Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013959.1 Kokia drynarioides strain JFW-HI SEQ_128989, 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: 73227
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1228 original size:21 final size:21
Alignment explanation
Indices: 1204--1250 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1194 TTTACTAGCC
1204 TAATT-GTTACTATTATTATTT
1 TAATTAGTTA-TATTATTATTT
* *
1225 TAATTAGTTATTTTTTTATTT
1 TAATTAGTTATATTATTATTT
1246 TAATT
1 TAATT
1251 TCTACGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (21 bp):
TAATTAGTTATATTATTATTT
Found at i:8495 original size:15 final size:15
Alignment explanation
Indices: 8451--8496 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
8441 TCAGGTTACA
8451 TTTTAATCACTTATG
1 TTTTAATCACTTATG
* *
8466 TTTGAA--ATGTTATG
1 TTTTAATCA-CTTATG
8480 TTTTAATCACTTATG
1 TTTTAATCACTTATG
8495 TT
1 TT
8497 AGTATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (15 bp):
TTTTAATCACTTATG
Found at i:13942 original size:138 final size:133
Alignment explanation
Indices: 13641--14083 Score: 457
Period size: 138 Copynumber: 3.3 Consensus size: 133
13631 CGAAAATGCA
* * *
13641 ATATTAGCAAATATGAATGAGCATTGATCTCTTTTAATGAATGTTAGACATAACTGACAAACTAT
1 ATATTAGCAAATATGAATGAACATTGA--TCTTTTAATGAATCTTAGACATAAGTGACAAAC-AT
* * *** * *
13706 CAACATAAACATCCAAACAAACATATTGAGATAAATACATGATGGTTTGGTTTTTTACACTGCAC
63 CAACATAAA-ATCCAAACAAATAT-TTGAGATTAATACATGGCAGATTGGATTTTTACACTGCAC
*
13771 AGACATTT
126 AGACACTT
* * * * **
13779 ATACTAGCAATATGTGAATAAACATTGATCTTGTAATGAATCACAGACATAAGTGACAAAACAAA
1 ATATTAGCAA-ATATGAATGAACATTGATCTTTTAATGAATCTTAGACATAAGTGAC-AAAC---
* *
13844 ACCAACATAAAATCCAAACAAATATGTTGAGATTAATACATGGCAGATT-GATTTTTATACTGCA
61 ATCAACATAAAATCCAAACAAATAT-TTGAGATTAATACATGGCAGATTGGATTTTTACACTGCA
13908 CAGACACTT
125 CAGACACTT
* *
13917 ATATTAGCAAGACATGAATGAACATTGATCTTTTAATGAATCTTAGACATAAGTGACGAAGCATC
1 ATATTAGCAA-ATATGAATGAACATTGATCTTTTAATGAATCTTAGACATAAGTGAC-AAACATC
* * * * *
13982 AACATAAAATCCAAACAAATA-TTGAGATTAATACATGG-TGATCGGGTTTTTACATTGCAGA-A
64 AACATAAAATCCAAACAAATATTTGAGATTAATACATGGCAGATTGGATTTTTACACTGCACAGA
* *
14044 AAGC-A
129 CA-CTT
14049 ATATTAGCAAATATGAAT-AAGCATTGATCTTTTAA
1 ATATTAGCAAATATGAATGAA-CATTGATCTTTTAA
14084 AGAAAACATC
Statistics
Matches: 257, Mismatches: 41, Indels: 21
0.81 0.13 0.07
Matches are distributed among these distances:
130 2 0.01
131 21 0.08
132 15 0.06
133 31 0.12
135 23 0.09
137 24 0.09
138 86 0.33
139 45 0.18
140 10 0.04
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (133 bp):
ATATTAGCAAATATGAATGAACATTGATCTTTTAATGAATCTTAGACATAAGTGACAAACATCAA
CATAAAATCCAAACAAATATTTGAGATTAATACATGGCAGATTGGATTTTTACACTGCACAGACA
CTT
Found at i:14840 original size:2 final size:2
Alignment explanation
Indices: 14835--14865 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14825 AGATGAAAGC
14835 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
14866 CACAATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:15232 original size:31 final size:31
Alignment explanation
Indices: 15146--15244 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
15136 ACATCGAGAT
* ** **
15146 TTGAACTTGATAATTGTTCCCATATTCAAGC
1 TTGAACTTGATAATTATTCATATATTGGAGC
* * **
15177 TTAAACTTAATAATTATTTTTATATTGGAGC
1 TTGAACTTGATAATTATTCATATATTGGAGC
* * *
15208 TTGAACTTGATAGTTATTCATATATTGGGGT
1 TTGAACTTGATAATTATTCATATATTGGAGC
15239 TTGAAC
1 TTGAAC
15245 GTTTTTGTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (31 bp):
TTGAACTTGATAATTATTCATATATTGGAGC
Found at i:17257 original size:2 final size:2
Alignment explanation
Indices: 17250--17279 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
17240 AATCCTATTT
17250 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
