Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005379.1 Kokia drynarioides strain JFW-HI SEQ_119366, whole genome shotgun sequence
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: 153210
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:5297 original size:22 final size:23
Alignment explanation
Indices: 5239--5297 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
5229 AAAACAATGT
* *
5239 AAAAT-ATAAATTTAATAGATAT
1 AAAATAATAAATTAAATAGATAA
*
5261 AAAATAAACTCAATTAAATA-ATAA
1 AAAAT-AA-TAAATTAAATAGATAA
5285 AAAATAATAAATT
1 AAAATAATAAATT
5298 CTCAAATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 10 0.33
23 2 0.07
24 9 0.30
25 9 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAATAAATTAAATAGATAA
Found at i:5445 original size:14 final size:14
Alignment explanation
Indices: 5426--5478 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
5416 TCTAGAAAAG
5426 TAAATCATTTTTCA
1 TAAATCATTTTTCA
5440 TAAATCATTTTTCA
1 TAAATCATTTTTCA
5454 TAAATCATTTTTCA
1 TAAATCATTTTTCA
*
5468 GAAATCATTTT
1 TAAATCATTTT
5479 CAGTCAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (14 bp):
TAAATCATTTTTCA
Found at i:8649 original size:14 final size:13
Alignment explanation
Indices: 8600--8651 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
8590 AACGAATCAA
*
8600 ATCAAATGAAATT
1 ATCAAATTAAATT
8613 ATTCAAATTAAATT
1 A-TCAAATTAAATT
**
8627 AAAAAATTAAATAT
1 ATCAAATTAAAT-T
8641 ATCAAATTAAA
1 ATCAAATTAAA
8652 ATTTTGTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (13 bp):
ATCAAATTAAATT
Found at i:8877 original size:18 final size:17
Alignment explanation
Indices: 8854--8897 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
8844 TTTTTTAAAA
8854 TATAAATTTTGGAACTTT
1 TATAAATTTTGGAA-TTT
*
8872 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
8890 TA-AAATTT
1 TATAAATTT
8898 ATTTTGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 4 0.17
18 12 0.50
19 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:12267 original size:18 final size:18
Alignment explanation
Indices: 12227--12269 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12217 ATTTAAGTTA
12227 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
12245 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
12263 TAATTAA
1 TAATTAA
12270 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:12647 original size:19 final size:19
Alignment explanation
Indices: 12608--12651 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12598 CCAAAAAATT
12608 TAAAA-ATAATAAACTTTC
1 TAAAATATAATAAACTTTC
*
12626 TAAAATATAA-AAAGTTTCC
1 TAAAATATAATAAACTTT-C
12645 TAAAATA
1 TAAAATA
12652 GTTTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAATATAATAAACTTTC
Found at i:18829 original size:23 final size:23
Alignment explanation
Indices: 18786--18831 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18776 ATACAATAAA
* *
18786 TAATTAAACATATGATTTGAAAT
1 TAATTAAACATAGGATATGAAAT
18809 TAATTAATA-ATAGGATATGAAAT
1 TAATTAA-ACATAGGATATGAAAT
18832 ATTTACGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (23 bp):
TAATTAAACATAGGATATGAAAT
Found at i:19492 original size:30 final size:27
Alignment explanation
Indices: 19441--19504 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
19431 TTTTAATTAA
* *
19441 TAAAAATAAAATTATATTTTAACTCTTT
1 TAAAAATAAAATTATAATTTAA-TATTT
*
19469 TAAAAATGATAAATTTTAATTTAATATTT
1 TAAAAAT-A-AAATTATAATTTAATATTT
19498 TAAAAAT
1 TAAAAAT
19505 TATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 12 0.39
30 12 0.39
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
TAAAAATAAAATTATAATTTAATATTT
Found at i:20517 original size:185 final size:185
Alignment explanation
Indices: 20202--20570 Score: 553
Period size: 185 Copynumber: 2.0 Consensus size: 185
20192 TAAATTTAGT
* *
20202 AATTAGATCTATTTTGATCCTTAATTTGAATTTATTAAGATTTAATGACATGATTAGTGTTTTGA
1 AATTAGATCTATTTTGATCCTTAATTTGAATTTATTAAAATTTAATGACATGACTAGTGTTTTGA
** * *
20267 AATATAACCAAATTAGTTGGTTAGATCAACAATCAACCGGTATATTGATCCGAACAAAGGGTTTG
66 AATATAACCAAATTAGTTGAATAGATCAACAACCAACCGGTATATTGATCCGAACAAAAGGTTTG
*
20332 ACCCGATTGAATAAAAAATTATTTGAAATCGAT-AAAAAGACTAGCACAAAAATA
131 ACCCGATTGAATAAAAAATTATTTGAAATCGATAAAAAAAACTAGCACAAAAATA
* * *
20386 AATTAGATCTATTTTGATCCTTAATTTGGATTTCATTAAAATTTAATGACGTGGCTAGTGTTCTT
1 AATTAGATCTATTTTGATCCTTAATTTGAATTT-ATTAAAATTTAATGACATGACTAGTGTT-TT
* * * * * *
20451 GGAATCTGATCAAATTGGTTGAATAGATCAAGAACCAACC-GTATATTGATCCGAACAAAAGGTT
64 GAAATATAACCAAATTAGTTGAATAGATCAACAACCAACCGGTATATTGATCCGAACAAAAGGTT
*
20515 TGACTCGATTGAATAAAAAATTATTTGAAATCGATAAAAAAAACTAGCACAAAAAT
129 TGACCCGATTGAATAAAAAATTATTTGAAATCGATAAAAAAAACTAGCACAAAAAT
20571 TAGTAGTTGA
Statistics
Matches: 165, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
184 32 0.19
185 81 0.49
186 52 0.32
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (185 bp):
AATTAGATCTATTTTGATCCTTAATTTGAATTTATTAAAATTTAATGACATGACTAGTGTTTTGA
AATATAACCAAATTAGTTGAATAGATCAACAACCAACCGGTATATTGATCCGAACAAAAGGTTTG
ACCCGATTGAATAAAAAATTATTTGAAATCGATAAAAAAAACTAGCACAAAAATA
Found at i:25041 original size:20 final size:21
Alignment explanation
Indices: 25016--25063 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
25006 CCCTTGTACT
*
25016 AATACATCTAAAG-ATGTGTC
1 AATACATCTAAAGCATGTATC
*
25036 AATACATCTAAGGCATGTATC
1 AATACATCTAAAGCATGTATC
25057 AATACAT
1 AATACAT
25064 TACCCTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (21 bp):
AATACATCTAAAGCATGTATC
