Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 101 of 218
Found at i:29239979 original size:31 final size:31
Alignment explanation
Indices: 29239944--29240020 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
29239934 TAACCCCATG
* *
29239944 GAGAAAATCAAGGGAACTACCAACCAGCCTA
1 GAGAAAATCAAGGAAACCACCAACCAGCCTA
* **
29239975 GAGAAAATTAAGGAAACCACTTACCAGCCTA
1 GAGAAAATCAAGGAAACCACCAACCAGCCTA
*
29240006 GAGAAATTCAAGGAA
1 GAGAAAATCAAGGAA
29240021 CCGACGCTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (31 bp):
GAGAAAATCAAGGAAACCACCAACCAGCCTA
Found at i:29244538 original size:38 final size:38
Alignment explanation
Indices: 29244482--29244564 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
29244472 ATTTAACTAT
* *
29244482 TCAACCAATATGCAATATAGGCACCTCAAACACATAAA
1 TCAAGCAATATGCAATATAGGCACCCCAAACACATAAA
29244520 TCAAGCAATATGCAATATAGGCACCCCAAACACATAAA
1 TCAAGCAATATGCAATATAGGCACCCCAAACACATAAA
29244558 TCAAGCA
1 TCAAGCA
29244565 TACCTAAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.47, C:0.27, G:0.10, T:0.17
Consensus pattern (38 bp):
TCAAGCAATATGCAATATAGGCACCCCAAACACATAAA
Found at i:29264638 original size:21 final size:21
Alignment explanation
Indices: 29264612--29264662 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
29264602 ATAATTAGGT
29264612 TCAAGTGGTATGACCCTAAAG
1 TCAAGTGGTATGACCCTAAAG
*
29264633 TCAAGTGATATGACCCTAAAG
1 TCAAGTGGTATGACCCTAAAG
29264654 TCAAGTGGT
1 TCAAGTGGT
29264663 TTTAGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (21 bp):
TCAAGTGGTATGACCCTAAAG
Found at i:29267109 original size:39 final size:39
Alignment explanation
Indices: 29267066--29267156 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
29267056 ATGGCTCAAA
* *
29267066 TGGCATGTTTTGTGATGGAAGTGTTAGTGGTCATAATTG
1 TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
*
29267105 TGGCATGTTTTGTGATGAAAGTGTTAATTGTCATAATTG
1 TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
29267144 TGGCATGTTTTGT
1 TGGCATGTTTTGT
29267157 TAGAAGTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (39 bp):
TGGCATGTTTTGTGATGAAAGTGTTAATGGTCATAATTG
Found at i:29271706 original size:14 final size:15
Alignment explanation
Indices: 29271680--29271708 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29271670 TTATACAAGG
29271680 TTAAAAATGATTTTT
1 TTAAAAATGATTTTT
29271695 TTAAAAAT-ATTTTT
1 TTAAAAATGATTTTT
29271709 AAATTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAAAAATGATTTTT
Found at i:29278348 original size:41 final size:41
Alignment explanation
Indices: 29278188--29278353 Score: 163
Period size: 41 Copynumber: 4.0 Consensus size: 41
29278178 CGTGCCTCTA
* * * * *
29278188 TTTGTACTTCGATACCCCTAAATTGTAGATACGTG-CCATTG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCA-TG
* * * *
29278229 TTTGTACTTTGGTACCCCTAAATAGCACATACGTGCCCCTA
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
* * * * *
29278270 TTTATACTTCAGTACCCCTGAATCGCACATGCATGCCCATG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
* * *
29278311 TTTGTACTTCGGCACCCTTGAATAGCACATACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
29278352 TT
1 TT
29278354 AACACTCTGG
Statistics
Matches: 100, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 98 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (41 bp):
TTTGTACTTCGGTACCCCTGAATAGCACATACGTGCCCATG
Found at i:29278601 original size:14 final size:14
Alignment explanation
Indices: 29278582--29278609 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29278572 TGTGGCTATA
29278582 TAGGTTGTTATAGT
1 TAGGTTGTTATAGT
29278596 TAGGTTGTTATAGT
1 TAGGTTGTTATAGT
29278610 ACATTAAGAC
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:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TAGGTTGTTATAGT
Found at i:29290941 original size:50 final size:50
Alignment explanation
Indices: 29290879--29291163 Score: 435
Period size: 50 Copynumber: 5.7 Consensus size: 50
29290869 AATATGTGAG
*
29290879 CCATGTAAGACCATGTCTGGGACATTGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* *
29290929 CCTTGTAAGACCATGTCTGGGACTTGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
29290979 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* *
29291029 CCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
** * * * **
29291079 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
* * *
29291129 CCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
29291164 GTACAGAAAA
Statistics
Matches: 216, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 216 1.00
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
Found at i:29291199 original size:49 final size:49
Alignment explanation
Indices: 29290879--29291212 Score: 258
Period size: 50 Copynumber: 6.7 Consensus size: 49
29290869 AATATGTGAG
* * * * * **
29290879 CCATGTAAGACCATGTCTGGGACATTGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAAAACTC
* * * * * * **
29290929 CCTTGTAAGACCATGTCTGGGACTTGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAAAACTC
* * * * **
29290979 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAAAACTC
* * * * **
29291029 CCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAAAACTC
** * * *
29291079 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATAAGAAAACTC
* *
29291129 CCATGTAAGACCATATCTGGGATATGGCATTGGCA-G-TACAGAAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATA-AGAAAAC-TC
* * *
29291178 CTATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29291213 TGTTATTTTC
Statistics
Matches: 256, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
47 2 0.01
48 6 0.02
49 32 0.12
50 216 0.84
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATAAGAAAACTC
Found at i:29297036 original size:18 final size:19
Alignment explanation
Indices: 29296993--29297057 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
29296983 CTTAAAAGAT
* *
29296993 TATTTTTTATAATTTTTAA
1 TATTTTTTACAACTTTTAA
29297012 GTA--TTTTACAA-TTTTAA
1 -TATTTTTTACAACTTTTAA
*
29297029 TATTTTTTGCAACTCTTTAA
1 TATTTTTTACAACT-TTTAA
29297049 TATTTTTTA
1 TATTTTTTA
29297058 TTTCTTTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.05
17 6 0.16
18 14 0.37
19 1 0.03
20 15 0.39
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTTTTTACAACTTTTAA
Found at i:29298279 original size:13 final size:13
Alignment explanation
Indices: 29298261--29298285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29298251 TCTACTTTAT
29298261 TTTGAGATAATTA
1 TTTGAGATAATTA
29298274 TTTGAGATAATT
1 TTTGAGATAATT
29298286 CAAGAAGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTGAGATAATTA
Found at i:29301009 original size:32 final size:32
Alignment explanation
Indices: 29300966--29301131 Score: 152
Period size: 32 Copynumber: 5.2 Consensus size: 32
29300956 TAATGTGATT
* *
29300966 GGCACAAAGCCATCAGTAGTAGTGATATGGCC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
29300998 GGCACACAGCCATTAGTAACGGTAACATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* *
29301030 GGTACAAAGCCATCAGTAGCAGTGATATGACT
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
29301062 GGCACACAGCCATCAGCAACGGTAACATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* *
29301094 GGCACAAAGCCATTAGTAGCAGTGATATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
29301126 GGCACA
1 GGCACA
29301132 CAGTCATACC
Statistics
Matches: 100, Mismatches: 34, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 100 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAGCAGTGATATGACC
Found at i:29301042 original size:64 final size:64
Alignment explanation
Indices: 29300961--29301134 Score: 267
Period size: 64 Copynumber: 2.7 Consensus size: 64
29300951 TACAGTAATG
* * * * *
29300961 TGATTGGCACAAAGCCATCAGTAGTAGTGATATGGCCGGCACACAGCCATTAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
* *
29301025 TGATCGGTACAAAGCCATCAGTAGCAGTGATATGACTGGCACACAGCCATCAGCAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
* *
29301089 TGATCGGCACAAAGCCATTAGTAGCAGTGATATGATCGGCACACAG
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAG
29301135 TCATACCAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 99 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (64 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACACAGCCATCAGCAACGGTAACA
Found at i:29301265 original size:27 final size:27
Alignment explanation
Indices: 29301212--29301441 Score: 304
Period size: 27 Copynumber: 8.6 Consensus size: 27
29301202 AAATTAGTCA
* *
29301212 TTTACCC-ACCAGGGCATTACGGTCAT
1 TTTACCCTACAAGGGCATTACGATCAT
* *
29301238 TTTACCCTACAGGGGTATTACGATCAT
1 TTTACCCTACAAGGGCATTACGATCAT
* *
29301265 TTTACCCTACAGGGGCATTACGATTAT
1 TTTACCCTACAAGGGCATTACGATCAT
*
29301292 TTTTCCCTACAAGGGCATTACGATCAT
1 TTTACCCTACAAGGGCATTACGATCAT
* *
29301319 TTGACCCTACAGGGGCATTACGATCAT
1 TTTACCCTACAAGGGCATTACGATCAT
29301346 TTTACCCTACAAGGGCATTAC-AGTCAT
1 TTTACCCTACAAGGGCATTACGA-TCAT
*
29301373 TTTACCCTACAAGGGCATTACAATCAT
1 TTTACCCTACAAGGGCATTACGATCAT
* * *
29301400 TTTACCCTATAAGGGCATTACGGTTAT
1 TTTACCCTACAAGGGCATTACGATCAT
29301427 TTTATCCC-ACAAGGG
1 TTTA-CCCTACAAGGG
29301442 TATTTCAATA
Statistics
Matches: 181, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
26 8 0.04
27 169 0.93
28 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (27 bp):
