATAAA-ATATAAAAAT
1 AAAAATATATAAAAAT
3521823 A
1 A
3521824 TATAAGTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 11 0.37
16 14 0.47
17 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATATATAAAAAT
Found at i:3521811 original size:8 final size:8
Alignment explanation
Indices: 3521785--3521825 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
3521775 AAAAATTATT
3521785 TAAAAATA
1 TAAAAATA
3521793 -AAAATATA
1 TAAAA-ATA
3521801 TAAAAATA
1 TAAAAATA
3521809 T-AAAATA
1 TAAAAATA
3521816 TAAAAATA
1 TAAAAATA
3521824 TA
1 TA
3521826 TAAGTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 11 0.37
8 15 0.50
9 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAAATA
Found at i:3521815 original size:17 final size:17
Alignment explanation
Indices: 3521785--3521828 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3521775 AAAAATTATT
3521785 TAAAAATA-AAAATATA
1 TAAAAATATAAAATATA
3521801 TAAAAATATAAAATATA
1 TAAAAATATAAAATATA
3521818 -AAAATATATAA
1 TAAAA-ATATAA
3521829 GTTCAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATATAAAATATA
Found at i:3521816 original size:15 final size:16
Alignment explanation
Indices: 3521785--3521825 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
3521775 AAAAATTATT
*
3521785 TAAAAATAAAAATATA
1 TAAAAATATAAATATA
3521801 TAAAAATATAAA-ATA
1 TAAAAATATAAATATA
3521816 TAAAAATATA
1 TAAAAATATA
3521826 TAAGTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATATAAATATA
Found at i:3521859 original size:23 final size:23
Alignment explanation
Indices: 3521782--3521859 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
3521772 TTAAAAAATT
* *
3521782 ATTTAAAAATAAAAATATATAAAA
1 ATTT-AAAATATAAATATATATAA
* *
3521806 ATATAAAATATAAAAATATATAA
1 ATTTAAAATATAAATATATATAA
* *
3521829 GTTCAAAAT-TCAAATATATATAA
1 ATTTAAAATAT-AAATATATATAA
*
3521852 TTTTAAAA
1 ATTTAAAA
3521860 AACAACTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.02
23 39 0.91
24 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (23 bp):
ATTTAAAATATAAATATATATAA
Found at i:3530761 original size:13 final size:13
Alignment explanation
Indices: 3530745--3530775 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3530735 CAAAAAAATC
*
3530745 AAAATCAAAATAA
1 AAAATAAAAATAA
3530758 AAAATAAAAATAA
1 AAAATAAAAATAA
3530771 AAAAT
1 AAAAT
3530776 GAGAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:3530773 original size:19 final size:19
Alignment explanation
Indices: 3530737--3530773 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3530727 GATCCTTCCA
* *
3530737 AAAAAATCAAAATCAAAAT
1 AAAAAATAAAAATAAAAAT
3530756 AAAAAATAAAAATAAAAA
1 AAAAAATAAAAATAAAAA
3530774 ATGAGAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAAATAAAAAT
Found at i:3530843 original size:16 final size:15
Alignment explanation
Indices: 3530807--3530842 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3530797 AGAAGAAAAG
* *
3530807 AAAAAATCTAGATGA
1 AAAAAATCAAAATGA
3530822 AAAAAATCAAAATGA
1 AAAAAATCAAAATGA
3530837 AAAAAA
1 AAAAAA
3530843 AGGTAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAAATCAAAATGA
Found at i:3533169 original size:128 final size:128
Alignment explanation
Indices: 3532941--3533425 Score: 848
Period size: 128 Copynumber: 3.8 Consensus size: 128
3532931 CGGTGAAATT
3532941 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
3533006 AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
3533069 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
3533134 AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
3533197 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * *
3533262 AGTAGCGGAGCAGATCGAAGACG--GTAACTCTTATCTTCAAGAGTAAGGAAGCATATTTAAGCC
66 AGTAGCGGAGCAGATCAAAGACGACG-AA-TCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
** *
3533325 ACAAGTCCTATCTAACTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
1 ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
* * * *
3533390 AGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT
66 AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCT
3533426 CCCTGAAGTT
Statistics
Matches: 343, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
126 1 0.00
127 2 0.01
128 338 0.99
129 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (128 bp):
ACAAGTCCTATCTCCCTGGTCAGTAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGC
AGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAAGAGTAAGGAATCAAATTTAAGCC
Found at i:3533534 original size:44 final size:44
Alignment explanation
Indices: 3533416--3533537 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
3533406 AAAGATGGCA
** * *
3533416 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAGCCAAT
* * *
3533460 AATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAGCCAAT
* *
3533503 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGTGGAT
3533538 CGCATCAAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 3 0.05
44 63 0.95
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAGCCAAT
Found at i:3538854 original size:20 final size:20
Alignment explanation
Indices: 3538797--3538857 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3538787 CTCAATTAAT
*
3538797 TGTTTAGCACTTCTGTGCTCTC
1 TGTTT-GCACTTCGGTGC-CTC
*
3538819 TGTTTGCACTTTGGTGCCTC
1 TGTTTGCACTTCGGTGCCTC
*
3538839 TGTTTGCACTACGGTGCCT
1 TGTTTGCACTTCGGTGCCT
3538858 TTGTACAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 20 0.57
21 10 0.29
22 5 0.14
ACGTcount: A:0.08, C:0.26, G:0.23, T:0.43
Consensus pattern (20 bp):
TGTTTGCACTTCGGTGCCTC
Found at i:3539763 original size:10 final size:10
Alignment explanation
Indices: 3539734--3539763 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3539724 GTTTAAATGA
3539734 TATGTTTTGG
1 TATGTTTTGG
3539744 TATGTATTTGG
1 TATGT-TTTGG
3539755 TATGTTTTG
1 TATGTTTTG
3539764 TGCAGGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (10 bp):
TATGTTTTGG
Found at i:3541683 original size:36 final size:37
Alignment explanation
Indices: 3541636--3541731 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
3541626 GTCTCCAAAT
* *
3541636 TCACATTTCAATTCAATTCCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTCCACTTTTCCACTTTCAAG
*
3541672 TCACAATTCAATTCAAAATT-CACTTTTCCATTTTCAAG
1 TCACAATTCAATTC--AATTCCACTTTTCCACTTTCAAG
*
3541710 TCA-ATATTCATTTCAATTCCAC
1 TCACA-ATTCAATTCAATTCCAC
3541732 ACATATATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
36 17 0.33
37 19 0.37
38 15 0.29
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.42
Consensus pattern (37 bp):
TCACAATTCAATTCAATTCCACTTTTCCACTTTCAAG
Found at i:3545526 original size:25 final size:25
Alignment explanation
Indices: 3545492--3545546 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
3545482 TCAAAATAAC
*
3545492 TCAAATAAACTTCTATTTTATTACA
1 TCAAAAAAACTTCTATTTTATTACA
3545517 TCAAAAAAACTTCTATTTTATTACA
1 TCAAAAAAACTTCTATTTTATTACA
3545542 TCAAA
1 TCAAA
3545547 TAATATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (25 bp):
TCAAAAAAACTTCTATTTTATTACA
Found at i:3545753 original size:25 final size:25
Alignment explanation
Indices: 3545719--3545770 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3545709 GTTAGGATAC
3545719 AAACTTCTATTTTATTACATCAAAT
1 AAACTTCTATTTTATTACATCAAAT
*
3545744 AAACTTCTATTTTATTACATTAAAT
1 AAACTTCTATTTTATTACATCAAAT
3545769 AA
1 AA
3545771 TATCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (25 bp):
AAACTTCTATTTTATTACATCAAAT
Found at i:3546225 original size:18 final size:18
Alignment explanation
Indices: 3546199--3546241 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3546189 GACTCGGAAA
*
3546199 AGGAAACATATAAGGGTT
1 AGGAAACATATAAGGGCT
*
3546217 AGGATACATATAAGGGCT
1 AGGAAACATATAAGGGCT
3546235 AGGAAAC
1 AGGAAAC
3546242 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGAAACATATAAGGGCT
Found at i:3546524 original size:500 final size:500
Alignment explanation
Indices: 3545823--3546822 Score: 2000
Period size: 500 Copynumber: 2.0 Consensus size: 500
3545813 GGTAATCAAT
3545823 GTCTATGCCCGGGGGATTCAGTGCCACATGGCGGCCGTCGACGGTTACACGCTGGATTCCTCCTT
1 GTCTATGCCCGGGGGATTCAGTGCCACATGGCGGCCGTCGACGGTTACACGCTGGATTCCTCCTT
3545888 TCTCTAGCTTTCAGCGGCAGTTGTTGTTCCTCCGACGGGGATTTTGGTTCTTCTGGTACGGCGGA
66 TCTCTAGCTTTCAGCGGCAGTTGTTGTTCCTCCGACGGGGATTTTGGTTCTTCTGGTACGGCGGA
3545953 TGGTTGTCGGACTTGGGACGATGATCCACCTTCAAGGAATAGTATATGTGGAGGTGTTTGCATCA
131 TGGTTGTCGGACTTGGGACGATGATCCACCTTCAAGGAATAGTATATGTGGAGGTGTTTGCATCA
3546018 CGAGCGGCGACGGTGTTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCCCGAC
196 CGAGCGGCGACGGTGTTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCCCGAC
3546083 GGCCCTTCTTGCGATCCCTCATGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGTATAACAGG
261 GGCCCTTCTTGCGATCCCTCATGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGTATAACAGG
3546148 AAATAGAGCTGAACCGGGCATTTGGCTCTAACCTGCCATAGGACTCGGAAAAGGAAACATATAAG
326 AAATAGAGCTGAACCGGGCATTTGGCTCTAACCTGCCATAGGACTCGGAAAAGGAAACATATAAG
3546213 GGTTAGGATACATATAAGGGCTAGGAAACGCACTTGGCATTTTCTGAAAAGGTGGTTGCATGGCC
391 GGTTAGGATACATATAAGGGCTAGGAAACGCACTTGGCATTTTCTGAAAAGGTGGTTGCATGGCC
3546278 GCTGATGATGAGCTGGGTGAATGTCTGGGCCTCGTTGAGGGGCTG
456 GCTGATGATGAGCTGGGTGAATGTCTGGGCCTCGTTGAGGGGCTG
3546323 GTCTATGCCCGGGGGATTCAGTGCCACATGGCGGCCGTCGACGGTTACACGCTGGATTCCTCCTT
1 GTCTATGCCCGGGGGATTCAGTGCCACATGGCGGCCGTCGACGGTTACACGCTGGATTCCTCCTT
3546388 TCTCTAGCTTTCAGCGGCAGTTGTTGTTCCTCCGACGGGGATTTTGGTTCTTCTGGTACGGCGGA
66 TCTCTAGCTTTCAGCGGCAGTTGTTGTTCCTCCGACGGGGATTTTGGTTCTTCTGGTACGGCGGA
3546453 TGGTTGTCGGACTTGGGACGATGATCCACCTTCAAGGAATAGTATATGTGGAGGTGTTTGCATCA
131 TGGTTGTCGGACTTGGGACGATGATCCACCTTCAAGGAATAGTATATGTGGAGGTGTTTGCATCA
3546518 CGAGCGGCGACGGTGTTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCCCGAC
196 CGAGCGGCGACGGTGTTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCCCGAC
3546583 GGCCCTTCTTGCGATCCCTCATGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGTATAACAGG
261 GGCCCTTCTTGCGATCCCTCATGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGTATAACAGG
3546648 AAATAGAGCTGAACCGGGCATTTGGCTCTAACCTGCCATAGGACTCGGAAAAGGAAACATATAAG
326 AAATAGAGCTGAACCGGGCATTTGGCTCTAACCTGCCATAGGACTCGGAAAAGGAAACATATAAG
3546713 GGTTAGGATACATATAAGGGCTAGGAAACGCACTTGGCATTTTCTGAAAAGGTGGTTGCATGGCC
391 GGTTAGGATACATATAAGGGCTAGGAAACGCACTTGGCATTTTCTGAAAAGGTGGTTGCATGGCC
3546778 GCTGATGATGAGCTGGGTGAATGTCTGGGCCTCGTTGAGGGGCTG
456 GCTGATGATGAGCTGGGTGAATGTCTGGGCCTCGTTGAGGGGCTG
3546823 CCTTCGTCAT
Statistics
Matches: 500, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
500 500 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (500 bp):
GTCTATGCCCGGGGGATTCAGTGCCACATGGCGGCCGTCGACGGTTACACGCTGGATTCCTCCTT
TCTCTAGCTTTCAGCGGCAGTTGTTGTTCCTCCGACGGGGATTTTGGTTCTTCTGGTACGGCGGA
TGGTTGTCGGACTTGGGACGATGATCCACCTTCAAGGAATAGTATATGTGGAGGTGTTTGCATCA
CGAGCGGCGACGGTGTTTGAAACCTATACGTTGGTGGGGATTGGTAAAAAGGAGAGCTCCCCGAC
GGCCCTTCTTGCGATCCCTCATGCGCCGTTGGCCTATACATCGGCGGTCCACTCGGTATAACAGG
AAATAGAGCTGAACCGGGCATTTGGCTCTAACCTGCCATAGGACTCGGAAAAGGAAACATATAAG
GGTTAGGATACATATAAGGGCTAGGAAACGCACTTGGCATTTTCTGAAAAGGTGGTTGCATGGCC
GCTGATGATGAGCTGGGTGAATGTCTGGGCCTCGTTGAGGGGCTG
Found at i:3546725 original size:18 final size:18
Alignment explanation
Indices: 3546699--3546741 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3546689 GACTCGGAAA
*
3546699 AGGAAACATATAAGGGTT
1 AGGAAACATATAAGGGCT
*
3546717 AGGATACATATAAGGGCT
1 AGGAAACATATAAGGGCT
3546735 AGGAAAC
1 AGGAAAC
3546742 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGAAACATATAAGGGCT
Found at i:3548542 original size:22 final size:21
Alignment explanation
Indices: 3548498--3548591 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 21
3548488 TAGATATTTA
* * *
3548498 AGAGAAATTTAAGAAGAACTTG
1 AGAGAAATTGAA-AGGAAATTG
**
3548520 AGAGCAAATTGAAATTAAATTG
1 AGAG-AAATTGAAAGGAAATTG
3548542 AGAGAAATTTTG-AAGGAAATTG
1 AGAGAAA--TTGAAAGGAAATTG
3548564 AGAGGAAATTGAAAGGAAATTTG
1 AGA-GAAATTGAAAGGAAA-TTG
3548587 AGAGA
1 AGAGA
3548592 GGATTAGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.10
22 34 0.57
23 20 0.33
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (21 bp):
AGAGAAATTGAAAGGAAATTG
Found at i:3548565 original size:44 final size:45
Alignment explanation
Indices: 3548493--3548591 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
3548483 AAAAATAGAT
* * **
3548493 ATTTAAGAGAAATTTAAGAAGAACTTGAGAGCAAATTGAAATTAA
1 ATTTGAGAGAAATTTAAGAAGAAATTGAGAGCAAATTGAAAGGAA
* *
3548538 A-TTGAGAGAAATTT-TGAAGGAAATTGAGAGGAAATTGAAAGGAA
1 ATTTGAGAGAAATTTAAGAA-GAAATTGAGAGCAAATTGAAAGGAA
3548582 ATTTGAGAGA
1 ATTTGAGAGA
3548592 GGATTAGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 3 0.07
44 34 0.74
45 9 0.20
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.25
Consensus pattern (45 bp):
ATTTGAGAGAAATTTAAGAAGAAATTGAGAGCAAATTGAAAGGAA
Found at i:3548571 original size:11 final size:11
Alignment explanation
Indices: 3548517--3548590 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
3548507 TAAGAAGAAC
*
3548517 TTGAGAGCAAA
1 TTGAGAGGAAA
* **
3548528 TTGAAATTAAA
1 TTGAGAGGAAA
3548539 TTGAGA-GAAA
1 TTGAGAGGAAA
3548549 TTTTGA-AGGAAA
1 --TTGAGAGGAAA
3548561 TTGAGAGGAAA
1 TTGAGAGGAAA
*
3548572 TTGAAAGGAAA
1 TTGAGAGGAAA
3548583 TTTGAGAG
1 -TTGAGAG
3548591 AGGATTAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
10 7 0.14
11 30 0.59
12 14 0.27
ACGTcount: A:0.46, C:0.01, G:0.27, T:0.26
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:3552416 original size:24 final size:23
Alignment explanation
Indices: 3552373--3552420 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3552363 ATAGATAAGC
*
3552373 TATCCTAATTTTCTATATAAATT
1 TATCCTAATTTTCTAAATAAATT
*
3552396 TATCCTAATTTTTTAAAATAAATT
1 TATCCTAATTTTCT-AAATAAATT
3552420 T
1 T
3552421 TTAATTTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (23 bp):
TATCCTAATTTTCTAAATAAATT
Found at i:3552610 original size:26 final size:26
Alignment explanation
Indices: 3552581--3552630 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3552571 ATTATTTGTG
3552581 TACCAAATACTAATTATTTATAAATA
1 TACCAAATACTAATTATTTATAAATA
3552607 TACCAAATACTAATTATTTATAAA
1 TACCAAATACTAATTATTTATAAA
3552631 CATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (26 bp):
TACCAAATACTAATTATTTATAAATA
Found at i:3554786 original size:3 final size:3
Alignment explanation
Indices: 3554771--3554801 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3554761 TTATAGTCTA
*
3554771 TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3554802 ACTACTACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:3559690 original size:25 final size:25
Alignment explanation
Indices: 3559613--3559709 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
3559603 AAAGCTCTCT
*
3559613 TGAGCTTCCTGATACT-TGGCTCT-TA
1 TGAGCTTCCCGATA-TATGGCT-TATA
* * * * * *
3559638 TGATCTTCCTGATAAATTGCTCACA
1 TGAGCTTCCCGATATATGGCTTATA
3559663 TGAGCTTCCCGATATATGGCTTATA
1 TGAGCTTCCCGATATATGGCTTATA
3559688 TGAGCTT-CCGATTATATGGCTT
1 TGAGCTTCCCGA-TATATGGCTT
3559710 GGAAGAGCTT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 4 0.07
25 54 0.93
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (25 bp):
TGAGCTTCCCGATATATGGCTTATA
Found at i:3559717 original size:25 final size:24
Alignment explanation
Indices: 3559664--3559720 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
3559654 TTGCTCACAT
* *
3559664 GAGCTTCCCGATATATGGCTTATAT
1 GAGCTT-CCGATATATGGCTTAGAA
*
3559689 GAGCTTCCGATTATATGGCTTGGAA
1 GAGCTTCCGA-TATATGGCTTAGAA
3559714 GAGCTTC
1 GAGCTTC
3559721 TCGTTTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (24 bp):
GAGCTTCCGATATATGGCTTAGAA
Found at i:3564075 original size:469 final size:469
Alignment explanation
Indices: 3563197--3564138 Score: 1866
Period size: 469 Copynumber: 2.0 Consensus size: 469
3563187 CTATATAGAA
3563197 TGGCTCCTACAGAGTTAAAAGAGTTGAAAGCACAGTTGCAAGAATTGATTGATAGGGGTTTTGCT
1 TGGCTCCTACAGAGTTAAAAGAGTTGAAAGCACAGTTGCAAGAATTGATTGATAGGGGTTTTGCT
3563262 TGACCTAGTTTTTCATATTGGGGTGCACCGGTTCTGTTTGTTAAGAAAAAAGACGGATTATTGAG
66 TGACCTAGTTTTTCATATTGGGGTGCACCGGTTCTGTTTGTTAAGAAAAAAGACGGATTATTGAG
3563327 GTTATGCATTGATTACCGTTAGCTCAAAAAAGTTACAATCAAGAATAAATATCCATTGCCTCGTA
131 GTTATGCATTGATTACCGTTAGCTCAAAAAAGTTACAATCAAGAATAAATATCCATTGCCTCGTA
3563392 TTGATGATTTGTTTGATTAGTTGAAAGGTGCCGTAGTGTTCTCAAAGATTGACCGATTTGCCAGT
196 TTGATGATTTGTTTGATTAGTTGAAAGGTGCCGTAGTGTTCTCAAAGATTGACCGATTTGCCAGT
* *
3563457 ATTTTGCTGGGCATTCATCAAGCTAGTTATGAGAGACTGTCGAGCAAAGGTAACTTGGCCTCCGA
261 ATTTTGCTAGGCATTCATCAAGCTAGTTATAAGAGACTGTCGAGCAAAGGTAACTTGGCCTCCGA
3563522 ACATGTCTTCTAGCTTATCTAGAATTGCTTTAGCAGTCTTACAACTCTCTAGTTGCTTATACAGA
326 ACATGTCTTCTAGCTTATCTAGAATTGCTTTAGCAGTCTTACAACTCTCTAGTTGCTTATACAGA
3563587 GTATTGAACACGCTTGCCAGCATATAGCAATAAGCTATCTCATTAGACTTTTCCTATCGTTTTCT
391 GTATTGAACACGCTTGCCAGCATATAGCAATAAGCTATCTCATTAGACTTTTCCTATCGTTTTCT
3563652 AGCCTTAGCTTGAG
456 AGCCTTAGCTTGAG
3563666 TGGCTCCTACAGAGTTAAAAGAGTTGAAAGCACAGTTGCAAGAATTGATTGATAGGGGTTTTGCT
1 TGGCTCCTACAGAGTTAAAAGAGTTGAAAGCACAGTTGCAAGAATTGATTGATAGGGGTTTTGCT
3563731 TGACCTAGTTTTTCATATTGGGGTGCACCGGTTCTGTTTGTTAAGAAAAAAGACGGATTATTGAG
66 TGACCTAGTTTTTCATATTGGGGTGCACCGGTTCTGTTTGTTAAGAAAAAAGACGGATTATTGAG
3563796 GTTATGCATTGATTACCGTTAGCTCAAAAAAGTTACAATCAAGAATAAATATCCATTGCCTCGTA
131 GTTATGCATTGATTACCGTTAGCTCAAAAAAGTTACAATCAAGAATAAATATCCATTGCCTCGTA
3563861 TTGATGATTTGTTTGATTAGTTGAAAGGTGCCGTAGTGTTCTCAAAGATTGACCGATTTGCCAGT
196 TTGATGATTTGTTTGATTAGTTGAAAGGTGCCGTAGTGTTCTCAAAGATTGACCGATTTGCCAGT