Found at i:30962 original size:58 final size:59
Alignment explanation
Indices: 30896--31198 Score: 439
Period size: 59 Copynumber: 5.2 Consensus size: 59
30886 ATTAATCGCA
* * * * * *
30896 TTAATCACATGAGTACTTAAGCATTTAACACAACACATATTAATCACATTTAATCACA-
1 TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
*
30954 TTAGTCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
1 TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
* * * *
31013 TTAATCACATTAATATTTCAACATTTATCACATAACATATTAATCACAATTAGTCACAT
1 TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
* *
31072 TTAATCACATTAATATTTCAG-TTTTATCACATCACATATTAATCACATTTAGTCACAT
1 TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
* * *
31130 TTAATCATATAAATATTTCAGCATTTATCACATCACATATTAATCACTTTTAGTCACAT
1 TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
*
31189 TTAGTCACAT
1 TTAATCACAT
31199 ATAATCACAT
Statistics
Matches: 221, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
58 104 0.47
59 117 0.53
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (59 bp):
TTAATCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCACAT
Found at i:30963 original size:9 final size:9
Alignment explanation
Indices: 30934--31085 Score: 62
Period size: 10 Copynumber: 17.7 Consensus size: 9
30924 CACAACACAT
30934 ATTAATCAC
1 ATTAATCAC
30943 ATTTAATCAC
1 A-TTAATCAC
*
30953 ATTAGTCAC
1 ATTAATCAC
*
30962 ATGAAT---
1 ATTAATCAC
30968 ATT--TCAGC
1 ATTAATCA-C
*
30976 ATTTATCAC
1 ATTAATCAC
* *
30985 A-TCA-CAT
1 ATTAATCAC
30992 ATTAATCAC
1 ATTAATCAC
*
31001 ATTTAGTCAC
1 A-TTAATCAC
31011 ATTTAATCAC
1 A-TTAATCAC
31021 ATTAAT---
1 ATTAATCAC
31027 ATT--TCAAC
1 ATTAATC-AC
*
31035 ATTTATCAC
1 ATTAATCAC
*
31044 A-TAA-CAT
1 ATTAATCAC
31051 ATTAATCAC
1 ATTAATCAC
*
31060 AATTAGTCAC
1 -ATTAATCAC
31070 ATTTAATCAC
1 A-TTAATCAC
31080 ATTAAT
1 ATTAAT
31086 ATTTCAGTTT
Statistics
Matches: 108, Mismatches: 15, Indels: 40
0.66 0.09 0.25
Matches are distributed among these distances:
4 2 0.02
6 5 0.05
7 6 0.06
8 15 0.14
9 33 0.31
10 47 0.44
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (9 bp):
ATTAATCAC
Found at i:30978 original size:23 final size:25
Alignment explanation
Indices: 30938--31012 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
30928 ACACATATTA
30938 ATCACAT-TTAATCACA-TTAGTCAC
1 ATCACATATT-ATCACATTTAGTCAC
*
30962 ATGA-ATATT-TCAGCATTTA-TCAC
1 ATCACATATTATCA-CATTTAGTCAC
30985 ATCACATATTAATCACATTTAGTCAC
1 ATCACATATT-ATCACATTTAGTCAC
31011 AT
1 AT
31013 TTAATCACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
22 3 0.07
23 11 0.26
24 13 0.31
25 6 0.14
26 9 0.21
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (25 bp):
ATCACATATTATCACATTTAGTCAC
Found at i:31012 original size:10 final size:10
Alignment explanation
Indices: 30985--31136 Score: 72
Period size: 10 Copynumber: 15.4 Consensus size: 10
30975 CATTTATCAC
30985 ATCACATATTA
1 ATCACAT-TTA
30996 ATCACATTTA
1 ATCACATTTA
*
31006 GTCACATTTA
1 ATCACATTTA
31016 ATCACATTAATA
1 ATCACATT--TA
*
31028 TTTCAACATTT-
1 -ATC-ACATTTA
31039 ATCACA--TA
1 ATCACATTTA
*
31047 A-CATA-TTA
1 ATCACATTTA
*
31055 ATCACAATTA
1 ATCACATTTA
*
31065 GTCACATTTA
1 ATCACATTTA
*
31075 ATCACATTAA
1 ATCACATTTA
** *
31085 TATTTCAGTTTT
1 -ATCACA-TTTA
31097 ATCAC-----
1 ATCACATTTA
31102 ATCACATATTA
1 ATCACAT-TTA
31113 ATCACATTTA
1 ATCACATTTA
*
31123 GTCACATTTA
1 ATCACATTTA
31133 ATCA
1 ATCA
31137 TATAAATATT
Statistics
Matches: 107, Mismatches: 18, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
5 5 0.05
7 4 0.04
8 4 0.04
9 6 0.06
10 55 0.51
11 21 0.20
12 5 0.05
13 2 0.02
14 5 0.05
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (10 bp):
ATCACATTTA
Found at i:31060 original size:117 final size:117
Alignment explanation
Indices: 30917--31198 Score: 433
Period size: 117 Copynumber: 2.4 Consensus size: 117
30907 AGTACTTAAG
* *
30917 CATTTAACACA-ACACATATTAATCACATTTAATCACA-TTAGTCACATGAATATTTCAGCATTT
1 CATTTATCACATA-ACATATTAATCACATTTAGTCACATTTAGTCACATGAATATTTCAG-ATTT
*
30980 ATCACATCACATATTAATCACATTTAGTCACATTTAATCACATTAATATTTCAA
64 ATCACATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAA
* * * *
31034 CATTTATCACATAACATATTAATCACAATTAGTCACATTTAATCACATTAATATTTCAGTTTTAT
1 CATTTATCACATAACATATTAATCACATTTAGTCACATTTAGTCACATGAATATTTCAGATTTAT
* *
31099 CACATCACATATTAATCACATTTAGTCACATTTAATCATATAAATATTTCAG
66 CACATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAA
* *
31151 CATTTATCACATCACATATTAATCACTTTTAGTCACATTTAGTCACAT
1 CATTTATCACATAACATATTAATCACATTTAGTCACATTTAGTCACAT
31199 ATAATCACAT
Statistics
Matches: 150, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
117 130 0.87
118 20 0.13
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (117 bp):
CATTTATCACATAACATATTAATCACATTTAGTCACATTTAGTCACATGAATATTTCAGATTTAT
CACATCACATATTAATCACATTTAGTCACATTTAATCACATAAATATTTCAA
Found at i:31191 original size:10 final size:10
Alignment explanation
Indices: 31161--31208 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
31151 CATTTATCAC
31161 ATCACATATTA
1 ATCACAT-TTA
*
31172 ATCACTTTTA
1 ATCACATTTA
*
31182 GTCACATTTA
1 ATCACATTTA
* *
31192 GTCACATATA
1 ATCACATTTA
31202 ATCACAT
1 ATCACAT
31209 GAAACACATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 26 0.81
11 6 0.19
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (10 bp):
ATCACATTTA
Found at i:34773 original size:39 final size:39
Alignment explanation
Indices: 34714--34796 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