TTTACCCTACAAGGGCATTACGATCAT
Found at i:29301496 original size:27 final size:27
Alignment explanation
Indices: 29301342--29301591 Score: 162
Period size: 27 Copynumber: 9.4 Consensus size: 27
29301332 GGCATTACGA
* *
29301342 TCATTTTACCCTA-CAAGGGCATTACAG
1 TCATTTTA-CCTATCAAGGGTATTTCAG
* * *
29301369 TCATTTTACCCTA-CAAGGGCATTACAA
1 TCATTTTA-CCTATCAAGGGTATTTCAG
* * *
29301396 TCATTTTACCCTAT-AAGGGCATTACGG
1 TCATTTTA-CCTATCAAGGGTATTTCAG
* * *
29301423 TTATTTTATCCCA-CAAGGGTATTTCAA
1 TCATTTTA-CCTATCAAGGGTATTTCAG
* ** *
29301450 T-ATTCTACCCTA-CGGGGGTATTTTAG
1 TCATTTTA-CCTATCAAGGGTATTTCAG
*
29301476 TCATTTTATCCTA-CGAA-GGTATTTCGG
1 TCATTTTA-CCTATC-AAGGGTATTTCAG
* *
29301503 T-ATTCTACCCTA-C-TGGGTATTTCAG
1 TCATTTTA-CCTATCAAGGGTATTTCAG
*
29301528 TCATTTTACCTATCAATGGTATTTCAG
1 TCATTTTACCTATCAAGGGTATTTCAG
* *
29301555 TTATTTTACCTATCAAGGGTATTTCGG
1 TCATTTTACCTATCAAGGGTATTTCAG
29301582 TCATTTTACC
1 TCATTTTACC
29301592 CTTCGGGGTA
Statistics
Matches: 181, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
25 14 0.08
26 35 0.19
27 132 0.73
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (27 bp):
TCATTTTACCTATCAAGGGTATTTCAG
Found at i:29304892 original size:16 final size:16
Alignment explanation
Indices: 29304871--29304904 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29304861 AATTATTGAA
29304871 TATATTGTAATTAATG
1 TATATTGTAATTAATG
29304887 TATATTGTAATTAATG
1 TATATTGTAATTAATG
29304903 TA
1 TA
29304905 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATTGTAATTAATG
Found at i:29308198 original size:24 final size:24
Alignment explanation
Indices: 29308143--29308201 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
29308133 GGTTTAATGC
* *
29308143 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
29308167 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
29308191 AAATGGATATA
1 AAATGGATATA
29308202 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:29308293 original size:37 final size:37
Alignment explanation
Indices: 29308242--29308354 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
29308232 TTATGTGTTA
*
29308242 ATTC-AAGACTTATGTAATATTTTTAACTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
29308278 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
29308315 ATTCAAATATTTATGTAATTTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
29308352 ATT
1 ATT
29308355 TAATTCGGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 4 0.06
37 68 0.94
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:29308369 original size:9 final size:9
Alignment explanation
Indices: 29308355--29308489 Score: 153
Period size: 9 Copynumber: 14.3 Consensus size: 9
29308345 TGTAGTGATT
29308355 TAATTCGGG
1 TAATTCGGG
29308364 TAATTCGGG
1 TAATTCGGG
*
29308373 TAATTTGGG
1 TAATTCGGG
*
29308382 TAATTTTTGGG
1 TAA--TTCGGG
29308393 TAATTCGGG
1 TAATTCGGG
*
29308402 TAATTTGGG
1 TAATTCGGG
29308411 TAATTTTCGGG
1 TAA--TTCGGG
*
29308422 TAATTCAGG
1 TAATTCGGG
29308431 TAATTTTCGGG
1 TAA--TTCGGG
29308442 TAATTCGGG
1 TAATTCGGG
29308451 TAATTCGGG
1 TAATTCGGG
*
29308460 TAAGTCGGG
1 TAATTCGGG
*
29308469 TAAGTCGGG
1 TAATTCGGG
*
29308478 TAAGTCGGG
1 TAATTCGGG
29308487 TAA
1 TAA
29308490 ATTTTAACCA
Statistics
Matches: 113, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
9 88 0.78
11 25 0.22
ACGTcount: A:0.23, C:0.08, G:0.33, T:0.36
Consensus pattern (9 bp):
TAATTCGGG
Found at i:29308395 original size:20 final size:20
Alignment explanation
Indices: 29308358--29308494 Score: 137
Period size: 20 Copynumber: 7.1 Consensus size: 20
29308348 AGTGATTTAA
29308358 TTCGGGTAATTCGGGTAA-T
1 TTCGGGTAATTCGGGTAATT
*
29308377 TT-GGGTAATTTTTGGGTAA--
1 TTCGGGTAA--TTCGGGTAATT
*
29308396 TTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATT
*
29308416 TTCGGGTAATTCAGGTAATT
1 TTCGGGTAATTCGGGTAATT
29308436 TTCGGGTAATTCGGGTAA--
1 TTCGGGTAATTCGGGTAATT
*
29308454 TTCGGGTAAGTCGGGTAA--
1 TTCGGGTAATTCGGGTAATT
* *
29308472 GTCGGGTAAGTCGGGTAAATT
1 TTCGGGTAATTCGGGT-AATT
29308493 TT
1 TT
29308495 AACCAGAAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
18 47 0.46
19 6 0.06
20 49 0.48
21 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.38
Consensus pattern (20 bp):
TTCGGGTAATTCGGGTAATT
Found at i:29308395 original size:29 final size:29
Alignment explanation
Indices: 29308358--29308489 Score: 164
Period size: 29 Copynumber: 4.6 Consensus size: 29
29308348 AGTGATTTAA
29308358 TTCGGGTAATTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
*
29308387 TTTGGGTAATTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
*
29308416 TTCGGGTAATTCAGGTAATTTTCGGGTAA--
1 TTCGGGTAATTCGGGTAA-TTT-GGGTAATT
* *
29308445 TTCGGGTAATTCGGGTAAGTCGGGTAA--
1 TTCGGGTAATTCGGGTAATTTGGGTAATT
* *
29308472 GTCGGGTAAGTCGGGTAA
1 TTCGGGTAATTCGGGTAA
29308490 ATTTTAACCA
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
27 22 0.24
28 1 0.01
29 61 0.66
30 3 0.03
31 6 0.06
ACGTcount: A:0.22, C:0.08, G:0.33, T:0.36
Consensus pattern (29 bp):
TTCGGGTAATTCGGGTAATTTGGGTAATT
Found at i:29312140 original size:73 final size:72
Alignment explanation
Indices: 29311996--29312141 Score: 179
Period size: 73 Copynumber: 2.0 Consensus size: 72
29311986 TGAAATCAAT
* **
29311996 ATTTTTATCTATAAGTATGATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTGGTA
1 ATTTTTATCTATAAGTATAATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTACTA
29312061 AAATTAA
66 AAATTAA
* * * *
29312068 ATTTCTTATTTATAAGTATAAT-AAATTTTCTTATTAAGTAAATTTATTTATA-CAAATATTTTA
1 ATTT-TTATCTATAAGTATAATAAAAATTT-TTATCAAATAAATTTATTTA-ACCAAATATTTTA
*
29312131 CTAACATTAA
63 CTAAAATTAA
29312141 A
1 A
29312142 ATTATCATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
72 10 0.16
73 52 0.83
74 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (72 bp):
ATTTTTATCTATAAGTATAATAAAAATTTTTATCAAATAAATTTATTTAACCAAATATTTTACTA
AAATTAA
Found at i:29312804 original size:17 final size:17
Alignment explanation
Indices: 29312782--29312822 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
29312772 TTATATTATT
29312782 AAAATATTAATTGTATA
1 AAAATATTAATTGTATA
29312799 AAAATATTAATTGTATA
1 AAAATATTAATTGTATA
29312816 AAAATAT
1 AAAATAT
29312823 AAGCAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
AAAATATTAATTGTATA
Found at i:29313242 original size:20 final size:20
Alignment explanation
Indices: 29313217--29313254 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29313207 TCCTCTTTCA
29313217 ATCTGTTT-TAATATAATTGG
1 ATCTGTTTGTAAT-TAATTGG
29313237 ATCTGTTTGTAATTAATT
1 ATCTGTTTGTAATTAATT
29313255 TAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
ATCTGTTTGTAATTAATTGG
Found at i:29317589 original size:34 final size:35
Alignment explanation
Indices: 29317545--29317611 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
29317535 TAGTAAAATA
29317545 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
29317579 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
29317612 CTGATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:29332959 original size:42 final size:43
Alignment explanation
Indices: 29332895--29333017 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 43
29332885 TGATTTGAGA
*
29332895 ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA-TG
1 ATTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTATAGTG
** * *
29332937 ATTTTGTGTAAGACCCTGTCTGGGATAGTGGCATCG-ATAGTTG
1 ATTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTATAG-TG
* * *
29332980 ATTACATGTAAGACCAC-GTCTGGAACGTTGGCATCGTA
1 ATTACGTGTAAGACC-CTGTCTGGGACATTGGCATCGTA
29333018 CGAGCTTTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
41 3 0.05
42 31 0.48
43 29 0.45
44 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
ATTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTATAGTG
Found at i:29335059 original size:28 final size:26
Alignment explanation
Indices: 29335001--29335071 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
29334991 TAATCAAAAT
*
29335001 TTATTATAA-AATTAAGTAAAATTCA
1 TTATTTTAATAATTAAGTAAAATTCA
**
29335026 AAATTTTAATAATTGAAGTAAAATTTCA
1 TTATTTTAATAATT-AAGTAAAA-TTCA
29335054 TTATTTTATAATAATTAA
1 TTA-TTT-TAATAATTAA
29335072 ATATTTTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 6 0.17
26 4 0.11
27 8 0.22
28 5 0.14
29 5 0.14
30 8 0.22
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (26 bp):
TTATTTTAATAATTAAGTAAAATTCA
Found at i:29353437 original size:27 final size:27
Alignment explanation
Indices: 29353410--29353480 Score: 96
Period size: 25 Copynumber: 2.8 Consensus size: 27
29353400 GCGGGCCAAT
29353410 TTTCACAACTCGTGTGAGCATTC-GAA
1 TTTCACAACTCGTGTGAGCATTCTGAA
* *
29353436 -TTCATAGCTCGTGTGAGCATTCTG-A
1 TTTCACAACTCGTGTGAGCATTCTGAA
29353461 TTT-ACAACTCGTGTGAGCAT
1 TTTCACAACTCGTGTGAGCAT
29353481 ACATGTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 36 0.92
26 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
TTTCACAACTCGTGTGAGCATTCTGAA
Found at i:29355929 original size:21 final size:20
Alignment explanation
Indices: 29355905--29355943 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29355895 GGACTGAATT
* *
29355905 GAAAACATTCGAAACATTTAA
1 GAAAAAATTC-AAAAATTTAA
29355926 GAAAAAATTCAAAAATTT
1 GAAAAAATTCAAAAATTT
