Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011641.1 Kokia drynarioides strain JFW-HI SEQ_126632, 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: 197057
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 195 characters in sequence are not A, C, G, or T
Found at i:1790 original size:24 final size:25
Alignment explanation
Indices: 1763--1812 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1753 AAATCCAAAG
*
1763 ACAGATGCAGGAACAAATG-CAAGA
1 ACAGATACAGGAACAAATGACAAGA
* *
1787 ACAGTTACAGGAAGAAATGACAAGA
1 ACAGATACAGGAACAAATGACAAGA
1812 A
1 A
1813 TGTTTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.52, C:0.14, G:0.24, T:0.10
Consensus pattern (25 bp):
ACAGATACAGGAACAAATGACAAGA
Found at i:7918 original size:122 final size:121
Alignment explanation
Indices: 7695--8340 Score: 923
Period size: 122 Copynumber: 5.3 Consensus size: 121
7685 CAATGAGGTG
* * * * *
7695 GTCATCTTCCTTATGAGAATAGAGAAGTATACCAAATCAATGAAATGAAGCTTAATACGAATGAG
1 GTCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAG
* * *
7760 ACTTCAAACCCCATCTTCCTGATGAGATGCAAAGAAGTGGGTCAAAGCAATAAAGC
66 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATC
* *
7816 AGTCATTTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAATCTCAATACGAATGA
1 -GTCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
* * *
7881 GACTTCAAACCCCGTCTTCCTAATGAGATACAGAGAAGTGGGTGAAAGCAATAAATC
65 GACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATC
* *
7938 GATCACCTTCCTAATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
1 G-TCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
* *
8003 GACTTCAAACCCCATCTTCCTAATGAGATACAGAGAAGTGAGTCAAAGCAATAAATC
65 GACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATC
* *
8060 GATCATCTTCTTGATAAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
1 G-TCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
* * *
8125 GACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATTAAAGCAATAAATC
65 GACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATC
* * * * * *
8182 GGTCATCTTCCTGATGAAAATAGAGAAGTAAACTAAATTAATGAAATGAAGCTCAATACGAATGA
1 -GTCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGA
* * **
8247 GACTTCAAACCCTATCTTCCTGATGAGATACAGAGAAGCGGGTCAAAGCAATAAAGAG
65 GACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAA-TC
* * *
8305 GTTATCTTCTTGATGAGATATAGAGAAGTAGACCAA
1 GTCATCTTCCTGATGAGA-ACAGAGAAGTAGACCAA
8341 GAAATGAAGT
Statistics
Matches: 471, Mismatches: 49, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
121 1 0.00
122 454 0.96
123 16 0.03
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (121 bp):
GTCATCTTCCTGATGAGAACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAATACGAATGAG
ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATC
Found at i:9331 original size:15 final size:16
Alignment explanation
Indices: 9307--9336 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9297 AACTACATAA
9307 TAAATAAATATAATAT
1 TAAATAAATATAATAT
9323 TAAAT-AATATAATA
1 TAAATAAATATAATA
9337 AATAAAAAAG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATAAATATAATAT
Found at i:10274 original size:30 final size:29
Alignment explanation
Indices: 10204--10384 Score: 184
Period size: 30 Copynumber: 6.1 Consensus size: 29
10194 ATAATTTCAT
*
10204 TTTTA-CCCCAAACTTCTCCAAAATCACA
1 TTTTACCCCCAAACTTTTCCAAAATCACA
*
10232 TTTTAGCCCCAAACTTTTCCAAAATCACA
1 TTTTACCCCCAAACTTTTCCAAAATCACA
* *
10261 TTTTATCCCCCAAAATTATCCCAAAATCACA
1 TTTTA-CCCCCAAACTT-TTCCAAAATCACA
* * *
10292 TTTTAACCCTAAATTTTTCCAAAATCACA
1 TTTTACCCCCAAACTTTTCCAAAATCACA
* * **
10321 TTTTAACCCCCAAAATTCTCCAAAATTTCA
1 TTTT-ACCCCCAAACTTTTCCAAAATCACA
* ** *
10351 TTTTGACACTTAAACTTTTACAAAATCACA
1 TTTT-ACCCCCAAACTTTTCCAAAATCACA
10381 TTTT
1 TTTT
10385 TACATTGAAA
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
28 5 0.04
29 43 0.34
30 61 0.48
31 17 0.13
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.34
Consensus pattern (29 bp):
TTTTACCCCCAAACTTTTCCAAAATCACA
Found at i:10293 original size:60 final size:59
Alignment explanation
Indices: 10201--10384 Score: 219
Period size: 60 Copynumber: 3.1 Consensus size: 59
10191 TCCATAATTT
* * * *
10201 CATTTTTA-CCCCAAACTTCTCCAAAATCACATTTTAGCCCCAAACTTTTCCAAAATCA
1 CATTTTAACCCCCAAAATTATCCAAAATCACATTTTAGCCCTAAACTTTTCCAAAATCA
* * *
10259 CATTTTATCCCCCAAAATTATCCCAAAATCACATTTTAACCCTAAATTTTTCCAAAATCA
1 CATTTTAACCCCCAAAATTAT-CCAAAATCACATTTTAGCCCTAAACTTTTCCAAAATCA
* ** * *
10319 CATTTTAACCCCCAAAATTCTCCAAAATTTCATTTT-GACACTTAAACTTTTACAAAATCA
1 CATTTTAACCCCCAAAATTATCCAAAATCACATTTTAG-C-CCTAAACTTTTCCAAAATCA
10379 CATTTT
1 CATTTT
10385 TACATTGAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
58 6 0.06
59 24 0.22
60 77 0.72
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.34
Consensus pattern (59 bp):
CATTTTAACCCCCAAAATTATCCAAAATCACATTTTAGCCCTAAACTTTTCCAAAATCA
Found at i:27548 original size:7 final size:7
Alignment explanation
Indices: 27536--27561 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27526 TCTACTTTTA
27536 TTTTATT
1 TTTTATT
27543 TTTTATT
1 TTTTATT
27550 TTTTATT
1 TTTTATT
27557 TTTTA
1 TTTTA
27562 GAACTTTCTA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:30921 original size:21 final size:19
Alignment explanation
Indices: 30895--30979 Score: 82
Period size: 21 Copynumber: 4.1 Consensus size: 19
30885 CTCTCACAAT
*
30895 AAAAATTACAAAATAATTTTC
1 AAAAATT-CAAAAT-ATTTTA
30916 AAAAATTCAAAATATTTATAA
1 AAAAATTCAAAATATTT-T-A
30937 AAAAATTCAAAATTTATATTTA
1 AAAAATTCAAAA--TAT-TTTA
30959 AAAAATTACAAAA-ATTTTA
1 AAAAATT-CAAAATATTTTA
30978 AA
1 AA
30980 TACGTATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
19 10 0.18
20 9 0.16
21 19 0.33
22 8 0.14
23 9 0.16
24 2 0.04
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTTA
Found at i:34423 original size:16 final size:16
Alignment explanation
Indices: 34395--34435 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
34385 TTGGAATTGA
34395 ATTTTTT-ACAAAAAT
1 ATTTTTTGACAAAAAT
*
34410 ATTTTTTGATAAAAAT
1 ATTTTTTGACAAAAAT
*
34426 ATATTTTGAC
1 ATTTTTTGAC
34436 TAATTGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
ATTTTTTGACAAAAAT
Found at i:34885 original size:20 final size:20
Alignment explanation
Indices: 34860--34914 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
