Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 88 of 313
Found at i:29206237 original size:44 final size:45
Alignment explanation
Indices: 29206184--29206286 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
29206174 TGTCTTTGAC
* * * *
29206184 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
29206228 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
29206274 ATGGACTTACATG
1 ATGGACTTACATG
29206287 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.64
46 18 0.36
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:29206285 original size:46 final size:44
Alignment explanation
Indices: 29206206--29206291 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
29206196 GAATTATTCT
*
29206206 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
*
29206250 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
29206292 TTTCTATTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 15 0.39
46 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
Found at i:29209453 original size:13 final size:13
Alignment explanation
Indices: 29209435--29209461 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29209425 ATGTTAATTG
29209435 AGTTTAGCTTTGT
1 AGTTTAGCTTTGT
29209448 AGTTTAGCTTTGT
1 AGTTTAGCTTTGT
29209461 A
1 A
29209462 AGACTCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (13 bp):
AGTTTAGCTTTGT
Found at i:29213334 original size:15 final size:15
Alignment explanation
Indices: 29213314--29213358 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
29213304 AAGAAAACTG
29213314 AATAAAGAAATCCAA
1 AATAAAGAAATCCAA
* *
29213329 AATAAAGAGATCCAG
1 AATAAAGAAATCCAA
*
29213344 GATAAAGAAA-CCAA
1 AATAAAGAAATCCAA
29213358 A
1 A
29213359 GATACGATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (15 bp):
AATAAAGAAATCCAA
Found at i:29217174 original size:4 final size:4
Alignment explanation
Indices: 29217165--29217189 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29217155 AAACTAAGTA
29217165 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
29217190 GATATAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:29226803 original size:25 final size:25
Alignment explanation
Indices: 29226774--29226824 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29226764 CAAAGGAAAA
**
29226774 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29226799 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29226824 T
1 T
29226825 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:29231475 original size:25 final size:25
Alignment explanation
Indices: 29231447--29231497 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29231437 AAAAGGAAAA
**
29231447 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29231472 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29231497 T
1 T
29231498 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:29233150 original size:12 final size:13
Alignment explanation
Indices: 29233135--29233167 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29233125 GTTTATATTT
29233135 AAAATGTTAC-TA
1 AAAATGTTACTTA
*
29233147 AAAATGTTACTTC
1 AAAATGTTACTTA
29233160 AAAATGTT
1 AAAATGTT
29233168 TATATAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (13 bp):
AAAATGTTACTTA
Found at i:29236166 original size:15 final size:15
Alignment explanation
Indices: 29236142--29236175 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29236132 CTACATCAGT
29236142 GACCCGAAAACCATC
1 GACCCGAAAACCATC
*
29236157 GACCCTAAAACCATC
1 GACCCGAAAACCATC
29236172 GACC
1 GACC
29236176 TTAACTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.41, G:0.12, T:0.09
Consensus pattern (15 bp):
GACCCGAAAACCATC
Found at i:29239357 original size:26 final size:25
Alignment explanation
Indices: 29239309--29239368 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
29239299 TTATTTCATT
* *
29239309 AAATAAAA-A-ATTTTAAAATATAA
1 AAATAAAATATATTTAAAAACATAA
*
29239332 TAAATTAAATATATTTAAAAACATAA
1 -AAATAAAATATATTTAAAAACATAA
29239358 AAATAAAATAT
1 AAATAAAATAT
29239369 TAAAACAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 12 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAAAATATATTTAAAAACATAA
Found at i:29251587 original size:2 final size:2
Alignment explanation
Indices: 29251580--29251621 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
29251570 TAACTAGCTT
* * *
29251580 TA TA TA TA TA TA TA AA TA TA TA AA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29251622 ACACCTTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:29251593 original size:8 final size:8
Alignment explanation
Indices: 29251580--29251617 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
29251570 TAACTAGCTT
*
29251580 TATATATA
1 TATATAAA
29251588 TATATAAA
1 TATATAAA
29251596 TATATAAA
1 TATATAAA
29251604 TATATAAA
1 TATATAAA
29251612 TATATA
1 TATATA
29251618 TATAACACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:29259066 original size:17 final size:17
Alignment explanation
Indices: 29259044--29259085 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
29259034 TACTATAATG
*
29259044 GCAAAAGAATGAAGAGT
1 GCAAAAGAACGAAGAGT
29259061 GCAAAAGAACGAAGAGT
1 GCAAAAGAACGAAGAGT
*
29259078 ACAAAAGA
1 GCAAAAGA
29259086 TGGAGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.10, G:0.26, T:0.07
Consensus pattern (17 bp):
GCAAAAGAACGAAGAGT
Found at i:29262539 original size:284 final size:286
Alignment explanation
Indices: 29262025--29262603 Score: 1126
Period size: 284 Copynumber: 2.0 Consensus size: 286
29262015 AAATAAAACA
29262025 ATAAAAATCACTATTTAAGAAAAACAAAATATTTAGAAATCGAATCTAAAATTGATGAAAAATTA
1 ATAAAAATCACTATTTAAGAAAAACAAAATATTTAGAAATCGAATCTAAAATTGATGAAAAATTA
29262090 TATATAAATACTTTACAACTTTACTTATAATCTAATTGTTGAACATGTATATAATAAATGCCATT
66 TATATAAATACTTTACAA--TTACTTATAATCTAATTGTTGAACATGTATATAATAAATGCCATT
29262155 TGTATATAAAGATTATTCTTTTTTTTTTTAACAATCTCAATATAGATTTTTAGGGGTGAACAAAA
129 TGTATATAAAGATTATTCTTTTTTTTTTTAACAATCTCAATATAGATTTTTAGGGGTGAACAAAA
29262220 TTCGATTCTATTCGAAAAATTCGATAAAAAATTTAAATTTTGAATTAAGTAGTTTGAGTTATTTG
194 TTCGATTCTATTCGAAAAATTCGATAAAAAATTTAAATTTTGAATTAAGTAGTTTGAGTTATTTG
29262285 AGTTAATCAAGTTATTCGGATCAACTAG
259 AGTTAATCAAGTTATTCGGATCAACTAG
29262313 ATAAAAATCACTATTTAAGAAAAACAAAATATTTAGAAATCGAATCTAAAATTGATGAAAAATTA
1 ATAAAAATCACTATTTAAGAAAAACAAAATATTTAGAAATCGAATCTAAAATTGATGAAAAATTA
29262378 TATATAAATACTTTAC-A-TACTTATAATCTAATTGTTGAACATGTATATAATAAATGCCATTTG
66 TATATAAATACTTTACAATTACTTATAATCTAATTGTTGAACATGTATATAATAAATGCCATTTG
29262441 TATATAAAGATTATTCTTTTTTTTTTTAACAATCTCAATATAGATTTTTAGGGGTGAACAAAATT
131 TATATAAAGATTATTCTTTTTTTTTTTAACAATCTCAATATAGATTTTTAGGGGTGAACAAAATT
29262506 CGATTCTATTCGAAAAATTCGATAAAAAATTTAAATTTTGAATTAAGTAGTTTGAGTTATTTGAG
196 CGATTCTATTCGAAAAATTCGATAAAAAATTTAAATTTTGAATTAAGTAGTTTGAGTTATTTGAG
29262571 TTAATCAAGTTATTCGGATCAACTAG
261 TTAATCAAGTTATTCGGATCAACTAG
29262597 ATAAAAA
1 ATAAAAA
29262604 ATTAAGTTTT
Statistics
Matches: 291, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
284 209 0.72
287 1 0.00
288 81 0.28
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (286 bp):
ATAAAAATCACTATTTAAGAAAAACAAAATATTTAGAAATCGAATCTAAAATTGATGAAAAATTA
TATATAAATACTTTACAATTACTTATAATCTAATTGTTGAACATGTATATAATAAATGCCATTTG
TATATAAAGATTATTCTTTTTTTTTTTAACAATCTCAATATAGATTTTTAGGGGTGAACAAAATT
CGATTCTATTCGAAAAATTCGATAAAAAATTTAAATTTTGAATTAAGTAGTTTGAGTTATTTGAG
TTAATCAAGTTATTCGGATCAACTAG
Found at i:29264170 original size:22 final size:22
Alignment explanation
Indices: 29264142--29264186 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29264132 CCAATGATTG
29264142 ACATAATTTCACCGCTTAAAAA
1 ACATAATTTCACCGCTTAAAAA
*
29264164 ACATAATTTCACTGCTTAAAAA
1 ACATAATTTCACCGCTTAAAAA
29264186 A
1 A
29264187 ATCCTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (22 bp):
ACATAATTTCACCGCTTAAAAA
Found at i:29272667 original size:20 final size:19
Alignment explanation
Indices: 29272642--29272698 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
29272632 AATTAAATTA
29272642 AATTTAATATTAAGATAAT
1 AATTTAATATTAAGATAAT
29272661 CAATTTAATATTAA-ATTAAT
1 -AATTTAATATTAAGA-TAAT
* *
29272681 AAATTACTATTAAGATAA
1 AATTTAATATTAAGATAA
29272699 GTATTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (19 bp):
AATTTAATATTAAGATAAT
Found at i:29293357 original size:28 final size:29
Alignment explanation
Indices: 29293325--29293423 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
29293315 ATAATAAGCC
*
29293325 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
29293353 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * *
29293381 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
29293410 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29293424 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 35 0.57
29 17 0.28
30 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:29295886 original size:43 final size:43
