Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:3733312 original size:7 final size:7
Alignment explanation
Indices: 3733300--3733508 Score: 418
Period size: 7 Copynumber: 29.9 Consensus size: 7
3733290 ATTGCTAAAT
3733300 AAAATTA
1 AAAATTA
3733307 AAAATTA
1 AAAATTA
3733314 AAAATTA
1 AAAATTA
3733321 AAAATTA
1 AAAATTA
3733328 AAAATTA
1 AAAATTA
3733335 AAAATTA
1 AAAATTA
3733342 AAAATTA
1 AAAATTA
3733349 AAAATTA
1 AAAATTA
3733356 AAAATTA
1 AAAATTA
3733363 AAAATTA
1 AAAATTA
3733370 AAAATTA
1 AAAATTA
3733377 AAAATTA
1 AAAATTA
3733384 AAAATTA
1 AAAATTA
3733391 AAAATTA
1 AAAATTA
3733398 AAAATTA
1 AAAATTA
3733405 AAAATTA
1 AAAATTA
3733412 AAAATTA
1 AAAATTA
3733419 AAAATTA
1 AAAATTA
3733426 AAAATTA
1 AAAATTA
3733433 AAAATTA
1 AAAATTA
3733440 AAAATTA
1 AAAATTA
3733447 AAAATTA
1 AAAATTA
3733454 AAAATTA
1 AAAATTA
3733461 AAAATTA
1 AAAATTA
3733468 AAAATTA
1 AAAATTA
3733475 AAAATTA
1 AAAATTA
3733482 AAAATTA
1 AAAATTA
3733489 AAAATTA
1 AAAATTA
3733496 AAAATTA
1 AAAATTA
3733503 AAAATT
1 AAAATT
3733509 TAGTATATAA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 202 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:3740567 original size:16 final size:17
Alignment explanation
Indices: 3740539--3740572 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3740529 TTAAACAAGT
*
3740539 ATAAAAGACAAAATAAA
1 ATAAAAGACAAAACAAA
3740556 ATAAAA-ACAAAACAAA
1 ATAAAAGACAAAACAAA
3740572 A
1 A
3740573 CATTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (17 bp):
ATAAAAGACAAAACAAA
Found at i:3741589 original size:22 final size:22
Alignment explanation
Indices: 3741564--3741605 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3741554 TGATTCATAA
* *
3741564 ATGTTAGCTTGTGTGAGCAAAT
1 ATGTCAGCTTGTATGAGCAAAT
3741586 ATGTCAGCTTGTATGAGCAA
1 ATGTCAGCTTGTATGAGCAA
3741606 TTCTAATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (22 bp):
ATGTCAGCTTGTATGAGCAAAT
Found at i:3767615 original size:22 final size:21
Alignment explanation
Indices: 3767590--3767633 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3767580 TGATAAACTT
3767590 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
3767612 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
3767633 T
1 T
3767634 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:3773283 original size:18 final size:17
Alignment explanation
Indices: 3773257--3773290 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3773247 AAGAAAAAGA
3773257 ATATAAGTTTGGTAATTG
1 ATATAAG-TTGGTAATTG
*
3773275 ATATTAGTTGGTAATT
1 ATATAAGTTGGTAATT
3773291 CATTTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
ATATAAGTTGGTAATTG
Found at i:3777171 original size:27 final size:27
Alignment explanation
Indices: 3777140--3777194 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3777130 AATAAGACAT
3777140 ACTATACCTTTGATAATAATTCAAATC
1 ACTATACCTTTGATAATAATTCAAATC
3777167 ACTATACCTTTGATAATAATTCAAATC
1 ACTATACCTTTGATAATAATTCAAATC
3777194 A
1 A
3777195 TACTTACCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (27 bp):
ACTATACCTTTGATAATAATTCAAATC
Found at i:3779451 original size:11 final size:11
Alignment explanation
Indices: 3779437--3779499 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
3779427 AATTCGAGGC
3779437 TAATTTAAAAA
1 TAATTTAAAAA
3779448 TAATTTAAAAA
1 TAATTTAAAAA
*
3779459 TCCA-TTAAAAA
1 T-AATTTAAAAA
**
3779470 T-ATGGAAAAA
1 TAATTTAAAAA
3779480 TAAATTT-AAAA
1 T-AATTTAAAAA
3779491 T-ATTTAAAA
1 TAATTTAAAA
3779500 TTACCCTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.12
10 9 0.21
11 25 0.60
12 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (11 bp):
TAATTTAAAAA
Found at i:3779499 original size:21 final size:21
Alignment explanation
Indices: 3779438--3779499 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3779428 ATTCGAGGCT
*
3779438 AATTTAAAAATAATTTAAAAATC
1 AATTT-AAAAT-ATTTAAAAATA
* * **
3779461 CATTAAAAATATGGAAAAATA
1 AATTTAAAATATTTAAAAATA
3779482 AATTTAAAATATTTAAAA
1 AATTTAAAATATTTAAAA
3779500 TTACCCTAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 22 0.73
22 5 0.17
23 3 0.10
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AATTTAAAATATTTAAAAATA
Found at i:3784044 original size:160 final size:160
Alignment explanation
Indices: 3783780--3784090 Score: 525
Period size: 160 Copynumber: 1.9 Consensus size: 160
3783770 CTGTTTTCCA
3783780 TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
1 TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
* *
3783845 GTATGGAAAAGTTGTTGGTACCATACGATATGTTTGTCTTACCAGACTAGATATTTCTTACAGTG
66 GTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGTG
3783910 AACAAAGTAAGTCAATACATGCTATTCACT
131 AACAAAGTAAGTCAATACATGCTATTCACT
* ** * *
3783940 TACTTGAGGCCTTTTATGGCCTAAACTTTA-TGCTATTGATGGTCAACCATTTTCAGATTGCATC
1 TACTTGAAGCCTTTTATGGCCTAAAC-ACACTGCTATTGATGGTAAACAATTTTCAGATTGCATC
* *
3784004 TGTCTGGAAAAGTGGTTGGTACCCTACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGT
65 TGTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGT
3784069 GAACAAAGTAAGTCAATACATG
130 GAACAAAGTAAGTCAATACATG
3784091 AATATTCCTT
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
160 140 0.99
161 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (160 bp):
TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
GTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGTG
AACAAAGTAAGTCAATACATGCTATTCACT
Found at i:3784292 original size:12 final size:12
Alignment explanation
Indices: 3784275--3784300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3784265 TCTATCTTGA
3784275 TGATAATCCTAT
1 TGATAATCCTAT
3784287 TGATAATCCTAT
1 TGATAATCCTAT
3784299 TG
1 TG
3784301 GGTGGTGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (12 bp):
TGATAATCCTAT
Found at i:3785326 original size:13 final size:13
Alignment explanation
Indices: 3785288--3785327 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3785278 TTTAAACTAA
*
3785288 ACTTTTCAAAAGC
1 ACTTTTCAAAAGT
3785301 ACTTCTT-AAAAGT
1 ACTT-TTCAAAAGT
3785314 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
3785327 A
1 A
3785328 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:3802411 original size:15 final size:16
Alignment explanation
Indices: 3802391--3802421 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3802381 TATTATTTAT
3802391 TTATTTAATTA-CTAA
1 TTATTTAATTATCTAA
3802406 TTATTTAATTATCTAA
1 TTATTTAATTATCTAA
3802422 CCTAATTGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAATTATCTAA
Found at i:3806730 original size:14 final size:14
Alignment explanation
Indices: 3806711--3806738 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3806701 CCAATTTATT
3806711 AATGAATTATTAAA
1 AATGAATTATTAAA
3806725 AATGAATTATTAAA
1 AATGAATTATTAAA
3806739 TATAAATTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:3822140 original size:33 final size:33
Alignment explanation
Indices: 3822103--3822170 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
3822093 GGCAAAAAGA
*
3822103 AAAAAAGGAAACAAG-AATAAA-ATAAAATAGAAT
1 AAAAAAGAAAACAAGAAATAAATA-AAAATA-AAT
**
3822136 AAAAACTAAAACAAGAAATAAATAAAAATAAAT
1 AAAAAAGAAAACAAGAAATAAATAAAAATAAAT
3822169 AA
1 AA
3822171 GAAGAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 17 0.57
34 12 0.40
35 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.13
Consensus pattern (33 bp):
AAAAAAGAAAACAAGAAATAAATAAAAATAAAT
Found at i:3822166 original size:10 final size:10
Alignment explanation
Indices: 3822122--3822182 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
3822112 AACAAGAATA
3822122 AAAT-AAAAT
1 AAATAAAAAT
3822131 AGAATAAAAACT
1 A-AATAAAAA-T
*
3822143 AAAACAAGAAAT
1 -AAATAA-AAAT
3822155 AAATAAAAAT
1 AAATAAAAAT
* *
3822165 AAATAAGAAG
1 AAATAAAAAT
3822175 AAATAAAA
1 AAATAAAA
3822183 TTATTAACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 1 0.02
10 22 0.52
11 9 0.21
12 6 0.14
13 4 0.10
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:3822175 original size:24 final size:23
Alignment explanation
Indices: 3822127--3822181 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
3822117 GAATAAAATA
3822127 AAATAGAATAAAAACTAAAACAAG
1 AAATA-AATAAAAACTAAAACAAG
*
3822151 AAATAAATAAAAA-TAAATAAGAAG
1 AAATAAATAAAAACT-AA-AACAAG
3822175 AAATAAA
1 AAATAAA
3822182 ATTATTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 10 0.36
24 17 0.61
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.15
Consensus pattern (23 bp):
AAATAAATAAAAACTAAAACAAG
Found at i:3823369 original size:21 final size:21
Alignment explanation
Indices: 3823339--3823456 Score: 85
Period size: 21 Copynumber: 5.5 Consensus size: 21