34850 ACTTGACATT
34860 TTTTTCTTAATTTGGGACAC
1 TTTTTCTTAATTTGGGACAC
34880 TTTTTCTTAATTTGGGACAC
1 TTTTTCTTAATTTGGGACAC
34900 TTTTTCTTAATTTGG
1 TTTTTCTTAATTTGG
34915 TACCTAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTTTCTTAATTTGGGACAC
Found at i:42995 original size:291 final size:291
Alignment explanation
Indices: 42471--43047 Score: 1109
Period size: 291 Copynumber: 2.0 Consensus size: 291
42461 AGGGGAAGAA
*
42471 TTAAGGAGTGGGTAAACTTAGTATCTTCATTCATGGTTATCAACAGGAACTCTCAACTCTCGAGT
1 TTAAGGAGTGGGTAAACTTAGTATCTTCATTCATGGTTATCAACAGGAACTCTCAACTCTCGAAT
42536 TAGGTCAACCTCACTCGTCTATGGTAAATTCAGTAAAATGGTCCCCTCTTCCAATGGGCTTTATG
66 TAGGTCAACCTCACTCGTCTATGGTAAATTCAGTAAAATGGTCCCCTCTTCCAATGGGCTTTATG
*
42601 AAAGTCAATGTTGACGCTAGTTTTAACGCCAATATGAAGAAAGAAGTATTAGGCATCATTATTAG
131 AAAGTCAATGTTGACGCTAGTTTTAACGCCAATATGAAGAAAGAAGTATCAGGCATCATTATTAG
42666 AAATGAAACAAGGGAAATTTTGGGTACATGTCATAGAGTTACTCACCACGTGCTTTCAGGTTTTG
196 AAATGAAACAAGGGAAATTTTGGGTACATGTCATAGAGTTACTCACCACGTGCTTTCAGGTTTTG
42731 CAGCAGAGGCACTCATCGTGATCCATCGTGC
261 CAGCAGAGGCACTCATCGTGATCCATCGTGC
42762 TTAAGGAGTGGGTAAACTTAGTATCTTCATTCATGGTTATCAACAGGAACTCTCAACTCTCGAAT
1 TTAAGGAGTGGGTAAACTTAGTATCTTCATTCATGGTTATCAACAGGAACTCTCAACTCTCGAAT
42827 TAGGTCAACCTCACTCGTCTATGGTAAATTCAGTAAAATGGTCCCCTCTTCCAATGGGCTTTATG
66 TAGGTCAACCTCACTCGTCTATGGTAAATTCAGTAAAATGGTCCCCTCTTCCAATGGGCTTTATG
* *
42892 AAAGTCAATGTTGACGTTGGTTTTAACGCCAATATGAAGAAAGAAGTATCAGGCATCATTATTAG
131 AAAGTCAATGTTGACGCTAGTTTTAACGCCAATATGAAGAAAGAAGTATCAGGCATCATTATTAG
*
42957 AAATGAAACAAGGGAAATTTTGGGTACATGTCATAGAGTTACTCACCACGTGCTTTCGGGTTTTG
196 AAATGAAACAAGGGAAATTTTGGGTACATGTCATAGAGTTACTCACCACGTGCTTTCAGGTTTTG
43022 CAGCAGAGGCACTCATCGTGATCCAT
261 CAGCAGAGGCACTCATCGTGATCCAT
43048 GGCCTTCGGT
Statistics
Matches: 281, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 281 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (291 bp):
TTAAGGAGTGGGTAAACTTAGTATCTTCATTCATGGTTATCAACAGGAACTCTCAACTCTCGAAT
TAGGTCAACCTCACTCGTCTATGGTAAATTCAGTAAAATGGTCCCCTCTTCCAATGGGCTTTATG
AAAGTCAATGTTGACGCTAGTTTTAACGCCAATATGAAGAAAGAAGTATCAGGCATCATTATTAG
AAATGAAACAAGGGAAATTTTGGGTACATGTCATAGAGTTACTCACCACGTGCTTTCAGGTTTTG
CAGCAGAGGCACTCATCGTGATCCATCGTGC
Found at i:79678 original size:27 final size:28
Alignment explanation
Indices: 79600--79680 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 28
79590 TAAAGAAATG
*
79600 TGGAAGCCTTTGTGGTTGTTCTCTGATA
1 TGGAAGCCTTTGTGGATGTTCTCTGATA
* **
79628 TGTGAAAGTCTTTAAGGATGTTCT-TGATA
1 TG-G-AAGCCTTTGTGGATGTTCTCTGATA
* *
79657 TGGAAGCCTTTGTGGCTATTCTCT
1 TGGAAGCCTTTGTGGATGTTCTCT
79681 ATTACATGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
27 14 0.34
28 4 0.10
29 8 0.20
30 15 0.37
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (28 bp):
TGGAAGCCTTTGTGGATGTTCTCTGATA
Found at i:79876 original size:30 final size:30
Alignment explanation
Indices: 79842--79899 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
79832 AATGTGTCTA
79842 GATGCCATTATGGCTATCTAACGATGTGGG
1 GATGCCATTATGGCTATCTAACGATGTGGG
* * * *
79872 GATGCCTTTGTGGCTATCTGATGATGTG
1 GATGCCATTATGGCTATCTAACGATGTG
79900 TGAATACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (30 bp):
GATGCCATTATGGCTATCTAACGATGTGGG
Found at i:96972 original size:19 final size:20
Alignment explanation
Indices: 96940--96978 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
96930 CTAAATTACC
*
96940 ATATTTACTTAAAAT-AAAT
1 ATATTTACTCAAAATGAAAT
*
96959 ATATTTAGTCAAAATGAAAT
1 ATATTTACTCAAAATGAAAT
96979 TAGGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
ATATTTACTCAAAATGAAAT
Found at i:107248 original size:45 final size:45
Alignment explanation
Indices: 107176--107336 Score: 218
Period size: 45 Copynumber: 3.6 Consensus size: 45
107166 ATCGGCATGA
* *
107176 GTAAAACCATAGTTGAAATATACTATGGCATTATCCTGGAAATGT
1 GTAAGACCATAGTTGAAAGATACTATGGCATTATCCTGGAAATGT
* * * *
107221 GTAAGACAATAGTTGAATGATACTATGGCATT-TAACT-GACATGT
1 GTAAGACCATAGTTGAAAGATACTATGGCATTAT-CCTGGAAATGT
* *
107265 GTAAGACCATAGTTGAAAGATACTATGGCATTATCCCGAAAATGT
1 GTAAGACCATAGTTGAAAGATACTATGGCATTATCCTGGAAATGT
*
107310 GTAAGACCATAGTTGAAAGATATTATG
1 GTAAGACCATAGTTGAAAGATACTATG
107337 ACATCATATC
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
44 38 0.38
45 62 0.62
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (45 bp):
GTAAGACCATAGTTGAAAGATACTATGGCATTATCCTGGAAATGT
Found at i:133109 original size:56 final size:56
Alignment explanation
Indices: 133049--133300 Score: 373
Period size: 56 Copynumber: 4.5 Consensus size: 56
133039 GCAATATTCA
* * * *
133049 GAATCTTGCTCGGGTAGAGCATTATTCTATATTTGGCTCGGGTAGAGTATTACTCT
1 GAATCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAGGTAGAGCATTACTCT
*
133105 GAATCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAAGTAGAGCATTACTCT
1 GAATCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAGGTAGAGCATTACTCT
* * *
133161 GAATCTTGCTCGGGTAGAGCATTATTATACATCTAGCTCAGGTAGAGCGTTACTCT
1 GAATCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAGGTAGAGCATTACTCT
* * *
133217 -AACTCTTGCTCTGGTAGAGCATTATTCTACATCTGG-TCCGCGTAGAGCGTTACTCT
1 GAA-TCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAG-GTAGAGCATTACTCT
133273 GAATCTTGCTCGGGTAGAGCATTATTCT
1 GAATCTTGCTCGGGTAGAGCATTATTCT
133301 GATTCTAGCT
Statistics
Matches: 179, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
55 5 0.03
56 172 0.96
57 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (56 bp):
GAATCTTGCTCGGGTAGAGCATTATTCTACATCTGGCTCAGGTAGAGCATTACTCT
Found at i:133301 original size:28 final size:28
Alignment explanation
Indices: 133000--133313 Score: 264
Period size: 28 Copynumber: 11.2 Consensus size: 28
132990 CAAATGGAAG
** * * * *
133000 GCTCGGGTATTGCAATATTTTGATTCTA
1 GCTCGGGTAGAGCATTATTCTGAATCTT
* * * *
133028 GCTCGGATAAAGCAATATTCAGAATCTT
1 GCTCGGGTAGAGCATTATTCTGAATCTT
133056 GCTCGGGTAGAGCATTATTCT-ATAT-TT
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* *
133083 GGCTCGGGTAGAGTATTACTCTGAATCTT
1 -GCTCGGGTAGAGCATTATTCTGAATCTT
*
133112 GCTCGGGTAGAGCATTATTCT-ACATCTG
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
** *
133140 GCTCAAGTAGAGCATTACTCTGAATCTT
1 GCTCGGGTAGAGCATTATTCTGAATCTT
* *
133168 GCTCGGGTAGAGCATTATTAT-ACATCTA
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* * *