34704 CACATTAGTG
* * * * *
34714 ACATGAATATTTCAGCATTTACCATATTACATATTTATC
1 ACATTAATATTTCAACATTTACCACATCACATATTAATC
*
34753 ACATTAATATTTCAACATTTATCACATCACATATTAATC
1 ACATTAATATTTCAACATTTACCACATCACATATTAATC
34792 ACATT
1 ACATT
34797 TAGTCACATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (39 bp):
ACATTAATATTTCAACATTTACCACATCACATATTAATC
Found at i:34805 original size:10 final size:10
Alignment explanation
Indices: 34778--34816 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
34768 CATTTATCAC
34778 ATCACATATTA
1 ATCACAT-TTA
34789 ATCACATTTA
1 ATCACATTTA
*
34799 GTCACATTTA
1 ATCACATTTA
*
34809 ACCACATT
1 ATCACATT
34817 AATATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (10 bp):
ATCACATTTA
Found at i:37421 original size:68 final size:68
Alignment explanation
Indices: 37289--37422 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
37279 TACATATTTC
* * * *
37289 AAATTTAGTCTTTGTACTTTTCATATTTCAAAGTTTAAGTGAAATTGTTAACATTGCTAATTTTT
1 AAATTTAGTCTTTGTACTTTTCATATTTCAAAATTAAAGTGAAATTGTTAACACTACTAATTTTT
37354 TTG
66 TTG
* *
37357 AAATTTAGTCTTTGTACTTTTCATATTTCAAAATTAAAATTG-AATTGTTAATACTACT-ATTTT
1 AAATTTAGTCTTTGTACTTTTCATATTTCAAAATT-AAAGTGAAATTGTTAACACTACTAATTTT
37420 TTT
65 TTT
37423 ATCGAAATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 8 0.14
68 47 0.80
69 4 0.07
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (68 bp):
AAATTTAGTCTTTGTACTTTTCATATTTCAAAATTAAAGTGAAATTGTTAACACTACTAATTTTT
TTG
Found at i:40435 original size:60 final size:60
Alignment explanation
Indices: 40278--40472 Score: 239
Period size: 60 Copynumber: 3.2 Consensus size: 60
40268 TAAATGAAAA
*
40278 AGGTCCGATGACTATGTGTCATCGTTAGTATTAAATGAAATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTATGGATTATG
* * * * *
40338 AGGTCCGATGACTATGAGTCATCGTGAGAAATAAATGAATTGAATCCTTTATGGATTTTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTATGGATTATG
* * * * * * *
40398 AGGTTCGACGACTATGTGTCATCGTGAGTATTTAATGAGAAATTAATCCTATTACGAATTA-A
1 AGGTCCGATGACTATGTGTCATCGTGAGTATTAAAT--GAAATGAATCCT-TTATGGATTATG
40460 AGGTCCGATGACT
1 AGGTCCGATGACT
40473 CTATGTCAGC
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 84 0.75
62 21 0.19
63 7 0.06
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (60 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTATGGATTATG
Found at i:47606 original size:60 final size:60
Alignment explanation
Indices: 47511--47721 Score: 226
Period size: 60 Copynumber: 3.5 Consensus size: 60
47501 TAAATGAAAA
* *
47511 AGGTTCGACAACTATGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTACGAATTATG
1 AGGTTCGACGACTATGTGTCATCATGAGTATTAAATGAAATGAATCCTTTACGAATTATG
* * * * *
47571 AGGTTCGATGACTATGTGTCATCATGAGAAATAAATGGACTGAATCCTTTACGAATTATG
1 AGGTTCGACGACTATGTGTCATCATGAGTATTAAATGAAATGAATCCTTTACGAATTATG
* * * * * * * *
47631 AGGTCCGACGACTATGTGTTATCGTGAGTATTTAATGAGAAATGAATCTTATTATGGATTA-A
1 AGGTTCGACGACTATGTGTCATCATGAGTATTAAAT--GAAATGAATCCT-TTACGAATTATG
* * *
47693 AGGTTCGATGACTTTCTGTCATCATGAGT
1 AGGTTCGACGACTATGTGTCATCATGAGT
47722 TACCAAATGC
Statistics
Matches: 122, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
60 82 0.67
62 32 0.26
63 8 0.07
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (60 bp):
AGGTTCGACGACTATGTGTCATCATGAGTATTAAATGAAATGAATCCTTTACGAATTATG
Found at i:49313 original size:13 final size:13
Alignment explanation
Indices: 49295--49329 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
49285 TGTGAAAAAT
49295 TAAATTATTAAGA
1 TAAATTATTAAGA
* *
49308 TAAATTGTTAAGC
1 TAAATTATTAAGA
49321 TAAATTATT
1 TAAATTATT
49330 GCGACTATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (13 bp):
TAAATTATTAAGA
Found at i:51921 original size:17 final size:17
Alignment explanation
Indices: 51888--51937 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
51878 ATTAAATTAT
51888 AATGACAAATGGAAATGC
1 AATGAC-AATGGAAATGC
51906 AATGACAATGCG-AATGC
1 AATGACAATG-GAAATGC
* *
51923 AATAACAATAGAAAT
1 AATGACAATGGAAAT
51938 ATGATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.04
17 20 0.71
18 7 0.25
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AATGACAATGGAAATGC
Found at i:60544 original size:17 final size:16
Alignment explanation
Indices: 60522--60570 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
60512 AACTATGTTA
60522 ACAAAAGGAATGCAGTG
1 ACAAAA-GAATGCAGTG
*
60539 ACAAAACAAAATGCAGTG
1 AC-AAA-AGAATGCAGTG
60557 ACAATAAGAATGCA
1 ACAA-AAGAATGCA
60571 TGAAAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 11 0.41
18 15 0.56
19 1 0.04
ACGTcount: A:0.53, C:0.14, G:0.20, T:0.12
Consensus pattern (16 bp):
ACAAAAGAATGCAGTG
Found at i:68534 original size:20 final size:20
Alignment explanation
Indices: 68518--68553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68508 GAAAATAAAC
68518 AAATT-AGTA-AAAAAATAA
1 AAATTAAGTATAAAAAATAA
68536 AAATTAAGTATAAAAAAT
1 AAATTAAGTATAAAAAAT
68554 TAATTGCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.31
19 4 0.25
20 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
AAATTAAGTATAAAAAATAA
Found at i:69051 original size:41 final size:39
Alignment explanation
Indices: 69006--69089 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
68996 GAGGTAAAGC
*
69006 ATTAGCGGTGCTTATGATAAAGCGCCGCTAAAGGTCAGGGA
1 ATTAGCGATGCTTAT-AT-AAGCGCCGCTAAAGGTCAGGGA
** * *
69047 ATTAGCGATTTTTCTATAAGCGCCGCTAAAGGTCAGGGC
1 ATTAGCGATGCTTATATAAGCGCCGCTAAAGGTCAGGGA
69086 ATTA
1 ATTA