17280 TTGAGGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18884 original size:6 final size:6
Alignment explanation
Indices: 18805--18886 Score: 60
Period size: 6 Copynumber: 13.7 Consensus size: 6
18795 GGTTGGCTCA
* * * * * *
18805 TCATCT TCGTCT TCACCT CCATCT TGATCT TGATCT TGATCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* *
18853 CTGA-CAT TGA-CT TCATCT TCATCT TCATCT TCAT
1 -TCATC-T TCATCT TCATCT TCATCT TCATCT TCAT
18887 GTACATCTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
5 3 0.05
6 57 0.90
7 3 0.05
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (6 bp):
TCATCT
Found at i:22180 original size:3 final size:3
Alignment explanation
Indices: 22172--22203 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
22162 TTATTAGTTT
22172 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22204 CGTAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22446 original size:17 final size:17
Alignment explanation
Indices: 22407--22439 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22397 AAATGAACGG
*
22407 AATTTAACAATAATAAA
1 AATTTAAAAATAATAAA
22424 AATTTAAAAATAATAA
1 AATTTAAAAATAATAA
22440 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
AATTTAAAAATAATAAA
Found at i:27886 original size:29 final size:31
Alignment explanation
Indices: 27823--27890 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
27813 ATATTTTTCA
* *
27823 TTTA-ATTTAAATAATATATATAATATTTATT
1 TTTATATTTAAATAAAATATATAATA-TTATC
*
27854 TTTATATTTTAATAAAAT-TATAATA-TATC
1 TTTATATTTAAATAAAATATATAATATTATC
27883 TTTATATT
1 TTTATATT
27891 AATGTATGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 11 0.33
31 11 0.33
32 11 0.33
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTATATTTAAATAAAATATATAATATTATC
Found at i:28056 original size:29 final size:29
Alignment explanation
Indices: 28023--28115 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
28013 TTTAAATTCT
*
28023 TAAAATTATAATAAATTTTTATACTTTAA
1 TAAAATTATAATATATTTTTATACTTTAA
*
28052 TAAAATTA-AATCATTATTTTAATAC-TT-A
1 TAAAATTATAAT-A-TATTTTTATACTTTAA
* * *
28080 -AAAATTATAATATACTTCTATATTTTAA
1 TAAAATTATAATATATTTTTATACTTTAA
28108 TAAAATTA
1 TAAAATTA
28116 AATCATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 7 0.13
27 10 0.19
28 8 0.15
29 18 0.35
30 9 0.17
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTATAATATATTTTTATACTTTAA
Found at i:28090 original size:56 final size:56
Alignment explanation
Indices: 27993--28126 Score: 164
Period size: 56 Copynumber: 2.4 Consensus size: 56
27983 AAAATATATA
* * * * * *
27993 TTAATTAAATTTAATTATT-TTTTAAATTCTTAAAATTATAATAAATTTTTATACT
1 TTAATAAAATTAAATCATTATTTTAAATACTTAAAATTATAATAAACTTCTATACT
* *
28048 TTAATAAAATTAAATCATTATTTT-AATACTTAAAAATTATAATATACTTCTATATT
1 TTAATAAAATTAAATCATTATTTTAAATACTT-AAAATTATAATAAACTTCTATACT
*
28104 TTAATAAAATTAAATCATAATTT
1 TTAATAAAATTAAATCATTATTT
28127 CATCAATTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 22 0.32
56 46 0.68
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (56 bp):
TTAATAAAATTAAATCATTATTTTAAATACTTAAAATTATAATAAACTTCTATACT
Found at i:28323 original size:29 final size:29
Alignment explanation
Indices: 28260--28326 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
28250 GGTTTTTTTA
* *
28260 TAAAAGTAATTTTTTTTTTGATTAATTATG
1 TAAAA-TAATTTTTTTTTTAATTAAATATG
28290 T-AAATAATTTATTTTTTTAATTAAATAT-
1 TAAAATAATTT-TTTTTTTAATTAAATATG
28318 TAAAATAAT
1 TAAAATAAT
28327 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 25 0.76
30 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TAAAATAATTTTTTTTTTAATTAAATATG
Found at i:28803 original size:22 final size:21
Alignment explanation
Indices: 28750--28803 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
28740 AATTTAAATT
28750 TTTAAAAATTAAATAATAAACA
1 TTTAAAAA-TAAATAATAAACA