133196 GCTCAGGTAGAGCGTTACTCT-AACTCTT
1 GCTCGGGTAGAGCATTATTCTGAA-TCTT
*
133224 GCTCTGGTAGAGCATTATTCT-ACATC-T
1 GCTCGGGTAGAGCATTATTCTGA-ATCTT
* * * *
133251 GGTCCGCGTAGAGCGTTACTCTGAATCTT
1 GCT-CGGGTAGAGCATTATTCTGAATCTT
* *
133280 GCTCGGGTAGAGCATTATTCTGATTCTA
1 GCTCGGGTAGAGCATTATTCTGAATCTT
133308 GCTCGG
1 GCTCGG
133314 AAAGAGTGAT
Statistics
Matches: 230, Mismatches: 44, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
27 9 0.04
28 212 0.92
29 9 0.04
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (28 bp):
GCTCGGGTAGAGCATTATTCTGAATCTT
Found at i:133319 original size:28 final size:28
Alignment explanation
Indices: 133260--133354 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 28
133250 TGGTCCGCGT
* * * * **
133260 AGAGCGTTACTCTGAATCTTGCTCGGGT
1 AGAGCATTATTCTGATTCTAGCTCGGAA
133288 AGAGCATTATTCTGATTCTAGCTCGGAA
1 AGAGCATTATTCTGATTCTAGCTCGGAA
* *
133316 AGAGTGA-TATT-TCGATTCTGGCTCGGAA
1 AGAG-CATTATTCT-GATTCTAGCTCGGAA
133344 AGAGCATTATT
1 AGAGCATTATT
133355 TTGTTCTGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
27 2 0.04
28 52 0.95
29 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (28 bp):
AGAGCATTATTCTGATTCTAGCTCGGAA
Found at i:133348 original size:112 final size:110
Alignment explanation
Indices: 133049--133354 Score: 336
Period size: 112 Copynumber: 2.7 Consensus size: 110
133039 GCAATATTCA
* *
133049 GAATCTTGCTCGGGTAGAGCATTATTCTATATTTGGCTCGGGTAGAGT-AT-TACTCTGAATCTT
1 GAATCTTGCTCGGGTAGAGCATTATTCTAT-TCTAGCTC-GGTAGAGTGATAT-CTCTGAATCTT
133112 GCTCGGGTAGAGCATTATTCTACATCTGGCTCAAGTAGAGCATTACTCT
63 GCTC-GGTAGAGCATTATTCTACATCTGGCTCAAGTAGAGCATTACTCT
* * * *
133161 GAATCTTGCTCGGGTAGAGCATTATTATACATCTAGCTCAGGTAGAGCGTTA-CTCT-AACTCTT
1 GAATCTTGCTCGGGTAGAGCATTATTCTA-TTCTAGCTC-GGTAGAGTGATATCTCTGAA-TCTT
** *
133224 GCTCTGGTAGAGCATTATTCTACATCTGG-TCCGCGTAGAGCGTTACTCT
63 GCTC-GGTAGAGCATTATTCTACATCTGGCT-CAAGTAGAGCATTACTCT
* * * *
133273 GAATCTTGCTCGGGTAGAGCATTATTCTGATTCTAGCTCGGAAAGAGTGATATTTC-GATTCTGG
1 GAATCTTGCTCGGGTAGAGCATTATTCT-ATTCTAGCTCGG-TAGAGTGATATCTCTGAATCTTG
*
133337 CTCGGAAAGAGCATTATT
64 CTCGG-TAGAGCATTATT
133355 TTGTTCTGGG
Statistics
Matches: 164, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
111 7 0.04
112 152 0.93
113 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (110 bp):
GAATCTTGCTCGGGTAGAGCATTATTCTATTCTAGCTCGGTAGAGTGATATCTCTGAATCTTGCT
CGGTAGAGCATTATTCTACATCTGGCTCAAGTAGAGCATTACTCT
Found at i:133355 original size:28 final size:28
Alignment explanation
Indices: 133288--133368 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
133278 TTGCTCGGGT
*
133288 AGAGCATTA-TTCTGATTCTAGCTCGGAA
1 AGAGCATTATTTC-GATTCTGGCTCGGAA
*
133316 AGAGTGA-TATTTCGATTCTGGCTCGGAA
1 AGAG-CATTATTTCGATTCTGGCTCGGAA
*
133344 AGAGCATTATTTTG-TTCTGGGCTCG
1 AGAGCATTATTTCGATTCT-GGCTCG
133369 AATGGGCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.11
28 36 0.80
29 4 0.09
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (28 bp):
AGAGCATTATTTCGATTCTGGCTCGGAA
Found at i:145724 original size:15 final size:15
Alignment explanation
Indices: 145688--145728 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
145678 AGAACCTGAG
*
145688 AAGAAG-GAA-AATA
1 AAGAAGAGAAGAACA
145701 AAGAAGAGAAGAACA
1 AAGAAGAGAAGAACA
*
145716 AAGAGGAGAAGAA
1 AAGAAGAGAAGAA
145729 AGAAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.25
14 3 0.12
15 15 0.62
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.02
Consensus pattern (15 bp):
AAGAAGAGAAGAACA
Found at i:149389 original size:21 final size:21
Alignment explanation
Indices: 149363--149404 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
149353 CAAACAAAGA
149363 CAAAAAGTATTGATACCTTTT
1 CAAAAAGTATTGATACCTTTT
149384 CAAAAAGTATTGATACCTTTT
1 CAAAAAGTATTGATACCTTTT
149405 ATCATGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
CAAAAAGTATTGATACCTTTT
Found at i:152249 original size:82 final size:81
Alignment explanation
Indices: 152120--152322 Score: 289
Period size: 82 Copynumber: 2.5 Consensus size: 81
152110 TATGGACCCC
* *
152120 TATGATGGCTAAGTTTCTACATACGTTGTGGATTCTCATCAGCTTGTGTGAGCAGCATCATGAGT
1 TATGATGGCTGAGTTTCTGCATACGTTGTGGATTCTCATCAGCTTGTGTGAGCAGCATCATGAGT
*
152185 GGGTAATTCTGGACCG
66 GGGTAATTCTAGACCG
* * *
152201 TAATGATGACTGAGTTTCTGCATACGTTGTGGATTCTCATCAGCTTGTGTGAGTAGCATCGTGAG
1 T-ATGATGGCTGAGTTTCTGCATACGTTGTGGATTCTCATCAGCTTGTGTGAGCAGCATCATGAG
*
152266 TGGGTAATTTTAGACCG
65 TGGGTAATTCTAGACCG
* * * *
152283 TATCGATGGTTGACTTTCTGCATATGTTGTAGATTCTCAT
1 TAT-GATGGCTGAGTTTCTGCATACGTTGTGGATTCTCAT
152323 TTTGTGTGAG
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
81 3 0.03
82 105 0.97
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (81 bp):
TATGATGGCTGAGTTTCTGCATACGTTGTGGATTCTCATCAGCTTGTGTGAGCAGCATCATGAGT
GGGTAATTCTAGACCG
Found at i:156838 original size:82 final size:82
Alignment explanation
Indices: 156701--156924 Score: 292
Period size: 82 Copynumber: 2.7 Consensus size: 82
156691 ATGGTCCCCT
* * *
156701 ACAATGGCTAAGTTTCTGCAAACGTTATGGATTCTCATCAGCTTGTGTGAGCAGCATTGTGAGTG
1 ACAATGGCTGAGTTTCTGCATACGTTATGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGAGTG
* *
156766 GGTAATTTTGG-ACTGTA
66 GGTAATTATGGAAC-ATA
*
156783 ACAATGG-TCGAGTTTCTGCATACGTTATGGATTCTCATCAGCTTGTGTGACCAGCATCGTGAGT
1 ACAATGGCT-GAGTTTCTGCATACGTTATGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGAGT
156847 GGGTAATTATGGAACATA
65 GGGTAATTATGGAACATA
* * * * * *
156865 TCAATGGCTGACTTT-TCGCATATGTTACGGATTTTCATAAGCTTGTGTGAGCAGCATCGT
1 ACAATGGCTGAGTTTCT-GCATACGTTATGGATTCTCATCAGCTTGTGTGAGCAGCATCGT
156925 ATACTGGTTA
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
81 2 0.02
82 120 0.96
83 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (82 bp):
ACAATGGCTGAGTTTCTGCATACGTTATGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGAGTG
GGTAATTATGGAACATA
Found at i:161789 original size:22 final size:22
Alignment explanation
Indices: 161747--161790 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
161737 TAATTGGAAG
161747 ATAAAAGAACTAAAAAAATAAA
1 ATAAAAGAACTAAAAAAATAAA
161769 ATAAAA-AAC-AAAACAAGATAAA
1 ATAAAAGAACTAAAA-AA-ATAAA
161791 TTCTTGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.11
Consensus pattern (22 bp):
ATAAAAGAACTAAAAAAATAAA