69090 AGCGCCGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 25 0.66
40 2 0.05
41 11 0.29
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (39 bp):
ATTAGCGATGCTTATATAAGCGCCGCTAAAGGTCAGGGA
Found at i:69112 original size:25 final size:25
Alignment explanation
Indices: 69063--69114 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
69053 GATTTTTCTA
*
69063 TAAGCGCCGCTAAAGGTCAGGGCAT
1 TAAGCGCCGCTAAAGATCAGGGCAT
69088 TAAGCGCCGCTAAAGATC-GGAGCAT
1 TAAGCGCCGCTAAAGATCAGG-GCAT
69113 TA
1 TA
69115 GCAGCGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (25 bp):
TAAGCGCCGCTAAAGATCAGGGCAT
Found at i:69180 original size:41 final size:41
Alignment explanation
Indices: 69089--69183 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
69079 TCAGGGCATT
*
69089 AAGCGCCGCTAAAGATCGGAGCATTAGCAGCGCTTATAAAA
1 AAGCGCCGCTAAAGATCAGAGCATTAGCAGCGCTTATAAAA
* * * *
69130 AAGCACCGCTAAAGGTCAGAGCATTAGCAGCGCTTATAGAG
1 AAGCGCCGCTAAAGATCAGAGCATTAGCAGCGCTTATAAAA
*
69171 AAGTGCCGCTAAA
1 AAGCGCCGCTAAA
69184 AGTTGCTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (41 bp):
AAGCGCCGCTAAAGATCAGAGCATTAGCAGCGCTTATAAAA
Found at i:69254 original size:20 final size:20
Alignment explanation
Indices: 69229--69268 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
69219 TATTTAATTT
69229 ATATTTCAATAAAAATATTA
1 ATATTTCAATAAAAATATTA
***
69249 ATATTTGTTTAAAAATATTA
1 ATATTTCAATAAAAATATTA
69269 TACTATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATTTCAATAAAAATATTA
Found at i:72787 original size:43 final size:43
Alignment explanation
Indices: 72655--72966 Score: 369
Period size: 43 Copynumber: 7.3 Consensus size: 43
72645 ATCTGTTAAT
72655 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
* ** *
72698 TTTAGCGACGTTTGT-GAAAAAGCGCTACTAAAGACCATGTTT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
* * * *
72740 TTTAGCGGTGTTTGTGGAAAGAGCACCGCTAAAGACCACGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
*** *
72783 TTTAGCGAAATTTGTGGAAAAAACGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
* * * * *
72826 TTTAGTGGCATTTGTGG-GAAAGCGTCGCTAAAGACCATGTTT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
* * * *
72868 TTTATCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATATTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
* *
72911 TTTAGCGGCGTTTGTGAGAAAAA-CGCCACTAAAGACCTTGTTC
1 TTTAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGACCATGTTC
* *
72954 TATAGTGGCGTTT
1 TTTAGCGGCGTTT
72967 TTGAACGCCG
Statistics
Matches: 224, Mismatches: 42, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
42 72 0.32
43 147 0.66
44 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
Found at i:72797 original size:85 final size:85
Alignment explanation
Indices: 72655--72954 Score: 368
Period size: 85 Copynumber: 3.5 Consensus size: 85
72645 ATCTGTTAAT
72655 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGT-GAAAAA
1 TTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAA
** *
72719 GCGCTACTAAAGACCATGTTT
65 GCGCCGCTAAAGACCATGTTC
* * * **
72740 TTTAGCGGTGTTTGTGGAAAGAGCACCGCTAAAGACCACGTTCTTTAGCGAAATTTGTGGAAAAA
1 TTTAGCGGCGTTTGTGGAAA-AGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAA
*
72805 ACGCCGCTAAAGACCATGTTC
65 GCGCCGCTAAAGACCATGTTC
* * * * * * * *
72826 TTTAGTGGCATTTGTGGGAAAGCGTCGCTAAAGACCATGTTTTTTATCGGCGTTTGTGGGAAAAG
1 TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAG
* *
72891 CGCCGCTAAAGATCATATTC
66 CGCCGCTAAAGACCATGTTC
* * *
72911 TTTAGCGGCGTTTGTGAGAAAAACGCCACTAAAGACCTTGTTCT
1 TTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCT
72955 ATAGTGGCGT
Statistics
Matches: 179, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
84 3 0.02
85 116 0.65
86 60 0.34
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGGAAAAAG
CGCCGCTAAAGACCATGTTC
Found at i:72883 original size:128 final size:128
Alignment explanation
Indices: 72665--72971 Score: 377
Period size: 128 Copynumber: 2.4 Consensus size: 128
72655 TTTAGCGGCG
* * * *
72665 TTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACGTTTGTGAAAAAGCGCTACTAAA
1 TTTGTGGAAAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCATTTGTGAAAAAGCGCTACTAAA
* *
72730 GACCATGTTTTTTAGCGGTGTTTGT-GGAAAGAGCACCGCTAAAGACCACGTTCTTTAGCGAAA
66 GACCATGTTTTTTAGCGGCGTTTGTGGGAAA-AGCACCGCTAAAGACCACATTCTTTAGCGAAA
** *
72793 TTTGTGGAAAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCATTTGTGGGAAAGCG-TCGCTAA
1 TTTGTGGAAAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCATTTGTGAAAAAGCGCT-ACTAA
* * * * ***
72857 AGACCATGTTTTTTATCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATATTCTTTAGCGGCG
65 AGACCATGTTTTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACCACATTCTTTAGCGAAA
* * * * *
72921 TTTGT-GAGAAAAACGCCACTAAAGACCTTGTTCTATAGTGGCGTTTTTGAA
1 TTTGTGGA-AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCATTTGTGAA
72972 CGCCGCGACT
Statistics
Matches: 153, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
127 3 0.02
128 145 0.95
129 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (128 bp):
TTTGTGGAAAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCATTTGTGAAAAAGCGCTACTAAA
GACCATGTTTTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGACCACATTCTTTAGCGAAA
Found at i:75651 original size:19 final size:19
Alignment explanation
Indices: 75627--75670 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
75617 AGTAAATATG
75627 TGCAAGCATACACTGCCAA
1 TGCAAGCATACACTGCCAA