29355944 GAACTACAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
GAAAAAATTCAAAAATTTAA
Found at i:29357038 original size:41 final size:41
Alignment explanation
Indices: 29356977--29357246 Score: 309
Period size: 41 Copynumber: 6.6 Consensus size: 41
29356967 ATCAGAGTGT
*
29356977 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTTC
1 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTTC
* * **
29357018 AAATAGGGGCACGTATGTGCAATTC-AGGGTTGCTGAAGTTC
1 AAACAGGGGCACGTATGTGCAATTCAAGGG-TACCAAAGTTC
* * * * * *
29357059 AAAAAGGGGCACATATGTGTAATTTAAAGGTA-CAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTTC
* *
29357099 AAGA-A-GGGCACGTATGTGCAATTCAGGGGTACTAAA-TTAC
1 AA-ACAGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTT-C
29357139 AAACAGGGGCACGTATGTGCAATTC-AGAGGTACCAAAGTTC
1 AAACAGGGGCACGTATGTGCAATTCAAG-GGTACCAAAGTTC
* * *
29357180 AAACAGGGGCACGTGTGTGCAATTCAAAGGTACCAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTTC
*
29357221 AAACAGGGGCACGTATATGCAATTCA
1 AAACAGGGGCACGTATGTGCAATTCA
29357247 GGGAATAATT
Statistics
Matches: 193, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
39 23 0.12
40 20 0.10
41 144 0.75
42 6 0.03
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAAGGGTACCAAAGTTC
Found at i:29357209 original size:121 final size:123
Alignment explanation
Indices: 29356977--29357249 Score: 367
Period size: 121 Copynumber: 2.2 Consensus size: 123
29356967 ATCAGAGTGT
* * *
29356977 AAACAGGGGCACGTATGTGCAATTCAAGGGTACCGAAGTTCAAATAGGGGCACGTATGTGCAATT
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAATTCAAACAGGGGCACGTATGTGCAATT
* ** * *
29357042 CAGGGTTGCTGAAGTTCAAAAAGGGGCACATATGTGTAATTTAAAGGTA-CAAAGTAC
66 CAGGGTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTAC
*
29357099 AAGA-A-GGGCACGTATGTGCAATTCAGGGGTA-CTAAATTACAAACAGGGGCACGTATGTGCAA
1 AA-ACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAATT-CAAACAGGGGCACGTATGTGCAA
* * *
29357161 TTCAGAGG-TACCAAAGTTCAAACAGGGGCACGTGTGTGCAATTCAAAGGTACCAAAGTAC
64 TTCAG-GGTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTAC
*
29357221 AAACAGGGGCACGTATATGCAATTCAGGG
1 AAACAGGGGCACGTATGTGCAATTCAGGG
29357250 AATAATTAAC
Statistics
Matches: 132, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
120 5 0.04
121 88 0.67
122 16 0.12
123 23 0.17
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (123 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAATTCAAACAGGGGCACGTATGTGCAATT
CAGGGTTACCAAAGTTCAAAAAGGGGCACATATGTGCAATTCAAAGGTACCAAAGTAC
Found at i:29363177 original size:29 final size:28
Alignment explanation
Indices: 29363132--29363193 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
29363122 ATAGGGCCAT
* *
29363132 GTGTCACACATGGCTGAGTCACATGCCC
1 GTGTCACACACGACTGAGTCACATGCCC
*
29363160 GTGTCAACACACGACTGAGTCACATGCCT
1 GTGTC-ACACACGACTGAGTCACATGCCC
29363189 GTGTC
1 GTGTC
29363194 TCAGGCAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (28 bp):
GTGTCACACACGACTGAGTCACATGCCC
Found at i:29367600 original size:25 final size:24
Alignment explanation
Indices: 29367537--29367601 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
29367527 TTTTCTTAGT
*
29367537 TTTATTTTTATTTCTCATTTTTATC
1 TTTATTTTTATTT-TCATTTTAATC
* * * *
29367562 TTTGTCTATAATTTTGATTTTAATC
1 TTTAT-TTTTATTTTCATTTTAATC
29367587 TTTATTTTTGATTTT
1 TTTATTTTT-ATTTT
29367602 AATGTTAGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
24 2 0.07
25 22 0.73
26 6 0.20
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (24 bp):
TTTATTTTTATTTTCATTTTAATC
Found at i:29367613 original size:19 final size:19
Alignment explanation
Indices: 29367573--29367617 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
29367563 TTGTCTATAA
*
29367573 TTTTGATTTTAATCTTTAT
1 TTTTGATTTTAATCGTTAT
*
29367592 TTTTGATTTTAAT-GTTAG
1 TTTTGATTTTAATCGTTAT
29367610 TTTT-ATTT
1 TTTTGATTT
29367618 ATTTTAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 7 0.29
19 13 0.54
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTTGATTTTAATCGTTAT
Found at i:29379619 original size:115 final size:115
Alignment explanation
Indices: 29379417--29379760 Score: 593
Period size: 115 Copynumber: 3.0 Consensus size: 115
29379407 AATGCCTTAT
*
29379417 TGGCATATTGGTTGTG-TGGAATAATGGTATAGTGAATTGGTCATTTCAAGCATGTTTTGGTATG
1 TGGCATATTGGTTG-GATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATG
*
29379481 GTTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTAGGTACATGCTTGAAA
65 TTTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTAGGTACATGCTTGAAA
* *
29379532 TGGCATATTGATTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTAGGTATGT
1 TGGCATATTGGTTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
29379597 TTTGATGCTTTGCAA-AAGGGTGCAAATGGCTTGTAGGTACATGCTTGAAA
66 TTTGATGCTTTG-AACAAGGGTGCAAATGGCTTGTAGGTACATGCTTGAAA
* *
29379647 TTGTATATTGGTTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
1 TGGCATATTGGTTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
*
29379712 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTAGGTACAGGCTTGAA
66 TTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTAGGTACATGCTTGAA
29379761 TGGGTGATGG
Statistics
Matches: 217, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
114 3 0.01
115 212 0.98
116 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (115 bp):
TGGCATATTGGTTGGATGGAATAATGGTATAGTGAATTGGTCATTTCATGCATGTTTTGGTATGT
TTTGATGCTTTGAACAAGGGTGCAAATGGCTTGTAGGTACATGCTTGAAA
Found at i:29387158 original size:20 final size:20
Alignment explanation
Indices: 29387133--29387171 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29387123 CCCTTCCAAT
29387133 CTCTTCGTCTGCTTCTCCTC
1 CTCTTCGTCTGCTTCTCCTC
* *
29387153 CTCTTCTTCTTCTTCTCCT
1 CTCTTCGTCTGCTTCTCCT
29387172 TCTTCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.44, G:0.05, T:0.51
Consensus pattern (20 bp):
CTCTTCGTCTGCTTCTCCTC
Found at i:29387160 original size:3 final size:3
Alignment explanation
Indices: 29387154--29387203 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
29387144 CTTCTCCTCC
*
29387154 TCT TCT TCT TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
29387202 TC
1 TC
29387204 ACATAATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:29387286 original size:21 final size:21
Alignment explanation
Indices: 29387271--29387317 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
29387261 ATGGCTCCGT
29387271 GAAGAGCAACGCTGGCTAAGA
1 GAAGAGCAACGCTGGCTAAGA
*
29387292 GAAGAGCAGCGCTGGCTTAAAGA
1 GAAGAGCAACGCTGGC-T-AAGA
29387315 GAA
1 GAA
29387318 AGAATCGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.38, C:0.17, G:0.34, T:0.11
Consensus pattern (21 bp):
GAAGAGCAACGCTGGCTAAGA
Found at i:29388462 original size:26 final size:26
Alignment explanation
Indices: 29388432--29388481 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
29388422 AACTTGTTTA
29388432 TTGTTCCACTAATATATAATAAAACG
1 TTGTTCCACTAATATATAATAAAACG
29388458 TTGTTCCACTAATATATAATAAAA
1 TTGTTCCACTAATATATAATAAAA
29388482 TTATTATGGA
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:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (26 bp):
TTGTTCCACTAATATATAATAAAACG
Found at i:29388595 original size:6 final size:6
Alignment explanation
Indices: 29388584--29388608 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29388574 AGATATTATA
29388584 TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG T
29388609 TTATTTATTG
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:29390840 original size:15 final size:14
Alignment explanation
Indices: 29390815--29390878 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 14
29390805 ATAATATTTT
*
29390815 ATTTATTTTATAT-
1 ATTTATTTTTTATA
29390828 ATTTATTTTTTATAA
1 ATTTATTTTTTAT-A
29390843 ATTT-TTAATTTTA-A
1 ATTTATT--TTTTATA
29390857 ATTTATTTTTTTAATA
1 ATTTA-TTTTTT-ATA
29390873 ATTTAT
1 ATTTAT
29390879 ATAAGATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
13 12 0.29
14 11 0.26
15 6 0.14
16 13 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTATTTTTTATA
Found at i:29390974 original size:25 final size:26
Alignment explanation
Indices: 29390926--29390979 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29390916 TATTATAGGC
**
29390926 TTTTTATTTATTTATAATTGTATATA
1 TTTTTATAAATTTATAATTGTATATA
*
29390952 TTTTTATAAATTTGTAATT-TATATA
1 TTTTTATAAATTTATAATTGTATATA
29390977 TTT
1 TTT
29390980 AAAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTATAAATTTATAATTGTATATA
Found at i:29394050 original size:3 final size:3
Alignment explanation
Indices: 29394042--29394087 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29394032 TTTGAGACAT
29394042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29394088 CTTCTTTCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29394713 original size:144 final size:145
Alignment explanation
Indices: 29394522--29394809 Score: 352
Period size: 144 Copynumber: 2.0 Consensus size: 145
29394512 AAAAAGAGAA
* * *
29394522 AGTTTAGATTTTAAAAATAAAAATATGTTTTCTTTAGTCATTTTAAAGGAAA-GTTTA-AAATTT
1 AGTTTAGATTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAATGTGTAGAAATTT
* *
29394585 TAAAGCAAAGTTTTAATTTTTTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAAATA
66 TAAAACAAAGTTTTAA-TCTTTTTCAACTATTTCAAAAT-AAAACTTTGATCTTTAAGAAAAATA