Found at i:166862 original size:3 final size:3
Alignment explanation
Indices: 166854--166908 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
166844 ACTCTAAAAC
166854 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
166902 TTA TTA T
1 TTA TTA T
166909 ATATGTAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:166963 original size:2 final size:2
Alignment explanation
Indices: 166950--166995 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
166940 AATCAAGATG
* * * *
166950 TA TA TT TA TA TA TA TA TT TA TG TA CA TA TA TA 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
166992 TA TA
1 TA TA
166996 ATAAAAGGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:168315 original size:78 final size:78
Alignment explanation
Indices: 168181--168947 Score: 610
Period size: 78 Copynumber: 9.8 Consensus size: 78
168171 GATAACTGCA
* * * * *** * * * *
168181 ATCTGCCCCATGATCGGGGTAAAAGATTAGACGGTTGTGATTTGCCCTATGGTCGGGGTAAGAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
* * *
168246 TCGGGTGACGGTG
66 TTGGCTGATGGTG
* * * * * *
168259 ATCTGCCCTATGATCAGGGTAAAAGATCAGATGGCTTCAATCTGCCTCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
*
168324 TTAGCTGATGGTG
66 TTGGCTGATGGTG
* * * * * *
168337 ATCTGCCCCAAGCTCGAGCTAAAAGATCAGAAGGCTACAATTTGCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
* *
168402 TTGCCTGATAGTG
66 TTGGCTGATGGTG
* * * **
168415 ATCTGCCCCAAGCTCGGGGTAAAATATCAAATGGCTACAATCTAACCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
*
168480 TTGGCTAATGGTG
66 TTGGCTGATGGTG
* * * * * * *
168493 ATTTGCCCCAA-ACTTGGGGTAAAAGATCGGATGGTTGCGATCTGCCCCAAGCTCGGGGTAAGAA
1 ATCTGCCCCAAGA-TCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAG
** * *
168557 ATTGATTAATAGTG
65 ATTGGCTGATGGTG
* * * * * *
168571 ATTTGCCCCAAGCTCGAGGTAAAAGATC-GAATGGTTACAATTTGCCCCAAGCTCGAGGTAAGAG
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAG-ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAG
*
168635 ATTGGTTGATGGTG
65 ATTGGCTGATGGTG
* *** * * * * ** ** * **
168649 ATTTGCCCTGGGCTCGAGGTAAAAAATC-GAATGGTTGTAAT-TTACCCTAGTCTCAAGGTAAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAG-ATGGCTACAATCTGCCCCAAG-CTCGGGGTAAGA
*
168712 GATTGGTTGATGGTG
64 GATTGGCTGATGGTG
* * * * * * **
168727 ATCTACCCCAAGCTCGGGGTAAAAGAT-TGAATGGCTGCAATATACCCCAAGCTCGGCATAAGAG
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAG-ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAG
168791 ATTGGCTGATGGTG
65 ATTGGCTGATGGTG
* * * * *
168805 ATCTGCCCCAGGCTCGGGGTAAAAGATC-GAATGGATGCAATCTACCCCAAGCTCGGGGTAAGAG
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAG-ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAG
*
168869 ATTGGTTGATGGTG
65 ATTGGCTGATGGTG
* * * ** * * * *
168883 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTATGATCTACCCTATGATCGGGGTAAGAGA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
168948 ACGAAATCTT
Statistics
Matches: 570, Mismatches: 111, Indels: 16
0.82 0.16 0.02
Matches are distributed among these distances:
77 7 0.01
78 556 0.98
79 7 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
ATCTGCCCCAAGATCGGGGTAAAAGATCAGATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
TTGGCTGATGGTG
Found at i:168469 original size:156 final size:156
Alignment explanation
Indices: 168220--168947 Score: 749
Period size: 156 Copynumber: 4.7 Consensus size: 156
168210 GACGGTTGTG
* * * * * * * *
168220 ATTTGCCCTATGG-TCGGGGTAAGAGATCGGGTGACGGTGATCTGCCCTATGATCAGGGTAAAAG
1 ATTTGCCCCA-GGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
* * * * * *
168284 ATCAGATGGCTTCAATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAG
65 ATCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG
* * *
168349 CTCGAGCTAAAAGATCAGAA-GGCTACA
130 CTCGAGGTAAAAGATC-GAATGGTTGCA
** * *
168376 ATTTGCCCCAGGCTCGGGGTAAGAGATTGCCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAATA
1 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * * *
168441 TCAAATGGCTACAATCTAACCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATTTGCCCCAAAC
66 TCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* * * *
168506 TTGGGGTAAAAGATCGGATGGTTGCG
131 TCGAGGTAAAAGATCGAATGGTTGCA
* * * * * * * *
168532 ATCTGCCCCAAGCTCGGGGTAAGAAATTGATTAATAGTGATTTGCCCCAAGCTCGAGGTAAAAGA
1 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
* * * * * * * ***
168597 TCGAATGGTTACAATTTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATGGTGATTTGCCCTGGGC
66 TCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
168662 TCGAGGTAAAAAATCGAATGGTTGTA
131 TCGAGGTAAAAGATCGAATGGTTGCA
* * * ** *
168688 ATTTACCCTAGTCTCAAGGTAAGAGATTGGTTGATGGTGATCTACCCCAAGCTCGGGGTAAAAGA
1 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
** * * ** *
168753 TTGAATGGCTGCAATATACCCCAAGCTCGGCATAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
66 TCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
* *
168818 TCGGGGTAAAAGATCGAATGGATGCA
131 TCGAGGTAAAAGATCGAATGGTTGCA
* * *
168844 ATCTACCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
** * ** * * *
168909 TCGGATGACTATGATCTACCCTATGATCGGGGTAAGAGA
66 TCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGA
168948 ACGAAATCTT
Statistics
Matches: 466, Mismatches: 104, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
155 4 0.01
156 462 0.99
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (156 bp):
ATTTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
TCAAATGGCTACAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGC
TCGAGGTAAAAGATCGAATGGTTGCA
Found at i:168503 original size:39 final size:39
Alignment explanation
Indices: 168298--168909 Score: 265
Period size: 39 Copynumber: 15.7 Consensus size: 39
168288 GATGGCTTCA
* * * *
168298 ATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* * * ** *
168337 ATCTGCCCCAAGCTCGAGCTAAAAGATCAG--AA-GGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGG-T--G
* * * * *
168376 ATTTGCCCCAGGCTCGGGGTAAGAGATTGCCTGATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* *
168415 ATCTGCCCCAAGCTCGGGGTAA-A-ATAT--CAAATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGCTAATGG-T--G
**
168454 ATCTAACCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* * * * * * ** * *