75646 TGCAAGCATACACTGCCAA
1 TGCAAGCATACACTGCCAA
75665 TGCAAG
1 TGCAAG
75671 TATAGTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (19 bp):
TGCAAGCATACACTGCCAA
Found at i:77274 original size:79 final size:79
Alignment explanation
Indices: 77167--77326 Score: 232
Period size: 79 Copynumber: 2.0 Consensus size: 79
77157 TGACTAAAGT
* * * * *
77167 TGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGAT-AGGATTTGACGGATTTTGTTGGT
1 TGGGCTCACATTTGCCGTTTATCAGCTAGGCACTGAGT-ATCAGGATTTGACAGATGTTGTTGGT
77231 TAATCCAACTAGAGC
65 TAATCCAACTAGAGC
* *
77246 TGGGCTCACATTTGCCGTTTATTAGCTAGGCACTGAGTTTCAGGATTTGACAGATGTTGTTGGTT
1 TGGGCTCACATTTGCCGTTTATCAGCTAGGCACTGAGTATCAGGATTTGACAGATGTTGTTGGTT
*
77311 AATTCAACTAGAGC
66 AATCCAACTAGAGC
77325 TG
1 TG
77327 AGTTTACTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 71 0.99
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (79 bp):
TGGGCTCACATTTGCCGTTTATCAGCTAGGCACTGAGTATCAGGATTTGACAGATGTTGTTGGTT
AATCCAACTAGAGC
Found at i:77375 original size:79 final size:78
Alignment explanation
Indices: 77170--77363 Score: 226
Period size: 79 Copynumber: 2.4 Consensus size: 78
77160 CTAAAGTTGG
* * *
77170 GCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGATAGGATTTGACGGATTTTGTTGGTTAAT
1 GCTCACATTTGC-GTTTATCCGCTAGGCACTGGGTGACAGGATTTGACAGATGTTGTTGGTTAAT
*
77235 CCAACTAGAGCTGG
65 CCAACTAGAGCTGA
** * **
77249 GCTCACATTTGCCGTTTATTAGCTAGGCACTGAGTTTCAGGATTTGACAGATGTTGTTGGTTAAT
1 GCTCACATTTG-CGTTTATCCGCTAGGCACTGGGTGACAGGATTTGACAGATGTTGTTGGTTAAT
*
77314 TCAACTAGAGCTGA
65 CCAACTAGAGCTGA
* * * * *
77328 GTTTACTTTTGCGATATATCCGCTAGGCACCGGGTG
1 GCTCACATTTGCG-TTTATCCGCTAGGCACTGGGTG
77364 CCATGAATTG
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
78 2 0.02
79 91 0.97
80 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (78 bp):
GCTCACATTTGCGTTTATCCGCTAGGCACTGGGTGACAGGATTTGACAGATGTTGTTGGTTAATC
CAACTAGAGCTGA
Found at i:79005 original size:14 final size:14
Alignment explanation
Indices: 78986--79012 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
78976 GGGTTTAGAT
78986 TTAAGGTTTCATGG
1 TTAAGGTTTCATGG
79000 TTAAGGTTTCATG
1 TTAAGGTTTCATG
79013 AATATATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (14 bp):
TTAAGGTTTCATGG
Found at i:82098 original size:18 final size:18
Alignment explanation
Indices: 82071--82124 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
82061 TTACTTTCTA
*
82071 TTGCACTGACAATTTAAC
1 TTGCATTGACAATTTAAC
*
82089 TTGCATTGACAACTT-A-
1 TTGCATTGACAATTTAAC
*
82105 TTGCATTTACAATTTTAAC
1 TTGCATTGACAA-TTTAAC
82124 T
1 T
82125 ATTTAGTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 14 0.48
19 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (18 bp):
TTGCATTGACAATTTAAC
Found at i:88926 original size:20 final size:20
Alignment explanation
Indices: 88901--88945 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
88891 CTGGACGATA
*
88901 AAGGAACTGACCAGGTCATG
1 AAGGAACTGACCAAGTCATG
88921 AAGGAACTGACCAAGTCATG
1 AAGGAACTGACCAAGTCATG
88941 AAGGA
1 AAGGA
88946 CCTCTACGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.13
Consensus pattern (20 bp):
AAGGAACTGACCAAGTCATG
Found at i:98057 original size:19 final size:20
Alignment explanation
Indices: 98030--98079 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
98020 TGCAGATTGC
* *
98030 TACCAATACAAGAGACAA-T
1 TACCGATACAAGAGAAAATT
*
98049 TACCGATACAAGTGAAAATTT
1 TACCGATACAAGAGAAAA-TT
98070 TACCGATACA
1 TACCGATACA
98080 TGTCTTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (20 bp):
TACCGATACAAGAGAAAATT
Found at i:98878 original size:40 final size:40
Alignment explanation
Indices: 98747--98880 Score: 189
Period size: 40 Copynumber: 3.4 Consensus size: 40
98737 AAGTTCATGT
* * * * *
98747 GTCTTCCTTTTTAATAATTTTAT-CTCTACCAAGTCAAAA
1 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
*
98786 GTCTTCCCTTTTAACAATCTTATGCTCTACCGATTCATAA
1 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
*
98826 GTCTTCCCTTTTAACAATCTTATGCTCTACTGAGTCATAA
1 GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
*
98866 GTCTTCCTTTTTAAC
1 GTCTTCCCTTTTAAC
98881 TATATTCTCA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 20 0.24
40 65 0.76
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (40 bp):
GTCTTCCCTTTTAACAATCTTATGCTCTACCGAGTCATAA
Found at i:103948 original size:27 final size:27
Alignment explanation
Indices: 103898--104023 Score: 135
Period size: 27 Copynumber: 4.7 Consensus size: 27
103888 CCCTAAAATT
* * * *
103898 AACGATACTCTATTTCTAGTTCGAATG
1 AACGATACTCTGTTTTTGGCTCGAATG
*
103925 AACGATATTCTGTTTTTGGCTCGAATG
1 AACGATACTCTGTTTTTGGCTCGAATG
* *
103952 AACGATACTCAGTTTTTAGCTCGAATG
1 AACGATACTCTGTTTTTGGCTCGAATG
* * * *
103979 AGCAATACTCTGTTTCTGGTTCGAATG
1 AACGATACTCTGTTTTTGGCTCGAATG
* *
104006 AGCGATACTCTATTTTTG
1 AACGATACTCTGTTTTTG
104024 ACCCGAATTA
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (27 bp):
AACGATACTCTGTTTTTGGCTCGAATG
Found at i:104022 original size:54 final size:54
Alignment explanation
Indices: 103898--104022 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
103888 CCCTAAAATT
* * * * *
103898 AACGATACTCTATTTCTAGTTCGAATGAACGATATTCTGTTTTTGGCTCGAATG
1 AACGATACTCTATTTTTAGCTCGAATGAACAATACTCTGTTTCTGGCTCGAATG
* *
103952 AACGATACTC-AGTTTTTAGCTCGAATGAGCAATACTCTGTTTCTGGTTCGAATG
1 AACGATACTCTA-TTTTTAGCTCGAATGAACAATACTCTGTTTCTGGCTCGAATG
*
104006 AGCGATACTCTATTTTT
1 AACGATACTCTATTTTT
104023 GACCCGAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.02