Alignment explanation
Indices: 29295839--29295978 Score: 156
Period size: 43 Copynumber: 3.3 Consensus size: 43
29295829 AATGTATTAG
** *
29295839 CACTAAGTGTGCGATACAATTATAGTTTTGACTAATTAATTGA
1 CACTAAGTGTGCGATACAATTATAGCCTCGACTAATTAATTGA
* * *
29295882 CACTAAGTGTGGGATACAATTATAGCCTCGGCTAATTAATTGG
1 CACTAAGTGTGCGATACAATTATAGCCTCGACTAATTAATTGA
* * * **
29295925 CACTAAGTGCGCGAAACAATTATAGCTTC-AGCTAATTAATCAA
1 CACTAAGTGTGCGATACAATTATAGCCTCGA-CTAATTAATTGA
*
29295968 CACTAAATGTG
1 CACTAAGTGTG
29295979 TGAGTTTGTT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (43 bp):
CACTAAGTGTGCGATACAATTATAGCCTCGACTAATTAATTGA
Found at i:29312854 original size:17 final size:17
Alignment explanation
Indices: 29312832--29312869 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
29312822 TTGTTTAATT
29312832 CAGCCTTTTCTTTCCAA
1 CAGCCTTTTCTTTCCAA
29312849 CAGCCTTTTCTTTCCAA
1 CAGCCTTTTCTTTCCAA
29312866 CAGC
1 CAGC
29312870 TTCATAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.37, G:0.08, T:0.37
Consensus pattern (17 bp):
CAGCCTTTTCTTTCCAA
Found at i:29315773 original size:43 final size:43
Alignment explanation
Indices: 29315599--29315771 Score: 147
Period size: 43 Copynumber: 4.0 Consensus size: 43
29315589 ACATAGGATT
* * *
29315599 TCGATATTTGATTTCGTGTACGACCACGTCTGGGACGTTGGCA
1 TCGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
* * * *
29315642 TCGAT-TTGAGATTTACATGTAAGACCATGTCTGGGACATCGGCA
1 TCGATATT-TGA-TTACATGTAAGACCACGTCTGGGACGTTGGCA
* *** * *
29315686 TCG-TATGTGATTTTGTGTAAGACC-CTATCTTGGACAG-TGGCA
1 TCGATATTTGATTACATGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
29315728 TTGATATTTGATTACATGTAAGACCACGTCTGGGATGTTGGCA
1 TCGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
29315771 T
1 T
29315772 TGTACAAGCT
Statistics
Matches: 97, Mismatches: 25, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
42 27 0.28
43 39 0.40
44 31 0.32
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (43 bp):
TCGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
Found at i:29318759 original size:18 final size:19
Alignment explanation
Indices: 29318725--29318763 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29318715 GATAAACTCA
*
29318725 TTATTATGTATGTAAGACT
1 TTATTATCTATGTAAGACT
29318744 TTATTATCTA-GTAAGACT
1 TTATTATCTATGTAAGACT
29318762 TT
1 TT
29318764 TCCTGTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.49
Consensus pattern (19 bp):
TTATTATCTATGTAAGACT
Found at i:29334528 original size:13 final size:13
Alignment explanation
Indices: 29334500--29334540 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
29334490 ACTTTGTTCT
*
29334500 TTTTTTCTA-TTC
1 TTTTTTCTATTTA
29334512 TTTTTTCTATTTA
1 TTTTTTCTATTTA
29334525 TTTTATT-TATTTA
1 TTTT-TTCTATTTA
29334538 TTT
1 TTT
29334541 ATTTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 15 0.58
14 2 0.08
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCTATTTA
Found at i:29334541 original size:12 final size:13
Alignment explanation
Indices: 29334519--29334547 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29334509 TTCTTTTTTC
29334519 TATTTATTTTATT
1 TATTTATTTTATT
29334532 TATTTA-TTTATT
1 TATTTATTTTATT
29334544 TATT
1 TATT
29334548 ATAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:29334564 original size:5 final size:5
Alignment explanation
Indices: 29334547--29334576 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
29334537 ATTTATTTAT
29334547 TATAA TAATAA TATAA TATAA TATAA TATA
1 TATAA T-ATAA TATAA TATAA TATAA TATA
29334577 TATTCTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:29338946 original size:49 final size:49
Alignment explanation
Indices: 29338795--29338970 Score: 146
Period size: 49 Copynumber: 3.6 Consensus size: 49
29338785 TGTGTGTGCT
*
29338795 AGTGTAAGACCTGTCTGGGACATGGCA-TCGACATCGATAG-AT-GAGAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATTAG-CATCGAT-GTATGGA-AGTC
* * * * ** * * * *
29338843 TAATATAAGACCTGCCTAGGACATGGCATCGGCTTC-AAGATATGCAAGTT
1 -AGTGTAAGACCTGTCTGGGACATGGCATTAGCATCGATG-TATGGAAGTC
*
29338893 AGTGTAAGACCTGTCTGGGACATGGCATTAGCCTCGATGTATGGAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATTAGCATCGATGTATGGAAGTC
* *
29338942 AGTGTAATACCTATCTGGGACATGGCATT
1 AGTGTAAGACCTGTCTGGGACATGGCATT
29338971 GACTTAGATG
Statistics
Matches: 99, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 93 0.94
50 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATTAGCATCGATGTATGGAAGTC
Found at i:29345348 original size:54 final size:54
Alignment explanation
Indices: 29345286--29345392 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 54
29345276 AACTTGAACA
*
29345286 GCTCAAGTTATCGATTGTGCTAAATTCGAGTATCCTAATACTTACCTTTGAGCT
1 GCTCAAGTTATCAATTGTGCTAAATTCGAGTATCCTAATACTTACCTTTGAGCT
* *
29345340 GCTCAAGTTATCAATTTTGCTAAATTTGAGTATCCTAATACTTACCTTTGAGC
1 GCTCAAGTTATCAATTGTGCTAAATTCGAGTATCCTAATACTTACCTTTGAGC
29345393 AGTTCACGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (54 bp):
GCTCAAGTTATCAATTGTGCTAAATTCGAGTATCCTAATACTTACCTTTGAGCT
Found at i:29347949 original size:25 final size:25
Alignment explanation
Indices: 29347897--29347949 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
29347887 ATAAAATAAC
* * * *
29347897 TTAAATACTAAAATGGATAGAAAAA
1 TTAAATACCAAAATGAAAACAAAAA
*
29347922 TTAAATACCAAAATGAAAACAAATA
1 TTAAATACCAAAATGAAAACAAAAA
29347947 TTA
1 TTA
29347950 TTCAATGGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (25 bp):
TTAAATACCAAAATGAAAACAAAAA
Found at i:29351600 original size:210 final size:210
Alignment explanation
Indices: 29351044--29351668 Score: 934
Period size: 212 Copynumber: 3.0 Consensus size: 210
29351034 ATGAAAAACT
*
29351044 TAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGATTGACTTGAGCCTGGGTA
1 TAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGA-TCACTTGAGCCTGGGTA
* * *
29351109 ACATACCTCATACTGAATGAAGTAAAGAAAA-AAATTTGAAAAAACCACATTCAATGGGAAATAA
65 ACATAGCTCATACCGAATGAAGTAATGAAAACAAA-TTGAAAAAACCACATTCAATGGGAAATAA
*
29351173 AGTACATGAAAGAATTGAAGATGATTCTTTTTGCAATC-TTGGATTCAACCCAAGCAGTGAAGCA
129 AGTACATGAAAGAATTGAAGATCATTCTTTTTGCAA-CATTGGATTCAACCCAAGCAGTGAAGCA
29351237 AACAAATAAAAGATTCACC
193 AACAAAT-AAAGATTCACC
* *
29351256 TAGAAAGGTTTAGCATACCAGTGTTGGACAAAAGTCAGCATCCAAGAGTCACTTGAGCCTGGGTA
1 TAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGA-TCACTTGAGCCTGGGTA
* * * *
29351321 ACATAGCTCATATCAAATGAAGTAATGAAAACAAACTGAAAAAACCACATTCAATGGGAAATGAA
65 ACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAATAAA
* * *
29351386 GTACATGAGAGAACTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGACGCAAA
130 GTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGCAAA
*
29351451 CAAATAAAGATTCACTT
195 CAAATAAAGATTCAC-C
* * * *
29351468 TA-AAAGGTTTAGCATATCAATGTTAGACAAATGTCAGCAACCAAGATCCAC-CGAGCCTGGGTA
1 TAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGAT-CACTTGAGCCTGGGTA
* * *
29351531 ACATAGCTCATACCGAATGATGCAATGAAAACAAATTGAAAAAGCCACATTCAATGGGAAATAAA
65 ACATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAATAAA
* * *
29351596 GTACATGAAAGGATTGAATATCATCCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGCAAA
130 GTACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGCAAA
29351661 CAAATAAA
195 CAAATAAA
29351669 AGCTTCTCAT
Statistics
Matches: 374, Mismatches: 35, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
210 137 0.37
211 53 0.14
212 181 0.48
213 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (210 bp):
TAGAAAGGTTTAGCATATCAGTGTTGGACAAATGTCAGCATCCAAGATCACTTGAGCCTGGGTAA
CATAGCTCATACCGAATGAAGTAATGAAAACAAATTGAAAAAACCACATTCAATGGGAAATAAAG
TACATGAAAGAATTGAAGATCATTCTTTTTGCAACATTGGATTCAACCCAAGCAGTGAAGCAAAC
AAATAAAGATTCACC
Found at i:29355015 original size:43 final size:43
Alignment explanation
Indices: 29354954--29355038 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
29354944 TTACTAAAAT
*
29354954 TAGGATTTAGTCCTAAAACTTTGCTTTAAATAATTAATTAAAC
1 TAGGATTTAGTCCTAAAACTTTGCTTTAAATAAATAATTAAAC
29354997 TAGGATTTAGTCCTAAAACTTTGCTTTAAATAAATAATTAAA
1 TAGGATTTAGTCCTAAAACTTTGCTTTAAATAAATAATTAAA
29355039 GTATTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (43 bp):
TAGGATTTAGTCCTAAAACTTTGCTTTAAATAAATAATTAAAC
Found at i:29357501 original size:12 final size:12
Alignment explanation
Indices: 29357470--29357505 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29357460 TATCAATTCC
* *
29357470 ATTATTATTATT
1 ATTATTACTACT
29357482 ATTATTACTACT
1 ATTATTACTACT
29357494 ATTATTACTACT
1 ATTATTACTACT
29357506 GTTGTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTACTACT
Found at i:29362932 original size:18 final size:20
Alignment explanation
Indices: 29362911--29362950 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29362901 ATTAATTACC
29362911 AAAAAT-AG-CTTAATGGAT
1 AAAAATAAGCCTTAATGGAT
*
29362929 AAAAATAAGCCTTATTGGAT