168493 ATTTGCCCCAAACTTGGGGTAAAAGATCGGATGGTTGCG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* ** *
168532 ATCTGCCCCAAGCTCGGGGTAAGAAATTGATTAATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* * * * *
168571 ATTTGCCCCAAGCTCGAGGTAAAAGA-T--CGAATGGTTACA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGG-T--G
* * * *
168610 ATTTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* *** * * * *
168649 ATTTGCCCTGGGCTCGAGGTAA-AAAAT--CGAATGGTTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGG-TG
** * ** * *
168686 TAAT-TTACCCTAGTCTCAAGGTAAGAGATTGGTTGATGGTG
1 --ATCTGCCCCAAG-CTCGGGGTAAGAGATTGGCTAATGGTG
* *
168727 ATCTACCCCAAGCTCGGGGTAAAAGATT-G--AATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGG-TG
* * ** *
168764 CAATATACCCCAAGCTCGGCATAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
* * *
168805 ATCTGCCCCAGGCTCGGGGTAAAAGA-T--CGAATGGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGG-TG
* * *
168842 CAATCTACCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
*
168883 ATCTGCCCCAAGCTCGGGGTAAAAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
168910 CGGATGACTA
Statistics
Matches: 420, Mismatches: 113, Indels: 80
0.69 0.18 0.13
Matches are distributed among these distances:
36 23 0.05
37 12 0.03
38 12 0.03
39 324 0.77
40 14 0.03
41 12 0.03
42 23 0.05
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
Found at i:168924 original size:39 final size:38
Alignment explanation
Indices: 168181--168943 Score: 258
Period size: 39 Copynumber: 19.6 Consensus size: 38
168171 GATAACTGCA
* * ** * *
168181 ATCTGCCCCATGATCGGGGTAAAAGATTAGACGGTTGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGA-TGATGTG
* * * * * * *
168220 ATTTGCCCTATGGTCGGGGTAAGAGATCGGGTGACGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGA-TGTG
* * * * * * *
168259 ATCTGCCCTATGATCAGGGTAAAAGATCAGATGGCT-TCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGT-G
* * * ** *
168298 ATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
* * * * * ***
168337 ATCTGCCCCAAGCTCGAGCTAAAAGATCAGAAGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATC-GGATGATGTG
* * * * **
168376 ATTTGCCCCAGGCTCGGGGTAAGAGATTGCCTGATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
* ** * ***
168415 ATCTGCCCCAAGCTCGGGGTAAAATATCAAATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGTG
** * * * *
168454 ATCTAACCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
* * * * *
168493 ATTTGCCCCAAACTTGGGGTAAAAGATCGGATGGTTGCG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGTG
* *
168532 ATCTGCCCCAAGCTCGGGGTAAGAA-AT-TGATTAATAGTG
1 ATCTGCCCCAAGCTCGGGGTAA-AAGATCGGA-TGAT-GTG
* * * * *
168571 ATTTGCCCCAAGCTCGAGGTAAAAGATCGAATGGT-TACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATGT--G
* * * * *
168610 ATTTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
* *** * * * * *
168649 ATTTGCCCTGGGCTCGAGGTAAAAAATCGAATGGTTGTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGTG
** * ** * * *
168688 AT-TTACCCTAGTCTCAAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAG-CTCGGGGTAAAAGATCGGATGAT-GTG
* * * * **
168727 ATCTACCCCAAGCTCGGGGTAAAAGATTGAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGTG
* * ** * * *
168766 ATATACCCCAAGCTCGGCATAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
* * **
168805 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGATGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGAT-GATGTG
* * * *
168844 ATCTACCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGAT-GTG
*
168883 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGACTATG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGA-TGTG
* * * *
168922 ATCTACCCTATGATCGGGGTAA
1 ATCTGCCCCAAGCTCGGGGTAA
168944 GAGAACGAAA
Statistics
Matches: 513, Mismatches: 183, Indels: 56
0.68 0.24 0.07
Matches are distributed among these distances:
37 1 0.00
38 24 0.05
39 463 0.90
40 24 0.05
41 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (38 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATGTG
Found at i:169342 original size:12 final size:13
Alignment explanation
Indices: 169325--169353 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
169315 GTCTAAGTCC
169325 TATCATG-ATGTG
1 TATCATGTATGTG
169337 TATCATGTATGTG
1 TATCATGTATGTG
169350 TATC
1 TATC
169354 TTTATCGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (13 bp):
TATCATGTATGTG
Found at i:175518 original size:30 final size:29
Alignment explanation
Indices: 175484--175734 Score: 231
Period size: 30 Copynumber: 8.5 Consensus size: 29
175474 GGTCAAAACA
175484 TAATTTTAGAAAAGTTTGAGAGGTAAAATG
1 TAATTTTAGAAAAGTTTGAG-GGTAAAATG
* * * *
175514 TAATTTTGGGAAAGTTT-AGAGTTAAAATA
1 TAATTTTAGAAAAGTTTGAG-GGTAAAATG
* * *
175543 TAATTTTGGAAAAGTGTGGGGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGT-AAAATG
*
175573 TAATTTT-GAAGAAGTTTGGGGGTTAAAATG
1 TAATTTTAGAA-AAGTTTGAGGG-TAAAATG
*
175603 CAATTTTAGAAAAGTTTGAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTGAGGG-TAAAATG
* *
175633 TAATTTTA-AAGAAGTTTG-GGATTAAATG
1 TAATTTTAGAA-AAGTTTGAGGGTAAAATG
* *
175661 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGGT-AAAATG
* * *
175691 TAATTTTTGAAAATTTTGAGGATGAAAATG
1 TAATTTTAGAAAAGTTTGAGGGT-AAAATG
* *
175721 TGATTTTAAAAAAG
1 TAATTTTAGAAAAG
175735 AGCTTAATCT
Statistics
Matches: 184, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
28 19 0.10
29 39 0.21
30 122 0.66
31 4 0.02
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.35
Consensus pattern (29 bp):
TAATTTTAGAAAAGTTTGAGGGTAAAATG
Found at i:175616 original size:60 final size:59
Alignment explanation
Indices: 175484--175734 Score: 267
Period size: 60 Copynumber: 4.2 Consensus size: 59
175474 GGTCAAAACA
* * * *
175484 TAATTTTAGAAAAGTTTGAGAGGT-AAAATGTAATTTTG-GGAAAGTTTAGAGTTAAAATA
1 TAATTTTAGAAAAGTTTGAG-GGTCAAAATGTAATTTTGAAG-AAGTTTGGGGTTAAAATG
* * *
175543 TAATTTTGGAAAAGTGTGGGGGTCAAAATGTAATTTTGAAGAAGTTTGGGGGTTAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGTTT-GGGGTTAAAATG
* * * *
175603 CAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTTAAAGAAGTTTGGGATT-AAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGTTTGGGGTTAAAATG
* * * * *
175661 TAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTTGAA-AATTTTGAGGATGAAAATG
1 TAATTTTAGAAAAGTTTGAGGGTCAAAATGTAA-TTTTGAAGAAGTTTG-GGGTTAAAATG