3823329 TGCTAGTACA
* *
3823339 GTGTAAATAAACCACTCATTG
1 GTGTAGATAAACCACTCAATG
* *
3823360 GTGTAGATAAAAACTACTACACT-
1 GTGTAGAT--AAACCACT-CAATG
* * *
3823383 ATGTGGATAAACCACTCAACG
1 GTGTAGATAAACCACTCAATG
* **
3823404 ATGTAGATAAACTGCTCAAATG
1 GTGTAGATAAACCACTC-AATG
*
3823426 GTGTGGATAAACCACTCAATG
1 GTGTAGATAAACCACTCAATG
*
3823447 GTGCAGATAA
1 GTGTAGATAA
3823457 TTTGTTCACA
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
20 2 0.03
21 40 0.54
22 16 0.22
23 13 0.18
24 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
GTGTAGATAAACCACTCAATG
Found at i:3837158 original size:11 final size:12
Alignment explanation
Indices: 3837130--3837157 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3837120 TTGTTTATAA
3837130 TTTTTAACAATT
1 TTTTTAACAATT
3837142 TTTTTAACAATT
1 TTTTTAACAATT
3837154 TTTT
1 TTTT
3837158 ATGTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTAACAATT
Found at i:3838969 original size:8 final size:8
Alignment explanation
Indices: 3838956--3838989 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
3838946 ATATGGATGC
3838956 TTGTGAAA
1 TTGTGAAA
3838964 TTGTGAAA
1 TTGTGAAA
3838972 TTGTGAAA
1 TTGTGAAA
3838980 TTGTGAAA
1 TTGTGAAA
3838988 TT
1 TT
3838990 AAGAACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (8 bp):
TTGTGAAA
Found at i:3849791 original size:39 final size:39
Alignment explanation
Indices: 3849748--3849849 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
3849738 CACAGCCTTG
* *
3849748 CCCAACACCTACATCCCCGTGTGGGCCAACAC-GACCTGA
1 CCCAACACCTACATGCTCGTGTGGGCCAACACGGA-CTGA
* * *
3849787 CCCAACACCAACATGCTTGTGTGGGCCCACACGGACTGA
1 CCCAACACCTACATGCTCGTGTGGGCCAACACGGACTGA
*
3849826 CCCAACACTTACATGCTCGTGTGG
1 CCCAACACCTACATGCTCGTGTGG
3849850 TATGTCCGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
39 52 0.96
40 2 0.04
ACGTcount: A:0.25, C:0.38, G:0.21, T:0.17
Consensus pattern (39 bp):
CCCAACACCTACATGCTCGTGTGGGCCAACACGGACTGA
Found at i:3857105 original size:15 final size:15
Alignment explanation
Indices: 3857085--3857114 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3857075 TTCGTCGCGC
3857085 CCACGAATACCACGA
1 CCACGAATACCACGA
*
3857100 CCACGAATTCCACGA
1 CCACGAATACCACGA
3857115 GCGCTCATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.40, G:0.13, T:0.10
Consensus pattern (15 bp):
CCACGAATACCACGA
Found at i:3859043 original size:17 final size:17
Alignment explanation
Indices: 3859021--3859065 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
3859011 AAAGAATGTG
3859021 AATTTGGAAAAAGGCAA
1 AATTTGGAAAAAGGCAA
3859038 AATTTGGAAAAAGGCAA
1 AATTTGGAAAAAGGCAA
3859055 AATTTGGAAAA
1 AATTTGGAAAA
3859066 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (17 bp):
AATTTGGAAAAAGGCAA
Found at i:3860315 original size:16 final size:16
Alignment explanation
Indices: 3860294--3860324 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3860284 ATATGTACGC
*
3860294 TTGTGAAATTGTGAAG
1 TTGTGAAATTATGAAG
3860310 TTGTGAAATTATGAA
1 TTGTGAAATTATGAA
3860325 CATACATGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (16 bp):
TTGTGAAATTATGAAG
Found at i:3863447 original size:22 final size:22
Alignment explanation
Indices: 3863422--3863466 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3863412 AGATACAAAA
3863422 GTAGAAAATATCAGATATAGAT
1 GTAGAAAATATCAGATATAGAT
* * *
3863444 GTAGGACATATTAGATATAGAT
1 GTAGAAAATATCAGATATAGAT
3863466 G
1 G
3863467 CAAACTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
GTAGAAAATATCAGATATAGAT
Found at i:3866599 original size:22 final size:22
Alignment explanation
Indices: 3866574--3866618 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3866564 ATACAGAAAT
*
3866574 AGAAAATATCATATACAAATGC
1 AGAAAATATCAAATACAAATGC
* *
3866596 AGAACATATCAAATACAGATGC
1 AGAAAATATCAAATACAAATGC
3866618 A
1 A
3866619 AATTCCTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (22 bp):
AGAAAATATCAAATACAAATGC
Found at i:3867347 original size:63 final size:62
Alignment explanation
Indices: 3867231--3867353 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
3867221 TCCTAGGCCT
* * * *
3867231 GTGTGACCTTAAATCCAAACAATGAGTTACACGGCCTCGGCACATGCCCGTGTCTCTAGCTC
1 GTGTGACCTTAAATCCAAACAATAAGTTACACAGCCTCGGCACACGCCCGTGTCCCTAGCTC
* * * *
3867293 GTGTGACCTTAAATCCAAAACAGTAAGTTATACAG-CTTGGACGCACGCCCGTGTCCCTAGC
1 GTGTGACCTTAAATCC-AAACAATAAGTTACACAGCCTCGG-CACACGCCCGTGTCCCTAGC
3867354 CCGTATGCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 20 0.39
63 31 0.61
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (62 bp):
GTGTGACCTTAAATCCAAACAATAAGTTACACAGCCTCGGCACACGCCCGTGTCCCTAGCTC
Found at i:3867941 original size:17 final size:17
Alignment explanation
Indices: 3867871--3867943 Score: 51
Period size: 17 Copynumber: 4.1 Consensus size: 17
3867861 ATAAAAAATG
*
3867871 AAAGAAGAAA-TAAGAAA
1 AAAGAAGAAAGGAA-AAA
* *
3867888 TAAGAAGAAAAGGAAAACG
1 AAAGAAG-AAAGGAAAA-A
*
3867907 AAA-AATAAAGGAAGAAAA
1 AAAGAAGAAAGG-A-AAAA
3867925 AAAGAAGAAAGGAAAAA
1 AAAGAAGAAAGGAAAAA
3867942 AA
1 AA
3867944 CATTAAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
17 17 0.40
18 12 0.28
19 14 0.33
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (17 bp):
AAAGAAGAAAGGAAAAA
Found at i:3871608 original size:16 final size:17
Alignment explanation
Indices: 3871587--3871618 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3871577 AAATATGCAA
3871587 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
3871603 TCACATAACTTCATAT
1 TCACATAACTTCATAT
3871619 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:3871846 original size:43 final size:43
Alignment explanation
Indices: 3871779--3871949 Score: 145
Period size: 43 Copynumber: 4.0 Consensus size: 43
3871769 GACTCGTACA
* * * * *
3871779 ATGCCAAC-GTCCCAGACGTTGTCTTACATGTAATCACATATTG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
* * * *
3871822 ATGCCACTGTCCCAGACAAGGTCTTACA-CAAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
* * * * *
3871863 ATGCTAATGTCCTAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATA-TCG
*
3871906 ATGCCAAC-ATCCCAGACATGGTCTTACATGAAAACACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
3871949 A
1 A
3871950 AATCCTATGT
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 26 0.26
42 15 0.15
43 58 0.57
44 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
Found at i:3877633 original size:7 final size:7
Alignment explanation
Indices: 3877621--3877646 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3877611 TAAAAGAATT
3877621 GTCCAAA
1 GTCCAAA
3877628 GTCCAAA
1 GTCCAAA
3877635 GTCCAAA
1 GTCCAAA
3877642 GTCCA
1 GTCCA
3877647 CAAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (7 bp):
GTCCAAA
Found at i:3878064 original size:47 final size:47
Alignment explanation
Indices: 3878010--3878160 Score: 207
Period size: 47 Copynumber: 3.2 Consensus size: 47
3878000 GTCACAGTAA
*
3878010 TGCAGATAAACTT-CCAGTTAATAATATTGTGGACAAGCCACCACTTT
1 TGCAGATAAA-TTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
* * *
3878057 TGCAGAT-AATTCGCCACTTAATAAAATTATAGACAAGCCACCACTTT
1 TGCAGATAAATT-GCCACTTAATAATATTGTGGACAAGCCACCACTTT
* * *
3878104 TGTAGATAAATTGCCACTTTATAATATTGTGGACAAGCCACCATTTT
1 TGCAGATAAATTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
3878151 TGCAGATAAA
1 TGCAGATAAA
3878161 CTATCACTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 2 0.02
46 2 0.02
47 82 0.91
48 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (47 bp):
TGCAGATAAATTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
Found at i:3878241 original size:20 final size:20
Alignment explanation
Indices: 3878216--3878254 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3878206 TATGGCCACT
*
3878216 AAAATCACTTTTTAACTTTA
1 AAAATCAATTTTTAACTTTA
*
3878236 AAAATCAATTTTTCACTTT
1 AAAATCAATTTTTAACTTT
3878255 GGCATGTGAG
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCAATTTTTAACTTTA
Found at i:3882349 original size:3 final size:3
Alignment explanation
Indices: 3882341--3882381 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3882331 GTTTGATATA
3882341 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3882382 TTTGGTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3891833 original size:19 final size:19
Alignment explanation
Indices: 3891809--3891851 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3891799 GTGGGGTGGG
*
3891809 AATATACTT-TTTTAATATT
1 AATATAATTATTTTAA-ATT
*
3891828 AATATAATTATTTTTAATT
1 AATATAATTATTTTAAATT
3891847 AATAT
1 AATAT
3891852 TAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATAATTATTTTAAATT
Found at i:3891858 original size:31 final size:33
Alignment explanation
Indices: 3891820--3891881 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
3891810 ATATACTTTT
3891820 TTAATATTAATATAA-TTATT-TTTAATTAATA
1 TTAATATTAATATAATTTATTATTTAATTAATA
*
3891851 TTAATATTAATATAATTTTTTATTTAATTAA
1 TTAATATTAATATAATTTATTATTTAATTAA
3891882 ATTTTAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 15 0.54
32 4 0.14
33 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATATTAATATAATTTATTATTTAATTAATA
Found at i:3891888 original size:28 final size:31
Alignment explanation
Indices: 3891822--3891889 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
3891812 ATACTTTTTT
*
3891822 AATATTAATATAATTATTTTTAATTAATATT
1 AATATTAATATAATTATTTTTAATTAATATA
*
3891853 AATATTAATATAA-T-TTTTTATTTAAT-TA
1 AATATTAATATAATTATTTTTAATTAATATA
*
3891881 AATTTTAAT
1 AATATTAAT
3891890 GAAATGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 9 0.26
29 11 0.32
30 1 0.03
31 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATATTAATATAATTATTTTTAATTAATATA
Found at i:3892108 original size:16 final size:15
Alignment explanation
Indices: 3892087--3892118 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3892077 TTTAGGATAA
3892087 TAATTTAGAGTTAATT
1 TAATTTAGA-TTAATT
3892103 TAATTTAGATTAATT
1 TAATTTAGATTAATT
3892118 T
1 T
3892119 TTACTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TAATTTAGATTAATT
Found at i:3892317 original size:14 final size:15
Alignment explanation
Indices: 3892289--3892364 Score: 70
Period size: 14 Copynumber: 5.0 Consensus size: 15
3892279 GTTTGGCAGT
3892289 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3892303 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
3892317 AAAATGATTTATATTTCTGG
1 AAAATG----AT-TTTCTGG
*
3892337 AAAATGATTTACT-G
1 AAAATGATTTTCTGG
3892351 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3892365 TATTTGGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
13 6 0.12
14 21 0.40
15 9 0.17
16 2 0.04
18 2 0.04
19 3 0.06
20 9 0.17
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3892337 original size:20 final size:20
Alignment explanation
Indices: 3892309--3892347 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3892299 CTGGAAAATG
*
3892309 ATTTTTGGAAAATGATTTAT
1 ATTTCTGGAAAATGATTTAT
3892329 ATTTCTGGAAAATGATTTA
1 ATTTCTGGAAAATGATTTA
3892348 CTGAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTCTGGAAAATGATTTAT
Found at i:3892354 original size:34 final size:33
Alignment explanation
Indices: 3892296--3892359 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
3892286 AGTAAAATAT
*
3892296 TTTCTGGAAAATGATTTTTGGAAAATGATTTATA
1 TTTCTGGAAAATGATTTCTGGAAAAT-ATTTATA
3892330 TTTCTGGAAAATGATTTACT-GAAAATATTT
1 TTTCTGGAAAATGATTT-CTGGAAAATATTT
3892360 TCTGGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 23 0.82
35 1 0.04
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (33 bp):
TTTCTGGAAAATGATTTCTGGAAAATATTTATA
Found at i:3892425 original size:32 final size:32
Alignment explanation
Indices: 3892340--3892426 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
3892330 TTTCTGGAAA
3892340 ATGATTTACTGAAAATATTTTCTGGTATTTGG
1 ATGATTTACTGAAAATATTTTCTGGTATTTGG
* * *
3892372 ATGAATTT-GTGTAAAATATTTTCTGTTGTTTGG
1 ATG-ATTTACTG-AAAATATTTTCTGGTATTTGG
3892405 CA-GATTTACTGAAAATATTTTC
1 -ATGATTTACTGAAAATATTTTC
3892427 CGAAAAAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 20 0.43
33 26 0.55
34 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (32 bp):
ATGATTTACTGAAAATATTTTCTGGTATTTGG
Found at i:3894950 original size:13 final size:13
Alignment explanation
Indices: 3894932--3894957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3894922 CCATTATTCA
3894932 TATATCTCTCACT
1 TATATCTCTCACT
3894945 TATATCTCTCACT
1 TATATCTCTCACT
3894958 CCTAACCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATCTCTCACT
Found at i:3895811 original size:22 final size:22
Alignment explanation
Indices: 3895764--3895818 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3895754 GAATTCTTTT
*
3895764 TAAATTTATTATAATTTAATTG
1 TAAATTTATTATAATTTAATTC
*
3895786 TAAATTTATTCTAATTTACA-TC
1 TAAATTTATTATAATTTA-ATTC
*
3895808 TAAATATATTA
1 TAAATTTATTA
3895819 AATGTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTTATTATAATTTAATTC
Found at i:3899630 original size:69 final size:69
Alignment explanation
Indices: 3899552--3899851 Score: 407
Period size: 69 Copynumber: 4.4 Consensus size: 69
3899542 ATTTCATCCT
*
3899552 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAACTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
*
3899617 ATGA
66 ATTA
3899621 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
3899686 ATTA
66 ATTA
* * * *
3899690 TTTATATTTGTTATATCTATTTATTTATTTTTTTCATATTATTTTACTTTTTAAATACTTAAATT
1 TTTATATTTGTTTTATCTATTTATTTA--TTTAT--TATTCTTTTACTTTTTAAATACCTAAATT
3899755 T-A-A-TA
62 TAATATTA
* * * *
3899760 -TTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACTTAAATTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
3899824 ATTA
66 ATTA
* *
3899828 TGTATA--TATTTTATCTATTT-TTTA
1 TTTATATTTGTTTTATCTATTTATTTA
3899852 CTTTTTAAAT
Statistics
Matches: 209, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
65 28 0.13
66 5 0.02
67 18 0.09
68 2 0.01
69 120 0.57
70 2 0.01
71 5 0.02
72 1 0.00
73 28 0.13
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (69 bp):
TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
ATTA
Found at i:3899735 original size:23 final size:23
Alignment explanation
Indices: 3899687--3899733 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3899677 AAATTTAATA
3899687 TTATTTATATTTGTTATATCTAT
1 TTATTTATATTTGTTATATCTAT
*
3899710 TTATTTAT-TTTTTTCATAT-TAT
1 TTATTTATATTTGTT-ATATCTAT
3899732 TT
1 TT
3899734 TACTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTTATATTTGTTATATCTAT
Found at i:3899761 original size:32 final size:32
Alignment explanation
Indices: 3899725--3899828 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 32
3899715 TATTTTTTTC
3899725 ATATTATTTTACTTTTTAAATACTTAAATTTA
1 ATATTATTTTACTTTTTAAATACTTAAATTTA
* *
3899757 ATATTATATTTA-TTTTATCAAT--TTATTTATTTA
1 ATATTAT-TTTACTTTT-TAAATACTTA--AATTTA
* * *
3899790 TTATTCTTTTACTTCTTAAATACTTAAATTTA
1 ATATTATTTTACTTTTTAAATACTTAAATTTA
3899822 ATATTAT
1 ATATTAT
3899829 GTATATATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
31 3 0.05
32 29 0.52
33 21 0.38
34 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (32 bp):
ATATTATTTTACTTTTTAAATACTTAAATTTA
Found at i:3899799 original size:59 final size:62
Alignment explanation
Indices: 3899718--3899851 Score: 143
Period size: 65 Copynumber: 2.1 Consensus size: 62
3899708 ATTTATTTAT
*
3899718 TTTTTTCATATTATTTTAC-T-TT-TTAAATACTTAAATTTAATATTA-TATTTATTTTATCAA
1 TTTTTT-AT-TTATTTTACTTATTCTTAAATACTTAAATTTAATATTAGTATATATTTTATCAA
3899778 TTTATTTATTTATTATT-CTTTTACTTCTTAAATACTTAAATTTAATATTATGTATATATTTTAT
1 TTT-TTTATTTATT-TTAC--TTA-TTCTTAAATACTTAAATTTAATATTA-GTATATATTTTAT
*
3899842 CTA
60 CAA
3899845 TTTTTTA
1 TTTTTTA
3899852 CTTTTTAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
59 6 0.10
60 7 0.11
61 3 0.05
62 1 0.02
64 2 0.03
65 23 0.37
66 4 0.06
67 16 0.26
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (62 bp):
TTTTTTATTTATTTTACTTATTCTTAAATACTTAAATTTAATATTAGTATATATTTTATCAA
Found at i:3903524 original size:19 final size:20
Alignment explanation
Indices: 3903485--3903524 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3903475 CAATGTCGTA
*
3903485 TATGTAAAATGTATCCGTTT
1 TATGTAAAAAGTATCCGTTT
*
3903505 TATGTAAAAAG-ATTCGTTT
1 TATGTAAAAAGTATCCGTTT
3903524 T
1 T
3903525 CTAGTAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (20 bp):
TATGTAAAAAGTATCCGTTT
Found at i:3911246 original size:20 final size:19
Alignment explanation
Indices: 3911213--3911286 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 19
3911203 ATTCCAAAAA
**
3911213 TAATATTATTTTAATAGATT
1 TAATATTAAATTAATA-ATT
3911233 TAATATTAAATT-A-AATT
1 TAATATTAAATTAATAATT
*
3911250 TAATAATTATATTAATAAATT
1 TAAT-ATTAAATTAAT-AATT
** *
3911271 TTTTATTAATTTAATA
1 TAATATTAAATTAATA
3911287 TTAAAGTGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.16
18 8 0.19
19 3 0.07
20 19 0.44
21 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
TAATATTAAATTAATAATT
Found at i:3911250 original size:17 final size:18
Alignment explanation
Indices: 3911230--3911264 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3911220 ATTTTAATAG
3911230 ATTTAAT-ATTAAATTAA
1 ATTTAATAATTAAATTAA
*
3911247 ATTTAATAATTATATTAA
1 ATTTAATAATTAAATTAA