*
29394650 GT-ATTTTTTTTAAAGAG
129 GTGA-TTTTGTTAAAGAG
* * **
29394667 AGTTTAGATTTTTTAAAATAAAAATCT-ATTT-TTTAGTCATTTTAAAGAAAATGTGTAGATTTT
1 AGTTTAGA-TTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAATGTGTAGAAATT
* ** ** * *
29394730 TTAAAACAAAGTTTTGATCTTTTTCAACTATTTTGAAATAAAGTTTTGATTTTTAAGAAAAGTAG
65 TTAAAACAAAGTTTTAATCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTAAGAAAAATAG
29394795 TGATTTTGTTAAAGA
130 TGATTTTGTTAAAGA
29394810 AAACTTTTAT
Statistics
Matches: 122, Mismatches: 17, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
144 53 0.43
145 35 0.29
146 34 0.28
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (145 bp):
AGTTTAGATTTTAAAAATAAAAATATGATTTCTTTAGTCATTTTAAAGAAAATGTGTAGAAATTT
TAAAACAAAGTTTTAATCTTTTTCAACTATTTCAAAATAAAACTTTGATCTTTAAGAAAAATAGT
GATTTTGTTAAAGAG
Found at i:29394945 original size:12 final size:12
Alignment explanation
Indices: 29394928--29394959 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29394918 TTGCCAACAT
29394928 AGAAAGAGGAAG
1 AGAAAGAGGAAG
29394940 AGAAAGAGGAAG
1 AGAAAGAGGAAG
*
29394952 AGGAAGAG
1 AGAAAGAG
29394960 ATTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AGAAAGAGGAAG
Found at i:29395761 original size:26 final size:26
Alignment explanation
Indices: 29395732--29395797 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
29395722 TTAGTTAAGT
* *
29395732 AGGTGTTATATTTTAACGAAACTATA
1 AGGTGTTACATTTTAACGAAACCATA
* *
29395758 AGGTTTTTACATTTTAATGAAACCATA
1 AGG-TGTTACATTTTAACGAAACCATA
*
29395785 AGGTTTTTACATT
1 AGG-TGTTACATT
29395798 CAGATTTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (26 bp):
AGGTGTTACATTTTAACGAAACCATA
Found at i:29395771 original size:27 final size:27
Alignment explanation
Indices: 29395741--29395797 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
29395731 TAGGTGTTAT
*
29395741 ATTTTAACGAAACTATAAGGTTTTTAC
1 ATTTTAACGAAACCATAAGGTTTTTAC
*
29395768 ATTTTAATGAAACCATAAGGTTTTTAC
1 ATTTTAACGAAACCATAAGGTTTTTAC
29395795 ATT
1 ATT
29395798 CAGATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
ATTTTAACGAAACCATAAGGTTTTTAC
Found at i:29397778 original size:23 final size:24
Alignment explanation
Indices: 29397743--29397796 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
29397733 CTCCACCCGG
*
29397743 TCCCTCTCTCCCCCTCCCCTCCC-C
1 TCCCTCTCACCCCCT-CCCTCCCTC
*
29397767 TCCC-CTCACCCCGTCCCTCCCTC
1 TCCCTCTCACCCCCTCCCTCCCTC
29397790 TCCCTCT
1 TCCCTCT
29397797 GTGACCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 13 0.50
24 6 0.23
ACGTcount: A:0.02, C:0.70, G:0.02, T:0.26
Consensus pattern (24 bp):
TCCCTCTCACCCCCTCCCTCCCTC
Found at i:29398067 original size:11 final size:11
Alignment explanation
Indices: 29398045--29398088 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
29398035 AACTAATCCT
29398045 CTCTCAAATTTC
1 CTCTC-AATTTC
29398057 CTCTCAATTTC
1 CTCTCAATTTC
*
29398068 CTCTAAATTTC
1 CTCTCAATTTC
29398079 CTCTCAATTT
1 CTCTCAATTT
29398089 TGGAGTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 25 0.83
12 5 0.17
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:29398077 original size:22 final size:23
Alignment explanation
Indices: 29398045--29398088 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
29398035 AACTAATCCT
29398045 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
29398068 CTCT-AAATTTCCTCTCAATTT
1 CTCTCAAATTTCCTCTCAATTT
29398089 TGGAGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:29398751 original size:24 final size:23
Alignment explanation
Indices: 29398712--29398757 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
29398702 TTTGGTGCTA
29398712 TTATTTTTCTACTGTTTTTGTTG
1 TTATTTTTCTACTGTTTTTGTTG
*
29398735 TTATTTTTGCTATTGTTTTTGTT
1 TTATTTTT-CTACTGTTTTTGTT
29398758 ATTTGTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.72
Consensus pattern (23 bp):
TTATTTTTCTACTGTTTTTGTTG
Found at i:29399859 original size:9 final size:9
Alignment explanation
Indices: 29399809--29399858 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
29399799 TTTGGTTAAA
29399809 AATTAACCG
1 AATTAACCG
*
29399818 AATTAACTG
1 AATTAACCG
*
29399827 AATTAACCA
1 AATTAACCG
29399836 AATTAACCG
1 AATTAACCG
*
29399845 AATTACCCG
1 AATTAACCG
29399854 AATTA
1 AATTA
29399859 CTCGAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:29399864 original size:9 final size:9
Alignment explanation
Indices: 29399809--29399866 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
29399799 TTTGGTTAAA
*
29399809 AATTAACCG
1 AATTACCCG
* *
29399818 AATTAACTG
1 AATTACCCG
* *
29399827 AATTAACCA
1 AATTACCCG
*
29399836 AATTAACCG
1 AATTACCCG
29399845 AATTACCCG
1 AATTACCCG
*
29399854 AATTACTCG
1 AATTACCCG
29399863 AATT
1 AATT
29399867 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTACCCG
Found at i:29399864 original size:18 final size:19
Alignment explanation
Indices: 29399809--29399866 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
29399799 TTTGGTTAAA
29399809 AATTAACCGAATTAACT-G
1 AATTAACCGAATTAACTCG
*
29399827 AATTAACCAAATTAAC-CG
1 AATTAACCGAATTAACTCG
*
29399845 AATTACCCGAATT-ACTCG
1 AATTAACCGAATTAACTCG
29399863 AATT
1 AATT
29399867 GAATCACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.06
18 33 0.94
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTAACCGAATTAACTCG
Found at i:29399896 original size:17 final size:17
Alignment explanation
Indices: 29399874--29399936 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
29399864 ATTGAATCAC
29399874 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
29399891 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
29399911 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
29399928 TACATAATT
1 TACATAATT
29399937 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:29399911 original size:37 final size:37
Alignment explanation
Indices: 29399865--29399939 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29399855 ATTACTCGAA
*
29399865 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
29399902 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
29399939 T
1 T
29399940 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:29400152 original size:39 final size:38
Alignment explanation
Indices: 29400068--29400184 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 38
29400058 ACTTAAGAGT
*
29400068 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
29400106 TAGACTTTAGTTTTAGTTTTATTGGGTTGGATAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGG-TAATTGGG
29400145 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGG
29400184 T
1 T
29400185 TGGGTTGGAT
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
38 29 0.38
39 45 0.59
40 2 0.03
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
Found at i:29400183 original size:13 final size:13
Alignment explanation
Indices: 29400165--29400189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29400155 TTTTAGTTTT
29400165 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
29400178 ATTGGGTTGGGT
1 ATTGGGTTGGGT
29400190 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:29409241 original size:18 final size:18
Alignment explanation
Indices: 29409218--29409254 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29409208 GCCAAGTGTA
* *
29409218 TATCCTAGCCTTTATATG
1 TATCCTAACCCTTATATG
29409236 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
29409254 T
1 T
29409255 TTTCTTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:29409779 original size:18 final size:18
Alignment explanation
Indices: 29409731--29409779 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
29409721 TTTGGTTAAA
*
29409731 AATTAACCGAATTAACTG
1 AATTACCCGAATTAACTG
* *
29409749 AATTACCCAAATTACCTG
1 AATTACCCGAATTAACTG
*
29409767 AATTACTCGAATT
1 AATTACCCGAATT
29409780 GAATCACTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (18 bp):
AATTACCCGAATTAACTG
Found at i:29409809 original size:17 final size:17
Alignment explanation
Indices: 29409787--29409849 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
29409777 ATTGAATCAC
29409787 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
29409804 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
29409824 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
29409841 TACATAATT
1 TACATAATT
29409850 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:29409824 original size:37 final size:37
Alignment explanation
Indices: 29409778--29409852 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29409768 ATTACTCGAA
*
29409778 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
29409815 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
29409852 T
1 T
29409853 GAAATTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:29410070 original size:13 final size:13
Alignment explanation
Indices: 29410045--29410080 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
29410035 TTTTATTGGG
29410045 TTGGGTT-GGTAA
1 TTGGGTTGGGTAA
29410057 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
29410070 TTGGGTTGGGT
1 TTGGGTTGGGT
29410081 TGGATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.11, C:0.00, G:0.47, T:0.42
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:29413765 original size:126 final size:126