* *
175721 TGATTTTAAAAAAG
1 TAATTTTAGAAAAG
175735 AGCTTAATCT
Statistics
Matches: 162, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
58 43 0.27
59 52 0.32
60 67 0.41
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.35
Consensus pattern (59 bp):
TAATTTTAGAAAAGTTTGAGGGTCAAAATGTAATTTTGAAGAAGTTTGGGGTTAAAATG
Found at i:175689 original size:88 final size:87
Alignment explanation
Indices: 175484--175732 Score: 261
Period size: 88 Copynumber: 2.8 Consensus size: 87
175474 GGTCAAAACA
* * * *
175484 TAATTTTAGAAAAGTTTGAGAGGTAAAATGTAATTTTGGGAAAGTTT-AGAGTTAAAATATAATT
1 TAATTTT-GAAAAGTTTGAG-GGTAAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATT
* *
175548 TTGGAAAAGTGTGGGGGTCAAAATG
64 TT-AAAAAGTGTGGGGATCAAAATG
* *
175573 TAATTTTGAAGAAGTTTGGGGGTTAAAATGCAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATT
1 TAATTTTGAA-AAGTTTGAGGG-TAAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATT
* *
175638 TTAAAGAAGT-TTGGGAT-TAAATG
64 TTAAA-AAGTGTGGGGATCAAAATG
* * * * * *
175661 TAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTTGAAAATTTTGAGGATGAAAATGTGATT
1 TAATTTT-GAAAAGTTTGAGGGT-AAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATT
175726 TTAAAAA
64 TTAAAAA
175733 AGAGCTTAAT
Statistics
Matches: 136, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
87 3 0.02
88 66 0.49
89 46 0.34
90 21 0.15
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (87 bp):
TAATTTTGAAAAGTTTGAGGGTAAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTT
AAAAAGTGTGGGGATCAAAATG
Found at i:177664 original size:95 final size:96
Alignment explanation
Indices: 177483--177673 Score: 253
Period size: 95 Copynumber: 2.0 Consensus size: 96
177473 CTTTTGCGAA
* *
177483 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTGAGTTAAGGCGCAATATTTCG
* * * * *
177548 GAATCGGAGATAAGGATATATTGCCTCGATT
66 AAACCCGAAATAAAGATATATTGCCTCGATT
* * *
177579 AAGGGTATTCGATTATTTCGATTTGAAGAAA-ATTGCACCTAGTGAGTTAATGCGCAA-AGTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTGAGTTAAGGCGCAATA-TTTC
177642 GAAACCCGAAATAAAAGA-ATATTGCCTCGATT
65 GAAACCCGAAAT-AAAGATATATTGCCTCGATT
177674 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
94 1 0.01
95 50 0.60
96 32 0.39
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTGAGTTAAGGCGCAATATTTCG
AAACCCGAAATAAAGATATATTGCCTCGATT
Found at i:178191 original size:60 final size:60
Alignment explanation
Indices: 178126--178484 Score: 447
Period size: 60 Copynumber: 6.2 Consensus size: 60
178116 AAAATGGGAC
* * *
178126 TTTGGAAGGCTCGAGGTCAAAAATGGGACTTTTCGGAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
* * *
178186 TTTGGAAGGTTTGGGGTCAAAAATGGGACTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
* * * * * *
178246 ATTGGAATGTTCGGGGTTAAAAATGGG-TTTTTTGGAAGTTTGGGGGGTAAAATAGT-ATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAG-TTCGGGGGTAAAATGGTAATT
* *
178305 TTTGGAAGGTTCGAGGTCAAAAATTGG-TTTTTTGGAAGTTC----NT--AA---TAATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
* * *
178355 TTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTTGGAAGTTCGAGGGTAAAATAGTAATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
* *
178414 TTTGGAAGGTTCGAGTTCAAAATTGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
178474 TTTGGAAGGTT
1 TTTGGAAGGTT
178485 TAAGGACCTC
Statistics
Matches: 260, Mismatches: 26, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
49 8 0.03
50 34 0.13
52 2 0.01
54 2 0.01
56 2 0.01
58 2 0.01
59 67 0.26
60 143 0.55
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.35
Consensus pattern (60 bp):
TTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATT
Found at i:178238 original size:89 final size:87
Alignment explanation
Indices: 178027--178405 Score: 277
Period size: 89 Copynumber: 4.4 Consensus size: 87
178017 GTTCGAGGGT
* * *
178027 AAAATGGTAATTTTTGGAAGATTTGGGGTAAAAATGGGACTTTTGGAAGTT-GGGGGTTAAAATG
1 AAAATGGGACTTTTTGGAAG-TTCGGGGTAAAAATGGGACTTTTGGAAGTTCGGGGG-TAAAATG
* * ***
178091 GTCATTTTTAGAAGGATCAAGGTCA
64 GT-ATTTTTGGAAGGTTTGGGGTCA
* *
178116 AAAATGGGAC--TTTGGAAGGCTCGAGGTCAAAAATGGGACTTTTCGGAAGTTCGGGGGTAAAAT
1 AAAATGGGACTTTTTGGAA-GTTCGGGGT-AAAAATGGGACTTTT-GGAAGTTCGGGGGTAAAAT
178179 GGTAATTTTTGGAAGGTTTGGGGTCA
63 GGT-ATTTTTGGAAGGTTTGGGGTCA
* * *
178205 AAAATGGGACTTTTTGGAAGTTCGGGGGT-AAAATGGTAATTATTGGAATGTTCGGGGTTAAAAA
1 AAAATGGGACTTTTTGGAAGTTC-GGGGTAAAAATGGGACTT-TTGGAA-GTTCGGGGGT-AAAA
***
178269 TGGGT-TTTTTGGAA-GTTTGGGGGGT
62 T-GGTATTTTTGGAAGGTTTGGGGTCA
* * * * ** *
178294 AAAATAGTA-TTTTTGGAAGGTTCGAGGTCAAAAATTGGTTTTTTGGAAGTTC----NT--AAT-
1 AAAATGGGACTTTTTGGAA-GTTCGGGGT-AAAAATGGGACTTTTGGAAGTTCGGGGGTAAAATG
* *
178351 -AATTTTTGGAAGGTTCGGGGTC-
64 GTATTTTTGGAAGGTTTGGGGTCA
*
178373 AAAATGGGATTTTTTGGAAGTTCGAGGGTAAAA
1 AAAATGGGACTTTTTGGAAGTTCG-GGGTAAAA
178406 TAGTAATTTT
Statistics
Matches: 238, Mismatches: 34, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
79 25 0.11
80 19 0.08
81 3 0.01
84 1 0.00
87 12 0.05
88 33 0.14
89 90 0.38
90 36 0.15
91 16 0.07
92 3 0.01
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.33
Consensus pattern (87 bp):
AAAATGGGACTTTTTGGAAGTTCGGGGTAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAATGGT
ATTTTTGGAAGGTTTGGGGTCA
Found at i:178345 original size:29 final size:27
Alignment explanation
Indices: 177959--178481 Score: 183
Period size: 29 Copynumber: 18.0 Consensus size: 27
177949 AATTTCAAAC
*
177959 GTTCAGGGGT-AAAATGGTAATTTTGGAA
1 GTTC-GGGGTAAAAATGGT-TTTTTGGAA
** * * *
177987 GGTTCAAGGTCAAGAATGGGATTTTTAGAA
1 -GTTCGGGGT-AAAAAT-GGTTTTTTGGAA
178017 GTTCGAGGGT-AAAATGGTAATTTTTGGAA
1 GTTCG-GGGTAAAAATGGT--TTTTTGGAA
* **
178046 GATTTGGGGTAAAAATGGGACTTTTGGAA
1 G-TTCGGGGTAAAAAT-GGTTTTTTGGAA
* * *
178075 GTTGGGGGTTAAAATGGTCATTTTTAGAA
1 GTTCGGGGTAAAAATGGT--TTTTTGGAA
* ** ***
178104 GGATCAAGGTCAAAAATGGGACTTTGGAA
1 -GTTCGGGGT-AAAAATGGTTTTTTGGAA
* * * *
178133 GGCTCGAGGTCAAAAATGGGACTTTTCGGAA
1 -GTTCGGGGT-AAAAAT-GG-TTTTTTGGAA
178164 GTTCGGGGGT-AAAATGGTAATTTTTGGAA
1 GTTC-GGGGTAAAAATGGT--TTTTTGGAA
* *
178193 GGTTTGGGGTCAAAAATGGGACTTTTTGGAA
1 -GTTCGGGGT-AAAAAT-GG-TTTTTTGGAA
*
178224 GTTCGGGGGT-AAAATGGTAATTATTGGAA
1 GTTC-GGGGTAAAAATGGT--TTTTTGGAA
178253 TGTTCGGGGTTAAAAATGGGTTTTTTGGAA
1 -GTTCGGGG-TAAAAAT-GGTTTTTTGGAA
* *
178283 GTTTGGGGGGT-AAAATAGTATTTTTGGAA