3911265 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAATAATTAAATTAA
Found at i:3911251 original size:26 final size:23
Alignment explanation
Indices: 3911217--3911291 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 23
3911207 CAAAAATAAT
3911217 ATTATTTTAATAGATTTAATATTAA
1 ATTA-TTTAATA-ATTTAATATTAA
* *
3911242 ATTAAATTTAATAATTATATTAATAA
1 ATT--ATTTAATAATT-TAATATTAA
* *
3911268 ATTTTTTATTAATTTAATATTAA
1 ATTATTTAATAATTTAATATTAA
3911291 A
1 A
3911292 GTGATTATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 8 0.20
24 9 0.22
25 6 0.15
26 17 0.41
27 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATTATTTAATAATTTAATATTAA
Found at i:3912897 original size:15 final size:15
Alignment explanation
Indices: 3912879--3912918 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3912869 TTAATTTTCA
3912879 TTTTAATTATTTATT
1 TTTTAATTATTTATT
*
3912894 TTTTAAATATTTATT
1 TTTTAATTATTTATT
3912909 TTTT-ATTATT
1 TTTTAATTATT
3912919 GAATTTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTATTTATT
Found at i:3914071 original size:3 final size:3
Alignment explanation
Indices: 3914063--3914124 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
3914053 GGATGTTAAC
*
3914063 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3914111 GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
3914125 GCACCCTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:3918380 original size:5 final size:5
Alignment explanation
Indices: 3918372--3918397 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3918362 GAGACGAAAT
3918372 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
3918398 ATATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:3918911 original size:20 final size:20
Alignment explanation
Indices: 3918877--3918926 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3918867 AGGTAAAGGT
3918877 GAAAAGTAAAAG-TTTAGGAG
1 GAAAA-TAAAAGTTTTAGGAG
* *
3918897 GAAAATAAAAGGTTTTGGGGG
1 GAAAATAAAA-GTTTTAGGAG
3918918 GAAAATAAA
1 GAAAATAAA
3918927 TGGGGNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 6 0.23
21 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (20 bp):
GAAAATAAAAGTTTTAGGAG
Found at i:3919921 original size:15 final size:16
Alignment explanation
Indices: 3919893--3919922 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3919883 GAAAAAAAAT
3919893 TTAAATTCTATTTTCC
1 TTAAATTCTATTTTCC
3919909 TTAAATT-TATTTTC
1 TTAAATTCTATTTTC
3919923 TGTTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATTCTATTTTCC
Found at i:3920645 original size:21 final size:21
Alignment explanation
Indices: 3920619--3920659 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3920609 CTAAAAGGGT
3920619 TCAGTTGGACAACTATTTTCC
1 TCAGTTGGACAACTATTTTCC
3920640 TCAGTTGGACAACTATTTTC
1 TCAGTTGGACAACTATTTTC
3920660 TATCCATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (21 bp):
TCAGTTGGACAACTATTTTCC
Found at i:3925893 original size:29 final size:30
Alignment explanation
Indices: 3925872--3925934 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
3925862 TCATGTGTAC
3925872 AATTACAC-CAAATCAAAATTCATGTATCA
1 AATTACACACAAATCAAAATTCATGTATCA
* *
3925901 AATTACACATTAAATCAAAATTCATATAT-A
1 AATTACACA-CAAATCAAAATTCATGTATCA
3925931 AATT
1 AATT
3925935 TAATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 5 0.17
31 17 0.57
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (30 bp):
AATTACACACAAATCAAAATTCATGTATCA
Found at i:3928586 original size:2 final size:2
Alignment explanation
Indices: 3928579--3928616 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3928569 AACAAAAACC
3928579 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3928617 ATGAAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3934896 original size:22 final size:22
Alignment explanation
Indices: 3934862--3935086 Score: 252
Period size: 22 Copynumber: 10.2 Consensus size: 22
3934852 AAGTAAAAAT
3934862 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * *
3934884 TATGGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
3934906 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * *
3934928 TATTGATTGAATGATGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
**
3934950 TGTTGATTAAATACTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * *
3934972 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
*
3934994 TGTTGATTAAATGTTGTCTAAA
1 TGTTGATTAAATGTTGTCCAAA
*** * *
3935016 TGTTGATTGGTTGATGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
3935038 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* **
3935060 TGTTAATTAAATGTTGTCTGAA
1 TGTTGATTAAATGTTGTCCAAA
3935082 TGTTG
1 TGTTG
3935087 GATAATTGTT
Statistics
Matches: 164, Mismatches: 39, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 164 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (22 bp):
TGTTGATTAAATGTTGTCCAAA
Found at i:3935086 original size:44 final size:44
Alignment explanation
Indices: 3934859--3935077 Score: 312
Period size: 44 Copynumber: 5.0 Consensus size: 44
3934849 TTGAAGTAAA
* * *
3934859 AATTGTTGATTAAATGTTGTCCAAATATGGATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTCC
*
3934903 AATTGTTGATTAAATGTTGTCCAAATATTGATTGAATGATGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTCC
** * *
3934947 AATTGTTGATTAAATACTGTCCAAATGTTGATTTAATGCTGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTCC
* **
3934991 AATTGTTGATTAAATGTTGTCTAAATGTTGATTGGTTGATGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTCC
* * *
3935035 AATTGTTGATTAAATGTTGTCCAAATGTTAATTAAATGTTGTC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTC
3935078 TGAATGTTGG
Statistics
Matches: 155, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 155 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (44 bp):
AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGATGTCC
Found at i:3937052 original size:160 final size:161
Alignment explanation
Indices: 3936870--3937190 Score: 536
Period size: 160 Copynumber: 2.0 Consensus size: 161
3936860 TTTTAATATA
* *
3936870 CACGGTCATCCATAAGAATTTCCAATGATGAGTTAAGAATTTCAGATAATTATAAAAATCAAGAA
1 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
* *
3936935 GTTTAATAGTGTTATGTAAAAATTCATC-GTTAAAGGTCAAGATAAAAACTTTTGTTGCAAGAGA
66 GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
* ** *
3936999 AAATATTTAAAATGGTTTAAGAAAACTTATT
131 AAATATGTAAAATACTTTAAAAAAACTTATT
3937030 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
1 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
** *
3937095 GTTTAATCTTATTATGTAAAAATTCATCATTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
66 GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
3937160 AAATATGTAAAATACTTTAAAAAAACTTATT
131 AAATATGTAAAATACTTTAAAAAAACTTATT
3937191 TAATGCAAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
160 88 0.59
161 61 0.41
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (161 bp):
CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
AAATATGTAAAATACTTTAAAAAAACTTATT
Found at i:3937562 original size:8 final size:7
Alignment explanation
Indices: 3937540--3937571 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3937530 AGAAACACCA
3937540 CTAAACC
1 CTAAACC
3937547 CTAAACC
1 CTAAACC
3937554 CTAAAACC
1 CT-AAACC
3937562 CTAAACC
1 CTAAACC
3937569 CTA
1 CTA
3937572 GGGTAAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:3937562 original size:15 final size:15
Alignment explanation
Indices: 3937542--3937571 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3937532 AAACACCACT
3937542 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
3937557 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
3937572 GGGTAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:3939180 original size:13 final size:14
Alignment explanation
Indices: 3939139--3939180 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3939129 AATCCAAGTC
* *
3939139 AAATAAAACAATTA
1 AAATAAAATAACTA
3939153 AAAT-AAATAACTA
1 AAATAAAATAACTA
3939166 AAATAAAATAA-TA
1 AAATAAAATAACTA
3939179 AA
1 AA
3939181 TCAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:3941381 original size:62 final size:59
Alignment explanation
Indices: 3941277--3941477 Score: 156
Period size: 62 Copynumber: 3.2 Consensus size: 59
3941267 ATCACTTTAA
* * * *
3941277 TATTAAATTAATATAATACTTTTCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
3941336 TATTAAATTAATAGAATA-TTAATCTACAAGATAAACATTAAATTAAATTAAATATTAAGATAAT
1 TATTAAATTAATAGAATACTT--T-T-CAAGATAAACATTAAATTAAATTAAATATT---A-AAT
3941400 CACTTT
58 --C--T
* * * ** *
3941406 AATATTAAATTAATAAAATAATATT-AAGATAATTATTAAATTAAATTTAATATTAAATC-