1 AAAAATAAGCCTTAATGGAT
29362949 AA
1 AA
29362951 GGCAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAAATAAGCCTTAATGGAT
Found at i:29366722 original size:27 final size:27
Alignment explanation
Indices: 29366692--29366745 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29366682 ATACGGAAGT
*
29366692 GTTCGACGATGAAATCGACAAGCGAAA
1 GTTCGACGATGAAATCAACAAGCGAAA
29366719 GTTCGACGATGAAATCAACAAGCGAAA
1 GTTCGACGATGAAATCAACAAGCGAAA
29366746 CTTTTCGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (27 bp):
GTTCGACGATGAAATCAACAAGCGAAA
Found at i:29366908 original size:47 final size:47
Alignment explanation
Indices: 29366847--29366976 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 47
29366837 ATGCGAATAA
* * * * *
29366847 TACCTTGATTTGGCTACGGCCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGT
* * *
29366894 TACCTTGATTTGGCTACGGGCCATGGTATAGGTGCTTCGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGT
*
29366941 TACCTTGATTTGCCTACGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
29366977 ATCAATTACG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGT
Found at i:29378340 original size:15 final size:13
Alignment explanation
Indices: 29378318--29378361 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 13
29378308 TATATATCCC
29378318 TTATTATATTATAT
1 TTATTATATT-TAT
29378332 TTCATTATATTCTAT
1 TT-ATTATATT-TAT
29378347 TTATATATATTTAT
1 TTAT-TATATTTAT
29378361 T
1 T
29378362 ACATATNTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:29378906 original size:90 final size:90
Alignment explanation
Indices: 29378699--29378895 Score: 394
Period size: 90 Copynumber: 2.2 Consensus size: 90
29378689 AAAGCGTTGT
29378699 GTCCTAACTTACTGGATACGGCGTTTTGTTGTTTCGAGATAGAGATTTTCAAAAAGGTTAGCTTA
1 GTCCTAACTTACTGGATACGGCGTTTTGTTGTTTCGAGATAGAGATTTTCAAAAAGGTTAGCTTA
29378764 GCTTCGAATGTTTTAAAAATATTGC
66 GCTTCGAATGTTTTAAAAATATTGC
29378789 GTCCTAACTTACTGGATACGGCGTTTTGTTGTTTCGAGATAGAGATTTTCAAAAAGGTTAGCTTA
1 GTCCTAACTTACTGGATACGGCGTTTTGTTGTTTCGAGATAGAGATTTTCAAAAAGGTTAGCTTA
29378854 GCTTCGAATGTTTTAAAAATATTGC
66 GCTTCGAATGTTTTAAAAATATTGC
29378879 GTCCTAACTTACTGGAT
1 GTCCTAACTTACTGGAT
29378896 GCGATATTTT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 107 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (90 bp):
GTCCTAACTTACTGGATACGGCGTTTTGTTGTTTCGAGATAGAGATTTTCAAAAAGGTTAGCTTA
GCTTCGAATGTTTTAAAAATATTGC
Found at i:29389571 original size:28 final size:28
Alignment explanation
Indices: 29389532--29389586 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
29389522 CAATCAAATA
29389532 TGGCACTCAGTGTACGAAATATTGAGAC
1 TGGCACTCAGTGTACGAAATATTGAGAC
* * *
29389560 TGGCACTTAGTGTGCGAGATATTGAGA
1 TGGCACTCAGTGTACGAAATATTGAGA
29389587 ACGAAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (28 bp):
TGGCACTCAGTGTACGAAATATTGAGAC
Found at i:29390049 original size:21 final size:22
Alignment explanation
Indices: 29390016--29390058 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29390006 AAGAATGTAT
*
29390016 TATGATGTATGTGGAAATGAAA
1 TATGATGTATGTGCAAATGAAA
*
29390038 TATGAT-TATGTGCCAATGAAA
1 TATGATGTATGTGCAAATGAAA
29390059 CATAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (22 bp):
TATGATGTATGTGCAAATGAAA
Found at i:29390926 original size:66 final size:66
Alignment explanation
Indices: 29390820--29390991 Score: 344
Period size: 66 Copynumber: 2.6 Consensus size: 66
29390810 TAAGTGGTAA
29390820 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATTGGTATGGGTTCAAATGGTTAATGAT
1 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATTGGTATGGGTTCAAATGGTTAATGAT
29390885 G
66 G
29390886 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATTGGTATGGGTTCAAATGGTTAATGAT
1 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATTGGTATGGGTTCAAATGGTTAATGAT
29390951 G
66 G
29390952 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATT
1 GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATT
29390992 TGCACTTACC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 106 1.00
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (66 bp):
GTAATGAATATATTTTATGATTGTTTTGGTTGATTGTATTGGTATGGGTTCAAATGGTTAATGAT
G
Found at i:29399567 original size:70 final size:70
Alignment explanation
Indices: 29399454--29400293 Score: 1680
Period size: 70 Copynumber: 12.0 Consensus size: 70
29399444 CTAAACGATA
29399454 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399519 CCGGC
66 CCGGC
29399524 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399589 CCGGC
66 CCGGC
29399594 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399659 CCGGC
66 CCGGC
29399664 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399729 CCGGC
66 CCGGC
29399734 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399799 CCGGC
66 CCGGC
29399804 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399869 CCGGC
66 CCGGC
29399874 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29399939 CCGGC
66 CCGGC
29399944 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29400009 CCGGC
66 CCGGC
29400014 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29400079 CCGGC
66 CCGGC
29400084 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29400149 CCGGC
66 CCGGC
29400154 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29400219 CCGGC
66 CCGGC
29400224 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
1 ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
29400289 CCGGC
66 CCGGC
29400294 CGTGTATCTC
Statistics
Matches: 770, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 770 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (70 bp):
ACTCAGGAAATTTTTAGGAAACTTAGAAAATTTTTCAAAATACAGGGGACAAACGCCTGTGTGGC
CCGGC
Found at i:29403653 original size:18 final size:17
Alignment explanation
Indices: 29403613--29403653 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29403603 CATGCCCGTA
*
29403613 TGGCCTACACGCCTGTG
1 TGGCCTACACGCCAGTG
*
29403630 TGGCCTACACGCCCAGTT
1 TGGCCTACACG-CCAGTG
29403648 TGGCCT
1 TGGCCT
29403654 TGCCCGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.24
Consensus pattern (17 bp):
TGGCCTACACGCCAGTG
Found at i:29408260 original size:12 final size:12
Alignment explanation
Indices: 29408243--29408276 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
29408233 TTTTCAAGAG
29408243 AAATAAAATAAA
1 AAATAAAATAAA
*
29408255 AAATAAAATAAC
1 AAATAAAATAAA
29408267 AAA-AAAATAA
1 AAATAAAATAA
29408277 TTATATACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:29416538 original size:56 final size:56
Alignment explanation
Indices: 29416452--29416571 Score: 224
Period size: 56 Copynumber: 2.1 Consensus size: 56
29416442 ACAAGGGATG
29416452 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAA-AATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAAT-GAAAGAATAAAATAAGAAGC
29416508 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGAAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGAAAGAATAAAATAAGAAGC
29416564 ATGGGCAA
1 ATGGGCAA
29416572 TAAACTAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 4 0.06
56 59 0.94
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGAAAGAATAAAATAAGAAGC
Found at i:29417894 original size:40 final size:40
Alignment explanation
Indices: 29417702--29417887 Score: 205
Period size: 40 Copynumber: 4.7 Consensus size: 40
29417692 TCGAATGATG
* * * * *
29417702 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTTACTAAA
* ** * *
29417742 TCCGGACTAAGATTCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29417782 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29417822 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29417863 -CCGGGCTATGACCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTG
29417888 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
40 115 0.93
41 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29417894 original size:80 final size:79
Alignment explanation
Indices: 29417756--29417920 Score: 199
Period size: 80 Copynumber: 2.1 Consensus size: 79
29417746 GACTAAGATT
* * **
29417756 CGAAGGCATTTGTGCGAGATACTAATTCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTA
1 CGAAGGCATTTGTGCGAGATACTAATACCGGACTAAGACCCGAAGGCATTTGAACGAG-TAGCTA
*
29417820 AATCCGGGTTAAGTCC
65 AATCC-GGTTAAATCC
* * *
29417836 CGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGACCCGAAGGCATTTGAACGAGTAGCTA
1 CGAAGGCATTTGTGCGAGATACTAAT-ACCGGACTAAGACCCGAAGGCATTTGAACGAGTAGCTA
* *
29417900 TATCCGGTTAAATTC
65 AATCCGGTTAAATCC
29417915 CGAAGG
1 CGAAGG
29417921 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 18 0.25
80 55 0.75
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGATACTAATACCGGACTAAGACCCGAAGGCATTTGAACGAGTAGCTAA
ATCCGGTTAAATCC
Found at i:29419622 original size:21 final size:21
Alignment explanation
Indices: 29419584--29419628 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29419574 GTGAGGGTCT