54 59 0.97
55 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (54 bp):
AACGATACTCTATTTTTAGCTCGAATGAACAATACTCTGTTTCTGGCTCGAATG
Found at i:104031 original size:54 final size:54
Alignment explanation
Indices: 103919--104042 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
103909 ATTTCTAGTT
* * * * *
103919 CGAATGAACGATATTCTGTTTTTGGCTCGAATGAACGATACTCAGTTTTTAGCT
1 CGAATGAGCAATACTCTGTTTCTGGCTCGAATGAACGATACTCAGTTTTTAGCC
* *
103973 CGAATGAGCAATACTCTGTTTCTGGTTCGAATGAGCGATACTCTA-TTTTT-GACC
1 CGAATGAGCAATACTCTGTTTCTGGCTCGAATGAACGATACTC-AGTTTTTAG-CC
* *
104027 CGAATTAGTAATACTC
1 CGAATGAGCAATACTC
104043 GAGTAGGGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.02
54 57 0.97
55 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (54 bp):
CGAATGAGCAATACTCTGTTTCTGGCTCGAATGAACGATACTCAGTTTTTAGCC
Found at i:104984 original size:46 final size:46
Alignment explanation
Indices: 104885--104994 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 46
104875 ACTTCATTTA
* * * * *
104885 TAGTCGTTTA-CCCCTCTATTTTCAATTTATACCAACTCTATTTAT
1 TAGTCGTTTATCTCCTCTATCTTCAATTTATACCAACCCCATATAT
* *
104930 TAATCGTTTATCTCC-CTATCTTCCATTTATACCATACCCCATATAT
1 TAGTCGTTTATCTCCTCTATCTTCAATTTATACCA-ACCCCATATAT
*
104976 TAGTCGTTTCTCTCTCTCT
1 TAGTCGTTTATCTC-CTCT
104995 CGAACTAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
45 26 0.50
46 23 0.44
47 1 0.02
48 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.05, T:0.45
Consensus pattern (46 bp):
TAGTCGTTTATCTCCTCTATCTTCAATTTATACCAACCCCATATAT
Found at i:105117 original size:173 final size:174
Alignment explanation
Indices: 104828--105175 Score: 608
Period size: 173 Copynumber: 2.0 Consensus size: 174
104818 CCCTAAAAAC
* ** *
104828 AAATTTAAGACAACTAAACTAATTACACATCCTAACTACAGAAATCCACTTCATTTATAGTCGTT
1 AAATTTAAGACAAATAAACTAATTACACATCCTAACTACAGAAATCCACCCCATTTATAATCGTT
104893 TACCCCTCTATTTTCAATTTATACCAACTCTATTTATTAATCGTTTATCTCCCTATCTTCCATTT
66 TACCCCTCTATTTTCAATTTATACCAACTCTATTTATTAATCGTTTATCTCCCTATCTTCCATTT
*
104958 ATACCATA-CCCCATATATTAGTCGTTTCTCTCTCTCTCGAACT
131 ATACCATACCCCCATATATTAGTCGTTTATCTCTCTCTCGAACT
* *
105001 AAATTTAAGACAAATAAATTAATTACACATCCTAACTAGAGAAATCCACCCCATTTATAATCGTT
1 AAATTTAAGACAAATAAACTAATTACACATCCTAACTACAGAAATCCACCCCATTTATAATCGTT
*
105066 TACCCCTCTATTTTCAATTTATACCAACTCTATTTATTAATCGTTTATCTCCTTATCTTCCATTT
66 TACCCCTCTATTTTCAATTTATACCAACTCTATTTATTAATCGTTTATCTCCCTATCTTCCATTT
*
105131 ATACCATACCCCCATATATTAGTCGTTTATCTCTCTCTTGAACT
131 ATACCATACCCCCATATATTAGTCGTTTATCTCTCTCTCGAACT
105175 A
1 A
105176 CTTTTCCTTT
Statistics
Matches: 165, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
173 131 0.79
174 34 0.21
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.39
Consensus pattern (174 bp):
AAATTTAAGACAAATAAACTAATTACACATCCTAACTACAGAAATCCACCCCATTTATAATCGTT
TACCCCTCTATTTTCAATTTATACCAACTCTATTTATTAATCGTTTATCTCCCTATCTTCCATTT
ATACCATACCCCCATATATTAGTCGTTTATCTCTCTCTCGAACT
Found at i:105131 original size:45 final size:48
Alignment explanation
Indices: 105049--105168 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 48
105039 GAGAAATCCA
* *
105049 CCCCATTTA-TAATCGTTTA-CCCCTCTATTTTCAATTTATACCA-A-
1 CCCCATTTATTAATCGTTTATCTCCTCTATCTTCAATTTATACCATAC
* * *
105093 CTCTATTTATTAATCGTTTATCTCCT-TATCTTCCATTTATACCATAC
1 CCCCATTTATTAATCGTTTATCTCCTCTATCTTCAATTTATACCATAC
* *
105140 CCCCATATATTAGTCGTTTATCTCTCTCT
1 CCCCATTTATTAATCGTTTATCTC-CTCT
105169 TGAACTACTT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 7 0.11
45 26 0.43
46 5 0.08
47 20 0.33
48 2 0.03
49 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.45
Consensus pattern (48 bp):
CCCCATTTATTAATCGTTTATCTCCTCTATCTTCAATTTATACCATAC
Found at i:108784 original size:23 final size:23
Alignment explanation
Indices: 108749--109241 Score: 626
Period size: 23 Copynumber: 21.3 Consensus size: 23
108739 AGTCACATTC
* *
108749 AATCACATGAACATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
108772 AATCATATTAACATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
108795 AATCACATTAACATTTAAGTATA
1 AATCACATTAATATTTAAGCATA
*
108818 GATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* * **
108841 AATCATATTAACATTTAATTATA
1 AATCACATTAATATTTAAGCATA
108864 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
*
108887 AATCACATTAATATTTAAGCTTA
1 AATCACATTAATATTTAAGCATA
* *
108910 AATCAGATTAATATTTAAGCACA
1 AATCACATTAATATTTAAGCATA
*
108933 AATCACATTAATATTTAAGCACA
1 AATCACATTAATATTTAAGCATA
* *
108956 AATCACATTAATATTTAAGTACA
1 AATCACATTAATATTTAAGCATA
* *
108979 AATCACATTAATATTTAAGGACA
1 AATCACATTAATATTTAAGCATA
109002 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
109025 AATCACATTAACATTTAAGCACA
1 AATCACATTAATATTTAAGCATA
* *
109048 AATCACATTAATATTTAAGTACA
1 AATCACATTAATATTTAAGCATA
* *
109071 AATCACATTAATATTTAAGGAAA
1 AATCACATTAATATTTAAGCATA
109094 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* *
109117 AATCACATTAACATTTAAGCGTA
1 AATCACATTAATATTTAAGCATA
** * *
109140 AATCATGTTGATATTTAAGCACA
1 AATCACATTAATATTTAAGCATA
109163 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
* * * * *
109186 AATCATATTAACAGTGAAGCTTA
1 AATCACATTAATATTTAAGCATA
* *
109209 AACCACATTAATATTTAACACATA
1 AATCACATTAATATTTAA-GCATA
109233 TAATCACAT
1 -AATCACAT
109242 ATAACCACAT
Statistics
Matches: 410, Mismatches: 58, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
23 400 0.98
24 3 0.01
25 7 0.02