1 --TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
*
3941465 TATTAAAATAATA
1 TATTAAATTAATA
3941478 TTATATTTGG
Statistics
Matches: 117, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
57 12 0.10
58 2 0.02
59 17 0.15
60 1 0.01
61 1 0.01
62 28 0.24
64 3 0.03
65 2 0.02
66 3 0.03
68 27 0.23
70 2 0.02
71 1 0.01
72 17 0.15
73 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
Found at i:3941418 original size:37 final size:35
Alignment explanation
Indices: 3941372--3941480 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
3941362 CAAGATAAAC
3941372 ATTAAATTAA-ATTAAATATTAAGATAATCACTTTAA
1 ATTAAATTAATATTAAATATTAAGATAATCA--TTAA
** *
3941408 TATTAAATTAATAAAATAATATTAAGATAATTATTAA
1 -ATTAAATTAATATTA-AATATTAAGATAATCATTAA
*
3941445 ATTAAATTTAATATTAAATCTATTAAAATAAT-ATTA
1 ATTAAA-TTAATATTAAA--TATTAAGATAATCATTA
3941481 TATTTGGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
36 8 0.13
37 25 0.41
38 13 0.21
39 15 0.25
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (35 bp):
ATTAAATTAATATTAAATATTAAGATAATCATTAA
Found at i:3941439 original size:23 final size:25
Alignment explanation
Indices: 3941377--3941480 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 25
3941367 TAAACATTAA
*
3941377 ATTAA-ATTAAA-TATTAAGATAAT
1 ATTAAGATTAAATTATTAAAATAAT
* *
3941400 CACTTTAATATTAAATTAATAAAATAAT
1 -A--TTAAGATTAAATTATTAAAATAAT
*
3941428 ATTAAGA-T-AATTATTAAATTAA-
1 ATTAAGATTAAATTATTAAAATAAT
*
3941450 ATTTAATATTAAATCTATTAAAATAAT
1 A-TTAAGATTAAAT-TATTAAAATAAT
3941477 ATTA
1 ATTA
3941481 TATTTGGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.02
23 17 0.27
24 3 0.05
25 8 0.12
26 17 0.27
27 8 0.12
28 10 0.16
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTAAGATTAAATTATTAAAATAAT
Found at i:3942965 original size:14 final size:14
Alignment explanation
Indices: 3942948--3942978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3942938 AATATTTGCT
*
3942948 TATCACAATTTCGC
1 TATCACAATTTCAC
3942962 TATCACAATTTCAC
1 TATCACAATTTCAC
3942976 TAT
1 TAT
3942979 GCATGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (14 bp):
TATCACAATTTCAC
Found at i:3943562 original size:22 final size:22
Alignment explanation
Indices: 3943537--3943581 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3943527 AATAAAGAAA
*
3943537 TATAATTCTATAAGGATTTTAC
1 TATAATTCTATAAGAATTTTAC
*
3943559 TATAATTCTATGAGAATTTTAC
1 TATAATTCTATAAGAATTTTAC
3943581 T
1 T
3943582 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TATAATTCTATAAGAATTTTAC
Found at i:3948263 original size:5 final size:5
Alignment explanation
Indices: 3948253--3948281 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3948243 NNNNNNNNNN
3948253 TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATA TAATA TAATA TAATA TAATA TAAT
3948282 GTGATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:3955137 original size:175 final size:175
Alignment explanation
Indices: 3954845--3955194 Score: 655
Period size: 175 Copynumber: 2.0 Consensus size: 175
3954835 CCTCTTCCAT
3954845 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
1 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
* * *
3954910 CTGTGTTAATGCCTTTCGATCCTTGCGCTTCTTCTCTTCTTCCGTTAATGTTGAAGGCATCTTAT
66 CTGTGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCCGTCAATGTTGAAGGCATCTTAT
3954975 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
131 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
3955020 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
1 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
*
3955085 CTGTGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
66 CTGTGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCCGTCAATGTTGAAGGCATCTTAT
*
3955150 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGTAAGAACTA
131 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
3955195 CATGCATCTT
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 170 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (175 bp):
AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
CTGTGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCCGTCAATGTTGAAGGCATCTTAT
CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
Found at i:3962734 original size:44 final size:44
Alignment explanation
Indices: 3962684--3962860 Score: 354
Period size: 44 Copynumber: 4.0 Consensus size: 44
3962674 ACTTTTGAAC
3962684 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
3962728 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
3962772 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
3962816 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
3962860 A
1 A
3962861 TTATATAAAT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 133 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (44 bp):
AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
Found at i:3962816 original size:24 final size:24
Alignment explanation
Indices: 3962789--3962864 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 24
3962779 ATGATACTTC
3962789 ATGAATTATGATGATATCAATAAA
1 ATGAATTATGATGATATCAATAAA
* ** **
3962813 ATGAGA-CACAATGATA-C--TTCA
1 ATGA-ATTATGATGATATCAATAAA
3962834 -TGAATTATGATGATATCAATAAA
1 ATGAATTATGATGATATCAATAAA
3962857 ATG-ATTAT
1 ATGAATTAT
3962865 ATAAATTTGG
Statistics
Matches: 36, Mismatches: 10, Indels: 13
0.61 0.17 0.22
Matches are distributed among these distances:
19 1 0.03
20 10 0.28
21 3 0.08
23 8 0.22
24 13 0.36
25 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (24 bp):
ATGAATTATGATGATATCAATAAA
Found at i:3965187 original size:15 final size:15
Alignment explanation
Indices: 3965169--3965199 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3965159 GAAGAAGAGG
*
3965169 AGAAGGAGGAGAAAA
1 AGAAGGAGAAGAAAA
3965184 AGAAGGAGAAGAAAA
1 AGAAGGAGAAGAAAA
3965199 A
1 A
3965200 AAATAGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAGGAGAAGAAAA
Found at i:3966276 original size:21 final size:21
Alignment explanation
Indices: 3966251--3966304 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3966241 ATCTTTTTGG
*
3966251 TGAGTTGGGGCAGATTGTTGA-
1 TGAGTTGGGGCAGATTG-TAAC
* *
3966272 TGAGTTTGGGCAGTTTGTAAC
1 TGAGTTGGGGCAGATTGTAAC
3966293 TGAGTTGGGGCA
1 TGAGTTGGGGCA
3966305 ACCACTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.19, C:0.07, G:0.41, T:0.33
Consensus pattern (21 bp):
TGAGTTGGGGCAGATTGTAAC
Found at i:3967108 original size:77 final size:77
Alignment explanation
Indices: 3966996--3967170 Score: 251
Period size: 77 Copynumber: 2.3 Consensus size: 77
3966986 AAAAAACAAT
* * * * *
3966996 CACTGCATGCATATTAAAAAATAGTCAATAGCATGTGACCATCCCCACCAAAAATCATACACAGA
1 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
* * *
3967061 TAGATTAGAAAA
66 CAAATTAAAAAA
* *
3967073 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACTAGCCCCACCAACAATCATACACAAA
1 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
3967138 CAAATTAAAAAA
66 CAAATTAAAAAA
*
3967150 CACTACATGCATGTTAAAAAA
1 CACTACATGCATATTAAAAAA
3967171 CACTCACTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 87 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (77 bp):
CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
CAAATTAAAAAA
Found at i:3971555 original size:26 final size:26
Alignment explanation
Indices: 3971525--3971577 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3971515 CCATAAAGGT
3971525 AGACAAAAACCAAACCATTTAATACA
1 AGACAAAAACCAAACCATTTAATACA
*
3971551 AGACAATAACCAAACCATTTAATACA
1 AGACAAAAACCAAACCATTTAATACA
3971577 A
1 A
3971578 CATAGGCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.04, T:0.17
Consensus pattern (26 bp):
AGACAAAAACCAAACCATTTAATACA
Found at i:3971859 original size:48 final size:48
Alignment explanation
Indices: 3971790--3971923 Score: 207
Period size: 48 Copynumber: 2.8 Consensus size: 48
3971780 TAGGATACAA
3971790 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
1 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
** *
3971838 ACAATGGTTGATACAAACAATAAACATCAGTTTCATAATGTCATTCAT
1 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
*
3971886 ACAAT-GACAGATACAAAACAATAAACACCAGTTTGATA
1 ACAATGGA-AGATAC-AAACAATAAACATCAGTTTGATA
3971924 CAAACAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 55 0.71
49 21 0.27
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (48 bp):
ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
Found at i:3972066 original size:35 final size:34
Alignment explanation
Indices: 3972017--3972083 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
3972007 CATTAATAAA
* *
3972017 AAAATAAAACCAAAATTAAAATAACCCTAAATCC