*
29419584 ACACGCCCATGCGGAGGCCAC
1 ACACGCCCATGCGAAGGCCAC
* * *
29419605 ACACTCCCATGTGAAGGCCCC
1 ACACGCCCATGCGAAGGCCAC
29419626 ACA
1 ACA
29419629 TGACCGTGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.42, G:0.22, T:0.09
Consensus pattern (21 bp):
ACACGCCCATGCGAAGGCCAC
Found at i:29421984 original size:24 final size:24
Alignment explanation
Indices: 29421954--29422032 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
29421944 AAAATACAAC
*
29421954 ATATAATGAAATTTATGAATGTAT
1 ATATAATGAAATTAATGAATGTAT
**
29421978 ATATAATGTTAAA--AAT-AATAAAT
1 ATATAATG--AAATTAATGAATGTAT
*
29422001 ATATAATGAAATTGATGAATGTAT
1 ATATAATGAAATTAATGAATGTAT
29422025 ATATAATG
1 ATATAATG
29422033 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.07
23 15 0.34
24 23 0.52
26 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (24 bp):
ATATAATGAAATTAATGAATGTAT
Found at i:29421992 original size:47 final size:47
Alignment explanation
Indices: 29421940--29422046 Score: 180
Period size: 47 Copynumber: 2.3 Consensus size: 47
29421930 AATAAAAAAA
*
29421940 TAAAAA-AATACAACATATAATGAAATTTATGAATGTATATATAATGT
1 TAAAAATAATA-AACATATAATGAAATTGATGAATGTATATATAATGT
*
29421987 TAAAAATAATAAATATATAATGAAATTGATGAATGTATATATAATGT
1 TAAAAATAATAAACATATAATGAAATTGATGAATGTATATATAATGT
29422034 TAAAAATAATAAA
1 TAAAAATAATAAA
29422047 AATAAAACAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
47 53 0.93
48 4 0.07
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (47 bp):
TAAAAATAATAAACATATAATGAAATTGATGAATGTATATATAATGT
Found at i:29421992 original size:53 final size:52
Alignment explanation
Indices: 29421935--29422062 Score: 167
Period size: 47 Copynumber: 2.5 Consensus size: 52
29421925 AAATAAATAA
*
29421935 AAAAATAAAAAAATACAACATATAATGAAATTTATGAATGTATATATAATGTT
1 AAAAATAAAAAAATA-AACATATAATGAAATTGATGAATGTATATATAATGTT
*
29421988 AAAAAT-----AATAAATATATAATGAAATTGATGAATGTATATATAATGTT
1 AAAAATAAAAAAATAAACATATAATGAAATTGATGAATGTATATATAATGTT
29422035 AAAAATAATAAAAATAAAACAATATAAT
1 AAAAATAA-AAAAAT-AAAC-ATATAAT
29422063 TAACGTTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
47 41 0.64
48 4 0.06
53 9 0.14
54 3 0.05
55 7 0.11
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (52 bp):
AAAAATAAAAAAATAAACATATAATGAAATTGATGAATGTATATATAATGTT
Found at i:29422311 original size:21 final size:22
Alignment explanation
Indices: 29422281--29422323 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29422271 CATTAAAGCT
29422281 AAATTAAAAAATA-AATAAAATG
1 AAATTAAAAAATATAA-AAAATG
29422303 AAATT-AAAAATATAAAAAATG
1 AAATTAAAAAATATAAAAAATG
29422324 CAAGAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAATTAAAAAATATAAAAAATG
Found at i:29422432 original size:29 final size:29
Alignment explanation
Indices: 29422392--29422447 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
29422382 GTAATCGGGC
29422392 CAACACGCGGGTCCTCAAGTTTTAAAAGT
1 CAACACGCGGGTCCTCAAGTTTTAAAAGT
*
29422421 CAACATGCGGGTCCTCAAGTTTTAAAA
1 CAACACGCGGGTCCTCAAGTTTTAAAA
29422448 CGAGGTCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (29 bp):
CAACACGCGGGTCCTCAAGTTTTAAAAGT
Found at i:29423770 original size:87 final size:87
Alignment explanation
Indices: 29423619--29424375 Score: 468
Period size: 87 Copynumber: 8.7 Consensus size: 87
29423609 CAGTGCAGAG
* * * * * ** * * * *
29423619 ATGCCAAACCATCTTAGATTTGCTTCAGCATAAACA-CGTGAAAGCCAAATCTACTGTGTTTTCG
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATC-TGAAGGTTAGATCTGCTATGTATTCG
* *
29423683 ATTTGCTCCTTGTGAACACAAGG
65 ATTTGCTCCTTGTAAACACAAGA
29423706 ATGCCAAATCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATTCG
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTATTCG
*
29423770 ATTTGTTCCTTGTAAACACAAGA
65 ATTTGCTCCTTGTAAACACAAGA
* * *
29423793 ATGTCAAATCATCTTTGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATGTA-TC--
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATTCGA
* * ***
29423855 TGCT-CTCCATCG-AAA-TGGAG-
66 T-TTGCTCC-TTGTAAACACAAGA
* * * ** * * * * *
29423875 ATTCCAGATCTGTTCTCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTTAAATATGCTATGT
1 ATGCCAAATC----ATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATGT
*
29423940 CTTCGATTTGCTCCTTGTAAACACAAGA
60 ATTCGATTTGCTCCTTGTAAACACAAGA
*
29423968 ATGCCAAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATGTA-TC--
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATTCGA
* **
29424030 --TGCT-CTCTGTCGAA-A-TGGA
66 TTTGCTCCT-TGT-AAACACAAGA
* * ** * * * * * *
29424049 GATGTCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTACTATG
1 -ATGCCAAATC----ATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATG
* *
29424114 TCTTCGATTTGTTCCTTGTAAACACAAGA
59 TATTCGATTTGCTCCTTGTAAACACAAGA
*
29424143 ATGCCAAATCATCTTGGTTCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTA-TC--
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATTCGA
* * *
29424205 --TGCT-CTCCGTCGAA-A-TAGA
66 TTTGCTCCT-TGT-AAACACAAGA
* ** * * * * *
29424224 TATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATG
1 -ATGCCAAATC----ATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATG
* * *
29424289 TCTTCTATTTGTTCCTTGTAAACACAAGA
59 TATTCGATTTGCTCCTTGTAAACACAAGA
** *
29424318 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACA-CATGAAGGCCAGATCTGTTATG
1 ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATC-TGAAGGTTAGATCTGCTATG
29424376 CTTTGGTCTG
Statistics
Matches: 509, Mismatches: 108, Indels: 106
0.70 0.15 0.15
Matches are distributed among these distances:
81 9 0.02
82 38 0.07
83 6 0.01
84 7 0.01
85 3 0.01
86 61 0.12
87 187 0.37
88 75 0.15
89 59 0.12
90 3 0.01
91 8 0.02
92 6 0.01
93 38 0.07
94 9 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (87 bp):
ATGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATTCGA
TTTGCTCCTTGTAAACACAAGA
Found at i:29423957 original size:175 final size:175
Alignment explanation
Indices: 29423754--29424375 Score: 1032
Period size: 175 Copynumber: 3.6 Consensus size: 175
29423744 TGAAGGTTAG
* * *
29423754 ATCTGCTATGTATTCGATTTGTTCCTTGTAAACACAAGAATGTCAAATCATCTTTGATCTGCTTC
1 ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
* *
29423819 AATATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCGAAATGGAGATTCCAGAT
66 AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATTCCAGAT
* *
29423884 CTGTTCTCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTTAA
131 CTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
* * *
29423929 ATATGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTT
1 ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
*
29423994 AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGAGATGT-CAGA
66 AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGAT-TCCAGA
29424058 TCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
130 TCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
* *
29424104 ATCTACTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGTTCTGCTTC
1 ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
* * *
29424169 AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATAGATATGCCAGAT
66 AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATTCCAGAT
29424234 CTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
131 CTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
*
29424279 ATCTGCTATGTCTTCTATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
1 ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
** *
29424344 AGTATAAACA-CATGAAGGCCAGATCTGTTATG
66 AGTATAAACATC-TGAAGGTTAGATCTGCTATG
29424376 CTTTGGTCTG
Statistics
Matches: 418, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
174 1 0.00
175 416 1.00
176 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (175 bp):
ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTC
AGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATTCCAGAT
CTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAA
Found at i:29436730 original size:14 final size:15
Alignment explanation
Indices: 29436685--29436743 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
29436675 AGTAAAAACG
*
29436685 AATATATACATAATAA
1 AATATATATATAA-AA
29436701 AATATATATATAAAA
1 AATATATATATAAAA
29436716 AAT-TATATA-AGAAA
1 AATATATATATA-AAA
*
29436730 AATAAATATTATAA
1 AATATATA-TATAA
29436744 GGAATGTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 1 0.03
14 12 0.32
15 8 0.22
16 15 0.41
17 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AATATATATATAAAA
Found at i:29437179 original size:21 final size:22
Alignment explanation
Indices: 29437149--29437191 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29437139 CATTAAAGCT
29437149 AAATTAAAAAATA-AATAAAATG
1 AAATTAAAAAATATAA-AAAATG
29437171 AAATT-AAAAATATAAAAAATG
1 AAATTAAAAAATATAAAAAATG
29437192 CAAGAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAATTAAAAAATATAAAAAATG