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:109242 original size:10 final size:10
Alignment explanation
Indices: 109227--109300 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 10
109217 TAATATTTAA
109227 CACATATAAT
1 CACATATAAT
*
109237 CACATATAAC
1 CACATATAAT
* *
109247 CACATTTAGT
1 CACATATAAT
109257 CACATATAAT
1 CACATATAAT
* *
109267 CAAAT-TAAC
1 CACATATAAT
*
109276 CGCATATAAT
1 CACATATAAT
*
109286 CACATTTAAT
1 CACATATAAT
109296 CACAT
1 CACAT
109301 GAGTCACATG
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
9 6 0.12
10 44 0.88
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (10 bp):
CACATATAAT
Found at i:109378 original size:59 final size:59
Alignment explanation
Indices: 109278--109427 Score: 187
Period size: 59 Copynumber: 2.6 Consensus size: 59
109268 AAATTAACCG
* * * *
109278 CATA-TAATCACATTTAATCACA-TGAGTCACATGAATATTTCAGTATTTATCACATCA
1 CATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAGCATTTATCACATCA
* * *
109335 CATATTAATCACATCTAGTCACATTTAATCACATGAATGTTTCAGCATTTATTACATCA
1 CATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAGCATTTATCACATCA
* * * *
109394 CATATTAATAACTTTTAGTGACATTTAATAACAT
1 CATATTAATCACATTTAGTCACATTTAATCACAT
109428 TCAGTTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 4 0.05
58 16 0.20
59 59 0.75
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (59 bp):
CATATTAATCACATTTAGTCACATTTAATCACATGAATATTTCAGCATTTATCACATCA
Found at i:109617 original size:66 final size:66
Alignment explanation
Indices: 109509--109645 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 66
109499 AATACACGGA
* * * *
109509 TCTCCAAACACACCAAATGACTCACAGAGTCGAACATATCCCATAAGTGAAGCATATAGCTAACA
1 TCTCCAAACACACCAAATGACTCACAAAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACA
109574 C
66 C
** * *
109575 TCTCCAAACACACCGAAA-GACTCGTAAAGTCAAACATGTCCCAAAAGTGAAGCGTAAAGCTAAC
1 TCTCCAAACACACC-AAATGACTCACAAAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAAC
109639 AC
65 AC
109641 TCTCC
1 TCTCC
109646 TTATTTCCCC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 59 0.95
67 3 0.05
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (66 bp):
TCTCCAAACACACCAAATGACTCACAAAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACA
C
Found at i:109925 original size:36 final size:36
Alignment explanation
Indices: 109851--109958 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
109841 TAATATAATA
* * *
109851 ACTATCACATGACATGAAAAACATA-CTACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
*
109886 ACTATCACATGGCATGAATAACACACCCACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
*
109922 ACTATCACGTGGCATGAATAACATACCCACATATTT
1 ACTATCACATGGCATGAATAACATACCCACATATTT
109958 A
1 A
109959 ATTTCACAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
35 22 0.33
36 44 0.67
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (36 bp):
ACTATCACATGGCATGAATAACATACCCACATATTT
Found at i:112119 original size:30 final size:30
Alignment explanation
Indices: 112072--112151 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
112062 TCCACTTATC
* *
112072 TTAGATAGCCTCGAAGGCATCCACACATCA
1 TTAGATAGCCACAAAGGCATCCACACATCA
* * *
112102 TTATATAGCCACAAAGGCCTCCACACATTA
1 TTAGATAGCCACAAAGGCATCCACACATCA
* *
112132 TTAGATAACTACAAAGGCAT
1 TTAGATAGCCACAAAGGCAT
112152 TCTAGATACA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (30 bp):
TTAGATAGCCACAAAGGCATCCACACATCA
Found at i:112374 original size:30 final size:30
Alignment explanation
Indices: 112340--112398 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
112330 CACATGTAAT
112340 AGAGAACAACCACAAAGGCTTCCACATATC
1 AGAGAACAACCACAAAGGCTTCCACATATC
* *
112370 AGAGAACAACCACAAAGGTTTGCACATAT
1 AGAGAACAACCACAAAGGCTTCCACATAT
112399 TAGTAACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.15
Consensus pattern (30 bp):
AGAGAACAACCACAAAGGCTTCCACATATC
Found at i:114052 original size:17 final size:17
Alignment explanation
Indices: 114030--114066 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
114020 CCGTAATTTC
*
114030 CTTATTGCTGACATAAA
1 CTTATTGCTAACATAAA
*
114047 CTTATTTCTAACATAAA
1 CTTATTGCTAACATAAA
114064 CTT
1 CTT
114067 CTCAGCATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (17 bp):
CTTATTGCTAACATAAA
Found at i:116457 original size:19 final size:19
Alignment explanation
Indices: 116433--116472 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
116423 GTGACCTCTG
*
116433 TTTTCCAAATTTTTAAGTT
1 TTTTCCAAAATTTTAAGTT
*
116452 TTTTCCAAAATTTTATGTT
1 TTTTCCAAAATTTTAAGTT
116471 TT
1 TT
116473 GTTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTCCAAAATTTTAAGTT
Found at i:124056 original size:35 final size:36
Alignment explanation
Indices: 123974--124072 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
123964 TTGTATCTAA
* * *
123974 AAATACCAATAAGAC-ATTAAGTTCAATTGTATATTT
1 AAATACCAATAAAACAATGAAGTTCAA-TATATATTT
* *
124010 AAATACTAATAAAACAATGAAGTTCAA-ATATCTTT
1 AAATACCAATAAAACAATGAAGTTCAATATATATTT
*
124045 AAATACCAATAAAGCAATGAAGTTCAAT
1 AAATACCAATAAAACAATGAAGTTCAAT
124073 TAAAATAGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 31 0.57
36 13 0.24
37 10 0.19
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.30
Consensus pattern (36 bp):
AAATACCAATAAAACAATGAAGTTCAATATATATTT
Found at i:127374 original size:22 final size:21
Alignment explanation
Indices: 127323--127374 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
127313 ACAAATTATT
**
127323 TTTTATTTCATTCTTTTCTCTT