1 AAAATAAAACCAAAATCAAAATAACCCAAAATCC
* *
3972051 AAAATCAAAATCAAAATCGAAATAACCCAAAAT
1 AAAAT-AAAACCAAAATCAAAATAACCCAAAAT
3972084 AACCCTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.63, C:0.19, G:0.01, T:0.16
Consensus pattern (34 bp):
AAAATAAAACCAAAATCAAAATAACCCAAAATCC
Found at i:3972319 original size:44 final size:41
Alignment explanation
Indices: 3972242--3972348 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 41
3972232 GAAAAAGATC
* *
3972242 AATCGATTTCTAACCCTATACC-A-TGTTAATCGATTATTG
1 AATCGATTTCTAACCCTAAACCAACTGTTAATCGATTACTG
*
3972281 AATCGATATTCTAACCCTAAACCAACTTTGTTAATCGATTCCTG
1 AATCGAT-TTCTAACCCTAAACCAAC--TGTTAATCGATTACTG
*
3972325 AATCAATTTCTAACCC-AAACCAAC
1 AATCGATTTCTAACCCTAAACCAAC
3972349 CCAAATCACA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 7 0.12
40 14 0.24
41 1 0.02
42 8 0.14
43 9 0.15
44 20 0.34
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (41 bp):
AATCGATTTCTAACCCTAAACCAACTGTTAATCGATTACTG
Found at i:3973422 original size:15 final size:15
Alignment explanation
Indices: 3973402--3973434 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3973392 AATTTCATAA
3973402 TTATTT-TTTATATTT
1 TTATTTATTTA-ATTT
3973417 TTATTTATTTAATTT
1 TTATTTATTTAATTT
3973432 TTA
1 TTA
3973435 AAAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTATTTAATTT
Found at i:3982565 original size:275 final size:275
Alignment explanation
Indices: 3982074--3982623 Score: 1046
Period size: 275 Copynumber: 2.0 Consensus size: 275
3982064 AATCAACCTA
*
3982074 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAATCATTCCAACAACATAAATATTCATAGAT
1 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
**
3982139 ATGTTCATTATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
66 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
*
3982204 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCTGTTGTCCTCGTCGACAAAGGCTGCTAACAC
131 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
*
3982269 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGGCAAGACAGCA
196 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
3982334 AGAGAATTTTGGAAT
261 AGAGAATTTTGGAAT
*
3982349 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAATAACATAAATATTCATAGAT
1 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
3982414 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
66 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
3982479 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
131 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
3982544 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
196 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
3982609 AGAGAATTTTGGAAT
261 AGAGAATTTTGGAAT
3982624 GGAAAAGAAT
Statistics
Matches: 269, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
275 269 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (275 bp):
ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
AGAGAATTTTGGAAT
Found at i:3993090 original size:26 final size:26
Alignment explanation
Indices: 3993054--3993106 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3993044 GGGACAAAGG
3993054 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
3993080 CCTCGAATCCTGTCTTTGACGGCGAT
1 CCTCGAATCCTGTCTTTGACGGCGAT
3993106 C
1 C
3993107 ATAGCGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.30
Consensus pattern (26 bp):
CCTCGAATCCTGTCTTTGACGGCGAT
Found at i:4002021 original size:41 final size:40
Alignment explanation
Indices: 4001976--4002075 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 40
4001966 CCATAATAAT
4001976 TAAAGCAATAGTGGCATTTATGAT-AAAAACACCGCAAAAGG
1 TAAAGCAATAGTGGCATTT-T-ATCAAAAACACCGCAAAAGG
* * * * *
4002017 TAAAGCATTAGCGG-AGTTTTCTCATAAACGCCGCAAAAGG
1 TAAAGCAATAGTGGCA-TTTTATCAAAAACACCGCAAAAGG
*
4002057 T-GAGCAATAGTGGCATTTT
1 TAAAGCAATAGTGGCATTTT
4002076 TTGTCCAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
39 14 0.29
40 19 0.40
41 15 0.31
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (40 bp):
TAAAGCAATAGTGGCATTTTATCAAAAACACCGCAAAAGG
Found at i:4002362 original size:76 final size:74
Alignment explanation
Indices: 4002152--4002372 Score: 209
Period size: 75 Copynumber: 2.9 Consensus size: 74
4002142 ACCTTGATCG
* * **
4002152 TTTTCCCTAAATTAG-T-TCCCCTTCCCAAAATCCCTAAGTATTTTTCCCAAAATCCTTCCCTTT
1 TTTTCCCCAAATTAGTTCTCCCCTTCCCGAAATCCCTAAGT-TTTTTCCC-AAATCCTT-TATTT
*
4002215 TTGCCCAATTCA
63 TTCCCCAATTCA
* * * *
4002227 TTTCCCCCAAATTAATTC-CCCC-TCCACGAAATCCCT-AGTTTTATCCAAAAATCCCTTTATTT
1 TTTTCCCCAAATTAGTTCTCCCCTTCC-CGAAATCCCTAAGTTTTTTCC-CAAAT-CCTTTA-TT
* *
4002289 TTTCCCCATTTTA
62 TTTCCCCAATTCA
* * *
4002302 TTTTCCCCAAATCAGTTCTCCCCTTCCCGAAATCCCTAACTTTTTTCCCAATTCCTTTTATTTTT
1 TTTTCCCCAAATTAGTTCTCCCCTTCCCGAAATCCCTAAGTTTTTTCCCAAATCC-TTTATTTTT
4002367 CCCCAA
65 CCCCAA
4002373 ATTAGTTCCC
Statistics
Matches: 117, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
74 10 0.09
75 61 0.52
76 35 0.30
77 11 0.09
ACGTcount: A:0.23, C:0.34, G:0.03, T:0.39
Consensus pattern (74 bp):
TTTTCCCCAAATTAGTTCTCCCCTTCCCGAAATCCCTAAGTTTTTTCCCAAATCCTTTATTTTTC
CCCAATTCA
Found at i:4002388 original size:60 final size:61
Alignment explanation
Indices: 4002297--4002411 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
4002287 TTTTTCCCCA
*
4002297 TTTTATTTTCCCCAAATCAGTTCTCCCCTT-CCCGAAATCCCTAACTTTTTTCCCAATTCC
1 TTTTATTTTCCCCAAATCAGTTCTCCCCTTCCCCGAAATCCCTAACTCTTTTCCCAATTCC
* *
4002357 TTTTATTTTTCCCCAAATTAGTTC-CCCCTTCCCCGAAATCCCTGACTCTTTTCCC
1 TTTTA-TTTTCCCCAAATCAGTTCTCCCCTTCCCCGAAATCCCTAACTCTTTTCCC
4002412 CAACGTCAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
60 11 0.22
61 39 0.78
ACGTcount: A:0.18, C:0.37, G:0.04, T:0.40
Consensus pattern (61 bp):
TTTTATTTTCCCCAAATCAGTTCTCCCCTTCCCCGAAATCCCTAACTCTTTTCCCAATTCC
Found at i:4002452 original size:25 final size:25
Alignment explanation
Indices: 4002420--4002502 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
4002410 CCCAACGTCA
4002420 GCTGCATCATCGTCGGCAGCCCTCT
1 GCTGCATCATCGTCGGCAGCCCTCT
* *
4002445 GCTGCATCATCATCGGTAGCCCTCT
1 GCTGCATCATCGTCGGCAGCCCTCT
* *
4002470 GCTGCCTC-TCCGTCAGCAGCCCTCT
1 GCTGCATCAT-CGTCGGCAGCCCTCT
4002495 GCTGCATC
1 GCTGCATC
4002503 GCCGTGTAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 1 0.02
25 49 0.98
ACGTcount: A:0.12, C:0.41, G:0.22, T:0.25
Consensus pattern (25 bp):
GCTGCATCATCGTCGGCAGCCCTCT
Found at i:4003792 original size:11 final size:11
Alignment explanation
Indices: 4003771--4003799 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4003761 AATATTTAAC
4003771 TTTTA-ATAAT
1 TTTTATATAAT
4003781 TTTTATATAAT
1 TTTTATATAAT
4003792 TTTTATAT
1 TTTTATAT
4003800 TTCTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTATATAAT
Found at i:4004824 original size:20 final size:20
Alignment explanation
Indices: 4004801--4004864 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
4004791 TTTTATAATT
4004801 TATATTTTTTATAGAATTTA
1 TATATTTTTTATAGAATTTA
4004821 TATATTTTTTATAGAATTTA
1 TATATTTTTTATAGAATTTA
**
4004841 TATATATTTTTATTTAATTTA
1 TATAT-TTTTTATAGAATTTA
4004862 TAT
1 TAT
4004865 TTAGGCTGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TATATTTTTTATAGAATTTA
Found at i:4005054 original size:19 final size:19
Alignment explanation
Indices: 4005032--4005118 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
4005022 TCTATGAATA
4005032 ATTAATTAATTAATTTTTG
1 ATTAATTAATTAATTTTTG
* ** *
4005051 ATTAATTAATTAAATAATC
1 ATTAATTAATTAATTTTTG
* *
4005070 A-TATTTCATAATAATTTTATG
1 ATTAATT-A-ATTAATTTT-TG
* *
4005091 AATAATTAATTAATTTTTT
1 ATTAATTAATTAATTTTTG
4005110 ATTAATTAA
1 ATTAATTAA
4005119 ATAAATAATC
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
18 4 0.08
19 26 0.52
20 13 0.26
21 3 0.06
22 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTAATTAATTAATTTTTG
Found at i:4005126 original size:59 final size:59
Alignment explanation
Indices: 4004984--4005320 Score: 512
Period size: 59 Copynumber: 5.6 Consensus size: 59
4004974 GGAACCCTAA
** * *
4004984 TTTGATTAATTAGTTAAATAATCATAATTCATAATAATTCTATGAATAATTAATTAATTAATT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATG---AA-TAATTAATTAATT
*
4005047 TTTGATTAATTAATTAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
* * *
4005106 TTTTATTAATTAAATAAATAATCATATTTCATAATAATTCTACGAATAATTAATTAATT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
* * *
4005165 TTCGGTTAATTAAATAAATAATCATATGTCATAATAATTTTATGAATAATTAATTAATT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
* *
4005224 TTCGATTAATTAATTAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
*