** *
28772 AGTAATAAATAAATAATAATTCA
1 TTTAA-AAATAAATAATAA-ACA
28795 TTTAAAAAT
1 TTTAAAAAT
28804 TCATTTAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
TTTAAAAATAAATAATAAACA
Found at i:32213 original size:19 final size:19
Alignment explanation
Indices: 32184--32240 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
32174 TTTCTCAACA
*
32184 AAAAATATAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
32203 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
32222 AAAAATTTCAAA-ATTTAT
1 AAAAATTTAAAATATTTAT
32240 A
1 A
32241 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:35152 original size:34 final size:34
Alignment explanation
Indices: 35109--35210 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
35099 TTGCTACATT
35109 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
1 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
35143 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
1 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
35177 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
1 CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
35211 ATAACTGGTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (34 bp):
CACTTCAGGGAATGGAGCAGAACTGTTGGAACGA
Found at i:35950 original size:29 final size:29
Alignment explanation
Indices: 35915--36001 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 29
35905 CTTTTCCAGC
35915 ACAAAGTAAACATG-TTGATTTCCAGTAGT
1 ACAAAGTAAACATGCTT-ATTTCCAGTAGT
**
35944 ACAAAGTAAATGTGCTTATTTCCAGTAGT
1 ACAAAGTAAACATGCTTATTTCCAGTAGT
35973 ACAAAGTAAACATGCTTATTT-CAGTAGT
1 ACAAAGTAAACATGCTTATTTCCAGTAGT
36001 A
1 A
36002 GATTTTCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 8 0.15
29 43 0.81
30 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (29 bp):
ACAAAGTAAACATGCTTATTTCCAGTAGT
Found at i:38051 original size:23 final size:23
Alignment explanation
Indices: 38025--38071 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
38015 ATTAATGAAA
38025 TCAACACTAATTTAAAGGGTAAG
1 TCAACACTAATTTAAAGGGTAAG
38048 TCAACACTAATTTAAAGGGTAAG
1 TCAACACTAATTTAAAGGGTAAG
38071 T
1 T
38072 GTGAGCCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (23 bp):
TCAACACTAATTTAAAGGGTAAG
Found at i:39135 original size:27 final size:25
Alignment explanation
Indices: 39088--39170 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 25
39078 TAATTAAATT
39088 AAATTAAATAT-TTTTTAATTTTTA
1 AAATTAAATATATTTTTAATTTTTA
39112 AAATTATAATATATTTTTATATTTTAATA
1 AAATTA-AATATATTTTTA-ATTTT--TA
* * *
39141 AACTTAAATCATAATTTTAATTTTTG
1 AAATTAAAT-ATATTTTTAATTTTTA
39167 AAAT
1 AAAT
39171 GGTTATTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.12
25 5 0.10
26 10 0.20
27 5 0.10
28 8 0.16
29 15 0.31
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (25 bp):
AAATTAAATATATTTTTAATTTTTA
Found at i:40328 original size:28 final size:28
Alignment explanation
Indices: 40296--40414 Score: 84
Period size: 28 Copynumber: 4.2 Consensus size: 28
40286 AAAATAAGAC
40296 ATTTTGGATATCCGAGGGT-AAAATGGTA
1 ATTTTGGATATCCG-GGGTAAAAATGGTA
* *
40324 ATTTTGGAT-TCTCGGGGT-GAAATGATA
1 ATTTTGGATATC-CGGGGTAAAAATGGTA
* *
40351 ATTTTGGGAAAATTCGGGGTTAAAAATGGTA
1 ATTTT-GG-ATATCCGGGG-TAAAAATGGTA
* * * *
40382 TTTTTAGACATTCGAGGGTAAAAAT-GTA
1 ATTTTGGATATCCG-GGGTAAAAATGGTA
40410 ATTTT
1 ATTTT
40415 TAGAGTTTCG
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 18 0.24
28 20 0.27
29 19 0.26
30 6 0.08
31 11 0.15
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (28 bp):
ATTTTGGATATCCGGGGTAAAAATGGTA
Found at i:40347 original size:27 final size:28
Alignment explanation
Indices: 40296--40357 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
40286 AAAATAAGAC
*
40296 ATTTTGGATATCCGAGGGTAAAATGGTA
1 ATTTTGGATATCCGAGGGTAAAATGATA
*
40324 ATTTTGGAT-TCTCG-GGGTGAAATGATA