3563926 ATTTTGCTAGGCATTCATCAAGCTAGTTATAAGAGACTGTCGAGCAAAGGTAACTTGGCCTCCGA
261 ATTTTGCTAGGCATTCATCAAGCTAGTTATAAGAGACTGTCGAGCAAAGGTAACTTGGCCTCCGA
3563991 ACATGTCTTCTAGCTTATCTAGAATTGCTTTAGCAGTCTTACAACTCTCTAGTTGCTTATACAGA
326 ACATGTCTTCTAGCTTATCTAGAATTGCTTTAGCAGTCTTACAACTCTCTAGTTGCTTATACAGA
3564056 GTATTGAACACGCTTGCCAGCATATAGCAATAAGCTATCTCATTAGACTTTTCCTATCGTTTTCT
391 GTATTGAACACGCTTGCCAGCATATAGCAATAAGCTATCTCATTAGACTTTTCCTATCGTTTTCT
3564121 AGCCTTAGCTTGAG
456 AGCCTTAGCTTGAG
3564135 TGGC
1 TGGC
3564139 CGGTGGACAC
Statistics
Matches: 471, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
469 471 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (469 bp):
TGGCTCCTACAGAGTTAAAAGAGTTGAAAGCACAGTTGCAAGAATTGATTGATAGGGGTTTTGCT
TGACCTAGTTTTTCATATTGGGGTGCACCGGTTCTGTTTGTTAAGAAAAAAGACGGATTATTGAG
GTTATGCATTGATTACCGTTAGCTCAAAAAAGTTACAATCAAGAATAAATATCCATTGCCTCGTA
TTGATGATTTGTTTGATTAGTTGAAAGGTGCCGTAGTGTTCTCAAAGATTGACCGATTTGCCAGT
ATTTTGCTAGGCATTCATCAAGCTAGTTATAAGAGACTGTCGAGCAAAGGTAACTTGGCCTCCGA
ACATGTCTTCTAGCTTATCTAGAATTGCTTTAGCAGTCTTACAACTCTCTAGTTGCTTATACAGA
GTATTGAACACGCTTGCCAGCATATAGCAATAAGCTATCTCATTAGACTTTTCCTATCGTTTTCT
AGCCTTAGCTTGAG
Found at i:3567676 original size:20 final size:20
Alignment explanation
Indices: 3567614--3567758 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 20
3567604 TACTTCGGCA
* *
3567614 CCCTGATTGCACGTACGTGC
1 CCCTGATTGCACATACGTAC
* *
3567634 CCCT-ATT-CATACTTCAGTAC
1 CCCTGATTGCACA-TAC-GTAC
*
3567654 CCCTGATTGCACATACGTGC
1 CCCTGATTGCACATACGTAC
* * **
3567674 CCCT-ATTTGTACTTTGGTAC
1 CCCTGA-TTGCACATACGTAC
* *
3567694 CCCTAATTGCACATACGTAT
1 CCCTGATTGCACATACGTAC
* * *
3567714 CCCTG-TT-CATACTTCAATAC
1 CCCTGATTGCACA-TAC-GTAC
*
3567734 CCCTGATTGCACATACGTGC
1 CCCTGATTGCACATACGTAC
3567754 CCCTG
1 CCCTG
3567759 TTTGTACTTT
Statistics
Matches: 89, Mismatches: 26, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
18 5 0.06
19 10 0.11
20 58 0.65
21 10 0.11
22 6 0.07
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (20 bp):
CCCTGATTGCACATACGTAC
Found at i:3567728 original size:80 final size:80
Alignment explanation
Indices: 3567578--3567777 Score: 285
Period size: 80 Copynumber: 2.5 Consensus size: 80
3567568 AATTATTGAA
* * * * * * * *
3567578 TGATTGCACATGCGTGCTCCTGTTCGTACTTCGGCA-CCCTGATTGCACGTACGTGCCCCTATTC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTAATTGCACATACGTACCCCTATTC
*
3567642 ATACTTCAGTACCCC
66 ATACTTCAATACCCC
* * *
3567657 TGATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCCTAATTGCACATACGTATCCCTGTTC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTAATTGCACATACGTACCCCTATTC
3567722 ATACTTCAATACCCC
66 ATACTTCAATACCCC
3567737 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCT
3567778 GAACGCATTT
Statistics
Matches: 107, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 30 0.28
80 77 0.72
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (80 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTAATTGCACATACGTACCCCTATTC
ATACTTCAATACCCC
Found at i:3567758 original size:40 final size:40
Alignment explanation
Indices: 3567578--3567779 Score: 217
Period size: 40 Copynumber: 5.1 Consensus size: 40
3567568 AATTATTGAA
* * * * *
3567578 TGATTGCACATGCGTGCTCCTGTTCGTACTTCGGCA-CCC
1 TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
* *
3567617 TGATTGCACGTACGTGCCCCTATTCATACTTCAGTACCCC
1 TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
* ** **
3567657 TGATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
* ** *
3567697 TAATTGCACATACGTATCCCTGTTCATACTTCAATACCCC
1 TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
** **
3567737 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
3567777 TGA
1 TGA
3567780 ACGCATTTAC
Statistics
Matches: 133, Mismatches: 29, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
39 29 0.22
40 104 0.78
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.33
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTCATACTTCAGTACCCC
Found at i:3576736 original size:22 final size:23
Alignment explanation
Indices: 3576688--3576743 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3576678 ATGAGGTTAT
* * *
3576688 GCTTAATTAAGTGGTTTAATCAG
1 GCTTAATTAAGTGATTTAATAAA
*
3576711 GCTTAATTAA-TGATTTATTAAA
1 GCTTAATTAAGTGATTTAATAAA
3576733 GCTTAATTAAG
1 GCTTAATTAAG
3576744 AAAGTTGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (23 bp):
GCTTAATTAAGTGATTTAATAAA
Found at i:3577494 original size:37 final size:37
Alignment explanation
Indices: 3577415--3577507 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
3577405 CTGAAAGTAA
* * * *
3577415 CTCAAACGACCAAATTTTATTGTTATACAGAGTGAAG
1 CTCAAATGAGCAAATTCTATTGTTATACAGAATGAAG
* *
3577452 TTCAAATGAGCAAATTCTATTGTTATACTA-AATGGAG
1 CTCAAATGAGCAAATTCTATTGTTATAC-AGAATGAAG
* *
3577489 CTCAAATGAGTAAAATCTA
1 CTCAAATGAGCAAATTCTA
3577508 CAGATATACT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
37 45 0.98
38 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (37 bp):
CTCAAATGAGCAAATTCTATTGTTATACAGAATGAAG
Found at i:3582171 original size:33 final size:33
Alignment explanation
Indices: 3582141--3582218 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
3582131 GCAAATCCCT
*
3582141 CCAATACACCAATGCTCAAAAAAGCTAATCCAA
1 CCAACACACCAATGCTCAAAAAAGCTAATCCAA
* * * *
3582174 CCGACACACCAATTCTCATAAGAGCTAATCCAA
1 CCAACACACCAATGCTCAAAAAAGCTAATCCAA
3582207 CCAACACACCAA
1 CCAACACACCAA
3582219 ACAGAGAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.35, G:0.06, T:0.14
Consensus pattern (33 bp):
CCAACACACCAATGCTCAAAAAAGCTAATCCAA
Found at i:3584216 original size:37 final size:37
Alignment explanation
Indices: 3584174--3584277 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 37
3584164 CTATTGATTT
* * *
3584174 TACTAAAAGTAGCTCAAACGAGCAAATTCTTCTGTTA
1 TACTAAAAGTAGCTCAAACGAGCAAATTCTACAGATA
** * * * *
3584211 TACTAAGTGAAGCTCAAATGAGAAAAATCTACAGATA
1 TACTAAAAGTAGCTCAAACGAGCAAATTCTACAGATA
*
3584248 TACTAAAA-TAAAGCTCAATCGAGCAAATTC
1 TACTAAAAGT--AGCTCAAACGAGCAAATTC
3584278 CACTAAGCAT
Statistics
Matches: 49, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
37 34 0.69
38 15 0.31
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (37 bp):
TACTAAAAGTAGCTCAAACGAGCAAATTCTACAGATA
Found at i:3591039 original size:16 final size:15
Alignment explanation
Indices: 3591012--3591041 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3591002 TTTATTAACC
3591012 TAAATTAAATTAATA
1 TAAATTAAATTAATA
3591027 TAAATTAAAATTAAT
1 TAAATT-AAATTAAT
3591042 TATGCTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTAAATTAATA
Found at i:3593083 original size:26 final size:27
Alignment explanation
Indices: 3593054--3593110 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3593044 CCCCAACAAC
3593054 ATTTTGACGATTTTACCCCTGGTA-AA
1 ATTTTGACGATTTTACCCCTGGTAGAA
* * *
3593080 ATTTTGATGATTTTGCTCCTGGTAGAA
1 ATTTTGACGATTTTACCCCTGGTAGAA
3593107 ATTT
1 ATTT
3593111 AAGAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTGACGATTTTACCCCTGGTAGAA
Found at i:3603654 original size:29 final size:30
Alignment explanation
Indices: 3603596--3603679 Score: 143
Period size: 29 Copynumber: 2.8 Consensus size: 30
3603586 AGAGGGGAGG
3603596 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
*
3603626 GGAGTAAAAGTTTTG-GGGGGAAGTGGGAA
1 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
*
3603655 GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGAGTAAAAGTTTTGAGGGGAAAGT
3603680 AAAGTGGGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 28 0.56
30 22 0.44
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
Found at i:3606873 original size:171 final size:172
Alignment explanation
Indices: 3606565--3606946 Score: 457
Period size: 171 Copynumber: 2.2 Consensus size: 172
3606555 GGCTTCAGTA
* * * * * * *
3606565 TATTTGATGATGCACTGTATGTGCTAGTATAGATTCTTCAGTTTATCCGATAATGCATTGTATGT
1 TATTCGATGATGCACTGTATGTGCTAGTATAGATACTTCAGTATATCCAATAATGCACTATATAT
*
3606630 GCCAATATAGATACTTCAATTTATTCGATGATGCACCATGTGTGCCAATATAGTTACTTCGGTAT
66 GCCAATATAGATACTTCAATTTATTCGATAATGCACCATGTGTGCCAATATAGTTACTTCGGTAT
3606695 ATCCGATGATGCACTGTATATGTTAATATAGATTATTCAATT
131 ATCCGATGATGCACTGTATATGTTAATATAGATTATTCAATT
* * *
3606737 TATTCGATGATGCA-T-TGTGTGCCTAGTATATATACTTCAGTATATCCAATGATGCACTATATA
1 TATTCGATGATGCACTGTATGTG-CTAGTATAGATACTTCAGTATATCCAATAATGCACTATATA
*** ** * *
3606800 TGCCAATATAGATACTTTGGTTTATTCGATAATGCACTGTGTGTGCCAGTATAGTTATTTCGGTA
65 TGCCAATATAGATACTTCAATTTATTCGATAATGCACCATGTGTGCCAATATAGTTACTTCGGTA
* * * *
3606865 TATCCGATGATGCACTGTATGTGTCAGTA-A-ATATACTTCAGTT
130 TATCCGATGATGCACTGTATATGTTAATATAGAT-TA-TTCAATT
* * * * **
3606908 TATCCAATGATGCACTATATGTGCCAGCGTAGATACTTC
1 TATTCGATGATGCACTGTATGTGCTAGTATAGATACTTC
3606947 GATTTATCCG