Found at i:29439885 original size:47 final size:47
Alignment explanation
Indices: 29439807--29440821 Score: 1877
Period size: 47 Copynumber: 21.6 Consensus size: 47
29439797 CCCTTCGGGA
* * * * * *
29439807 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29439854 CCTGTCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29439901 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29439948 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29439995 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440042 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440089 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440136 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440183 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440230 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440277 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440324 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440371 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440418 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440465 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440512 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440559 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440606 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440653 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29440700 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29440747 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29440796 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
29440822 CACAATTATC
Statistics
Matches: 946, Mismatches: 20, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
47 901 0.95
49 45 0.05
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29447239 original size:26 final size:26
Alignment explanation
Indices: 29447208--29447315 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29447198 TGAAATGCCC
*
29447208 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29447234 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29447260 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29447286 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29447312 ATCA
1 ATCA
29447316 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29454172 original size:26 final size:26
Alignment explanation
Indices: 29454141--29454248 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29454131 TGAAATGCCC
*
29454141 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29454167 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29454193 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29454219 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29454245 ATCA
1 ATCA
29454249 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29483686 original size:13 final size:13
Alignment explanation
Indices: 29483668--29483693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29483658 CAGGACTCTG
29483668 ATTATCTGTATCT
1 ATTATCTGTATCT
29483681 ATTATCTGTATCT
1 ATTATCTGTATCT
29483694 GAGTAAGACA
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:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTATCTGTATCT
Found at i:29494256 original size:27 final size:27
Alignment explanation
Indices: 29494226--29494279 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
29494216 ATATATAATT
29494226 ATTA-TAAAATAGTTAAATTGTACTTAA
1 ATTATTAAAAT-GTTAAATTGTACTTAA
* * *
29494253 ATTATTAACATGTTTAATTTTACTTAA
1 ATTATTAAAATGTTAAATTGTACTTAA
29494280 TTTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTATTAAAATGTTAAATTGTACTTAA
Found at i:29506367 original size:36 final size:35
Alignment explanation
Indices: 29506314--29506384 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
29506304 GTTCCTACAG
29506314 TTAGGTTCAACAATACTAGCGATGTTATATCGTGA
1 TTAGGTTCAACAATACTAGCGATGTTATATCGTGA
* *
29506349 NTTAGGTTCAGCAGTACTAGCGATGTTATATCGTGA
1 -TTAGGTTCAACAATACTAGCGATGTTATATCGTGA
29506385 GCTTTTTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (35 bp):
TTAGGTTCAACAATACTAGCGATGTTATATCGTGA
Found at i:29509340 original size:23 final size:24
Alignment explanation
Indices: 29509314--29509360 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
29509304 ATGATTTATA
*
29509314 CTATGA-TTAATTGTTTTAAAATG
1 CTATGAGTTAATGGTTTTAAAATG
29509337 CTATGATGTTAATGGTTTTAAAAT
1 CTATGA-GTTAATGGTTTTAAAAT
29509361 TGTACGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
25 15 0.71
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
CTATGAGTTAATGGTTTTAAAATG
Found at i:29510306 original size:16 final size:16
Alignment explanation
Indices: 29510285--29510325 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
29510275 GACACAAATT
29510285 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAG
**
29510301 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGAAAAAG
29510317 AGAAAGAAA
1 AGAAAGAAA
29510326 AAACCCACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAG
Found at i:29510768 original size:7 final size:7
Alignment explanation
Indices: 29510758--29510783 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29510748 TTAAATTTTA
29510758 AATATTC
1 AATATTC
29510765 AATATTC
1 AATATTC
29510772 AATATTC
1 AATATTC
29510779 AATAT
1 AATAT
29510784 GAAATTGAAA
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:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:29519942 original size:18 final size:18
Alignment explanation
Indices: 29519919--29519957 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
29519909 ATAAAACATC
29519919 ATCAATGACAAATTTTTT
1 ATCAATGACAAATTTTTT
29519937 ATCAATGACAAATTTTTT
1 ATCAATGACAAATTTTTT
29519955 ATC
1 ATC
29519958 TTTAAGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (18 bp):
ATCAATGACAAATTTTTT
Found at i:29533909 original size:48 final size:48
Alignment explanation
Indices: 29533856--29534037 Score: 197
Period size: 48 Copynumber: 3.8 Consensus size: 48
29533846 AGGGTGAATT
* * * *
29533856 GCCGATACCATGTTCTAAACATGGTCTTACACTGGCTCATATGTCGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATATGTCGAG
* * *
29533904 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATGAT-GTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCAT-ATG-TCGAG
* * * * * * *
29533952 GCCGATGCCATGTCCCAGACATGGTTTTACACTAGCGCACATATCAAC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATATGTCGAG
*
29534000 ACCGATGCCATGTCCCAAACATGGTCTTACACTAGCTC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTC
29534038 TCACAACATC
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
47 2 0.02
48 110 0.97
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCATATGTCGAG
Found at i:29534060 original size:48 final size:48
Alignment explanation
Indices: 29533904--29534117 Score: 221
Period size: 48 Copynumber: 4.5 Consensus size: 48
29533894 ATATGTCGAG
* * ** ** *
29533904 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGATGTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
* * * * * * *
29533952 GCCGATGCCATGTCCCAGACATGGTTTTACACTAGCGCACATATCAAC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
*
29534000 ACCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
* * * * * * * *
29534048 GCGGATGTCATGTTCCAAACATGGTCTTACATTGGCTCTCACATCGTA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
29534096 GCCGATGCCATGTCCCAAACAT
1 GCCGATGCCATGTCCCAAACAT
29534118 AGTATTATAC
Statistics
Matches: 136, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 136 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATC
Found at i:29534101 original size:96 final size:96
Alignment explanation
Indices: 29533856--29534117 Score: 285
Period size: 96 Copynumber: 2.7 Consensus size: 96
29533846 AGGGTGAATT
* * * *
29533856 GCCGATACCATGTTCTAAACATGGTCTTACACTGGCTCAT-ATGTCGAGGCCGATGCCATGTCCC
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTC-TCATATCGACGCCGATGCCATGTCCC
* * ** ** *
29533920 AGACATGGTCTTACACTGGCTCTCATGATGTG
65 AAACATGGTCTTACACTAGCTCTCACAACATC
* * * * * * * *
29533952 GCCGATGCCATGTCCCAGACATGGTTTTACACTAGCGCACATATCAACACCGATGCCATGTCCCA
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGACGCCGATGCCATGTCCCA
29534017 AACATGGTCTTACACTAGCTCTCACAACATC
66 AACATGGTCTTACACTAGCTCTCACAACATC
* * * *
29534048 GCGGATGTCATGTTCCAAACATGGTCTTACATTGGCTCTCACATCGTA-GCCGATGCCATGTCCC
1 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCG-ACGCCGATGCCATGTCCC
29534112 AAACAT
65 AAACAT
29534118 AGTATTATAC
Statistics
Matches: 133, Mismatches: 31, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
96 132 0.99
97 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGACGCCGATGCCATGTCCCA
AACATGGTCTTACACTAGCTCTCACAACATC
Found at i:29537445 original size:11 final size:11
Alignment explanation
Indices: 29537426--29537461 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29537416 CTTTTGATGG