1 ATTTTGGATATC-CGAGGGTAAAATGATA
40351 ATTTTGG
1 ATTTTGG
40358 GAAAATTCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.37
Consensus pattern (28 bp):
ATTTTGGATATCCGAGGGTAAAATGATA
Found at i:40394 original size:29 final size:29
Alignment explanation
Indices: 40362--40418 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
40352 TTTTGGGAAA
40362 ATTCG-GGGTTAAAAATGGT-ATTTTTAGAC
1 ATTCGAGGG-TAAAAAT-GTAATTTTTAGAC
40391 ATTCGAGGGTAAAAATGTAATTTTTAGA
1 ATTCGAGGGTAAAAATGTAATTTTTAGA
40419 GTTTCGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 2 0.08
29 21 0.81
30 3 0.12
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (29 bp):
ATTCGAGGGTAAAAATGTAATTTTTAGAC
Found at i:40493 original size:117 final size:119
Alignment explanation
Indices: 40343--40657 Score: 333
Period size: 117 Copynumber: 2.7 Consensus size: 119
40333 TCTCGGGGTG
* * ** * * *
40343 AAATGATAATTTTGGGAAAATTCGGGGTTAAAAATGGTATTTTTAGACA-TTCGAGGGTAAAAAT
1 AAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTAGA-AGTTCGGGGGTAAAAAT
* * *
40407 GTAATTTTTAG-AGTTTCGAGATCGAGAAT-AGAGTTCTTGGACA-TTCGG-GGGCA
65 GTAATTTTTAGAAGTTTCGAGATCAAAAATGAGA-TTCTTGGA-AGTTCGGAGGGAA
* *
40460 AAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTA-AAGTTTGGGGGT-AAAAT
1 AAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAA-TTTTTAGAAGTTCGGGGGTAAAAAT
* * * * * * *
40523 GTAATTTTTGGAAGTTTCGGGATTAAAAATGGGATTTTTGGAAGTTTGGAGGTAA
65 GTAATTTTTAGAAGTTTCGAGATCAAAAATGAGATTCTTGGAAGTTCGGAGGGAA
* *
40578 AAATGG-AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-
1 AAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATG
40641 TGAATTTTTAGAAGTTT
66 T-AATTTTTAGAAGTTT
40658 TAGGGGTTAA
Statistics
Matches: 165, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
116 22 0.13
117 107 0.65
118 36 0.22
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (119 bp):
AAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATG
TAATTTTTAGAAGTTTCGAGATCAAAAATGAGATTCTTGGAAGTTCGGAGGGAA
Found at i:40501 original size:30 final size:29
Alignment explanation
Indices: 40459--40686 Score: 262
Period size: 30 Copynumber: 7.7 Consensus size: 29
40449 ATTCGGGGGC
40459 AAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGT-A
** *
40490 AAAATGGAATTTTTTAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* * *
40518 AAAATGTAATTTTTGGAAGTTTCGGGATTA
1 AAAATGGAATTTTTGGAAGTTTTGGG-GTA
*
40548 AAAATGGGATTTTTGGAAG-TTTGGAGGTA
1 AAAATGGAATTTTTGGAAGTTTTGG-GGTA
40577 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGG-TA
* **
40607 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* * *
40636 AAAATTGAATTTTTAGAAGTTTTAGGGGTT
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTA
*
40666 AAAATGGGATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
40687 CAAGGGTAGA
Statistics
Matches: 166, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
28 22 0.13
29 47 0.28
30 90 0.54
31 7 0.04
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:40687 original size:59 final size:60
Alignment explanation
Indices: 40450--40687 Score: 317
Period size: 59 Copynumber: 4.0 Consensus size: 60
40440 TTCTTGGACA
* * * **
40450 TTCGGGGG-CAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTAAAG
1 TTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
* * *
40509 TTTGGGGGT-AAAAT-GTAATTTTTGGAAGTTTCGGGATTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
* *
40567 TTTGGAGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
* *
40626 TTCGGGGGTAAAAATTG-AATTTTTAGAAGTTTTAGGGGTT-AAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTT-GGGGTTAAAAATGGGATTTTTGGAAG
40685 TTC
1 TTC
40688 AAGGGTAGAA
Statistics
Matches: 161, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
58 46 0.29
59 108 0.67
60 7 0.04
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (60 bp):
TTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
Found at i:40706 original size:59 final size:58
Alignment explanation
Indices: 40450--40717 Score: 308
Period size: 59 Copynumber: 4.5 Consensus size: 58
40440 TTCTTGGACA
* * * **
40450 TTCGGGGG-CAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTAAAG
1 TTCGGGGGTAAAAAT-G-AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
* * *
40509 TTTGGGGGT-AAAATGTAATTTTTGGAAGTTTCGGGATTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAATG-AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
* *
40567 TTTGGAGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAAT-GAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
*
40626 TTCGGGGGTAAAAATTGAATTTTTAGAAGTTTTAGGGGTT-AAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAA-TGAATTTTTGGAAGTTTT-GGGGTTAAAAATGGGATTTTTGGAAG
** * *
40685 TTCAAGGGTAGAAACGAAATTTTTGGAAAGTTT
1 TTCGGGGGTAAAAATG-AATTTTTGG-AAGTTT
40718 AGGGACCTCC
Statistics
Matches: 184, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
58 47 0.26
59 123 0.67
60 14 0.08
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.37
Consensus pattern (58 bp):
TTCGGGGGTAAAAATGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
Found at i:41510 original size:19 final size:20
Alignment explanation
Indices: 41486--41532 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
41476 AACTTCTTCC
* *
41486 TTTTTTTGTTTTA-AAACTA
1 TTTTTTTATTTTATAAACCA
41505 TTTTTTTATTTTATTAAACCA
1 TTTTTTTATTTTA-TAAACCA
41526 TTTTTTT
1 TTTTTTT
41533 TCTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTTTATTTTATAAACCA
Found at i:42405 original size:39 final size:39
Alignment explanation
Indices: 42331--42410 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
42321 TTTAGGCTAG
** *
42331 TTTGGGTCATTTAATTTGGGCTTATTTGGGCCTTTGTAA
1 TTTGGGTCATTTAATTTGGGCCCAATTGGGCCTTTGTAA
42370 TTTGGGTCATCTGT-ATTTGGGCCCAATTGGG-CTTTGTAA
1 TTTGGGTCAT-T-TAATTTGGGCCCAATTGGGCCTTTGTAA
42409 TT
1 TT
42411 GGACATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 20 0.56
40 15 0.42
41 1 0.03
ACGTcount: A:0.15, C:0.12, G:0.26, T:0.46
Consensus pattern (39 bp):
TTTGGGTCATTTAATTTGGGCCCAATTGGGCCTTTGTAA
Found at i:42526 original size:18 final size:17
Alignment explanation
Indices: 42445--42527 Score: 62
Period size: 17 Copynumber: 4.6 Consensus size: 17
42435 TTTAAATAAT
*
42445 TAAATTTTAAA-TTCAAA
1 TAAA-TTTAAACTTTAAA
*
42462 TTAATTTTAAAC-TTAATA
1 -TAAATTTAAACTTTAA-A
*
42480 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTTAAA
*
42497 GAAAAGTTTAAACTTTAAA
1 -TAAA-TTTAAACTTTAAA
42516 CTAAATTTAAAC
1 -TAAATTTAAAC
42528 CCAAAATGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
17 20 0.38
18 17 0.33
19 15 0.29
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTTAAA
Found at i:43331 original size:205 final size:205
Alignment explanation
Indices: 42882--43752 Score: 1246
Period size: 204 Copynumber: 4.3 Consensus size: 205
42872 TCTGGTTTAA
* * * * *** ** *** *
42882 TTGACTTGGCCTTTTTCTCAGTATCTCATCAAGAAGATGACCATATCACTTGTTTTGTTCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * * * * * * *
42947 CTCTGTGTTTCATCAGGAAGATGATTTTGGTTCACTTCCCTGTATTTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCG-
* * * * * * * *
43012 TTTATTACTTCGA-CTTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTT-GT-TCA
130 TTTATTGCTTCGATC-TGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACA
*
43074 TCGAGTGTGGGT
194 TCGAGCGTGGGT
* * *
43086 TTGATTTGGTGTTCTTCTTAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * *
43151 CTCTGTGTATCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
43216 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACATC
131 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACATC
43281 GAGCGTGGGT