Alignment explanation
Indices: 29413540--29413933 Score: 469
Period size: 126 Copynumber: 3.2 Consensus size: 126
29413530 AAGGGTAAGT
* * * **
29413540 AAGAACTATTGTAGAAAAAGAGCGTCCACATAGAAACTTTTTTCAGTAATTTTGCTAATGGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTCCACATAGGAACTTTTTTCAGTAATTTTGCTGACAGTGCA
* **
29413605 TCCTGCTTGAAGCGTTTTTTATATTAACTTTTCAGAACCATCTTCTCATAATTATTTTTTC
66 TCCTGCTTGAAGCGTTTTTTACATTATTTTTTCAGAACCATCTTCTCATAATTATTTTTTC
* *
29413666 AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTCCACATAGGAACTTTTTTCAGTAATTTTGCTGACAGTGCA
** * *
29413731 TCCTGCTTGAAGCGTTTTTTACATTATTTTTTCAGAACTGTCTTCTCAAAATTAATTTTTC
66 TCCTGCTTGAAGCGTTTTTTACATTATTTTTTCAGAACCATCTTCTCATAATTATTTTTTC
* * * * * * * * *
29413792 CAGAAACTATTATAAAAAAAGAGCATCCACAT-GAGAACTTTTTTTTAGTACTTTTGCTGAGAAT
1 AAG-AACTACTGTAGAAAAAGAGCGTCCACATAG-GAAC-TTTTTTCAGTAATTTTGCTGACAGT
* * *
29413856 GCATCCTGCTTGAAGCGTTTTTGT-CACTATTTTTTCAAAACCA---TCTCATTATTATTTTTTC
63 GCATCCTGCTTGAAGCGTTTTT-TACATTATTTTTTCAGAACCATCTTCTCATAATTATTTTTTC
29413917 -A-AACTACTGTAGAAAAA
1 AAGAACTACTGTAGAAAAA
29413934 AAAAACAAAA
Statistics
Matches: 229, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
122 13 0.06
124 1 0.00
125 15 0.07
126 115 0.50
127 26 0.11
128 58 0.25
129 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (126 bp):
AAGAACTACTGTAGAAAAAGAGCGTCCACATAGGAACTTTTTTCAGTAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTTACATTATTTTTTCAGAACCATCTTCTCATAATTATTTTTTC
Found at i:29414066 original size:34 final size:34
Alignment explanation
Indices: 29414028--29414107 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
29414018 ATTATTTTTA
29414028 AAAAACCCTAAACCCTAATTTAATTAA-TTTTCTT
1 AAAAACCCTAAACCCTAATTTAATTAATTTTTC-T
* *
29414062 AAAAACCTTAAA-CCTAATTTGATTAATTTTTCT
1 AAAAACCCTAAACCCTAATTTAATTAATTTTTCT
*
29414095 -AAAATCCTAAACC
1 AAAAACCCTAAACC
29414108 TTGATTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.22
33 15 0.38
34 16 0.40
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.36
Consensus pattern (34 bp):
AAAAACCCTAAACCCTAATTTAATTAATTTTTCT
Found at i:29414078 original size:33 final size:32
Alignment explanation
Indices: 29414028--29414108 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 32
29414018 ATTATTTTTA
29414028 AAAAACCCTAAACCCTAATTTAATTAA-TTTTCTT
1 AAAAA-CCTAAA-CCTAATTTAATTAATTTTTC-T
*
29414062 AAAAACCTTAAACCTAATTTGATTAATTTTTCT
1 AAAAACC-TAAACCTAATTTAATTAATTTTTCT
*
29414095 AAAATCCTAAACCT
1 AAAAACCTAAACCT
29414109 TGATTTATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 7 0.16
33 22 0.51
34 14 0.33
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (32 bp):
AAAAACCTAAACCTAATTTAATTAATTTTTCT
Found at i:29414112 original size:28 final size:29
Alignment explanation
Indices: 29414080--29414160 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
29414070 TAAACCTAAT
*
29414080 TTGATTAATTTTTCTAAAATC-CTAAA-CC
1 TTGATTTATTTTT-TAAAATCTCTAAATCC
*
29414108 TTGATTTATTGTTTAAAATCTCTAAATCC
1 TTGATTTATTTTTTAAAATCTCTAAATCC
*
29414137 -TGATTTA-TTTTTAAAATTTCTAAA
1 TTGATTTATTTTTTAAAATCTCTAAA
29414161 CCCTAAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 22 0.47
28 23 0.49
29 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (29 bp):
TTGATTTATTTTTTAAAATCTCTAAATCC
Found at i:29422028 original size:2 final size:2
Alignment explanation
Indices: 29422023--29422051 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29422013 AATATATATA
29422023 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29422052 ATTCAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29422786 original size:48 final size:48
Alignment explanation
Indices: 29422731--29422824 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
29422721 GCCAGCCTCA
29422731 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
1 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
29422779 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTT
1 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTT
29422825 GAGTTTCGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (48 bp):
GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
Found at i:29424944 original size:318 final size:319
Alignment explanation
Indices: 29424347--29424984 Score: 1134
Period size: 318 Copynumber: 2.0 Consensus size: 319
29424337 AATGCATGCT
*
29424347 TTTATATGTGTTTCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
1 TTTATATGTGTTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
*
29424412 AAATAATTTAAATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
66 AAATAATTTAAATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
*
29424477 TGTATCATGTCGAATATGGTTCGGTACTTCCTCGAGTTGACCTTCAGTGGGTTTAATCGTGTCTA
131 TGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
**
29424542 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTTGACTAACAGTTTCCCCAGATCGT
196 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
* *
29424607 TGAAATCGCTTTGTTGCATTTGAATTTGATTATCTATTTCCAAGAATATACAATGATAA
261 TGAAATCGCTCTATTGCATTTGAATTTGATTATCTATTTCCAAGAATATACAATGATAA
* *
29424666 TTTATGTGTGTTCCATCTATGGCCCCAATACAATCCTTTAAAATAAATAATGAGAT-AAAGTTAG
1 TTTATATGTGTTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
*
29424730 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
66 AAATAATTTAAATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
* *
29424795 TGTATCATGTCGAATATGGTTCGGTATTTCCTCGAATTGACCTTTAGTGGGTTTAATCGTGTCTA
131 TGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
*
29424860 TTCCCATTCGAGCAAATATATGTAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
196 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
* *
29424925 TGAAATCGCTCTATTGCATTTGAATTTGATTCTCTATTTCCAAGAATGTACAATGATAA
261 TGAAATCGCTCTATTGCATTTGAATTTGATTATCTATTTCCAAGAATATACAATGATAA
29424984 T
1 T
29424985 GCTAACTTCT
Statistics
Matches: 304, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
318 251 0.83
319 53 0.17
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (319 bp):
TTTATATGTGTTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
AAATAATTTAAATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
TGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
TGAAATCGCTCTATTGCATTTGAATTTGATTATCTATTTCCAAGAATATACAATGATAA
Found at i:29432466 original size:17 final size:17
Alignment explanation
Indices: 29432444--29432497 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
29432434 CAAATATGGA
*
29432444 ATGTAATCTTCGAAGAT
1 ATGTAATCTTAGAAGAT
* *
29432461 ATGTAATCTTGGATGAT
1 ATGTAATCTTAGAAGAT
29432478 ATGTAATCTTAGAAGAT
1 ATGTAATCTTAGAAGAT
29432495 ATG
1 ATG
29432498 ATTCTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (17 bp):
ATGTAATCTTAGAAGAT
Found at i:29432510 original size:24 final size:23
Alignment explanation
Indices: 29432482--29432528 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
29432472 GATGATATGT
29432482 AATCTTAGAAGATATGATTCTGTA
1 AATCTTAG-AGATATGATTCTGTA
* *
29432506 AATCTTAGAGATTTGATTTTGTA
1 AATCTTAGAGATATGATTCTGTA
29432529 GATTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (23 bp):
AATCTTAGAGATATGATTCTGTA
Found at i:29433934 original size:9 final size:9
Alignment explanation
Indices: 29433922--29433957 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
29433912 TCAAGATTTC
29433922 AAATCTTGG
1 AAATCTTGG
29433931 AAATCTTGG
1 AAATCTTGG
29433940 AAATCTTGG
1 AAATCTTGG
29433949 AAATCTTGG
1 AAATCTTGG
29433958 TCCAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
AAATCTTGG
Found at i:29436744 original size:30 final size:30
Alignment explanation
Indices: 29436708--29436782 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
29436698 ATGGTGACCC
* *
29436708 ATCCCTTTTCATAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
* * * *
29436738 ATCCCTTTTTATAGTTTGACAGCCGAAGCT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
29436768 ATCCC-TTTCATAATT
1 ATCCCTTTTCATAATT
29436783 TGATGGTAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCGAAGCT
Found at i:29436800 original size:29 final size:30
Alignment explanation
Indices: 29436768--29436846 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
29436758 AGCCGAAGCT
29436768 ATCCC-TTTCATAATTTGATGGTAGTCACC
1 ATCCCTTTTCATAATTTGATGGTAGTCACC
*** ** *
29436797 ATCCCTTTTCATTGCTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTAGTCACC
29436827 ATCCCTTTTCATAATTTGAT
1 ATCCCTTTTCATAATTTGAT
29436847 ACCTGAAGCT
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTAGTCACC
Found at i:29436891 original size:30 final size:30
Alignment explanation
Indices: 29436825--29436899 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
29436815 ATGGTCGTCA
* * *
29436825 CCATCCCTTTTCATAATTTGATACCTGAAG
1 CCATCCCTTTTCATAAATCGACACCTGAAG
* *
29436855 CTATCCCTTTTCATAAATCGACAGCC-GAAT
1 CCATCCCTTTTCATAAATCGACA-CCTGAAG
29436885 CCATCCCTTTTCATA
1 CCATCCCTTTTCATA
29436900 TTTCGATTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (30 bp):
CCATCCCTTTTCATAAATCGACACCTGAAG
Found at i:29436919 original size:30 final size:30
Alignment explanation
Indices: 29436885--29436958 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
29436875 ACAGCCGAAT
**
29436885 CCATCCCTTTTCATAT-TTCGATTGTCGTCA
1 CCATCCCTTTTCATATGTT-GACGGTCGTCA