Statistics
Matches: 176, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
169 2 0.01
170 8 0.05
171 135 0.77
172 26 0.15
173 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (172 bp):
TATTCGATGATGCACTGTATGTGCTAGTATAGATACTTCAGTATATCCAATAATGCACTATATAT
GCCAATATAGATACTTCAATTTATTCGATAATGCACCATGTGTGCCAATATAGTTACTTCGGTAT
ATCCGATGATGCACTGTATATGTTAATATAGATTATTCAATT
Found at i:3606941 original size:129 final size:129
Alignment explanation
Indices: 3606565--3607527 Score: 757
Period size: 129 Copynumber: 7.5 Consensus size: 129
3606555 GGCTTCAGTA
* * * * * *
3606565 TATTTGATGATGCACTGTATGTGCTAGTATAGATT-CTTCAGTTTATCCGATAATGCATTGTATG
1 TATTCGATGATGCACTGTATGTGCTAGTATAG-TTATTTCGGTATATCCGATGATGCACTGTATG
* * * * * * * * * *
3606629 TGCCAATATAGATACTTCAATTTATTCGATGATGCACCATGTGTGCCAATATAGTTACTTCGGTA
65 TGCCAGTATATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGTT
* * * * ** * * *
3606694 TATCCGATGATGCACTGTATATGTTAATATAGATTA-TTCAATTTATTCGATGATGCA-T-TGTG
1 TATTCGATGATGCACTGTATGTGCTAGTATAG-TTATTTCGGTATATCCGATGATGCACTGTATG
* * * *
3606756 TGCCTAGTATATATACTTCAGTATATCCAATGATGCACTATATATGCCAATATAGATACTTTGGT
65 TGCC-AGTATATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGT
3606821 T
129 T
* * *
3606822 TATTCGATAATGCACTGTGTGTGCCAGTATAGTTATTTCGGTATATCCGATGATGCACTGTATGT
1 TATTCGATGATGCACTGTATGTGCTAGTATAGTTATTTCGGTATATCCGATGATGCACTGTATGT
* * ** *
3606887 GTCAGTAAATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGCGTAGATACTTCGATT
66 GCCAGTATATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGTT
* * ** * * *
3606951 TATCCGATGATGCATTGCGTGTGCTAGTATAGTT-TCTTCGGTATATCAGATGAAGCATTGTATG
1 TATTCGATGATGCACTGTATGTGCTAGTATAGTTAT-TTCGGTATATCCGATGATGCACTGTATG
* * * * * * * * *
3607015 TGTCAATATAGATACTTCGGTTTATCCAATGATGCACTATGTGTGCTAGTATAGTTGCTTCGGTA
65 TGCCAGTATATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGTT
* * * * * * *
3607080 TATTCGATGATACACTGTATGTGCCAGTATAGATATTGT-AGTTTATCCGATGATGCACTGTGTC
1 TATTCGATGATGCACTGTATGTGCTAGTATAGTTATT-TCGGTATATCCGATGATGCACTGTATG
* ** * * * * * *
3607144 TGCAAGTATA-ATTACTTTGGTATATCCAATGATGCATTGTATGTGCTAGTATAGATAATTCAGT
65 TGCCAGTATATA-TACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGT
3607208 T
129 T
* * * ** * * * * *
3607209 TATCCGATGGTGCACTATGGGTGTTGGTATAGTTACTTCGTTATATCCGATGATGCACTGTTTGT
1 TATTCGATGATGCACTGTATGTGCTAGTATAGTTATTTCGGTATATCCGATGATGCACTGTATGT
* * * * * * * *
3607274 GCCAATATAGATACTTC-GATTTATCCGATGATGCACTTTGTGTGCCAATATAGTTACTTCGGTA
66 GCCAGTATATATACTTCAG-TTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGTT
* * * * * * * *
3607338 TATTCGATGATGCACTTTATGTACTGGTATAGATATTGT-GGTTTATCCAATGATGCACTATGTG
1 TATTCGATGATGCACTGTATGTGCTAGTATAGTTATT-TCGGTATATCCGATGATGCACTGTATG
* *** * * *
3607402 TGCCAGTATAGT-TACTTCAGTATATTTGATGATGCACTGTATTTGCC-GATATAGATACTTCGA
65 TGCCAGTATA-TATACTTCAGTTTATCCAATGATGCACTATATGTGCCAG-TATAGATACTTCGG
3607465 TT
128 TT
* * * *
3607467 CA-TCTGATGATGCACTGTGTGTGCTAGTATAGTTACTTTAC--TATATCTGATGGTGCACTGT
1 TATTC-GATGATGCACTGTATGTGCTAGTATAGTTA-TTT-CGGTATATCCGATGATGCACTGT
3607528 GTAGCCGATT
Statistics
Matches: 658, Mismatches: 156, Indels: 40
0.77 0.18 0.05
Matches are distributed among these distances:
127 10 0.02
128 98 0.15
129 537 0.82
130 13 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (129 bp):
TATTCGATGATGCACTGTATGTGCTAGTATAGTTATTTCGGTATATCCGATGATGCACTGTATGT
GCCAGTATATATACTTCAGTTTATCCAATGATGCACTATATGTGCCAGTATAGATACTTCGGTT
Found at i:3607488 original size:86 final size:86
Alignment explanation
Indices: 3606557--3607527 Score: 782
Period size: 86 Copynumber: 11.3 Consensus size: 86
3606547 TCCAATTAGG
* * * *
3606557 CTTCAGTATATTTGATGATGCACTGTATGTGCTAGTATAGATTCTTC-AGTTTATCCGATAATGC
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGA-TTTATCCGATGATGC
* * * *
3606621 ATTGTATGTGCCAATATAGATA
65 ACTGTGTGTGCCAGTATAGTTA
* * ** * * * * *
3606643 CTTCAATTTATTCGATGATGCACCATGTGTGCCAATATAGTTACTTCGGTATATCCGATGATGCA
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGCA
* * ** *
3606708 CTGTATATGTTAATATAGATTA
66 CTGTGTGTGCCAGTATAG-TTA
* * * * * *
3606730 -TTCAATTTATTCGATGATGCA-T-TGTGTGCCTAGTATATATACTTC-AGTATATCCAATGATG
1 CTTCAGTATATTCGATGATGCACTGTATGTGCC-AGTATAGATACTTCGA-TTTATCCGATGATG
* * * * *
3606791 CACTATATATGCCAATATAGATA
64 CACTGTGTGTGCCAGTATAGTTA
** * * * * * * *
3606814 CTTTGGTTTATTCGATAATGCACTGTGTGTGCCAGTATAGTTATTTCGGTATATCCGATGATGCA
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGCA
* * *
3606879 CTGTATGTGTCAGTA-AATATA
66 CTGTGTGTGCCAGTATAGT-TA
* * * * **
3606900 CTTCAGTTTATCCAATGATGCACTATATGTGCCAGCGTAGATACTTCGATTTATCCGATGATGCA
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGCA
* * * *
3606965 TTGCGTGTGCTAGTATAGTTT
66 CTGTGTGTGCCAGTATAGTTA
* * * * * * *
3606986 CTTCGGTATA-TCAGATGAAGCATTGTATGTGTCAATATAGATACTTCGGTTTATCCAATGATGC
1 CTTCAGTATATTC-GATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGC
* * *
3607050 ACTATGTGTGCTAGTATAGTTG
65 ACTGTGTGTGCCAGTATAGTTA
* *
3607072 CTTCGGTATATTCGATGATACACTGTATGTGCCAGTATAGATA-TT-GTAGTTTATCCGATGATG
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCG-A-TTTATCCGATGATG
* * *
3607135 CACTGTGTCTGCAAGTATAATTA
64 CACTGTGTGTGCCAGTATAGTTA
** * * * * * *
3607158 CTTTGGTATATCCAATGATGCATTGTATGTGCTAGTATAGATAATTC-AGTTTATCCGATGGTGC
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGA-TTTATCCGATGATGC
* * ***
3607222 ACTATGGGTGTTGGTATAGTTA
65 ACTGTGTGTGCCAGTATAGTTA
* * *
3607244 CTTC-GTTATATCCGATGATGCACTGTTTGTGCCAATATAGATACTTCGATTTATCCGATGATGC
1 CTTCAG-TATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGC
* *
3607308 ACTTTGTGTGCCAATATAGTTA
65 ACTGTGTGTGCCAGTATAGTTA
* * * ** * * *
3607330 CTTCGGTATATTCGATGATGCACTTTATGTACTGGTATAGATA-TTGTGGTTTATCCAATGATGC
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTT-CGATTTATCCGATGATGC
*
3607394 ACTATGTGTGCCAGTATAGTTA
65 ACTGTGTGTGCCAGTATAGTTA
* * * *
3607416 CTTCAGTATATTTGATGATGCACTGTATTTGCC-GATATAGATACTTCGATTCATCTGATGATGC
1 CTTCAGTATATTCGATGATGCACTGTATGTGCCAG-TATAGATACTTCGATTTATCCGATGATGC
*
3607480 ACTGTGTGTGCTAGTATAGTTA
65 ACTGTGTGTGCCAGTATAGTTA
* * *
3607502 CTTTACTATA-TCTGATGGTGCACTGT
1 CTTCAGTATATTC-GATGATGCACTGT
3607528 GTAGCCGATT
Statistics
Matches: 713, Mismatches: 149, Indels: 46
0.79 0.16 0.05
Matches are distributed among these distances:
84 11 0.02
85 67 0.09
86 615 0.86
87 20 0.03
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (86 bp):
CTTCAGTATATTCGATGATGCACTGTATGTGCCAGTATAGATACTTCGATTTATCCGATGATGCA
CTGTGTGTGCCAGTATAGTTA
Found at i:3607528 original size:43 final size:43
Alignment explanation
Indices: 3606557--3607529 Score: 601
Period size: 43 Copynumber: 22.7 Consensus size: 43
3606547 TCCAATTAGG
** *
3606557 CTTCAGTATATTTGATGATGCACTGTATGTGCTAGTATAGATT-
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAG-TTA
* * * * * * *
3606600 CTTCAGTTTATCCGATAATGCATTGTATGTGCCAATATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * ** * *
3606643 CTTCAATTTATTCGATGATGCACCATGTGTGCCAATATAGTTA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * *
3606686 CTTCGGTATATCCGATGATGCACTGTATATGTTAATATAGATTA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAG-TTA
* * *
3606730 -TTCAATTTATTCGATGATGCA-T-TGTGTGCCTAGTATA-TATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTG-CTAGTATAGT-TA
* * * * * * *
3606771 CTTCAGTATATCCAATGATGCACTATATATGCCAATATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
** * * * *
3606814 CTTTGGTTTATTCGATAATGCACTGTGTGTGCCAGTATAGTTA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * *
3606857 TTTCGGTATATCCGATGATGCACTGTATGTG-TCAGTA-AATATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCT-AGTATAGT-TA
* * * * * ** *
3606900 CTTCAGTTTATCCAATGATGCACTATATGTGCCAGCGTAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * *
3606943 CTTC-GATTTATCCGATGATGCATTGCGTGTGCTAGTATAGTTT
1 CTTCAG-TATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * * * *
3606986 CTTCGGTATATCAGATGAAGCATTGTATGTG-TCAATATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCT-AGTATAGTTA
* * * * *
3607029 CTTCGGTTTATCCAATGATGCACTATGTGTGCTAGTATAGTTG
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * * *
3607072 CTTCGGTATATTCGATGATACACTGTATGTGCCAGTATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * *
3607115 -TTGTAGTTTATCCGATGATGCACTGTGTCTGCAAGTATAATTA
1 CTT-CAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
** * * * *
3607158 CTTTGGTATATCCAATGATGCATTGTATGTGCTAGTATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * * * *
3607201 ATTCAGTTTATCCGATGGTGCACTATGGGTGTTGGTATAGTTA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * *
3607244 CTTC-GTTATATCCGATGATGCACTGTTTGTGCCAATATAGATA
1 CTTCAG-TATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * *
3607287 CTTC-GATTTATCCGATGATGCACTTTGTGTGCCAATATAGTTA
1 CTTCAG-TATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * * * * *
3607330 CTTCGGTATATTCGATGATGCACTTTATGTACTGGTATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
** * * * *
3607373 -TTGTGGTTTATCCAATGATGCACTATGTGTGCCAGTATAGTTA
1 CTT-CAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
** * * * *
3607416 CTTCAGTATATTTGATGATGCACTGTATTTGC-CGATATAGATA
1 CTTCAGTATATCCGATGATGCACTGTGTGTGCTAG-TATAGTTA
*
3607459 CTTC-G-ATTCATCTGATGATGCACTGTGTGTGCTAGTATAGTTA
1 CTTCAGTA-T-ATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
* * * *
3607502 CTTTACTATATCTGATGGTGCACTGTGT
1 CTTCAGTATATCCGATGATGCACTGTGT
3607530 AGCCGATTGA
Statistics
Matches: 708, Mismatches: 194, Indels: 56
0.74 0.20 0.06
Matches are distributed among these distances:
40 1 0.00
41 7 0.01
42 37 0.05
43 645 0.91
44 17 0.02
45 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (43 bp):
CTTCAGTATATCCGATGATGCACTGTGTGTGCTAGTATAGTTA
Found at i:3611545 original size:46 final size:43
Alignment explanation
Indices: 3611487--3611579 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 43
3611477 AACAGACACA
*
3611487 CGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATGATATC
1 CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAATGATA-C
* *
3611533 CGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAATGATAC
1 CGGT-GGATTCAGCACACAGCAACCACCTTATAATCAATGATAC
3611576 CGGT
1 CGGT
3611580 TCACATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 5 0.12
44 13 0.30
45 2 0.05
46 20 0.47
47 3 0.07
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
CGGTGGATTCAGCACACAGCAACCACCTTATAATCAATGATAC
Found at i:3611660 original size:51 final size:50
Alignment explanation
Indices: 3611576--3611771 Score: 182
Period size: 51 Copynumber: 3.9 Consensus size: 50
3611566 TTAATGATAC
* * *
3611576 CGGTTCACATAGTAGCCTGCACATAGTACTACAAATGTGACCATCACTATT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACAAACGTGACCAT-ACTATT
* * * * * *
3611627 CGATACACGTAGCAGCCTGTACATAGTACTACAAACATGATCGA-AGCTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACAAACGTGA-CCATA-CTATT
* * * * *
3611678 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TA-TCATT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACAAACGTGACCATACT-ATT
* *
3611727 CTGGTACACGTAGTAGCCTGCACATAGAACTACACACGTGACCAT
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACAAACGTGACCAT
3611772 CACTTTCACT
Statistics
Matches: 114, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 39 0.34
51 69 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACAAACGTGACCATACTATT
Found at i:3611796 original size:101 final size:102
Alignment explanation
Indices: 3611575--3611760 Score: 252
Period size: 102 Copynumber: 1.8 Consensus size: 102
3611565 ATTAATGATA
*
3611575 CCGGTTCACATAGTAGCCTGCACATAGTACTACAAATGTGACCATCACTATTCGATACACGTAGC
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACAAATGCGACCATCACTATTCGATACACGTAGC
* * *
3611640 AGCCTGTACATAGTACTACAAACATGATCGAAGCTAT
66 AGCCTGCACATAGAACTACAAACATGATCCAAGCTAT
* * * *
3611677 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-T-A-TCATTCTGGTACACGTA
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACAAATGCGACCATCACT-ATTC-GATACACGTA
*
3611739 GTAGCCTGCACATAGAACTACA
64 GCAGCCTGCACATAGAACTACA
3611761 CACGTGACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
99 1 0.01
100 5 0.07
101 29 0.39
102 39 0.53
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACAAATGCGACCATCACTATTCGATACACGTAGC
AGCCTGCACATAGAACTACAAACATGATCCAAGCTAT
Found at i:3614189 original size:42 final size:42
Alignment explanation
Indices: 3614109--3614190 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
3614099 CGTTTTCTCT
* **
3614109 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
3614151 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
3614191 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:3632838 original size:12 final size:12
Alignment explanation
Indices: 3632805--3632839 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3632795 CAGGTGATGC
*
3632805 GCAAGACCAAGG
1 GCAAGAGCAAGG
3632817 GCAAGAGCAAGG
1 GCAAGAGCAAGG
*
3632829 GCAAGCGCAAG
1 GCAAGAGCAAG
3632840 TTGCGAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.37, T:0.00
Consensus pattern (12 bp):
GCAAGAGCAAGG
Found at i:3639496 original size:824 final size:825
Alignment explanation
Indices: 3637684--3640984 Score: 5885
Period size: 824 Copynumber: 4.0 Consensus size: 825
3637674 TTTTTAACAA
3637684 AAATGTTAAAAGAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAG
1 AAATGTTAAAA-AAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAG
3637749 -AAACTTTGAAGATGCAGAAATCATCCC-GAAAAACCAAATAAGACTAGAAAATCACCAACAAAA
65 AAAACTTTGAAGATGCAGAAATCATCCCAG-AAAACCAAATAAGACTAGAAAATCACCAACAAAA
*
3637812 GATGCAAAAATTTCAAATAGAAAAGGAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATA
129 GATGCAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATA
3637877 GGCCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATT
194 GGCCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATT
*
3637942 TCCAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGTAATCCTTAGAATACATTTAT
259 TCCAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTAT
*
3638007 TGTAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACC
324 TGCAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACC
*
3638072 TATAAAAGAGAAAGTTAATAAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGA
389 TATAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGA
* * *
3638137 CTCGAAA-GGGGAAATATTATTATACCCCCCATCTGTGTCAAGACACATGGTAAGTAAACAGAAC
454 CTCGAAAGGGGGAAATATTGTTATACCCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAAC
*
3638201 ACACAAACAATAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATT
519 ACACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATT
*
3638266 TGAACAAGCACATACTATCCGTCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGT
584 TGAACAAGCACATACTATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGT
3638331 CACCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTC
649 CACCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTC
*
3638396 CCATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACACGTTCTGTAATGATGGCTTAAT
714 CCATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACGCGTTCTGTAATGATGGCTTAAT
*
3638461 GGAAAGCCCAACACGTTAATGTGACCTTACATGGAACCCTCAACTAT
779 GGAAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
*
3638508 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGTGAAACGAATCGAAGCAAGA
1 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAGA
*
3638573 AAACTTTGAAGATGCAGAAATCATCCCGGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
66 AAACTTTGAAGATGCAGAAATCATCCCAGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
*
3638638 TGCAAAAATTTCAAATAGAAAAGGAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
131 TGCAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
3638703 CCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
196 CCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
*
3638768 CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGTAATCCTTAGAATACATTTATTG
261 CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTATTG
3638833 CAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACCTA
326 CAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACCTA
3638898 TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGACT
391 TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGACT
* *
3638963 CGAAATGGGGAAATATTGTTATACCCCCCCATCTGTGTCAAGACACATGGTAAGTAAAGAGAACA
456 CGAAAGGGGGAAATATTGTTATA-CCCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAACA
*
3639028 CACAAACAGTAAGACAATTGACAAGAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATTT
520 CACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATTT
* *
3639093 GAACAAGCATATACTATCCATCATTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGTC
585 GAACAAGCACATACTATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGTC
* * *
3639158 ACCAAATACCACGTGAGTTCAACATCTCCATACCATCAAATTAGAATAAGTGATACGGTTTGTCC
650 ACCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTCC
*
3639223 CATCACAGACATCATCGTCCCATTAAAGGCATCCATCCCACGCGTTCTGTAATGATGGCTTAATG
715 CATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACGCGTTCTGTAATGATGGCTTAATG
3639288 GAAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
780 GAAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
*
3639334 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAATGAATCGAAGCAAGA
1 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAGA
*
3639399 AAACTTTGAAGATGCAGAAATCATCCCAGAAAACCAAATAAGACGAGAAAATCACCAACAAAAGA