196 GAGCGTGGGT
* *
43291 TTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* *
43356 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
* * * *
43421 TTATTGCTTCGATCTGCTTCTCGATGTCTCATCAAGAAGCTGAGATTTGAAGATTTACTCACATT
131 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACATC
43486 GAGCGTGGGT
196 GAGCGTGGGT
* *
43496 TTGATTTGGTCTTTTTCTCAGTATCTCAT-AGGAAGATGACTGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
43560 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
* * *
43625 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATTAGGAAGCTGGGATTCGAAGATTTACTCATATC
131 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACATC
43690 GAGCGTGGGT
196 GAGCGTGGGT
*
43700 TTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
43753 GGATGGTGAC
Statistics
Matches: 602, Mismatches: 61, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
203 49 0.08
204 300 0.50
205 253 0.42
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGATTTACTCACATC
GAGCGTGGGT
Found at i:43664 original size:409 final size:409
Alignment explanation
Indices: 42944--43752 Score: 1275
Period size: 409 Copynumber: 2.0 Consensus size: 409
42934 TTTTGTTCCA
* * * * * *
42944 CTTCTCTGTGTTTCATCAGGAAGATGATTTTGGTTCACTTCCCTGTATTTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAAC
* * * * * *
43009 CGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCA
66 CGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTCTACA
* * *
43074 TCGAGTGTGGGTTTGATTTGGTGTTCTTCTTAGTATCTCATCAAGAAGATGACCGCGTCGTTTGT
131 TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGT
*
43139 TTCAATCCGCTTCTCTGTGTATCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
196 TTCAATCCGCTTCTCTGTATATCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
*
43204 GAAGCTAATCGTTTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGA
261 GAAGCTAACCGTTTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGA
43269 TTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACCG
326 TTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACCG
*
43334 CGTTGTTTGTTTCAATCCG
391 CGTCGTTTGTTTCAATCCG
*
43353 CTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAAC
* * * *
43418 TG-TTTATTGCTTCGA-TCTGCTTCTC-GATGTCTCATCAAGAAGCTGAGATTTGAAGATTTACT
66 CGTTTTATTACTTCGACT-TGCTTCTCAG-TATCTCATCAAGAAGCTGAGATTCGAAGATTT-CT
* * * *
43480 CACATTGAGCGTGGGTTTGATTTGGTCTTTTTCTCAGTATCTCAT-AGGAAGATGACTGCGTCGT
128 -ACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGT
*
43544 TTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
192 TTGTTTCAATCCGCTTCTCTGTATATCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* *
43609 TCAGGAAGCTAACCGTTTATTGCTTCGATCTGCTTCTCGGTGTCTCATTAGGAAGCTGGGATTCG
257 TCAGGAAGCTAACCGTTTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCG
*
43674 AAGATTTACTCATATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATG
322 AAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATG
43739 ACCGCGTCGTTTGT
387 ACCGCGTCGTTTGT
43753 GGATGGTGAC
Statistics
Matches: 365, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
407 2 0.01
408 46 0.13
409 279 0.76
410 38 0.10
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (409 bp):
CTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAAC
CGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTCTACA
TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGT
TTCAATCCGCTTCTCTGTATATCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
GAAGCTAACCGTTTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGAGATTCGAAGA
TTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACCG
CGTCGTTTGTTTCAATCCG
Found at i:55348 original size:28 final size:28
Alignment explanation
Indices: 55312--55372 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
55302 AAAATGAGAC
* *