29436915 CCATCCCTTTTCAT-TGTTGACGGTCGTCA
1 CCATCCCTTTTCATATGTTGACGGTCGTCA
*
29436944 ACATCCCTTTTCATA
1 CCATCCCTTTTCATA
29436959 ATCGATAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.41
Consensus pattern (30 bp):
CCATCCCTTTTCATATGTTGACGGTCGTCA
Found at i:29436940 original size:119 final size:119
Alignment explanation
Indices: 29436706--29436986 Score: 363
Period size: 119 Copynumber: 2.4 Consensus size: 119
29436696 CGATGGTGAC
* * ** * *
29436706 CCATCCCTTTTCATAATTCGATAACC-GAAGTTATCCCTTTTTATAGTTTGACAGCCGAAGCTAT
1 CCATCCCTTTTCATAATTCGAT-ACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCAT
*
29436770 CCCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAATGGTCGTCA
65 CCCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
* *
29436825 CCATCCCTTTTCATAATTTGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAATCCATC
1 CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCATC
* * **
29436890 CCTTTTCAT-ATTTCGATTGTCGTCACCATCCCTTTTCATTG-TTGACGGTCGTCA
66 CC-TTTCATAATTT-GATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
* * *
29436944 ACATCCCTTTTCATAA-TCGATAACTGAAGCTATCCTTTTTCAT
1 CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCAT
29436987 TTGCTGATGA
Statistics
Matches: 142, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
118 27 0.19
119 84 0.59
120 31 0.22
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (119 bp):
CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCATC
CCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
Found at i:29439466 original size:25 final size:27
Alignment explanation
Indices: 29439427--29439496 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
29439417 TTGTACATGT
** *
29439427 ATGCTCACATAAGCTGT-A-AATTAGA
1 ATGCTCACACGAGCTGTGATAATGAGA
* *
29439452 ATGCTCACACGAGCTGTGATAATGGGC
1 ATGCTCACACGAGCTGTGATAATGAGA
*
29439479 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
29439497 GGTCGAAACG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 15 0.41
26 1 0.03
27 21 0.57
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (27 bp):
ATGCTCACACGAGCTGTGATAATGAGA
Found at i:29444062 original size:18 final size:18
Alignment explanation
Indices: 29444039--29444095 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
29444029 TCAGTGAAAA
*
29444039 TGGGCTCACACGCCTATG
1 TGGGCTCACACGCCCATG
29444057 TGGGCTCACACGCCCATG
1 TGGGCTCACACGCCCATG
* * *
29444075 TGGACCCACACGCCCGTG
1 TGGGCTCACACGCCCATG
29444093 TGG
1 TGG
29444096 CCCACTCGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.16, C:0.37, G:0.30, T:0.18
Consensus pattern (18 bp):
TGGGCTCACACGCCCATG
Found at i:29446722 original size:14 final size:13
Alignment explanation
Indices: 29446699--29446731 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
29446689 ATAGGATTGT
29446699 ATTTAGTGAAAGG
1 ATTTAGTGAAAGG
29446712 ATTTGAGTGAAAGG
1 ATTT-AGTGAAAGG
29446726 ATTTAG
1 ATTTAG
29446732 CTCAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
ATTTAGTGAAAGG
Found at i:29447168 original size:16 final size:16
Alignment explanation
Indices: 29447147--29447185 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
29447137 AGGTGGTCGT
29447147 GAGAATTGATCAATTA
1 GAGAATTGATCAATTA
29447163 GAGAATTGATCAATTA
1 GAGAATTGATCAATTA
29447179 GAGAATT
1 GAGAATT
29447186 TGTTTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (16 bp):
GAGAATTGATCAATTA
Found at i:29450287 original size:24 final size:23
Alignment explanation
Indices: 29450259--29450305 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
29450249 GATGATATGC
29450259 AATCTTAGA-AGTTATGATTTTGTA
1 AATCTTAGAGA-TT-TGATTTTGTA
29450283 AATCTTAGAGATTTGATTTTGTA
1 AATCTTAGAGATTTGATTTTGTA
29450306 GATTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.45
24 11 0.50
25 1 0.05
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (23 bp):
AATCTTAGAGATTTGATTTTGTA
Found at i:29450303 original size:23 final size:24
Alignment explanation
Indices: 29450259--29450305 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
29450249 GATGATATGC
29450259 AATCTTAGAAGTTATGATTTTGTA
1 AATCTTAGAAGTTATGATTTTGTA
29450283 AATCTTAG-AGATT-TGATTTTGTA
1 AATCTTAGAAG-TTATGATTTTGTA
29450306 GATTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (24 bp):
AATCTTAGAAGTTATGATTTTGTA
Found at i:29451241 original size:34 final size:34
Alignment explanation
Indices: 29451186--29451251 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
29451176 AATTATTGGA
*
29451186 AATTAATTAAAAAACATAAAATTTTATAAAAAAT
1 AATTAATTAAAAAACACAAAATTTTATAAAAAAT
* *
29451220 AATTGATTAAAAACCACAAAATTTTATAAAAA
1 AATTAATTAAAAAACACAAAATTTTATAAAAA
29451252 CAATTGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (34 bp):
AATTAATTAAAAAACACAAAATTTTATAAAAAAT
Found at i:29455527 original size:25 final size:25
Alignment explanation
Indices: 29455481--29455528 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29455471 TTTAGTTTGA
* *
29455481 TTAATTAATAAAATTTATATATAAT
1 TTAATTAATAAAATTGACATATAAT
* *
29455506 TTAATTAATGAAATTGGCATATA
1 TTAATTAATAAAATTGACATATA
29455529 TCTTAAGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
TTAATTAATAAAATTGACATATAAT
Found at i:29456919 original size:248 final size:248
Alignment explanation
Indices: 29456481--29456983 Score: 970
Period size: 248 Copynumber: 2.0 Consensus size: 248
29456471 AAAATATGAT
*
29456481 TTATTTTATTTTATAAATAATATATGACACGTTTAATGTTTAATAAAACATGGAAAAAGGAAAGA
1 TTATTTTATTTTATAAATAATATATGACACGTTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
*
29456546 AAATGTGAATTCTGTCATCTTTTTCATTAGAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
66 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
*
29456611 TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTGTAATTTTTATGTTTT
131 TGACAAGCTTAACCTTGCTAATTGGGAAGTTGTTTTTAGTCTGTTTCTTGTAATTTTTATGTTTT
29456676 TGGAATCTTAGGAGCTTGATCTATCTAACCCAAGGTGTAACTCCCCAAAATTC
196 TGGAATCTTAGGAGCTTGATCTATCTAACCCAAGGTGTAACTCCCCAAAATTC
29456729 TTATTTTATTTTATAAATAATATATGACACGTTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
1 TTATTTTATTTTATAAATAATATATGACACGTTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
29456794 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
66 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
29456859 TGACAAGCTTAACCTTGCTAATTGGGAAGTTGTTTTTAGTCTGTTTCTTGTAATTTTTATGTTTT
131 TGACAAGCTTAACCTTGCTAATTGGGAAGTTGTTTTTAGTCTGTTTCTTGTAATTTTTATGTTTT
*
29456924 TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
196 TGGAATCTTAGGAGCTTGATCTATCTAACCCAAGGTGTAACTCCCCAAAATTC
29456977 TTATTTT
1 TTATTTT
29456984 TGTTATTGTG
Statistics
Matches: 251, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
248 251 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (248 bp):
TTATTTTATTTTATAAATAATATATGACACGTTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
TGACAAGCTTAACCTTGCTAATTGGGAAGTTGTTTTTAGTCTGTTTCTTGTAATTTTTATGTTTT
TGGAATCTTAGGAGCTTGATCTATCTAACCCAAGGTGTAACTCCCCAAAATTC
Found at i:29459457 original size:18 final size:18
Alignment explanation
Indices: 29459422--29459466 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
29459412 TCAATAAGTG
*
29459422 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
29459440 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
29459458 AC-TTTTGAA
1 ACGTTTTGAA
29459467 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:29466689 original size:27 final size:27
Alignment explanation
Indices: 29466659--29466891 Score: 322
Period size: 27 Copynumber: 8.6 Consensus size: 27
29466649 TAAGATTTTG
*
29466659 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
29466686 CCACAAAGGCAATTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
29466713 CCACAAAGGCAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
29466740 CCACAAAGACAGTTCTTTCAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * * * **
29466767 CCACCAATGCAATTCTTTTAGAGTATG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
29466794 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
29466821 CCACAAAGGTAGTACTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * *
29466848 CCACAAAGGTAATTCTTTCAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
29466875 CCACAAAGGCAGTTCTT
1 CCACAAAGGCAGTTCTT
29466892 AGTTGTCGTG
Statistics
Matches: 182, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 182 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCAGTTCTTTCAGAGTACA
Found at i:29466754 original size:81 final size:81
Alignment explanation
Indices: 29466659--29466891 Score: 367
Period size: 81 Copynumber: 2.9 Consensus size: 81
29466649 TAAGATTTTG
*
29466659 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACACCACAAAGGCA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29466724 GTTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
** * * * * * *
29466740 CCACAAAGACAGTTCTTTCAGAGTACGCCACCAATGCAATTCTTTTAGAGTATGCCACAAAGGTA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29466805 GTTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
* *
29466821 CCACAAAGGTAGTACTTTCAGAGTACACCACAAAGGTAATTCTTTCAGAGTACGCCACAAAGGCA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29466886 GTTCTT
66 GTTCTT
29466892 AGTTGTCGTG