*
29537426 AAAATAAAAGA
1 AAAAGAAAAGA
*
29537437 AAAAGAAAAAA
1 AAAAGAAAAGA
29537448 AAAAGAAAAGA
1 AAAAGAAAAGA
29537459 AAA
1 AAA
29537462 GAAGGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:29537450 original size:16 final size:16
Alignment explanation
Indices: 29537426--29537461 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29537416 CTTTTGATGG
*
29537426 AAAATAAAAGAAAAAGA
1 AAAAAAAAAG-AAAAGA
29537443 AAAAAAAAAGAAAAGA
1 AAAAAAAAAGAAAAGA
29537459 AAA
1 AAA
29537462 GAAGGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAGA
Found at i:29539266 original size:22 final size:22
Alignment explanation
Indices: 29539241--29539285 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29539231 TATTATTTAA
29539241 ATTTAATTAATTTTTTAAA-AAT
1 ATTTAATTAA-TTTTTAAATAAT
*
29539263 ATTTTATTAATTTTTAAATAAT
1 ATTTAATTAATTTTTAAATAAT
29539285 A
1 A
29539286 AATGAGCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAATTAATTTTTAAATAAT
Found at i:29542465 original size:18 final size:19
Alignment explanation
Indices: 29542444--29542482 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29542434 CTAAAAAATT
29542444 AAATGAAATGA-AAATAAA
1 AAATGAAATGAGAAATAAA
* *
29542462 AAATTAAATGAGTAATAAA
1 AAATGAAATGAGAAATAAA
29542481 AA
1 AA
29542483 CATAGCATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
AAATGAAATGAGAAATAAA
Found at i:29544158 original size:93 final size:93
Alignment explanation
Indices: 29543999--29544170 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
29543989 CGCCCATAAG
*
29543999 CGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
29544064 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGAATGCCTAGTTACATCTCA
*
29544092 CGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
29544156 AACGAGTTCGAATGC
65 AACGAGTTCGAATGC
29544171 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGAATGCCTAGTTACATCTCA
Found at i:29544165 original size:46 final size:46
Alignment explanation
Indices: 29543992--29544165 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
29543982 TGTAACCCGC
* *
29543992 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
29544038 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
29544088 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
29544131 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG
29544166 AATGCTCAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 59 0.54
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29544186 original size:46 final size:46
Alignment explanation
Indices: 29543995--29544186 Score: 143
Period size: 46 Copynumber: 4.2 Consensus size: 46
29543985 AACCCGCCCA
* * * *
29543995 TAAGCGAACTCGGACTCAACTCAACGAGCTC--AGGCGTTC-GCATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGC--TCATCATCC
*
29544040 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACAT-C
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCTC-A--T-CATCC
* * *
29544089 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT--TC-GCATCC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GA-ATGCTCATCATCC
29544133 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCTCAATCATCC
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCTC-ATCATCC
29544181 T-AGTGA
1 TAAGTGA
29544187 CATGTCACTT
Statistics
Matches: 118, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
43 3 0.03
44 3 0.03
45 5 0.04
46 62 0.53
47 27 0.23
48 12 0.10
49 3 0.03
50 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCTCATCATCC
Found at i:29552748 original size:28 final size:29
Alignment explanation
Indices: 29552699--29552755 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
29552689 CTTCATTTAC
* * *
29552699 TAAAAAAAACATATCAAGTAT-ATTAAAT
1 TAAAAAAAACACATAAAATATAATTAAAT
*
29552727 TAAAAAAAATACATAAAATATAATTAAAT
1 TAAAAAAAACACATAAAATATAATTAAAT
29552756 AAACAAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (29 bp):
TAAAAAAAACACATAAAATATAATTAAAT
Found at i:29555665 original size:3 final size:3
Alignment explanation
Indices: 29555657--29555693 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
29555647 AGTAAAATTT
*
29555657 ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29555694 ATCTACTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29560260 original size:26 final size:26
Alignment explanation
Indices: 29560231--29560326 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
29560221 TTATATTAAG
29560231 AATTTTATTAAATTATATTTAATAAT
1 AATTTTATTAAATTATATTTAATAAT
* * * **
29560257 AATTATGTTAAAATATGGTTAACTTATTTATT
1 AATTTTATTAAATTATATTTAA--TA---A-T
* *
29560289 ATTTTTATTAAATTATTTTTAATAAT
1 AATTTTATTAAATTATATTTAATAAT
*
29560315 AATCTTATTAAA
1 AATTTTATTAAA
29560327 ATTTAATAAC
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
26 28 0.55
27 1 0.02
28 2 0.04
30 2 0.04
31 1 0.02
32 17 0.33
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (26 bp):
AATTTTATTAAATTATATTTAATAAT
Found at i:29561432 original size:20 final size:21
Alignment explanation
Indices: 29561407--29561461 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
29561397 ATAAATTTTT
*
29561407 TAATAATTTATTTAAA-TAAA
1 TAATAATTAATTTAAATTAAA
29561427 TAATAATTAATTTCAAATTAAA
1 TAATAATTAATTT-AAATTAAA
29561449 -AAT-ATTAATTTAA
1 TAATAATTAATTTAA
29561462 GTAATTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 6 0.19
22 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATTAATTTAAATTAAA
Found at i:29562536 original size:7 final size:7
Alignment explanation
Indices: 29562524--29562549 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29562514 TTTTGAAACA
29562524 TTAAATT
1 TTAAATT
29562531 TTAAATT
1 TTAAATT
29562538 TTAAATT
1 TTAAATT
29562545 TTAAA
1 TTAAA
29562550 ACTTCAAATC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:29574800 original size:28 final size:27
Alignment explanation
Indices: 29574757--29574854 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 27
29574747 GAAATCAGAG
29574757 TTAA-CTGGGCCTTAGCCCATATCAATA
1 TTAATCTGGGCC-TAGCCCATATCAATA
*
29574784 TTAATCTGGGCCATAGCCCCT-TACAATA
1 TTAATCTGGGCC-TAGCCCATAT-CAATA
*
29574812 TCATAGTATACTGGGCCTAGCCCATATCAGTA
1 T--TA--AT-CTGGGCCTAGCCCATATCAATA
*
29574844 TCAATCTGGGC
1 TTAATCTGGGC
29574855 TGTAGCCCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
27 11 0.19
28 22 0.38
30 3 0.05
32 14 0.24
33 8 0.14
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (27 bp):
TTAATCTGGGCCTAGCCCATATCAATA
Found at i:29574887 original size:60 final size:60
Alignment explanation
Indices: 29574750--29574901 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
29574740 CTATTCAGAA
* *
29574750 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAAT
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAAT
* * **
29574811 ATCATAGTATACTGGGCCTAGCCCATATCAGTATCAATCTGGGCTGTAGCCCTATTACAA-
1 ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAAT
* * * *
29574871 GTC-GAGATATATTGGGCATTGCCCATATCAA
1 ATCAGAG-TATACTGGGCCTAGCCCATATCAA
29574902 CACAGTTGGC
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 2 0.03
60 52 0.68
61 21 0.28
62 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (60 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAAT
Found at i:29576230 original size:22 final size:22
Alignment explanation
Indices: 29576204--29576245 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29576194 TACGAGGGAA
29576204 AAAAGAAAAGATGAAAGAAAAG
1 AAAAGAAAAGATGAAAGAAAAG
* *
29576226 AAAAGAAAATATGAACGAAA
1 AAAAGAAAAGATGAAAGAAA
29576246 GAGAGGGGAG
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:0.71, C:0.02, G:0.19, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAGATGAAAGAAAAG
Found at i:29586576 original size:45 final size:46
Alignment explanation
Indices: 29586509--29586632 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
29586499 CATATGACCT
*
29586509 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
29586552 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
29586598 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
29586633 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:29586615 original size:46 final size:45
Alignment explanation
Indices: 29586509--29586743 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
29586499 CATATGACCT
*
29586509 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
29586552 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
29586598 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
29586635 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
29586672 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
29586709 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
29586744 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:29586636 original size:37 final size:37
Alignment explanation
Indices: 29586594--29586770 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