4005283 TTTGATTAACTAAATAAATAATCATATTTCATAATAAT
1 TTTGATTAATTAAATAAATAATCATATTTCATAATAAT
4005321 GATTATTGTA
Statistics
Matches: 255, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
59 212 0.83
60 2 0.01
63 41 0.16
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (59 bp):
TTTGATTAATTAAATAAATAATCATATTTCATAATAATTTTATGAATAATTAATTAATT
Found at i:4006262 original size:111 final size:112
Alignment explanation
Indices: 4006114--4006354 Score: 346
Period size: 111 Copynumber: 2.1 Consensus size: 112
4006104 AATAAGATAT
4006114 AAAAATACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT-AAAA
1 AAAAATA--AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAA
**
4006178 AAAA-TTT-CTTT-TTTTTTTGTGTCAGAATCAAATATAAAAATACGAAA
64 AAAATTTTCCTTTCTTTTTTCATGTCAGAATCAAATATAAAAATACG-AA
*
4006225 AAAAATTAAAAAAAAAATTTTGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACACAGTAAAAA
1 AAAAA-TAAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT-AAAA
*
4006290 AAAAATTTTTTCCTTTCTTTTTTCATGTCAGAATCAGATATAAAAATACGAA
63 AAAAA--TTTTCCTTTCTTTTTTCATGTCAGAATCAAATATAAAAATACGAA
4006342 AAAAATAAAAAAA
1 AAAAATAAAAAAA
4006355 TTCTATTTCC
Statistics
Matches: 117, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
110 9 0.08
111 46 0.39
112 2 0.02
113 8 0.07
116 11 0.09
117 11 0.09
118 30 0.26
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (112 bp):
AAAAATAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAAAAAAA
AATTTTCCTTTCTTTTTTCATGTCAGAATCAAATATAAAAATACGAA
Found at i:4006825 original size:115 final size:113
Alignment explanation
Indices: 4006461--4006823 Score: 448
Period size: 115 Copynumber: 3.2 Consensus size: 113
4006451 CAAGTCCTAT
* *
4006461 AAAATTTCTTTTTATTTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAGAAAGGAAAAA
1 AAAATTT-TTTTTATTTTTTTCATATTTTTATATCTGATTCTGACACGAAAAAA-AAA-GAAAAA
*** * *
4006526 ATTTTTTTTTTACTGTGTACTGGGTGCTGGCCATTGACAGGCCAGCACCCAAA
63 A--AAATTTTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
** * *
4006579 AAAA----AATTATTTTTTTCCTATTTTTATGTCTGATTCTGACACGAAAAAAAAAGAAAAAAAA
1 AAAATTTTTTTTATTTTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAAA
* *
4006640 AATTTTACTGTTCACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
66 ATTTTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAA
** *
4006689 AAAATTTTTTAAATTTTTTTTCATATTTTTATATCTGACTCTGACACG-AAAAAAAAGAAAAAAA
1 AAAATTTTTTTTA-TTTTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAA
*
4006753 AACTTTTTACTGTTTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAA
65 AA-TTTTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
*
4006803 CAAAATTTTTTTTCTTTTTTT
1 -AAAATTTTTTTTATTTTTTT
4006824 TCTTTTTCAT
Statistics
Matches: 212, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
109 40 0.19
110 7 0.03
111 7 0.03
112 3 0.01
113 40 0.19
114 29 0.14
115 82 0.39
118 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (113 bp):
AAAATTTTTTTTATTTTTTTCATATTTTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAAA
ATTTTTACTGTTTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
Found at i:4012704 original size:43 final size:43
Alignment explanation
Indices: 4012634--4012724 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
4012624 TTTATTACAG
* * *
4012634 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCATGACCT
1 TTAGCGACACTTTTCCCACAAACGCCGCTAAAGAACATGACCT
*
4012677 TTAGCGACACTTTTCCCA-AAACTGCCGCTATAGAACATGACCT
1 TTAGCGACACTTTTCCCACAAAC-GCCGCTAAAGAACATGACCT
4012720 TTAGC
1 TTAGC
4012725 AGCGTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (43 bp):
TTAGCGACACTTTTCCCACAAACGCCGCTAAAGAACATGACCT
Found at i:4020063 original size:31 final size:31
Alignment explanation
Indices: 4020026--4020088 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
4020016 AATAATTAAA
*
4020026 TAAAAGAACACTTAAAGTAAACAGAGAATTT
1 TAAAAGAACACTTAAAGTAAACAAAGAATTT
4020057 TAAAAGAACACTTAAAGTAAACAAAGAATTT
1 TAAAAGAACACTTAAAGTAAACAAAGAATTT
4020088 T
1 T
4020089 CTCATATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.24
Consensus pattern (31 bp):
TAAAAGAACACTTAAAGTAAACAAAGAATTT
Found at i:4024781 original size:24 final size:22
Alignment explanation
Indices: 4024751--4024795 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
4024741 TTGATAAATT
4024751 AAAATTAAAAATTTAATTATTAAA
1 AAAATTAAAAA-TTAATT-TTAAA
*
4024775 AAAATTAAATATTAATTTTAA
1 AAAATTAAAAATTAATTTTAA
4024796 GTTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTAAAAATTAATTTTAAA
Found at i:4024782 original size:16 final size:16
Alignment explanation
Indices: 4024746--4024789 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
4024736 GATGTTTGAT
4024746 AAATTAAA-ATT-AAA
1 AAATTAAATATTAAAA
* *
4024760 AATTTAATTATTAAAA
1 AAATTAAATATTAAAA
4024776 AAATTAAATATTAA
1 AAATTAAATATTAA
4024790 TTTTAAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 6 0.25
15 3 0.12
16 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTAAATATTAAAA
Found at i:4024970 original size:207 final size:208
Alignment explanation
Indices: 4024615--4025029 Score: 823
Period size: 207 Copynumber: 2.0 Consensus size: 208
4024605 TTTACAACAC
4024615 TTATGAGATGTCTTATGCCCCTCATTTATTGTTTCACACTTTTAGTAATAAAATATTTATTTGTA
1 TTATGAGATGTCTTATGCCCCTCATTTATTGTTTCACACTTTTAGTAATAAAATATTTATTTGTA
4024680 GAAAAAAGACACTTGGTTTGTACATTTGATAAATTGTTGATAAAAATTTGTTAAGTGATGTTTGA
66 GAAAAAAGACACTTGGTTTGTACATTTGATAAATTGTTGATAAAAATTTGTTAAGTGATGTTTGA
4024745 TAAATTAAAATTAAAAATTTAATTATTAAAAAAATTAAATATTAATTTTAAGTTATAAATAGGGG
131 TAAATTAAAATTAAAAATTTAATTATTAAAAAAATTAAATATTAATTTTAAGTTATAAATAGGGG
4024810 TG-GACCTCTAAA
196 TGAGACCTCTAAA
4024822 TTATGAGATGTCTTATGCCCCTCATTTATTGTTTCACACTTTTAGTAATAAAATATTTATTTGTA
1 TTATGAGATGTCTTATGCCCCTCATTTATTGTTTCACACTTTTAGTAATAAAATATTTATTTGTA
4024887 GAAAAAAGACACTTGGTTTGTACATTTGATAAATTGTTGATAAAAATTTGTTAAGTGATGTTTGA
66 GAAAAAAGACACTTGGTTTGTACATTTGATAAATTGTTGATAAAAATTTGTTAAGTGATGTTTGA
4024952 TAAATTAAAATTAAAAATTTAATTATTAAAAAAATTAAATATTAATTTTAAGTTATAAATAGGGG
131 TAAATTAAAATTAAAAATTTAATTATTAAAAAAATTAAATATTAATTTTAAGTTATAAATAGGGG
4025017 TGAGACCTCTAAA
196 TGAGACCTCTAAA
4025030 ATAAAAAAAA
Statistics
Matches: 207, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 197 0.95
208 10 0.05
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (208 bp):
TTATGAGATGTCTTATGCCCCTCATTTATTGTTTCACACTTTTAGTAATAAAATATTTATTTGTA
GAAAAAAGACACTTGGTTTGTACATTTGATAAATTGTTGATAAAAATTTGTTAAGTGATGTTTGA
TAAATTAAAATTAAAAATTTAATTATTAAAAAAATTAAATATTAATTTTAAGTTATAAATAGGGG
TGAGACCTCTAAA
Found at i:4024988 original size:24 final size:22
Alignment explanation
Indices: 4024958--4025002 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
4024948 TTGATAAATT
4024958 AAAATTAAAAATTTAATTATTAAA
1 AAAATTAAAAA-TTAATT-TTAAA
*
4024982 AAAATTAAATATTAATTTTAA
1 AAAATTAAAAATTAATTTTAA
4025003 GTTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTAAAAATTAATTTTAAA
Found at i:4024989 original size:16 final size:16
Alignment explanation
Indices: 4024953--4024996 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
4024943 GATGTTTGAT
4024953 AAATTAAA-ATT-AAA
1 AAATTAAATATTAAAA
* *
4024967 AATTTAATTATTAAAA
1 AAATTAAATATTAAAA
4024983 AAATTAAATATTAA
1 AAATTAAATATTAA
4024997 TTTTAAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 6 0.25
15 3 0.12
16 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTAAATATTAAAA
Found at i:4025665 original size:9 final size:10
Alignment explanation
Indices: 4025646--4025700 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
4025636 GACATGTAAC
4025646 AAAAAATTAT
1 AAAAAATTAT
4025656 AAAAAA-TAT
1 AAAAAATTAT
*
4025665 --AAAATTGT
1 AAAAAATTAT
4025673 AATAAGAAGTTAT
1 AA-AA-AA-TTAT
4025686 AAAAAATTAT
1 AAAAAATTAT
4025696 AAAAA
1 AAAAA
4025701 TTGTATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 4 0.11
8 2 0.05
9 3 0.08
10 15 0.41
11 4 0.11
12 4 0.11
13 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:4025674 original size:30 final size:32
Alignment explanation
Indices: 4025640--4025705 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
4025630 TGATATGACA
4025640 TGTAACAAAAAATTATAAAAAA-TAT-AAAAT
1 TGTAACAAAAAATTATAAAAAATTATAAAAAT
* * *
4025670 TGTAATAAGAAGTTATAAAAAATTATAAAAAT
1 TGTAACAAAAAATTATAAAAAATTATAAAAAT
4025702 TGTA
1 TGTA
4025706 TAATGCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 19 0.61
31 3 0.10
32 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (32 bp):
TGTAACAAAAAATTATAAAAAATTATAAAAAT
Found at i:4025920 original size:20 final size:21
Alignment explanation
Indices: 4025886--4025953 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