66 AAACTTTGAAGATGCAGAAATCATCCCAGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
3639464 TGCAAAAATTTCAAATAG-AAAGAAGG-AATACAACTTCGAAGAAGAAAACCCATAATACATAGG
131 TGCAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
* * *
3639527 CCTATTTCCTAAAACGCATTGTTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
196 CCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
* * *
3639592 CAAAAAGCTATTGTACATCATTATCACGACTCCCTAGAAACACAATCCTTAGAATACATTTATGG
261 CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTATTG
* * * * *
3639657 CAAAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCTCCAACCGGAGCAACCTG
326 CAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACCTA
* * *
3639722 TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAATGAAGATCACTTTATAACCTTCTTCTCAACT
391 TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGACT
3639787 CGAAAGGGGGAAATATTGTTATA-CCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAACAC
456 CGAAAGGGGGAAATATTGTTATACCCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAACAC
* *
3639851 ACAAAAAGTAAGACAATTGACAATAAGTTGGAAGGTCATCTGTAACCCTTTACAAAGACTATTTG
521 ACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATTTG
*
3639916 AACAAGCACATACTATCCGTCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGTCA
586 AACAAGCACATACTATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGTCA
3639981 CCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTCCC
651 CCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTCCC
*
3640046 ATCACAGACATCATCGTCCCATTAAAGGCATCCATCCCACGCGTTCTGTAATGATGGCTTAATGG
716 ATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACGCGTTCTGTAATGATGGCTTAATGG
3640111 AAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
781 AAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
*
3640156 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCAAAGCAAGA
1 AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAGA
*
3640221 AAACTTTGAAGATGTAGAAATCATCCCAGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
66 AAACTTTGAAGATGCAGAAATCATCCCAGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
*
3640286 TGGAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
131 TGCAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
* * *
3640351 CCTATTTCCCAAAATGCACTGTTTTGAAAGACAAACAACATTTAATAGCATATCACCACCATTTC
196 CCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
3640416 CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTATTG
261 CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTATTG
* * * * *
3640481 CAGAATCTCAAAGTTTTTGATATAACGTTTCACTATAAAACAAAGTCACTAACCGGAGCAACCTG
326 CAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACCTA
* *
3640546 TAAAAGAGAAACTTAATGAATTAGAGTGTCTCATGGAAGATCACTTTATAACCTTCCTCTCGACT
391 TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGACT
*
3640611 CGAAAGGGGGAAATATTGTTATACCCCCCATCTGTGTCAAGACACATGGCAAGTGAAGAGAACAC
456 CGAAAGGGGGAAATATTGTTATACCCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAACAC
* *
3640676 ACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATTTGCAATCCCCTTTACAAAGACTATT
521 ACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAA--CCCTTTACAAAGACTATT
* *
3640741 TGAACAAGCACATACCATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTTGGT
584 TGAACAAGCACATACTATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGT
* *
3640806 CAGCAAATACCACATGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTC
649 CACCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTC
* * *
3640871 CCATCACATACATCATCGTCCCATCAAAGACATCCATCCCACGCGTTCTATAATGATGGCTTAAT
714 CCATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACGCGTTCTGTAATGATGGCTTAAT
* * *
3640936 GGAAAGTCCAACACGTTAATGTGACCTTACATGGAACCCTAAACTAT
779 GGAAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
3640983 AA
1 AA
3640985 CTACCTCCAA
Statistics
Matches: 2383, Mismatches: 85, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
822 479 0.20
823 60 0.03
824 1010 0.42
825 105 0.04
826 479 0.20
827 250 0.10
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (825 bp):
AAATGTTAAAAAAATAACACCAATGACAACAAAGAACAATAACTGCGAAACGAATCGAAGCAAGA
AAACTTTGAAGATGCAGAAATCATCCCAGAAAACCAAATAAGACTAGAAAATCACCAACAAAAGA
TGCAAAAATTTCAAATAGAAAAGAAGGCAATACAACTTCGAAGAAGAAAACCCATAATACATAGG
CCTATTTCCCAAAACGCACTATTTTGAAAGACAAACAACATTTAATAGCATCTCACCACCATTTC
CAAAAAGCTATTGTTCATCATTATCACGACTCCCTAGAAACGCAATCCTTAGAATACATTTATTG
CAGAATCTCAAAGGTTTTGATATAACGTTTCACTATAAAACAAAGTCACCAAACGGAGAAACCTA
TAAAAGAGAAAGTTAATGAATTAGAGTGTCTCAAGGAAGATCACTTTATAACCTTCCTCTCGACT
CGAAAGGGGGAAATATTGTTATACCCCCCATCTGTGTCAAGACACATGGCAAGTAAAGAGAACAC
ACAAACAGTAAGACAATTGACAATAAGCTGGAAGGTCATCTGTAACCCTTTACAAAGACTATTTG
AACAAGCACATACTATCCATCGTTCAGGTCCTTGAGCTTCATCGGGAACATGAAGTTGTAGGTCA
CCAAATACCACGTGGGTTCAACATCTCCATACCATCAAATTAGAATAAATGATACGATTTGTCCC
ATCACAGACATCATCGTCCCATTAAAGACATCCATCCCACGCGTTCTGTAATGATGGCTTAATGG
AAAGCCCAACACGTTAATATGACCTTACATGGAACCCTCAACTAT
Found at i:3641888 original size:9 final size:9
Alignment explanation
Indices: 3641869--3641941 Score: 94
Period size: 9 Copynumber: 8.2 Consensus size: 9
3641859 TCGGGTATTT
3641869 TTCGG-TAA
1 TTCGGTTAA
*
3641877 TTCAGTTAA
1 TTCGGTTAA
3641886 TTCGGTTAA
1 TTCGGTTAA
3641895 TTCGGTTAA
1 TTCGGTTAA
*
3641904 TTCGGGTAA
1 TTCGGTTAA
*
3641913 TTCGGGTAA
1 TTCGGTTAA
*
3641922 TTCGGGTAA
1 TTCGGTTAA
*
3641931 TTCGGGTAA
1 TTCGGTTAA
3641940 TT
1 TT
3641942 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
8 4 0.07
9 57 0.93
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:3641897 original size:18 final size:18
Alignment explanation
Indices: 3641872--3641941 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
3641862 GGTATTTTTC
*
3641872 GGTAATTCAGTTAATTCG
1 GGTAATTCGGTTAATTCG
*
3641890 GTTAATTCGGTTAATTCG
1 GGTAATTCGGTTAATTCG
*
3641908 GGTAATTCGGGTAATTCG
1 GGTAATTCGGTTAATTCG
*
3641926 GGTAATTCGGGTAATT
1 GGTAATTCGGTTAATT
3641942 TTTAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (18 bp):
GGTAATTCGGTTAATTCG
Found at i:3644211 original size:23 final size:23
Alignment explanation
Indices: 3644192--3644244 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
3644182 AGTGTTATTG
3644192 ATCAGTGGTAGCATCGGTTACAT
1 ATCAGTGGTAGCATCGGTTACAT
* *
3644215 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCATCGGTTACAT
3644238 ATCAGTG
1 ATCAGTG
3644245 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCATCGGTTACAT
Found at i:3646428 original size:24 final size:24
Alignment explanation
Indices: 3646401--3646452 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3646391 TTAGTAAGTC
*
3646401 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3646425 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3646449 AAAT
1 AAAT
3646453 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3648398 original size:24 final size:24
Alignment explanation
Indices: 3648371--3648422 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3648361 TTAGTAAGTC
*
3648371 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3648395 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3648419 AAAT
1 AAAT
3648423 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3648636 original size:3 final size:3
Alignment explanation
Indices: 3648628--3648677 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
3648618 AAGCTAAAGT
* *
3648628 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3648676 TA
1 TA
3648678 TATTATTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3649224 original size:15 final size:15
Alignment explanation
Indices: 3649190--3649236 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3649180 AATGTTGTTG
3649190 ATATAAAATATA-TA
1 ATATAAAATATATTA
* * *
3649204 TTTATAATATATTTTA
1 -ATATAAAATATATTA
3649220 ATATAAAATATATTA
1 ATATAAAATATATTA
3649235 AT
1 AT
3649237 CATTTGCAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAAATATATTA
Found at i:3657402 original size:15 final size:15
Alignment explanation
Indices: 3657382--3657414 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3657372 CTAGCTTTAT
3657382 ACATATAGTATAACC
1 ACATATAGTATAACC
3657397 ACATATAGTATAACC
1 ACATATAGTATAACC
3657412 ACA
1 ACA
3657415 CTCAACCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (15 bp):
ACATATAGTATAACC
Found at i:3658969 original size:25 final size:25
Alignment explanation
Indices: 3658937--3658995 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
3658927 AGCTGTAATC
* *
3658937 GGTAAGCTCATACGAGCTGAGTAAA
1 GGTAAGCTCATACGAACTGAATAAA
**
3658962 GGTAAGCTCATACGAACTGAATATT
1 GGTAAGCTCATACGAACTGAATAAA
3658987 GGTAAGCTC
1 GGTAAGCTC
3658996 TCTCGAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCATACGAACTGAATAAA
Found at i:3665634 original size:13 final size:13
Alignment explanation
Indices: 3665613--3665642 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3665603 TACTTTTTCA
*
3665613 ATTTTTTTTCTTT
1 ATTTCTTTTCTTT
3665626 ATTTCTTTTCTTT
1 ATTTCTTTTCTTT
3665639 ATTT
1 ATTT
3665643 TTTATACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTCTTTTCTTT
Found at i:3665696 original size:23 final size:23
Alignment explanation
Indices: 3665669--3665717 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
3665659 ACGAGATTTT
3665669 CTTATATGAGTCTTAAGGACCAA
1 CTTATATGAGTCTTAAGGACCAA
3665692 CTTATATGAGTCTTAAGGACCAA
1 CTTATATGAGTCTTAAGGACCAA
3665715 CTT
1 CTT
3665718 CAAGCTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (23 bp):
CTTATATGAGTCTTAAGGACCAA
Found at i:3666487 original size:25 final size:25
Alignment explanation
Indices: 3666453--3666516 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 25
3666443 TCTTTGAGTT
3666453 TTTCTTTTAAAGAATTTCTCTTGAG
1 TTTCTTTTAAAGAATTTCTCTTGAG
3666478 TTTCTTTTAAAGAATTTCTCTTGAG
1 TTTCTTTTAAAGAATTTCTCTTGAG
3666503 TTTCTTTTAGAAGA
1 TTTCTTTTA-AAGA
3666517 GTTTTAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 34 0.89
26 4 0.11
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTCTTTTAAAGAATTTCTCTTGAG
Found at i:3666721 original size:16 final size:15
Alignment explanation
Indices: 3666702--3666747 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
3666692 GTTCCAATAT
3666702 TTTATTTATTGTTATA
1 TTTATTTATT-TTATA
*
3666718 TTTATTTATCTTAGTA
1 TTTATTTATTTTA-TA
3666734 TTTATTTATTTTAT
1 TTTATTTATTTTAT
3666748 TTGACTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTATTTATTTTATA
Found at i:3666725 original size:20 final size:20
Alignment explanation
Indices: 3666699--3666749 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3666689 ATTGTTCCAA
* *
3666699 TATTTTATTTATTGTTATATT
1 TATTTTATTTAGTATT-TATT
3666720 TA-TTTATCTTAGTATTTATT
1 TATTTTAT-TTAGTATTTATT
3666740 TATTTTATTT
1 TATTTTATTT
3666750 GACTTGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (20 bp):
TATTTTATTTAGTATTTATT
Found at i:3668820 original size:42 final size:42
Alignment explanation
Indices: 3668682--3668865 Score: 216
Period size: 42 Copynumber: 4.4 Consensus size: 42
3668672 TTTAAACAGA
* * * *
3668682 TTCACCGGCACTT-AGCCTGCTAGGCTTAAAGCCTGAT-TCAG-
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATAT-TGT
* * * *
3668723 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATATTGT
3668764 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
3668806 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* *
3668848 TTCACTGGCAATAAGCCT
1 TTCACCGGCATTAAGCCT
3668866 ACGACGCGCT
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
40 3 0.02
41 61 0.48
42 62 0.49
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:3669832 original size:9 final size:9
Alignment explanation
Indices: 3669813--3669891 Score: 88
Period size: 9 Copynumber: 8.6 Consensus size: 9
3669803 TTTGGTTAAA
*
3669813 AATTGCCCG
1 AATTACCCG
*
3669822 AAATACCCG
1 AATTACCCG
*
3669831 AAATA-CCG
1 AATTACCCG
*
3669839 TAATTACCAG
1 -AATTACCCG
3669849 AATTACCCG
1 AATTACCCG
3669858 AATTACCCG
1 AATTACCCG
3669867 AAAATTACCCG
1 --AATTACCCG
3669878 AATTACCCG
1 AATTACCCG
3669887 AATTA
1 AATTA
3669892 AATCACTACA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
8 3 0.05
9 47 0.77
10 2 0.03
11 9 0.15
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:3669874 original size:20 final size:20
Alignment explanation
Indices: 3669811--3669888 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
3669801 TATTTGGTTA
* *
3669811 AAAATTGCCCGAAATACCCG
1 AAAATTACCCGAATTACCCG
3669831 -AAA-TA-CCGTAATTA-CC-
1 AAAATTACCCG-AATTACCCG
*
3669847 AGAATTACCCGAATTACCCG
1 AAAATTACCCGAATTACCCG
3669867 AAAATTACCCGAATTACCCG
1 AAAATTACCCGAATTACCCG
3669887 AA
1 AA
3669889 TTAAATCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.15
18 12 0.25
19 8 0.17
20 21 0.44
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (20 bp):
AAAATTACCCGAATTACCCG
Found at i:3669881 original size:29 final size:28
Alignment explanation
Indices: 3669811--3669891 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
3669801 TATTTGGTTA
* * *
3669811 AAAATTGCCCGAAATACCCGAAATACCG
1 AAAATTACCCGAATTACCCGAATTACCG
* *
3669839 -TAATTACCAGAATTACCCGAATTACCCG
1 AAAATTACCCGAATTACCCGAATTA-CCG
3669867 AAAATTACCCGAATTACCCGAATTA
1 AAAATTACCCGAATTACCCGAATTA
3669892 AATCACTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 19 0.43
28 3 0.07
29 22 0.50
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (28 bp):
AAAATTACCCGAATTACCCGAATTACCG
Found at i:3669920 original size:17 final size:17
Alignment explanation
Indices: 3669898--3670032 Score: 63
Period size: 17 Copynumber: 7.4 Consensus size: 17
3669888 ATTAAATCAC
3669898 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
3669915 TACATAAATCTTTGAATCAC
1 TACAT-AAT-TAAAAAT-AT
3669935 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
* *** *
3669952 TAAATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
3669972 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
3669989 TACATAAGTCTTTGAATCAA
1 TACATAA-T-TAAAAAT-AT
*
3670009 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
3670026 TACATAA
1 TACATAA
3670033 GTCTTGAATT
Statistics
Matches: 82, Mismatches: 27, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
17 28 0.34
18 16 0.20
19 17 0.21
20 21 0.26
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:3669938 original size:37 final size:37
Alignment explanation
Indices: 3669892--3670057 Score: 264
Period size: 37 Copynumber: 4.5 Consensus size: 37
3669882 ACCCGAATTA
*
3669892 AATCACTACATAATTAAAAATATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
3669929 AATCACTACATAATTAAAAATATTAAATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
3669966 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
* *
3670003 AATCAATACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
3670039 AATTAAC-ACATAATTAAAA
1 AA-TCACTACATAATTAAAA
3670058 TATAAGTCTT
Statistics
Matches: 121, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
36 17 0.14
37 104 0.86
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:3670014 original size:20 final size:20
Alignment explanation
Indices: 3669955--3670015 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
3669945 AAAATATTAA
*
3669955 ATAAGTCTTTGAATCACTAC
1 ATAAGTCTTTGAATCAATAC
*** *
3669975 ATAA-T-TAAAAAT-ATTAC
1 ATAAGTCTTTGAATCAATAC
3669992 ATAAGTCTTTGAATCAATAC
1 ATAAGTCTTTGAATCAATAC
3670012 ATAA
1 ATAA
3670016 TTAAAAACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 8 0.27
18 5 0.17
19 5 0.17
20 12 0.40
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (20 bp):
ATAAGTCTTTGAATCAATAC
Found at i:3672479 original size:20 final size:20
Alignment explanation
Indices: 3672454--3672495 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3672444 TTCTGCAAGA
3672454 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
3672474 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
3672494 AA
1 AA
3672496 TCAGCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGTATATAATAAATT
Found at i:3675787 original size:20 final size:20
Alignment explanation
Indices: 3675762--3675803 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3675752 TTCTGCAAGA
3675762 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
3675782 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
3675802 AA
1 AA
3675804 TCAGCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGTATATAATAAATT
Found at i:3677824 original size:4 final size:4
Alignment explanation
Indices: 3677815--3677852 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
3677805 TATACAATAG
3677815 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
3677853 TGATTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3703270 original size:21 final size:21
Alignment explanation
Indices: 3703256--3703313 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3703246 CAACACACTA
*
3703256 AGATTCATCCACAACAAAGCT
1 AGATGCATCCACAACAAAGCT
* *
3703277 AGATGCATCCACATCAGAATC-
1 AGATGCATCCACAACA-AAGCT
*
3703298 AGATGCAACCACAACA
1 AGATGCATCCACAACA
3703314 CTCTTTAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16
Consensus pattern (21 bp):
AGATGCATCCACAACAAAGCT
Found at i:3711738 original size:25 final size:25
Alignment explanation
Indices: 3711696--3711792 Score: 117
Period size: 25 Copynumber: 3.9 Consensus size: 25
3711686 GCCATANTAT
* * *
3711696 GAGCTAAGTAACGAGAAGCTCATAC
1 GAGCTAAATATCGGGAAGCTCATAC
*
3711721 GAG-TCATATATCGGGAAGCTCATAC
1 GAGCT-AAATATCGGGAAGCTCATAC
*
3711746 GAGCTAGAA-ATCGGGAAGCTCATAT
1 GAGCTA-AATATCGGGAAGCTCATAC
3711771 GAGCTAAATATCGGGAAGCTCA