29586584 AGCTGAAGCT
* **
29586594 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
29586631 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
29586668 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
29586705 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
29586742 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
29586771 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:29592457 original size:29 final size:29
Alignment explanation
Indices: 29592424--29592484 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
29592414 AATTGGTAAC
* *
29592424 TTAGTTTTAGTTTTAATAACTTCTTACGT
1 TTAGTTTTAGTTTCAATAACTTCTTACAT
29592453 TTAGTTTTAGTTTCAATAACTTCTTACAT
1 TTAGTTTTAGTTTCAATAACTTCTTACAT
29592482 TTA
1 TTA
29592485 ATTCTACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.54
Consensus pattern (29 bp):
TTAGTTTTAGTTTCAATAACTTCTTACAT
Found at i:29599575 original size:27 final size:27
Alignment explanation
Indices: 29599516--29599576 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
29599506 AGCGAGTATG
29599516 GAATTAAGAAATAAAAATATTGATAATT
1 GAATT-AGAAATAAAAATATTGATAATT
* * *
29599544 AAATTAGAAATAAAATTATTTAGTAA-T
1 GAATTAGAAATAAAAATATTGA-TAATT
29599571 GAATTA
1 GAATTA
29599577 AATAGAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (27 bp):
GAATTAGAAATAAAAATATTGATAATT
Found at i:29601043 original size:21 final size:20
Alignment explanation
Indices: 29601019--29601057 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29601009 GAGTATTTTG
29601019 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
29601040 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
29601058 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:29603198 original size:17 final size:17
Alignment explanation
Indices: 29603176--29603211 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29603166 TATGTATATA
29603176 TAGGTGTGCATATAGCC
1 TAGGTGTGCATATAGCC
29603193 TAGGTGTGCATATAGCC
1 TAGGTGTGCATATAGCC
29603210 TA
1 TA
29603212 TGTTATGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (17 bp):
TAGGTGTGCATATAGCC
Found at i:29604719 original size:14 final size:14
Alignment explanation
Indices: 29604702--29604732 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29604692 ACATATAATT
29604702 TGGCCCAATCGGAA
1 TGGCCCAATCGGAA
29604716 TGGCCCAATCGGAA
1 TGGCCCAATCGGAA
29604730 TGG
1 TGG
29604733 TCCATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (14 bp):
TGGCCCAATCGGAA
Found at i:29604823 original size:19 final size:19
Alignment explanation
Indices: 29604799--29604896 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
29604789 AATCTTTAAA
*
29604799 GATATGCAATCTTAGGTAT
1 GATATGCAATCTTAGATAT
29604818 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29604837 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29604854 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29604873 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
29604894 GAT
1 GAT
29604897 CTTGTAATCT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
21 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29604835 original size:14 final size:15
Alignment explanation
Indices: 29604818--29604874 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
29604808 TCTTAGGTAT
29604818 GATATG-CAATCTTA
1 GATATGACAATCTTA
29604832 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
29604849 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
29604868 GATATGA
1 GATATGA
29604875 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:29604845 original size:36 final size:37
Alignment explanation
Indices: 29604799--29604896 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
29604789 AATCTTTAAA
*
29604799 GATATGCAATCTTAGGTATGATATGCAATCTTAGATAT
1 GATA-GCAATCTTAGATATGATATGCAATCTTAGATAT
29604837 GATA-CAATCTTAGATATGATATGCAATCTTAGATAT
1 GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
29604873 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT--AGATATGAT
29604897 CTTGTAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
40 9 0.16
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (37 bp):
GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:29611897 original size:19 final size:19
Alignment explanation
Indices: 29611875--29611917 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
29611865 TGAAGTTAAA
29611875 TTATTTAATCATTTTTATT
1 TTATTTAATCATTTTTATT
* *
29611894 TTATTTTATTATTTTTATT
1 TTATTTAATCATTTTTATT
29611913 TTATT
1 TTATT
29611918 CCTTTCTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTAATCATTTTTATT
Found at i:29613732 original size:21 final size:21
Alignment explanation
Indices: 29613693--29613732 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29613683 AATTCCAATT
*
29613693 TAAGTTTTATTCGATTTATTC
1 TAAGTTTTATTCGACTTATTC
29613714 TAAGTTTTATTTCG-CTTAT
1 TAAGTTTTA-TTCGACTTAT
29613733 ATATATACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TAAGTTTTATTCGACTTATTC
Found at i:29630186 original size:18 final size:17
Alignment explanation
Indices: 29630159--29630193 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29630149 TATTATAATT
*
29630159 AAATAAAAATTCATTCA
1 AAATAAAAATTAATTCA
29630176 AAATGAAAAATTAATTCA
1 AAAT-AAAAATTAATTCA
29630194 GGTGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATAAAAATTAATTCA
Found at i:29630665 original size:14 final size:15
Alignment explanation
Indices: 29630631--29630669 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
29630621 AAAGTTAGAT
*
29630631 TATATAAATTTATTA
1 TATATAAAATTATTA
*
29630646 TTTATAAAATT-TTA
1 TATATAAAATTATTA
29630660 TATATAAAAT
1 TATATAAAAT
29630670 ATAAAATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATAAAATTATTA
Found at i:29631335 original size:11 final size:11
Alignment explanation
Indices: 29631319--29631368 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
29631309 TCAATTATTT
29631319 TCTCAATTTCC
1 TCTCAATTTCC
* *
29631330 TCTCAAATTGC
1 TCTCAATTTCC
29631341 TCTCAATTTCC
1 TCTCAATTTCC
*
29631352 TTCTAAATTT-C
1 -TCTCAATTTCC
29631363 TCTCAA
1 TCTCAA
29631369 ATCCATATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 5 0.16
11 19 0.59
12 8 0.25
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:29631346 original size:22 final size:22
Alignment explanation
Indices: 29631319--29631368 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
29631309 TCAATTATTT
29631319 TCTCAATTTCC-TCTCAAATTGC
1 TCTCAATTTCCTTCT-AAATTGC
*
29631341 TCTCAATTTCCTTCTAAATTTC
1 TCTCAATTTCCTTCTAAATTGC
29631363 TCTCAA
1 TCTCAA
29631369 ATCCATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (22 bp):
TCTCAATTTCCTTCTAAATTGC
Found at i:29631594 original size:6 final size:7
Alignment explanation
Indices: 29631577--29631601 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29631567 TTTAAAATAC
29631577 TTTTTTA
1 TTTTTTA
29631584 TTTTTTA
1 TTTTTTA
29631591 TTTTTTA
1 TTTTTTA
29631598 TTTT
1 TTTT
29631602 GAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:29632409 original size:13 final size:13
Alignment explanation
Indices: 29632393--29632420 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29632383 ATATTATAAA
29632393 AATTAACTATATT
1 AATTAACTATATT
29632406 AATTAACTATATT
1 AATTAACTATATT
29632419 AA
1 AA
29632421 ATAATAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTAACTATATT
Found at i:29633405 original size:25 final size:27
Alignment explanation
Indices: 29633372--29633421 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
29633362 ATTAATATAT
*
29633372 TTAAAAAAAT-TT-AATTCGATTAAAG
1 TTAAAAAAATATTCAATTCAATTAAAG
29633397 TTAAAAAAATATTCAATTCAATTAA
1 TTAAAAAAATATTCAATTCAATTAA
29633422 TAACCCATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 10 0.45
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (27 bp):
TTAAAAAAATATTCAATTCAATTAAAG
Found at i:29635731 original size:18 final size:18
Alignment explanation
Indices: 29635708--29635743 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29635698 TTCCCTTCTA
29635708 ATTTCTCACTCAAATTTT
1 ATTTCTCACTCAAATTTT
* *
29635726 ATTTCTCTCTCAACTTTT
1 ATTTCTCACTCAAATTTT
29635744 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTCTCACTCAAATTTT
Found at i:29636470 original size:90 final size:88
Alignment explanation
Indices: 29636303--29636473 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 88
29636293 GCTAGAAGCT
* *
29636303 TTTTTGTTATTTTGGCCCAATCCCGTAATTTTACAAAAAAAAAGCCTAATCCAGTAATTATTTTA
1 TTTTTATTATTTTGGCCCAATCCCGTAATTTTACAAAAAAAAAACCTAATCCAGTAATTATTTTA
29636368 AAAAATCAAGATTTTTTATAGCA
66 AAAAATCAAGATTTTTTATAGCA
*
29636391 TTTTTATTATTTCT-GCCCAA-CCCTGTAATTTTACAAAAAAAAACAACCTAATCCAGTTATTAT
1 TTTTTATTATTT-TGGCCCAATCCC-GTAATTTTAC-AAAAAAAA-AACCTAATCCAGTAATTAT
**
29636454 TTTAAAAAATTGAGATTTTT
62 TTTAAAAAATCAAGATTTTT