4025876 CTTCTTTTGG
4025886 TACGATAATTTTTATAGTTTTTT
1 TACGAT-A-TTTTATAGTTTTTT
*
4025909 TACGA-ATTTTATA-TTTCTT
1 TACGATATTTTATAGTTTTTT
* *
4025928 TAC-ATTTTTTTATAGTTTTGT
1 TACGA-TATTTTATAGTTTTTT
4025949 TACGA
1 TACGA
4025954 CTTTATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.03
19 8 0.22
20 14 0.38
21 8 0.22
22 1 0.03
23 5 0.14
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (21 bp):
TACGATATTTTATAGTTTTTT
Found at i:4025975 original size:40 final size:40
Alignment explanation
Indices: 4025894--4025978 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
4025884 GGTACGATAA
* * *
4025894 TTTTTATAGTTTTTTTACGAATTTTATATTTCTTTACATT
1 TTTTTATAGTTTTGTTACGAATTTTAAATTTCTATACATT
*
4025934 TTTTTATAGTTTTGTTACGACTTTATAAAATTT-TATA-ATT
1 TTTTTATAGTTTTGTTACGAATTT-T-AAATTTCTATACATT
4025974 TTTTT
1 TTTTT
4025979 TCTATAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 30 0.77
41 4 0.10
42 5 0.13
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (40 bp):
TTTTTATAGTTTTGTTACGAATTTTAAATTTCTATACATT
Found at i:4026007 original size:9 final size:9
Alignment explanation
Indices: 4025989--4026054 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
4025979 TCTATAGTTC
*
4025989 TATATATTT
1 TATATTTTT
4025998 TATATTTTT
1 TATATTTTT
*
4026007 TATAATATTT
1 TAT-ATTTTT
4026017 TATAATATTTT
1 TAT-AT-TTTT
*
4026028 TACGA-TTTT
1 TA-TATTTTT
4026037 TATATTTTT
1 TATATTTTT
*
4026046 TAAATTTTT
1 TATATTTTT
4026055 CATTAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 1 0.02
9 29 0.62
10 11 0.23
11 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TATATTTTT
Found at i:4026014 original size:19 final size:19
Alignment explanation
Indices: 4025992--4026047 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
4025982 ATAGTTCTAT
*
4025992 ATATTTTATATTTTTTATA
1 ATATTTTATATTTTTTACA
*
4026011 ATATTTTATAATATTTTTACG
1 ATATTTTAT-AT-TTTTTACA
4026032 AT-TTTTATATTTTTTA
1 ATATTTTATATTTTTTA
4026048 AATTTTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 11 0.33
20 8 0.24
21 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATATTTTATATTTTTTACA
Found at i:4026019 original size:10 final size:10
Alignment explanation
Indices: 4025955--4026027 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
4025945 TTGTTACGAC
*
4025955 TTTATAAAAT
1 TTTATAATAT
*
4025965 TTTATAATTT
1 TTTATAATAT
* *
4025975 TTTTTCTATAGT
1 TTTAT-AATA-T
*
4025987 TCTAT-ATAT
1 TTTATAATAT
*
4025996 TTTAT-ATTT
1 TTTATAATAT
4026005 TTTATAATAT
1 TTTATAATAT
4026015 TTTATAATAT
1 TTTATAATAT
4026025 TTT
1 TTT
4026028 TACGATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
9 13 0.26
10 31 0.62
11 2 0.04
12 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:4026730 original size:3 final size:3
Alignment explanation
Indices: 4026722--4026759 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4026712 TTAAGGTCAA
4026722 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4026760 AATTTTCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4027225 original size:18 final size:20
Alignment explanation
Indices: 4027194--4027231 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
4027184 CAAATCAGAA
4027194 ATAAATAAATAAACAAAAAT
1 ATAAATAAATAAACAAAAAT
4027214 ATAAAT-AA-AAACAAAAAT
1 ATAAATAAATAAACAAAAAT
4027232 TATTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
ATAAATAAATAAACAAAAAT
Found at i:4028696 original size:25 final size:26
Alignment explanation
Indices: 4028668--4028724 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
4028658 TTATTACACA
4028668 TTTAAAAAATATTATATATTAT-TAT
1 TTTAAAAAATATTATATATTATATAT
** *
4028693 TTTAAAATTTATTATGTATTATATAT
1 TTTAAAAAATATTATATATTATATAT
*
4028719 TGTAAA
1 TTTAAA
4028725 GATTCATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTAAAAAATATTATATATTATATAT
Found at i:4032676 original size:27 final size:27
Alignment explanation
Indices: 4032646--4032699 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
4032636 CAGAAAGAGG
4032646 TCAATT-TTTTTCAATTTTTTAAGGGGT
1 TCAATTGTTTTTCAA-TTTTTAAGGGGT
4032673 TCAATTGTTTTTCAATTTTTAAGGGGT
1 TCAATTGTTTTTCAATTTTTAAGGGGT
4032700 CCAAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (27 bp):
TCAATTGTTTTTCAATTTTTAAGGGGT
Found at i:4032711 original size:28 final size:27
Alignment explanation
Indices: 4032647--4032712 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
4032637 AGAAAGAGGT
*
4032647 CAATTTTTTTCAATTTTTTAAGGGGTT
1 CAATTTTTTTCAATTTTTTAAGGGGTC
4032674 CAATTGTTTTTCAA-TTTTTAAGGGGTC
1 CAATT-TTTTTCAATTTTTTAAGGGGTC
4032701 CAAAATTTTTTT
1 C--AATTTTTTT
4032713 TACTAACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 18 0.51
28 13 0.37
29 4 0.11
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (27 bp):
CAATTTTTTTCAATTTTTTAAGGGGTC
Found at i:4033412 original size:20 final size:20
Alignment explanation
Indices: 4033387--4033468 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
4033377 TGAGTGTAAA
*
4033387 ATTAAAAAATTTCAAAAATT
1 ATTAAAAAATTTCAAAAAAT
*
4033407 ATTAAAAAAATTCTAAAAAAT
1 ATTAAAAAATTTC-AAAAAAT
*
4033428 ATATAAAAATTTTC---AAAT
1 AT-TAAAAAATTTCAAAAAAT
* *
4033446 GTGAAAAAA-TTCAAAAAAT
1 ATTAAAAAATTTCAAAAAAT
4033465 ATTA
1 ATTA
4033469 TTTATTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
18 5 0.10
19 6 0.12
20 12 0.25
21 8 0.17
22 9 0.19
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTAAAAAATTTCAAAAAAT
Found at i:4033416 original size:21 final size:21
Alignment explanation
Indices: 4033389--4033444 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
4033379 AGTGTAAAAT
*
4033389 TAAAAAATTTCAAAAATTAT-
1 TAAAAAATTTCAAAAAATATA
*
4033409 TAAAAAAATTCTAAAAAATATA
1 TAAAAAATTTC-AAAAAATATA
*
4033431 TAAAAATTTTCAAA
1 TAAAAAATTTCAAA
4033445 TGTGAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.33
21 11 0.37
22 9 0.30
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAAATTTCAAAAAATATA
Found at i:4033768 original size:39 final size:40
Alignment explanation
Indices: 4033725--4033853 Score: 100
Period size: 40 Copynumber: 3.2 Consensus size: 40
4033715 AAAACGCTGA
* *
4033725 TATAGATCAAGAATTAGCGGCGCTATTTGAAAAA-GCCAC
1 TATAGATCAACAATTAGCGACGCTATTTGAAAAACGCCAC
* ** * *
4033764 TATAGGTTGACCATTAGCGACGCTATTTGAAAAACGCCGC
1 TATAGATCAACAATTAGCGACGCTATTTGAAAAACGCCAC
* * * * * * *
4033804 TATAGGTCGACCATTAGCGGCACT-TCTTTAAAAACGCCGC
1 TATAGATCAACAATTAGCGACGCTAT-TTGAAAAACGCCAC
*
4033844 TATATATCAA
1 TATAGATCAA
4033854 GCATTAGTGA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
39 29 0.39
40 45 0.61
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (40 bp):
TATAGATCAACAATTAGCGACGCTATTTGAAAAACGCCAC
Found at i:4033818 original size:40 final size:40
Alignment explanation
Indices: 4033737--4033847 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
4033727 TAGATCAAGA
* *
4033737 ATTAGCGGCGCTATTTGAAAAA-GCCACTATAGGTTGACC
1 ATTAGCGGCGCTATTTGAAAAACGCCGCTATAGGTCGACC
*
4033776 ATTAGCGACGCTATTTGAAAAACGCCGCTATAGGTCGACC
1 ATTAGCGGCGCTATTTGAAAAACGCCGCTATAGGTCGACC
* *
4033816 ATTAGCGGCACT-TCTTTAAAAACGCCGCTATA
1 ATTAGCGGCGCTAT-TTGAAAAACGCCGCTATA
4033848 TATCAAGCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 22 0.34
40 42 0.66
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (40 bp):
ATTAGCGGCGCTATTTGAAAAACGCCGCTATAGGTCGACC
Found at i:4033950 original size:40 final size:40
Alignment explanation
Indices: 4033906--4033986 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
4033896 AGCTTTTGTG
*
4033906 GCATTAGCGGCGCTTCCTG-AAAAACACCGCTATATATCGA
1 GCATTAGCGGCGCTT-CTGAAAAAACACCGCTATAGATCGA
* * * *
4033946 GCATTAGCGGGGCTTTTGAAAAAACGCCGCTGTAGATCGA
1 GCATTAGCGGCGCTTCTGAAAAAACACCGCTATAGATCGA
4033986 G
1 G
4033987 ATTTAGAGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (40 bp):
GCATTAGCGGCGCTTCTGAAAAAACACCGCTATAGATCGA
Found at i:4034054 original size:9 final size:9
Alignment explanation
Indices: 4034040--4034065 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4034030 ATGTTGAGCT
4034040 TTAGTGGCA
1 TTAGTGGCA
4034049 TTAGTGGCA
1 TTAGTGGCA
4034058 TTAGTGGC
1 TTAGTGGC
4034066 GCTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.35, T:0.35
Consensus pattern (9 bp):
TTAGTGGCA
Found at i:4034263 original size:30 final size:31
Alignment explanation
Indices: 4034204--4034262 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4034194 ATTTGAAAGT
4034204 AAAAAATATAAAAATATATTTGTTAAAAATG
1 AAAAAATATAAAAATATATTTGTTAAAAATG
*
4034235 AAAAAA-ATTAAAATACTATTAT-TTAAAA
1 AAAAAATATAAAAATA-TATT-TGTTAAAA
4034263 TAATTTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAAATATAAAAATATATTTGTTAAAAATG
Done.