55312 ATTTCGGATACCCGGGGGCAAAATGGTA
1 ATTTTGGATACCCAGGGGCAAAATGGTA
* * **
55340 ATTTTGGATTCTCAGGGGTGAAATGGTA
1 ATTTTGGATACCCAGGGGCAAAATGGTA
55368 ATTTT
1 ATTTT
55373 AGGAAAAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (28 bp):
ATTTTGGATACCCAGGGGCAAAATGGTA
Found at i:55517 original size:30 final size:29
Alignment explanation
Indices: 55388--55756 Score: 241
Period size: 29 Copynumber: 12.8 Consensus size: 29
55378 AAGTCAAGGT
* *
55388 TAAAAATGGGATTTTTAG-A-TATTCGGGGG
1 TAAAAATGGAATTTTTGGAAGT-TTC-GGGG
* * *
55417 TAAAAATGTAATTTTTAG-AGTTTCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * * *
55445 TCGAGAATAGAGTTTTTGGACA--TCCGGGG
1 T-AAAAATGGAATTTTTGGA-AGTTTCGGGG
55474 -AAAAATGGTAATTTTTGGAAGTTTCGGGG
1 TAAAAATGG-AATTTTTGGAAGTTTCGGGG
55503 TAAAAAATGGAATTTTT--AA-------GG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
* *
55524 TAAAAATAGAATTTTTGGAAGTTTTGGGGTTAG
1 TAAAAATGGAATTTTTGGAAG-TTTCGGG---G
* *
55557 TAAAAAT-GAATTTTTTTGAAAGTTTTGGGG
1 TAAAAATGGAA--TTTTTGGAAGTTTCGGGG
* * * *
55587 TTAAAATGGGATTTTTTGAAGTTTCGGGT
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
55616 TAAAAATGGAATTTTTGGAAGTTTCGGTG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
* * * *
55645 TTAAAATGGGATTTTTGAAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
55674 TAAAAATGGAATTTTTGAAAGGTTT-GGGG
1 TAAAAATGGAATTTTTGGAA-GTTTCGGGG
* * * *
55703 TTAAAATGGGATTTTTTGAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
55732 TAAAAATGGAATTTTTGGAAAGTTT
1 TAAAAATGGAATTTTTGG-AAGTTT
55757 AGGGACCTTT
Statistics
Matches: 268, Mismatches: 44, Indels: 55
0.73 0.12 0.15
Matches are distributed among these distances:
20 14 0.05
21 3 0.01
22 2 0.01
27 6 0.02
28 19 0.07
29 161 0.60
30 26 0.10
31 11 0.04
32 3 0.01
33 14 0.05
34 9 0.03
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:55553 original size:50 final size:52
Alignment explanation
Indices: 55474--55571 Score: 139
Period size: 50 Copynumber: 1.9 Consensus size: 52
55464 ACATCCGGGG
*
55474 AAAAATGGTAATTTTTGGAAGTTTCGGGG-TA-AAAAATGGAATTTTTAAGGT
1 AAAAATAGTAATTTTTGGAAGTTTCGGGGTTAGAAAAAT-GAATTTTTAAGGT
*
55525 AAAAATAG-AATTTTTGGAAGTTTTGGGGTTAGTAAAAATGAATTTTT
1 AAAAATAGTAATTTTTGGAAGTTTCGGGGTTAG-AAAAATGAATTTTT
55572 TTGAAAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 19 0.45
51 9 0.21
52 8 0.19
53 6 0.14
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (52 bp):
AAAAATAGTAATTTTTGGAAGTTTCGGGGTTAGAAAAATGAATTTTTAAGGT
Found at i:55572 original size:33 final size:34
Alignment explanation
Indices: 55523--55589 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
55513 AATTTTTAAG
*
55523 GTAAAAATAGAA-TTTTTGGAAGTTTTGGGGTTA
1 GTAAAAATAGAATTTTTTGAAAGTTTTGGGGTTA
55556 GTAAAAAT-GAATTTTTTTGAAAGTTTTGGGGTTA
1 GTAAAAATAGAA-TTTTTTGAAAGTTTTGGGGTTA
55590 AAATGGGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 3 0.10
33 8 0.26
34 20 0.65
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (34 bp):
GTAAAAATAGAATTTTTTGAAAGTTTTGGGGTTA
Found at i:57451 original size:39 final size:39
Alignment explanation
Indices: 57372--57451 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
57362 TTTAGGCTAG
** *
57372 TTTGAGTCATTTAGTTTGGGCTTATTTGGGCCTTTATAA
1 TTTGAGTCATTTAGTTTGGGCCCAATTGGGCCTTTATAA
*
57411 TTTGAGTCATCTGTA-TTTGGGCCCAATTGGG-CTTTGTAA
1 TTTGAGTCAT-T-TAGTTTGGGCCCAATTGGGCCTTTATAA
57450 TT
1 TT
57452 GAACATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 19 0.54
40 14 0.40
41 2 0.06
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.46
Consensus pattern (39 bp):
TTTGAGTCATTTAGTTTGGGCCCAATTGGGCCTTTATAA
Found at i:57523 original size:17 final size:17
Alignment explanation
Indices: 57485--57535 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
57475 TTTTAAATAA
*
57485 TTAAATTTTAAA-TTCAAA
1 TTAAA-TTTAAACTT-AAT
* *