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 133 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (81 bp):
CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
GTTCTTTCAGAGTACA
Found at i:29470415 original size:11 final size:11
Alignment explanation
Indices: 29470387--29470427 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
29470377 TAAAATTTAA
29470387 TTAAAAA-ATT
1 TTAAAAATATT
*
29470397 ATAAAAATATT
1 TTAAAAATATT
*
29470408 TTATAAATATT
1 TTAAAAATATT
29470419 TTAAAAATA
1 TTAAAAATA
29470428 CATAAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:29470448 original size:12 final size:12
Alignment explanation
Indices: 29470431--29470455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29470421 AAAAATACAT
29470431 AAAATTCTATAA
1 AAAATTCTATAA
29470443 AAAATTCTATAA
1 AAAATTCTATAA
29470455 A
1 A
29470456 TATTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTCTATAA
Found at i:29470487 original size:16 final size:17
Alignment explanation
Indices: 29470452--29470513 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 17
29470442 AAAAATTCTA
29470452 TAAATATTTTATGTTAT
1 TAAATATTTTATGTTAT
29470469 TAAATATTTT-T-TATAT
1 TAAATATTTTATGT-TAT
29470485 TAAATATTTTAATGTTAAAT
1 TAAATATTTT-ATGTT--AT
29470505 TAAATATTT
1 TAAATATTT
29470514 AAAACAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 14 0.36
17 10 0.26
18 2 0.05
19 1 0.03
20 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TAAATATTTTATGTTAT
Found at i:29470502 original size:15 final size:16
Alignment explanation
Indices: 29470452--29470504 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
29470442 AAAAATTCTA
**
29470452 TAAATATTTTATGTTAT
1 TAAATATTTT-TAATAT
*
29470469 TAAATATTTTTTATAT
1 TAAATATTTTTAATAT
*
29470485 TAAATA-TTTTAATGT
1 TAAATATTTTTAATAT
29470500 TAAAT
1 TAAAT
29470505 TAAATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 12 0.38
16 10 0.31
17 10 0.31
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TAAATATTTTTAATAT
Found at i:29470508 original size:20 final size:18
Alignment explanation
Indices: 29470452--29470513 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 18
29470442 AAAAATTCTA
29470452 TAAATATTTTATGTT-AT
1 TAAATATTTTATGTTAAT
29470469 TAAATA-TTT-T-TTATAT
1 TAAATATTTTATGTTA-AT
29470485 TAAATATTTTAATGTTAAAT
1 TAAATATTTT-ATGTT-AAT
29470505 TAAATATTT
1 TAAATATTT
29470514 AAAACAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 11 0.29
17 9 0.24
19 1 0.03
20 13 0.34
21 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAAATATTTTATGTTAAT
Found at i:29483337 original size:31 final size:31
Alignment explanation
Indices: 29483301--29483365 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
29483291 ATTAATCTAG
*
29483301 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTCGAATAGTTCAA
* *
29483332 TGACTTAAATGAAAACTTTCGAATAGTTTAA
1 TGACTTAAATAAAAACTTTCGAATAGTTCAA
29483363 TGA
1 TGA
29483366 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAGTTCAA
Found at i:29485465 original size:40 final size:40
Alignment explanation
Indices: 29485404--29485481 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
29485394 TGATTGAAAT
* * * *
29485404 TACCGAAGTATAAATAGGGGCACGTATGTGCAATCAGGGG
1 TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGGGG
*
29485444 TACCAAAGTACAAATAAGGGCACGTACGTGCATTCAGG
1 TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGG
29485482 TATAGTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (40 bp):
TACCAAAGTACAAATAAGGGCACGTACGTGCAATCAGGGG
Found at i:29487724 original size:28 final size:30
Alignment explanation
Indices: 29487676--29487740 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
29487666 ACTTACCTCA
*
29487676 TGTTTACTGTCCCAACGAACT-CTA-TTTG
1 TGTTTACTGTCCCAACAAACTCCTATTTTG
* *
29487704 TGTTTACTGTCCTAGCAAACTGCCTATTTTG
1 TGTTTACTGTCCCAACAAACT-CCTATTTTG
29487735 TGTTTA
1 TGTTTA
29487741 TTGTTGTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.58
30 3 0.10
31 10 0.32
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (30 bp):
TGTTTACTGTCCCAACAAACTCCTATTTTG
Found at i:29488312 original size:98 final size:98
Alignment explanation
Indices: 29488140--29488334 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
29488130 ACAATAAAAT
*
29488140 TTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
29488205 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
*
29488238 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
29488303 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
29488335 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:29488628 original size:15 final size:15
Alignment explanation
Indices: 29488610--29488642 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29488600 CAAATGCTAT
29488610 AATAATAAATACAAC
1 AATAATAAATACAAC
*
29488625 AATAATAAATACATC
1 AATAATAAATACAAC
29488640 AAT
1 AAT
29488643 GACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:29489095 original size:19 final size:19
Alignment explanation
Indices: 29489071--29489108 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29489061 TGTAAAATAT
29489071 TTTGAAAATATATGTATAC
1 TTTGAAAATATATGTATAC
29489090 TTTGAAAATATATGTATAC
1 TTTGAAAATATATGTATAC
29489109 GGAAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTGAAAATATATGTATAC
Found at i:29489113 original size:17 final size:18
Alignment explanation
Indices: 29489074--29489114 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
29489064 AAAATATTTT
*
29489074 GAAAATATATGTATACTTT
1 GAAAATATATGTATAC-TG
29489093 GAAAATATATGTATAC-G
1 GAAAATATATGTATACTG
29489110 GAAAA
1 GAAAA
29489115 ATGTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
19 16 0.76
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (18 bp):
GAAAATATATGTATACTG
Found at i:29490548 original size:33 final size:33
Alignment explanation
Indices: 29490510--29490590 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
29490500 ACAATTGTCT
*
29490510 TAGTGGACTATCT-TTGTCATGTGTTTATTGTCCC
1 TAGTGGACTATCTCTTGTC-TGTGTTTACTG-CCC
*
29490544 -AGTGGACTATCTCTTTTCTGTGTTTACTGCCC
1 TAGTGGACTATCTCTTGTCTGTGTTTACTGCCC
*
29490576 TAGCGGACTATCTCT
1 TAGTGGACTATCTCT
29490591 GTGGATGCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 3 0.07
33 35 0.83
34 4 0.10
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
TAGTGGACTATCTCTTGTCTGTGTTTACTGCCC
Found at i:29492673 original size:50 final size:50
Alignment explanation
Indices: 29492595--29492787 Score: 161
Period size: 50 Copynumber: 3.7 Consensus size: 50
29492585 TTTCTTGTAC
* * * * **
29492595 TGCCAATGCCATATCCTAGATATGGTCTTACACGGGAGTTCTCATATCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACACGGGACATCTCATATCAG
* * * * * * * *
29492645 TGCCCATGCTATGTCCCTGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACACGGGACATCTCATATCAG
* * *
29492695 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACATCTCATAACCTTAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACACGGGACATCTCAT-A---TCA-G
* *
29492750 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACACGGGA
29492788 TCTCTTTACC
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 77 0.68
54 1 0.01
55 1 0.01
56 35 0.31
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACACGGGACATCTCATATCAG
Found at i:29496423 original size:3 final size:3
Alignment explanation
Indices: 29496415--29496441 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29496405 AAATAAATGA
29496415 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
29496442 GGTAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29498707 original size:31 final size:28
Alignment explanation
Indices: 29498663--29498725 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
29498653 AGCGTAAAGG
*
29498663 CTAAATTTTAATTTTAT-CAAATTTAGTCT
1 CTAAATTTTAATTTT-TGAAAATTTAGT-T
29498692 CTAAACTTTTCAATTTTTGAAAATTTAGTT
1 CTAAA-TTTT-AATTTTTGAAAATTTAGTT
29498722 CTAA
1 CTAA
29498726 TCAAATGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 10 0.33
31 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (28 bp):
CTAAATTTTAATTTTTGAAAATTTAGTT
Found at i:29502790 original size:37 final size:36
Alignment explanation
Indices: 29502739--29502814 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
29502729 ACACCAAAAA
*
29502739 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
29502775 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
29502812 TAA
1 TAA
29502815 AGTGATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:29504270 original size:90 final size:90
Alignment explanation
Indices: 29504143--29504346 Score: 250
Period size: 90 Copynumber: 2.3 Consensus size: 90
29504133 AGCCAAAGCA
* * ** * * * *
29504143 TGGGATATGAATTCATTAAGAATATTTAGTGGCTCATCCTATAAATTTAGT-AGGTTTATCAAGT
1 TGGGTTATGAAATCATTAAGAGCATCTAGTAGCTCATCCTATAAATTTAGTGA-ATTCATCAAGT
*
29504207 CCGTCTTAATATGACCACCCAAAC-C
65 CCGTCTTAACATGACCACCCAAACTC
* *
29504232 TTGGGTTATGAAATCATTAAGAGCATCTAGTAGTTCATCCTATAAATTTAGTGAATTCATTAAGT
1 -TGGGTTATGAAATCATTAAGAGCATCTAGTAGCTCATCCTATAAATTTAGTGAATTCATCAAGT
*
29504297 TCGTCTTAACATGACCACCCAAACTC
65 CCGTCTTAACATGACCACCCAAACTC
* *
29504323 TGGGTTATGAACTTATTAAGAGCA
1 TGGGTTATGAAATCATTAAGAGCA
29504347 AGGAGCTCAT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
90 96 0.98