29636474 CATAAATTCA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
87 3 0.04
88 27 0.36
89 9 0.12
90 35 0.47
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (88 bp):
TTTTTATTATTTTGGCCCAATCCCGTAATTTTACAAAAAAAAAACCTAATCCAGTAATTATTTTA
AAAAATCAAGATTTTTTATAGCA
Found at i:29637850 original size:15 final size:16
Alignment explanation
Indices: 29637830--29637859 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29637820 ATTTGTACTG
29637830 TTATTTTTA-TTTTAA
1 TTATTTTTACTTTTAA
29637845 TTATTTTTACTTTTA
1 TTATTTTTACTTTTA
29637860 TTAGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTACTTTTAA
Found at i:29639582 original size:25 final size:25
Alignment explanation
Indices: 29639529--29639587 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
29639519 CTTATTTCAT
* * *
29639529 TAAATAAA-AAATTTTAAAATATAA
1 TAAATAAATACATTTAAAAACATAA
29639553 TAAATCAAATACATTTAAAAACATAA
1 TAAAT-AAATACATTTAAAAACATAA
29639579 -AAATAAATA
1 TAAATAAATA
29639588 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 7 0.23
26 13 0.43
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAATACATTTAAAAACATAA
Found at i:29641122 original size:17 final size:18
Alignment explanation
Indices: 29641085--29641123 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29641075 TTCCCTTCTA
*
29641085 ATTTCTCACTCAAATTTT
1 ATTTCTCACTCAAACTTT
*
29641103 ATTTCTCTCTC-AACTTT
1 ATTTCTCACTCAAACTTT
29641120 ATTT
1 ATTT
29641124 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTCTCACTCAAACTTT
Found at i:29641511 original size:20 final size:19
Alignment explanation
Indices: 29641477--29641529 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
29641467 TACATCTCAA
*
29641477 AAAAT-TATAAAAAAACTT
1 AAAATATATATAAAAACTT
29641495 AAAAATAATATATAAAAAACTT
1 -AAAAT-ATATAT-AAAAACTT
29641517 AAAATATATATAA
1 AAAATATATATAA
29641530 TAAAAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 9 0.30
22 8 0.27
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATATATATAAAAACTT
Found at i:29641512 original size:23 final size:22
Alignment explanation
Indices: 29641475--29641538 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 22
29641465 TTTACATCTC
29641475 AAAA-AAT-TATAAAAAAACTT
1 AAAATAATATATAAAAAAACTT
29641495 AAAAATAATATAT-AAAAAACTT
1 -AAAATAATATATAAAAAAACTT
29641517 AAAATATATATAATAAAAAAAC
1 AAAATA-ATAT-ATAAAAAAAC
29641539 CTCAAAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.26
22 16 0.42
23 5 0.13
24 7 0.18
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAATATATAAAAAAACTT
Found at i:29643697 original size:20 final size:21
Alignment explanation
Indices: 29643672--29643742 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 21
29643662 ATTATTACTT
29643672 TTATTCTT-TATTCACTATTA
1 TTATTCTTATATTCACTATTA
* *
29643692 TTATTCTTACTAATGCATTATTA
1 TTATTCTTA-T-ATTCACTATTA
29643715 TTATTCTTATATTCTACTTCATTA
1 TTATTCTTATATTC-AC-T-ATTA
29643739 TTAT
1 TTAT
29643743 ATTATTACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 8 0.20
21 3 0.07
22 3 0.07
23 19 0.46
24 8 0.20
ACGTcount: A:0.27, C:0.14, G:0.01, T:0.58
Consensus pattern (21 bp):
TTATTCTTATATTCACTATTA
Found at i:29647703 original size:21 final size:20
Alignment explanation
Indices: 29647678--29647723 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
29647668 TGCATCAAAT
29647678 ATAATCATTAATAAATAAAAA
1 ATAATCATTAATAAA-AAAAA
* *
29647699 ATAATCCTTAATAAAAACAA
1 ATAATCATTAATAAAAAAAA
29647719 ATAAT
1 ATAAT
29647724 TACTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAATCATTAATAAAAAAAA
Found at i:29654315 original size:22 final size:22
Alignment explanation
Indices: 29654288--29654339 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
29654278 GCTCTAATAG
*
29654288 TTTTATTTATTATTG-CATTTAT
1 TTTTATTTATTATAGTC-TTTAT
29654310 TTTTATTTATTATAGTCTTTAT
1 TTTTATTTATTATAGTCTTTAT
*
29654332 TTTAATTT
1 TTTTATTT
29654340 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTTATTATAGTCTTTAT
Found at i:29655085 original size:16 final size:16
Alignment explanation
Indices: 29655043--29655074 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29655033 TAATTACAGT
29655043 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
29655059 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
29655075 CTTATTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (16 bp):
TCTATTCCATTACAAC
Found at i:29656000 original size:15 final size:15
Alignment explanation
Indices: 29655980--29656045 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
29655970 ACTACAAAAC
29655980 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
29655995 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
29656014 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
29656029 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
29656042 ATTT
1 ATTT
29656046 TTCAATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:29658879 original size:131 final size:125
Alignment explanation
Indices: 29658590--29659031 Score: 337
Period size: 125 Copynumber: 3.4 Consensus size: 125
29658580 ACGGTAAATT
* * * * *
29658590 GAAACCCAGCACGATTGGGCACGATTTATCGAATTTCTAAATACGAAACATTGCCTCATTTTAAT
1 GAAACCCAGCACGATTGGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCATTTTATT
* * * ** *** **
29658655 TTGAGAAAACATGGACGAAACTTCAAAAGGATATTTTGTATTTTAGTCGAATGGAAAATT
66 TTAAGAAAACATAGACGAAACTTCAAAAAGATATTTCATATTTTAGTCGAAAAAAAAAAC
* * * *** ** *
29658715 GAAGCCCAGCATGATTGGGCACGACTCCCCAAACTTCCAAGCACGAAATATTGCCTCGTTTTATT
1 GAAACCCAGCACGATTGGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCATTTTATT
* * * *
29658780 TTAAGAAAGCGTAGATGAAAATTTCAAAAAAAAAAGATATTTCATATTTTAGTCGAAAAAAAAAA
66 TTAAGAAAACATAGACG-AAACTTC-----AAAAAGATATTTCATATTTTAGTCGAAAAAAAAAA
29658845 C
125 C
* * *
29658846 GAAACCCAGCACGATTGGGCACGATTTTTCAAACTCCCCAAATACGAAATATTGACTCATTTTAT
1 GAAACCCAGCACGATTGGGCACGATTTATCAAACT-TCCAAATACGAAATATTGCCTCA-TTT-T
* * * * * * * *
29658911 AATTTTTTTTAA-AAAACATGGACGAAATTTCCAAAGGATATTCCGTATTTTGGTCGAATGAAAA
63 -A----TTTTAAGAAAACATAGACGAAACTTCAAAAAGATATTTCATATTTTAGTCGAA-AAAAA
29658975 AAAC
122 AAAC
* * * * *
29658979 AAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCTAAATACGAGATATT
1 GAAACCCAGCACGATTGGGCACGATTTATCAAACTTCC-AAATACGAAATATT
29659032 TCCTTATGTT
Statistics
Matches: 248, Mismatches: 53, Indels: 24
0.76 0.16 0.07
Matches are distributed among these distances:
125 63 0.25
126 6 0.02
131 57 0.23
132 43 0.17
133 56 0.23
134 1 0.00
135 1 0.00
137 7 0.03
138 8 0.03
139 6 0.02
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (125 bp):
GAAACCCAGCACGATTGGGCACGATTTATCAAACTTCCAAATACGAAATATTGCCTCATTTTATT
TTAAGAAAACATAGACGAAACTTCAAAAAGATATTTCATATTTTAGTCGAAAAAAAAAAC
Found at i:29660372 original size:18 final size:18
Alignment explanation
Indices: 29660339--29660389 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
29660329 GTTTGCAAGG
29660339 AAAAGAAAGCAAGAAAAACA
1 AAAAGAAA--AAGAAAAACA
*
29660359 AAAAGAAAAAGAAATACA
1 AAAAGAAAAAGAAAAACA
* *
29660377 AAATGGAAAAGAA
1 AAAAGAAAAAGAA
29660390 TAAAGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 20 0.71
20 8 0.29
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAACA
Found at i:29669068 original size:20 final size:19
Alignment explanation
Indices: 29669045--29669087 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
29669035 AGATATTATA
29669045 AAAATATATTAGA-ACATTGT
1 AAAATATATTA-ACA-ATTGT
*
29669065 AAAATTTATTAACAATTGT
1 AAAATATATTAACAATTGT
29669084 AAAA
1 AAAA
29669088 ATTATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (19 bp):
AAAATATATTAACAATTGT
Found at i:29673705 original size:15 final size:15
Alignment explanation
Indices: 29673685--29673729 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
29673675 TTTCAAATTT
29673685 ACTTTTCTAATAAGC
1 ACTTTTCTAATAAGC
*
29673700 ACTTTTC-CAT-AGC
1 ACTTTTCTAATAAGC
29673713 ACTTTT-TAA-AAGC
1 ACTTTTCTAATAAGC
29673726 ACTT
1 ACTT
29673730 CTCACTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 17 0.65
14 2 0.08
15 7 0.27
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (15 bp):
ACTTTTCTAATAAGC
Found at i:29674271 original size:19 final size:19
Alignment explanation
Indices: 29674234--29674270 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29674224 TTATAAAAGT
29674234 TCAAAAAATATTTAAAAAA
1 TCAAAAAATATTTAAAAAA
*
29674253 TCAACAAAT-TTTAAAAAA
1 TCAAAAAATATTTAAAAAA
29674271 AAATTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAAAAATATTTAAAAAA
Found at i:29674412 original size:19 final size:19
Alignment explanation
Indices: 29674388--29674429 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
29674378 TTTTTTTATA
29674388 AAAAGAAAGTAATTTAACT
1 AAAAGAAAGTAATTTAACT
29674407 AAAAGAAAGTAATTTAACT
1 AAAAGAAAGTAATTTAACT
29674426 AAAA
1 AAAA
29674430 TTTAAAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAAGAAAGTAATTTAACT
Done.