1 TTTT-TTTCATTCTTTTCTCAA
*
127345 TTTCTTTTCTTTCTTTTTCTCAA
1 TTT-TTTTCATTC-TTTTCTCAA
127368 TTTTTTT
1 TTTTTTT
127375 ATAGGTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTCATTCTTTTCTCAA
Found at i:129055 original size:17 final size:18
Alignment explanation
Indices: 129033--129067 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
129023 ATCTGCCTGC
129033 TTTTCCTTCTT-CTTCTT
1 TTTTCCTTCTTCCTTCTT
*
129050 TTTTCCTTTTTCCTTCTT
1 TTTTCCTTCTTCCTTCTT
129068 CTTGGGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCCTTCTTCCTTCTT
Found at i:133436 original size:207 final size:207
Alignment explanation
Indices: 132996--133607 Score: 1056
Period size: 207 Copynumber: 3.0 Consensus size: 207
132986 TAATCTCCTT
*
132996 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTGAATGGATTGCTTCCCTTCAT
1 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTAAATGGATTGCTTCCCTTCAT
133061 CTTCCAGTCTAATCTTGTGCATGCAAAAAGAGGGACTGATGGCTCTGATATCT---A--CTCCAA
66 CTTCCAGTCTAATCTTGTGCATGCAAAAAGAGGGACTGATGGCTCTGATATCTGCAATGCTCCAA
*
133121 GCGATGGCTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTAGCATTGTGTCGAGGGT
131 GCGATGGCTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
133186 TGCACTGACTTC
196 TGCACTGACTTC
133198 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTAAATGGATTGCTTCCCTTCAT
1 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTAAATGGATTGCTTCCCTTCAT
** * *
133263 CTTTTAGTCTAATATTGTGCATGCAAAAAGAGGGACTAATGGCTCTGATATCTGCAATGCTCCAA
66 CTTCCAGTCTAATCTTGTGCATGCAAAAAGAGGGACTGATGGCTCTGATATCTGCAATGCTCCAA
*
133328 GCGATGACTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
131 GCGATGGCTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
133393 TGCACTGACTTC
196 TGCACTGACTTC
* * *
133405 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCTTTGTTGCTCAATGGATTGCTTCCCATCAT
1 TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTAAATGGATTGCTTCCCTTCAT
* * *
133470 CTTCCAGTCTGATCTTGTGCATCCAAAAAGAGGGACTGATGGCTCTGATAGCTGCAATGCTCCAA
66 CTTCCAGTCTAATCTTGTGCATGCAAAAAGAGGGACTGATGGCTCTGATATCTGCAATGCTCCAA
*
133535 GCAATGGCTCTTTTATGCTCCTTT-AAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
131 GCGATGGCTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
133599 TGCACTGAC
196 TGCACTGAC
133608 AATTACAGGT
Statistics
Matches: 386, Mismatches: 19, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
202 113 0.29
205 1 0.00
206 49 0.13
207 223 0.58
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (207 bp):
TTTCACTACTTCTTTCATTTTCTCATTAAGCCTTCGTTGTTGCTAAATGGATTGCTTCCCTTCAT
CTTCCAGTCTAATCTTGTGCATGCAAAAAGAGGGACTGATGGCTCTGATATCTGCAATGCTCCAA
GCGATGGCTCTTTTATGCTCCTTTAAAATTGCAACAAGCTTTTCTTCTTGCATTGTGTCGAGGGT
TGCACTGACTTC
Found at i:141659 original size:20 final size:20
Alignment explanation
Indices: 141630--141680 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
141620 TGTTAAAGAG
* *
141630 ATTTTGACTTG-GTACAAATT
1 ATTTTAACTTGTGTA-AAATC
*
141650 ATTTTAACTTGTTTAAAATC
1 ATTTTAACTTGTGTAAAATC
141670 ATTTTAACTTG
1 ATTTTAACTTG
141681 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (20 bp):
ATTTTAACTTGTGTAAAATC
Found at i:141694 original size:20 final size:19
Alignment explanation
Indices: 141649--141694 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
141639 TGGTACAAAT
141649 TATTTTAACTTGTTTAAAA
1 TATTTTAACTTGTTTAAAA
141668 TCATTTTAACTTGATTTTAAAA
1 T-ATTTTAACTTG--TTTAAAA
141690 T-TTTT
1 TATTTT
141695 CCAAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
22 8 0.33
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTTTAACTTGTTTAAAA
Found at i:142211 original size:36 final size:37
Alignment explanation
Indices: 142171--142243 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
142161 AAAAATTTAC
* * *
142171 TTGTATCTAAAAATACTAATAAGAC-ATTAAGTTCAA
1 TTGTATATAAAAATACTAATAAAACAATGAAGTTCAA
**
142207 TTGTATATTTAAATACTAATAAAACAATGAAGTTCAA
1 TTGTATATAAAAATACTAATAAAACAATGAAGTTCAA
142244 ATATAACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 21 0.68
37 10 0.32
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (37 bp):
TTGTATATAAAAATACTAATAAAACAATGAAGTTCAA
Found at i:142255 original size:37 final size:37
Alignment explanation
Indices: 142181--142280 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 37
142171 TTGTATCTAA
* * * *
142181 AAATACTAATAAGAC-ATTAAGTTCAATTGTATATTT
1 AAATACTAATAAAACAATGAAGTTCAAATATATATTT
142217 AAATACTAATAAAACAATGAAGTTCAAATATA-ACTTT
1 AAATACTAATAAAACAATGAAGTTCAAATATATA-TTT
* * * *
142254 AAATACCAATGAAGCAATGGAGTTCAA
1 AAATACTAATAAAACAATGAAGTTCAA
142281 TTAATATAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 15 0.28
37 39 0.72
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (37 bp):
AAATACTAATAAAACAATGAAGTTCAAATATATATTT
Found at i:145204 original size:5 final size:5
Alignment explanation
Indices: 145194--145218 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
145184 TCCTCACAAG
145194 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
145219 GTAAAGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:145862 original size:20 final size:22
Alignment explanation
Indices: 145839--145885 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
145829 GACTTGGTCC
*
145839 AAATTATTTTGACTT-A-TTTA
1 AAATTATTTTAACTTGATTTTA
*
145859 AAATCATTTTAACTTGATTTTA
1 AAATTATTTTAACTTGATTTTA
145881 AAATT
1 AAATT
145886 GTTTCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (22 bp):
AAATTATTTTAACTTGATTTTA
Done.