91 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (90 bp):
TGGGTTATGAAATCATTAAGAGCATCTAGTAGCTCATCCTATAAATTTAGTGAATTCATCAAGTC
CGTCTTAACATGACCACCCAAACTC
Found at i:29507638 original size:22 final size:23
Alignment explanation
Indices: 29507611--29507658 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
29507601 CCCATGCCAC
29507611 AGTCCAAAA-AACAATAATAA-AA
1 AGTCCAAAATAACAA-AATAATAA
*
29507633 AGTCCAAAATACCAAAATAATAA
1 AGTCCAAAATAACAAAATAATAA
29507656 AGT
1 AGT
29507659 GTAAAACGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.17
Consensus pattern (23 bp):
AGTCCAAAATAACAAAATAATAA
Found at i:29508073 original size:30 final size:27
Alignment explanation
Indices: 29508012--29508074 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
29508002 CCAAGCCACA
**
29508012 AGATAATGTGGACAAGCTGCCAAATAC
1 AGATAATGTGGACAAGCCACCAAATAC
29508039 AGATATATGTGGACAAGCCACCAGAATCAC
1 AGATA-ATGTGGACAAGCCACCA-AAT-AC
29508069 AGATAA
1 AGATAA
29508075 ACTGCCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.16
28 15 0.48
29 4 0.13
30 7 0.23
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (27 bp):
AGATAATGTGGACAAGCCACCAAATAC
Found at i:29512126 original size:24 final size:24
Alignment explanation
Indices: 29512094--29512213 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
29512084 AGGCATTCCC
*
29512094 GAATACGCCACAAAGGCACTTGCA
1 GAATACGCCACAAAGGCACTTACA
29512118 GAATACGCCACAAAGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* *
29512142 GAATACGCCATAAATGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * *
29512166 AAATACACCACAAAGGAACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * *
29512190 AAATACGCCATAATGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
29512214 TAATCACGTG
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.43, C:0.27, G:0.14, T:0.16
Consensus pattern (24 bp):
GAATACGCCACAAAGGCACTTACA
Found at i:29515528 original size:26 final size:27
Alignment explanation
Indices: 29515486--29515536 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
29515476 TAAACGAAAT
*
29515486 AATTATATGAATCTGTTATGTGAAAAC
1 AATTATATGAATCTGTTATATGAAAAC
*
29515513 AATTATATGAA-GTGTTATATGAAA
1 AATTATATGAATCTGTTATATGAAA
29515537 TGTTTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (27 bp):
AATTATATGAATCTGTTATATGAAAAC
Found at i:29521398 original size:27 final size:27
Alignment explanation
Indices: 29521368--29521600 Score: 322
Period size: 27 Copynumber: 8.6 Consensus size: 27
29521358 TAAGATTTTG
*
29521368 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
29521395 CCACAAAGGCAATTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
29521422 CCACAAAGGCAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
29521449 CCACAAAGGCAGTTCGTTCAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * * * **
29521476 CCACCAATGCAATTCTTTTAGAGTATG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
29521503 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
29521530 CCACAAAGGTAGTACTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * *
29521557 CCACAAAGGTAATTCTTTCAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
29521584 CCACAAAGGCAGTTCTT
1 CCACAAAGGCAGTTCTT
29521601 AGTTGTCGTG
Statistics
Matches: 182, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 182 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (27 bp):
CCACAAAGGCAGTTCTTTCAGAGTACA
Found at i:29521463 original size:81 final size:81
Alignment explanation
Indices: 29521368--29521600 Score: 367
Period size: 81 Copynumber: 2.9 Consensus size: 81
29521358 TAAGATTTTG
*
29521368 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACACCACAAAGGCA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29521433 GTTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
* * * * * * * *
29521449 CCACAAAGGCAGTTCGTTCAGAGTACGCCACCAATGCAATTCTTTTAGAGTATGCCACAAAGGTA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29521514 GTTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
* *
29521530 CCACAAAGGTAGTACTTTCAGAGTACACCACAAAGGTAATTCTTTCAGAGTACGCCACAAAGGCA
1 CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
29521595 GTTCTT
66 GTTCTT
29521601 AGTTGTCGTG
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 133 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (81 bp):
CCACAAAGGTAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGCA
GTTCTTTCAGAGTACA
Found at i:29526393 original size:31 final size:28
Alignment explanation
Indices: 29526349--29526411 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
29526339 AGCGTAAAGG
*
29526349 CTAAATTTTAATTTTAT-CAAATTTAGTCT
1 CTAAATTTTAATTTT-TGAAAATTTAGT-T
29526378 CTAAACTTTTCAATTTTTGAAAATTTAGTT
1 CTAAA-TTTT-AATTTTTGAAAATTTAGTT
29526408 CTAA
1 CTAA
29526412 TCAAATGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 10 0.33
31 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (28 bp):
CTAAATTTTAATTTTTGAAAATTTAGTT
Found at i:29532084 original size:24 final size:23
Alignment explanation
Indices: 29532037--29532082 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
29532027 CATGATGGTG
29532037 TCAGTGCAAATCTTTTTTAGAAA
1 TCAGTGCAAATCTTTTTTAGAAA
*
29532060 TCAGTGCAAATTTTTTTTAGAAA
1 TCAGTGCAAATCTTTTTTAGAAA
29532083 ATGTTCCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (23 bp):
TCAGTGCAAATCTTTTTTAGAAA
Found at i:29532208 original size:28 final size:29
Alignment explanation
Indices: 29532171--29532233 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
29532161 CCAAGCCACA
*
29532171 AGAT-AATGTGGACAAGCTGCCA-AAT-AC
1 AGATAAATGTGGACAAGC-ACCAGAATCAC
29532198 AGATAAATGTGGACAAGCACCAGAATCAC
1 AGATAAATGTGGACAAGCACCAGAATCAC
29532227 AGATAAA
1 AGATAAA
29532234 CTGCCAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.22
28 16 0.50
29 9 0.28
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (29 bp):
AGATAAATGTGGACAAGCACCAGAATCAC
Found at i:29536341 original size:24 final size:24
Alignment explanation
Indices: 29536289--29536377 Score: 101
Period size: 24 Copynumber: 3.7 Consensus size: 24
29536279 GGCATTCGCC
*
29536289 GAATACGCCA-AAAGGCAACTTGCA
1 GAATACGCCACAAAGGC-ACTTACA
29536313 G-ATACGCCACAAAGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* *
29536336 GAATACGCCATAAATGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
*
29536360 AATATACAGCCACAAAGG
1 GA-ATAC-GCCACAAAGG
29536378 AATACAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.27
24 28 0.51
25 4 0.07
26 8 0.15
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.15
Consensus pattern (24 bp):
GAATACGCCACAAAGGCACTTACA
Found at i:29546850 original size:24 final size:24
Alignment explanation
Indices: 29546818--29546937 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
29546808 AGGCATTCCC
*
29546818 GAATACGCCACAAAGGCACTTGCA
1 GAATACGCCACAAAGGCACTTACA
29546842 GAATACGCCACAAAGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* *
29546866 GAATACGCCATAAATGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * *
29546890 AAATACACCACAAAGGAACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * * *
29546914 AAATACGCCATAATGGAACTTACA
1 GAATACGCCACAAAGGCACTTACA
29546938 TAATCACGTG
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 85 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (24 bp):
GAATACGCCACAAAGGCACTTACA
Found at i:29568884 original size:260 final size:260
Alignment explanation
Indices: 29568378--29568902 Score: 910
Period size: 260 Copynumber: 2.0 Consensus size: 260
29568368 ATTCATAAGA
*
29568378 ACTTACCTGGCTAAATTGTAAAAATTTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
1 ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
*
29568443 CCATCCGATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
66 CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
* *
29568508 TTTTATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAATTTTTACTTTTGTTCA
131 TTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
* *
29568573 ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCCAAAATTGAGCTTAGTCGAAT
196 ATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAATTGAGCCTAGTCGAAT
*
29568638 ACTTACCTGGCTAAATTGTAGAAATGTCAAAGTAC-AGGAGCATTTTTACCATTCTCCTCGATTT
1 ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGG-GCATTTTTACCATTCTCCTCGATTT
* *
29568702 TCCATCCAATCTTGATCTAATTTACTAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGT
65 TCCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGT
*
29568767 ATTTAATGCAATTTAGTCATT-TTTACATTTTTACAAAATTACCCCTAAAGTTTTACTTTTGTTC
130 ATTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTC
* *
29568831 AATTTAGTCCCTGAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTATTCGA
195 AATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCC-AAAATTGAGCCTAGTCGA
29568896 AT
259 AT
29568898 ACTTA
1 ACTTA
29568903 TTGCATCCAA
Statistics
Matches: 251, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
259 88 0.35
260 163 0.65
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (260 bp):
ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
CCATCCAATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
TTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
ATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAATTGAGCCTAGTCGAAT
Done.