1 GAGCTAAATATCGGGAAGCTCA
3711793 AGAGAGTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
24 3 0.05
25 57 0.92
26 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (25 bp):
GAGCTAAATATCGGGAAGCTCATAC
Found at i:3715384 original size:15 final size:15
Alignment explanation
Indices: 3715364--3715397 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3715354 GTGTGATACT
3715364 ATATACCATAAAATA
1 ATATACCATAAAATA
3715379 ATATACCATAAAATA
1 ATATACCATAAAATA
3715394 ATAT
1 ATAT
3715398 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATACCATAAAATA
Found at i:3742641 original size:31 final size:31
Alignment explanation
Indices: 3742567--3742632 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3742557 TAAAATGGTC
*
3742567 ATTG-AATATTCGAAAGTTTTTATTCAAGTA
1 ATTGAAATATTCAAAAGTTTTTATTCAAGTA
* *
3742597 ATTGAAATATTCAAAAGTTTTTATTTAAGTC
1 ATTGAAATATTCAAAAGTTTTTATTCAAGTA
3742628 ATTGA
1 ATTGA
3742633 GCTGTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTGAAATATTCAAAAGTTTTTATTCAAGTA
Found at i:3760824 original size:27 final size:27
Alignment explanation
Indices: 3760794--3760866 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 27
3760784 TGGCTTGAAT
3760794 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
3760821 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
3760853 TTGTTGGATATTGA
1 TTGTTAGATATTGA
3760867 AATGATTGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 14 0.35
32 26 0.65
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:3760843 original size:32 final size:32
Alignment explanation
Indices: 3760807--3760867 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
3760797 TTAGATATTG
3760807 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
*
3760839 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
3760868 ATGATTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:3770665 original size:6 final size:6
Alignment explanation
Indices: 3770654--3770727 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
3770644 GGGATCACTA
3770654 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
3770697 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
3770728 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:3770671 original size:5 final size:5
Alignment explanation
Indices: 3770651--3770712 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
3770641 GCCGGGATCA
3770651 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
3770697 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
3770713 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:3770689 original size:11 final size:11
Alignment explanation
Indices: 3770650--3770726 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
3770640 AGCCGGGATC
3770650 ACTAA-CTAAT
1 ACTAATCTAAT
3770660 ACTAATCTAAT
1 ACTAATCTAAT
3770671 -CTAA-CTAAT
1 ACTAATCTAAT
3770680 ACTAATCTAAT
1 ACTAATCTAAT
**
3770691 ACTAATAGAAT
1 ACTAATCTAAT
3770702 ACTAATCTAAT
1 ACTAATCTAAT
3770713 AC---TCTAAT
1 ACTAATCTAAT
3770721 ACTAAT
1 ACTAAT
3770727 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:3770705 original size:22 final size:21
Alignment explanation
Indices: 3770650--3770726 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
3770640 AGCCGGGATC
3770650 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
3770671 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
3770691 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
3770713 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
3770727 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:3770741 original size:14 final size:14
Alignment explanation
Indices: 3770724--3770751 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3770714 CTCTAATACT
3770724 AATAGAATAGAAAA
1 AATAGAATAGAAAA
3770738 AATAGAATAGAAAA
1 AATAGAATAGAAAA
3770752 TACTAATATA
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:3774135 original size:46 final size:46
Alignment explanation
Indices: 3774083--3774173 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
3774073 TGATAAAAGT
3774083 TAGTTTTCTTAATTTTGAAATAAAATTAAATCAAAGTTAAATAAAC
1 TAGTTTTCTTAATTTTGAAATAAAATTAAATCAAAGTTAAATAAAC
*
3774129 TAGTTTTCTTAATTTTGAAATAAAATTAAATCAAATTTAAATAAA
1 TAGTTTTCTTAATTTTGAAATAAAATTAAATCAAAGTTAAATAAA
3774174 TTATTTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (46 bp):
TAGTTTTCTTAATTTTGAAATAAAATTAAATCAAAGTTAAATAAAC
Found at i:3774890 original size:20 final size:20
Alignment explanation
Indices: 3774842--3774895 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
3774832 TATTATTATT
3774842 TCAGAAAATAGAATTTATAC
1 TCAGAAAATAGAATTTATAC
3774862 TC-GAAAAATAGAATTTATAC
1 TCAG-AAAATAGAATTTATAC
3774882 TCAGAAAATA-AATT
1 TCAGAAAATAGAATT
3774896 CTCACTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 26 0.81
21 1 0.03
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (20 bp):
TCAGAAAATAGAATTTATAC
Found at i:3778895 original size:15 final size:16
Alignment explanation
Indices: 3778877--3778917 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
3778867 TGGGTTATTT
3778877 AATT-TAATAAATTCG
1 AATTATAATAAATTCG
3778892 AATTATATAATAAATTCG
1 AA-T-TATAATAAATTCG
3778910 AATTATAA
1 AATTATAA
3778918 ACTTTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 6 0.26
17 2 0.09
18 13 0.57
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (16 bp):
AATTATAATAAATTCG
Found at i:3778904 original size:18 final size:18
Alignment explanation
Indices: 3778881--3778916 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3778871 TTATTTAATT
3778881 TAATAAATTCGAATTATA
1 TAATAAATTCGAATTATA
3778899 TAATAAATTCGAATTATA
1 TAATAAATTCGAATTATA
3778917 AACTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
TAATAAATTCGAATTATA
Found at i:3779319 original size:3 final size:3
Alignment explanation
Indices: 3779311--3779345 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3779301 TCGCTCTTCC
3779311 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3779346 ATTTTAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3784925 original size:318 final size:318
Alignment explanation
Indices: 3784348--3784985 Score: 949
Period size: 318 Copynumber: 2.0 Consensus size: 318
3784338 GTAATTAAAC
*
3784348 TTGAAAATTAGACTTGAGATCATAAATTGGGTACGAGAGCCTAAAACTGAGACCAAGACCCAAAA
1 TTGAAAATTAGACTTGAGATCATAAATTGGGCACGAGAGCCTAAAACTGAGACCAAGACCCAAAA
* * * * *
3784413 ACTGGTTGAATTGGGCCTAGTATGTGAAATTAGGTCGACAATCCAACCGGTGGTTAGACCGGACC
66 ACTGATTAAATAGGCCCTAGTATGTGAAATTAGGTCGACAATCCAACCGGTGGCTAGACCGGACC
* * * * * * *
3784478 GATTGGGTCGTCATTGACCGGTACCAAATCGATAGTAATTGAACTTGTTTGGGGTGCCGTAAAAG
131 GATTGGGTCATCACTGACCGGTACCAAATCGATAGTAACTAAACTGGTTTGAGGTACCGTAAAAG
* * *
3784543 TGTCACAGCTGTATCACTAGACACAGCGGCTGCGACGACGGCGTTCCGGTGGCTGGCGGTGGTTG
196 TGTCACACCTGTATCACTAGACACAGCGACTGCGACGACGGCGTTCCGGTGGCTGGCAGTGGTTG
* * *
3784608 ATATTCGGTGGTTGAGCAGTGGAATAGTTACACTCCTATAGGGACTCTACCAGAAAAT
261 ATATTCGGTGGTTGAGCAGTGGAAGAGTTACACTCCCATAGGGACTCTAACAGAAAAT
*
3784666 TTGAAAATTGGACTTGAGATCATAAATTGGGCACGAGAGCCTAAAACTGAGACCAAGACCCAAAA
1 TTGAAAATTAGACTTGAGATCATAAATTGGGCACGAGAGCCTAAAACTGAGACCAAGACCCAAAA
3784731 ACTGATTAAATCAGGCCCT-GTATGTGAAATT-GAGTCGACAATCCAACCGGTGGCTAGACCGGA
66 ACTGATTAAAT-AGGCCCTAGTATGTGAAATTAG-GTCGACAATCCAACCGGTGGCTAGACCGGA
* *
3784794 CCGATTGGGTCATCACTGACCCGG-ACCGAATCGATAGTAACTAAACTGGTTTGAGGTACTGTAA
129 CCGATTGGGTCATCACTGA-CCGGTACCAAATCGATAGTAACTAAACTGGTTTGAGGTACCGTAA
** * * * * * *
3784858 AAGTGTTGCACCTGTATCACTAGACACGGCGATTGCGGCGACGGTGTTTCGGTGGTTGGCAGTGG
193 AAGTGTCACACCTGTATCACTAGACACAGCGACTGCGACGACGGCGTTCCGGTGGCTGGCAGTGG
*
3784923 TTGATATTCGGTGGTTGAGCAGTGGAAGAGTTACACTCCCATAGGGACTTTAACAGAAAAT
258 TTGATATTCGGTGGTTGAGCAGTGGAAGAGTTACACTCCCATAGGGACTCTAACAGAAAAT
3784984 TT
1 TT
3784986 TATTAATTTG
Statistics
Matches: 286, Mismatches: 31, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
317 1 0.00
318 276 0.97
319 9 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (318 bp):
TTGAAAATTAGACTTGAGATCATAAATTGGGCACGAGAGCCTAAAACTGAGACCAAGACCCAAAA
ACTGATTAAATAGGCCCTAGTATGTGAAATTAGGTCGACAATCCAACCGGTGGCTAGACCGGACC
GATTGGGTCATCACTGACCGGTACCAAATCGATAGTAACTAAACTGGTTTGAGGTACCGTAAAAG
TGTCACACCTGTATCACTAGACACAGCGACTGCGACGACGGCGTTCCGGTGGCTGGCAGTGGTTG
ATATTCGGTGGTTGAGCAGTGGAAGAGTTACACTCCCATAGGGACTCTAACAGAAAAT
Found at i:3786077 original size:24 final size:24
Alignment explanation
Indices: 3786035--3786090 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3786025 ACCTATCTCA
*
3786035 TTATATATATCTATTTTAT-AAATGT
1 TTATA-ATATCTATATTATGAAAT-T
* *
3786060 TTATAATATTTATATTATGTAATT
1 TTATAATATCTATATTATGAAATT
3786084 TTATAAT
1 TTATAAT
3786091 TGTGATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATAATATCTATATTATGAAATT
Done.