1 G-TT-CGGGGTAAAAATGGT-TTTTTGGAA
*
178312 GGTTCGAGGTCAAAAATTGGTTTTTTGGAA
1 -GTTCGGGGT-AAAAA-TGGTTTTTTGGAA
* *
178342 GTTC---NTAATAA----TTTTTGGAA
1 GTTCGGGGTAAAAATGGTTTTTTGGAA
*
178362 GGTTCGGGGTCAAAATGGGATTTTTTGGAA
1 -GTTCGGGGTAAAAAT-GG-TTTTTTGGAA
*
178392 GTTCGAGGGT-AAAATAGTAATTTTTGGAA
1 GTTCG-GGGTAAAAATGGT--TTTTTGGAA
* * *
178421 GGTTCGAGTTCAAAATTGGGATTTTTTGGAA
1 -GTTCGGGGT-AAAAAT-GG-TTTTTTGGAA
178452 GTTCGGGGGT-AAAATGGTAATTTTTGGAA
1 GTTC-GGGGTAAAAATGGT--TTTTTGGAA
178481 G
1 G
178482 GTTTAAGGAC
Statistics
Matches: 374, Mismatches: 62, Indels: 116
0.68 0.11 0.21
Matches are distributed among these distances:
20 9 0.02
21 4 0.01
24 4 0.01
25 4 0.01
26 1 0.00
27 6 0.02
28 32 0.09
29 149 0.40
30 90 0.24
31 68 0.18
32 6 0.02
33 1 0.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.33
Consensus pattern (27 bp):
GTTCGGGGTAAAAATGGTTTTTTGGAA
Found at i:178388 original size:109 final size:109
Alignment explanation
Indices: 178241--178455 Score: 312
Period size: 109 Copynumber: 2.0 Consensus size: 109
178231 GGTAAAATGG
* * *
178241 TAATTATTGGAATGTTCGGGGTTAAAAATGGGTTTTTTGGAAGTTTGGGGGGTAAAATAGT-ATT
1 TAATTATTGGAAGGTTCGGGGTTAAAAATGGGTTTTTTGGAAG-TTCGAGGGTAAAATAGTAATT
178305 TTTGGAAGGTTCGAGGTCAAAAATT-GG-TTTTTTGGAAGTTCNTAA
65 TTTGGAAGGTTCGAGGTC-AAAATTGGGATTTTTTGGAAGTTC-TAA
* *
178350 TAATTTTTGGAAGGTTCGGGG-TCAAAATGGGATTTTTTGGAAGTTCGAGGGTAAAATAGTAATT
1 TAATTATTGGAAGGTTCGGGGTTAAAAATGGG-TTTTTTGGAAGTTCGAGGGTAAAATAGTAATT
*
178414 TTTGGAAGGTTCGAGTTCAAAATTGGGATTTTTTGGAAGTTC
65 TTTGGAAGGTTCGAGGTCAAAATTGGGATTTTTTGGAAGTTC
178456 GGGGGTAAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
108 30 0.31
109 52 0.54
110 14 0.15
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (109 bp):
TAATTATTGGAAGGTTCGGGGTTAAAAATGGGTTTTTTGGAAGTTCGAGGGTAAAATAGTAATTT
TTGGAAGGTTCGAGGTCAAAATTGGGATTTTTTGGAAGTTCTAA
Found at i:179707 original size:7 final size:7
Alignment explanation
Indices: 179695--179733 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
179685 NNNTGTTTTT
179695 TTATTAA
1 TTATTAA
179702 TTATTAA
1 TTATTAA
*
179709 TTAATAA
1 TTATTAA
179716 TTATTAA
1 TTATTAA
179723 -TATT-A
1 TTATTAA
179728 TTATTA
1 TTATTA
179734 TTAATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 8 0.29
7 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:179735 original size:15 final size:15
Alignment explanation
Indices: 179695--179740 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
179685 NNNTGTTTTT
179695 TTATTAATTATTAAT-
1 TTATT-ATTATTAATA
* *
179710 TAATAATTATTAATA
1 TTATTATTATTAATA
179725 TTATTATTATTAATA
1 TTATTATTATTAATA
179740 T
1 T
179741 CAAAACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:179831 original size:18 final size:19
Alignment explanation
Indices: 179810--179851 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
179800 ATTAGTATTA
*
179810 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAAAAG
179828 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAAAAG
179847 TTATT
1 TTATT
179852 GAAATGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAAAAG
Found at i:180383 original size:15 final size:15
Alignment explanation
Indices: 180365--180434 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
180355 TTTGGGTAGC
*
180365 TTGTAATTGGACCAT
1 TTGTAATTGGGCCAT
*
180380 TTGTATTTGGGCCA-
1 TTGTAATTGGGCCAT
*
180394 TCGATAATTGGGCCAT
1 TTG-TAATTGGGCCAT
* *
180410 TTGTTATTGGGTCAT
1 TTGTAATTGGGCCAT
180425 TTGTAATTGG
1 TTGTAATTGG
180435 ACTTTGTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (15 bp):
TTGTAATTGGGCCAT
Found at i:180459 original size:13 final size:14
Alignment explanation
Indices: 180424--180464 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
180414 TATTGGGTCA
180424 TTTG-TAATTGGAC
1 TTTGTTAATTGGAC
180437 TTTGTT--TTGGAC
1 TTTGTTAATTGGAC
180449 TTT-TTAATTGGAC
1 TTTGTTAATTGGAC
180462 TTT
1 TTT
180465 CTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 13 0.52
14 1 0.04
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56
Consensus pattern (14 bp):
TTTGTTAATTGGAC
Found at i:180488 original size:17 final size:16
Alignment explanation
Indices: 180466--180521 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
180456 TTGGACTTTC
*
180466 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
180483 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
180500 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
180516 TAAATT
1 TAAATT
180522 CAATTTCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.23
17 26 0.74
18 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:182439 original size:22 final size:22
Alignment explanation
Indices: 182397--182439 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
182387 AGTAATATAT
*
182397 TAATATAATTTATAGAGTTTAG
1 TAATATAATTTATAAAGTTTAG
*
182419 TAATGATAATTT-TAAATTTTA
1 TAAT-ATAATTTATAAAGTTTA
182440 AGAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TAATATAATTTATAAAGTTTAG
Found at i:184252 original size:14 final size:15
Alignment explanation
Indices: 184222--184254 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
184212 AGATATCAAC
184222 TTTTTCAAAAATATA
1 TTTTTCAAAAATATA
*
184237 TTTTTTAAAAAT-TA
1 TTTTTCAAAAATATA
184251 TTTT
1 TTTT
184255 CAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTCAAAAATATA
Found at i:186257 original size:23 final size:23
Alignment explanation
Indices: 186226--186273 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
186216 CATACAAAGA
186226 TACTGTTGTCTATTTAAAATTTT
1 TACTGTTGTCTATTTAAAATTTT
*
186249 TACTTTTGTCTATTTAAAATTTT
1 TACTGTTGTCTATTTAAAATTTT
186272 TA
1 TA
186274 ATAAAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
TACTGTTGTCTATTTAAAATTTT
Found at i:191536 original size:47 final size:47
Alignment explanation
Indices: 191485--191634 Score: 146
Period size: 47 Copynumber: 3.2 Consensus size: 47
191475 CACCCTCAAC
191485 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGAT
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGAT
* * * * * * * * * *
191532 TTTTTTAATT-TTTGTTTTGTTCAT-AATTTCTTAGTTTTATTTCA--AC
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGT--TTTTA-GTCACGAT
191578 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGAT
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGAT
*
191625 TTTTTTAATT
1 TTTTTAAATT
191635 TTTGTTTTGT
Statistics
Matches: 75, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
45 9 0.12
46 24 0.32
47 33 0.44
48 9 0.12
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (47 bp):
TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGAT
Found at i:191537 original size:48 final size:48
Alignment explanation
Indices: 191485--191632 Score: 146
Period size: 48 Copynumber: 3.1 Consensus size: 48
191475 CACCCTCAAC
191485 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATT
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATT
* * * * * * * * *
191533 TTTTT-AATT-TTTGTTTTGTTCAT-AATTTCTTAGTTTTATTTCA--A-C
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGT--TTTTA-GTCACGATT
191578 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATT
1 TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATT
191626 TTTTTAA
1 TTTTTAA
191633 TTTTTGTTTT
Statistics
Matches: 73, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
45 14 0.19
46 19 0.26
47 19 0.26
48 21 0.29
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (48 bp):
TTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATT
Found at i:191606 original size:93 final size:93
Alignment explanation
Indices: 191480--191666 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
191470 AATTACACCC
191480 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATTTTTTTAATTTTT
1 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATTTTTTTAATTTTT
191545 GTTTTGTTCATAATTTCTTAGTTTTATT
66 GTTTTGTTCATAATTTCTTAGTTTTATT
191573 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATTTTTTTAATTTTT
1 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATTTTTTTAATTTTT
191638 GTTTTGTTCATAATTTCTTAGTTTTATT
66 GTTTTGTTCATAATTTCTTAGTTTTATT
191666 T
1 T
191667 TGTTTATATT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (93 bp):
TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAGTCACGATTTTTTTAATTTTT
GTTTTGTTCATAATTTCTTAGTTTTATT
Found at i:191614 original size:45 final size:45
Alignment explanation
Indices: 191480--191620 Score: 133
Period size: 46 Copynumber: 3.1 Consensus size: 45
191470 AATTACACCC
191480 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAG
1 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAG
* * * * * * * * * *
191525 TCACGATTTTTTTAATT-TTTGTTTTGTTCAT-AATTTCTTAGTTTTATT
1 TCA--ACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGT--TTTTA-G
191573 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAG
1 TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAG
191618 TCA
1 TCA
191621 CGATTTTTTT
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
45 12 0.17
46 24 0.35
47 24 0.35
48 9 0.13
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (45 bp):
TCAACTTTTTAAATTATATCTTTGGGTCCTCAACTTCGTTTTTAG
Found at i:192835 original size:41 final size:41
Alignment explanation
Indices: 192778--192860 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
192768 TCGGTCCGGC
*
192778 TCGAAAAATGGGTCTAAAATTTTGTCCAAACCCGACCCGAA
1 TCGAAAAATGGATCTAAAATTTTGTCCAAACCCGACCCGAA
* *
192819 TCGAAAAATGGATCTAAAATTTTGTCCAAGCTCGACCCGAA
1 TCGAAAAATGGATCTAAAATTTTGTCCAAACCCGACCCGAA
192860 T
1 T
192861 TTAGAAGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
TCGAAAAATGGATCTAAAATTTTGTCCAAACCCGACCCGAA
Found at i:193188 original size:21 final size:23
Alignment explanation
Indices: 193143--193192 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
193133 AATAACATTC
*
193143 AAACAACAAAAATAACAACATCA
1 AAACAACAAAAATAACAACACCA
*
193166 AAACAATAAAAA-AA-AACACCA
1 AAACAACAAAAATAACAACACCA
193187 AAACAA
1 AAACAA
193193 AAACCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.74, C:0.20, G:0.00, T:0.06
Consensus pattern (23 bp):
AAACAACAAAAATAACAACACCA
Found at i:193213 original size:24 final size:23
Alignment explanation
Indices: 193186--193258 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 23
193176 AAAAAACACC
*
193186 AAAACAAAAACCAAAACAGTTAGA
1 AAAACAAAAACCAAAACAGTCA-A
*
193210 AAAA-ACAACACCAAAACAG-CAA
1 AAAACA-AAAACCAAAACAGTCAA
** *
193232 AAAACACCAACCAAAACAGTAAA
1 AAAACAAAAACCAAAACAGTCAA
193255 AAAA
1 AAAA
193259 GCACCAAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 15 0.38
23 9 0.22
24 16 0.40
ACGTcount: A:0.68, C:0.22, G:0.05, T:0.04
Consensus pattern (23 bp):
AAAACAAAAACCAAAACAGTCAA
Found at i:193244 original size:22 final size:21
Alignment explanation
Indices: 193209--193269 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
193199 AAACAGTTAG
193209 AAAAAACAACACCAAAACAGC
1 AAAAAACAACACCAAAACAGC
* *
193230 AAAAAACACCAACCAAAACAGT
1 AAAAAACAAC-ACCAAAACAGC
*
193252 AAAAAA-AGCACCAAAACA
1 AAAAAACAACACCAAAACA
193270 ACAATATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.25
21 11 0.31
22 16 0.44
ACGTcount: A:0.67, C:0.26, G:0.05, T:0.02
Consensus pattern (21 bp):
AAAAAACAACACCAAAACAGC
Found at i:193263 original size:24 final size:23
Alignment explanation
Indices: 193194--193265 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
193184 CCAAAACAAA
*
193194 AACCAAAACAGTTAGAAAAAACAAC
1 AACCAAAACAG-TA-AAAAAACACC
*
193219 -ACCAAAACAG-CAAAAAACACC
1 AACCAAAACAGTAAAAAAACACC
193240 AACCAAAACAGTAAAAAAAGCACC
1 AACCAAAACAGTAAAAAAA-CACC
193264 AA
1 AA
193266 AACAACAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.22
22 10 0.24
23 6 0.15
24 16 0.39
ACGTcount: A:0.64, C:0.25, G:0.07, T:0.04
Consensus pattern (23 bp):
AACCAAAACAGTAAAAAAACACC
Found at i:193956 original size:15 final size:15
Alignment explanation
Indices: 193938--193981 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
193928 AAATTAATTT
193938 AATAAAAATTATAAA
1 AATAAAAATTATAAA
* **
193953 AATATAAATTATTCA
1 AATAAAAATTATAAA
193968 AATATAAAATTATA
1 AATA-AAAATTATA
193982 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAAAATTATAAA
Found at i:196584 original size:21 final size:21
Alignment explanation
Indices: 196557--196610 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
196547 CTAGGGATGG
*
196557 TTCTACCGATACAAGTGATAC
1 TTCTACCGATACAAGTCATAC
* * * *
196578 TTTTACCAAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
196599 TTCTACCGATAC
1 TTCTACCGATAC
196611 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Done.