57503 TTAATTTTGAACTTAAT
1 TTAAATTTAAACTTAAT
57520 TTAAATTTAAACTTAA
1 TTAAATTTAAACTTAA
57536 AAGAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAACTTAAT
Found at i:57610 original size:13 final size:13
Alignment explanation
Indices: 57592--57617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57582 AAATTTAAAA
57592 ATTTAAATATTGG
1 ATTTAAATATTGG
57605 ATTTAAATATTGG
1 ATTTAAATATTGG
57618 CCCGATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTAAATATTGG
Found at i:59681 original size:90 final size:90
Alignment explanation
Indices: 59587--59756 Score: 304
Period size: 90 Copynumber: 1.9 Consensus size: 90
59577 ATAAAAAGGA
* * **
59587 ATTTGATATGTTCCTTATCAGATAAGGAAATATAATTTTTTTATTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
59652 AATAATAATTAAAATTCAAAATCGG
66 AATAATAATTAAAATTCAAAATCGG
59677 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
59742 AATAATAATTAAAAT
66 AATAATAATTAAAAT
59757 AGAATTTAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (90 bp):
ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
AATAATAATTAAAATTCAAAATCGG
Found at i:59753 original size:26 final size:25
Alignment explanation
Indices: 59724--59818 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
59714 TAATTATTAT
59724 TTAAAAGAGTTTTAGATAAATAATAA
1 TTAAAAGAGTTTTA-ATAAATAATAA
* * * * * *
59750 TTAAAATAGAATTTAATTATTATTAT
1 TTAAAAGAG-TTTTAATAAATAATAA
59776 TTAAAAGAGTTTTAAATAAA-AGATAA
1 TTAAAAGAGTTTT-AATAAATA-ATAA
*
59802 TTAAATAGAATTTTAAT
1 TTAAA-AGAGTTTTAAT
59819 TAAAAGAGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
25 4 0.08
26 37 0.71
27 11 0.21
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
TTAAAAGAGTTTTAATAAATAATAA
Found at i:59822 original size:42 final size:42
Alignment explanation
Indices: 59776--59862 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
59766 TTATTATTAT
*
59776 TTAAAAGAGTTTTAAATAAA-AGATAATTA-AATAGAATTTTAA
1 TTAAAAGAGTTTTAAATAAATA-ATAATGATAATAGAA-TTTAA
* *
59818 TTAAAAGAGTTTTAGATAAATAATAATGATATTAGAATTTAA
1 TTAAAAGAGTTTTAAATAAATAATAATGATAATAGAATTTAA
59860 TTA
1 TTA
59863 TTATTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 33 0.82
43 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (42 bp):
TTAAAAGAGTTTTAAATAAATAATAATGATAATAGAATTTAA
Found at i:59863 original size:94 final size:98
Alignment explanation
Indices: 59715--59927 Score: 335
Period size: 97 Copynumber: 2.2 Consensus size: 98
59705 AATAGAATTT
*
59715 AATTATTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTT-A-ATTATTATTATTT
1 AATTATTATTTAAAAGAGTTTTAGATAAATAATAATGAAAATAGAATTTAATATTATTATTATTT
*
59778 AAAAGAGTTTTAAATAAAAGATAATTAAATAG-
66 AAAAGAGTTTTAAATAAAAAATAATTAAATAGA
* * *
59810 AATT-TTAATTAAAAGAGTTTTAGATAAATAATAATGATATTAGAATTTAATTATTATTATTATT
1 AATTATTATTTAAAAGAGTTTTAGATAAATAATAATGAAAATAGAATTTAA-TATTATTATTATT
*
59874 TAAAAGAGTTTTAAATAAAAAATAATTTAATAGA
65 TAAAAGAGTTTTAAATAAAAAATAATTAAATAGA
59908 AATTATTATTTAAAAGAGTT
1 AATTATTATTTAAAAGAGTT
59928 ATTAATATTT
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
94 40 0.38
95 5 0.05
97 43 0.41
98 4 0.04
99 14 0.13
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.41
Consensus pattern (98 bp):
AATTATTATTTAAAAGAGTTTTAGATAAATAATAATGAAAATAGAATTTAATATTATTATTATTT
AAAAGAGTTTTAAATAAAAAATAATTAAATAGA
Found at i:62363 original size:6 final size:6
Alignment explanation
Indices: 62352--62376 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62342 TGGATAATTT
62352 TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA T
62377 AATAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:63322 original size:50 final size:50
Alignment explanation
Indices: 63265--63378 Score: 176
Period size: 50 Copynumber: 2.3 Consensus size: 50
63255 AACATCTTGT
63265 TAATGTTAAAAGTTTTAAGATTATAAATAGAAACAGACATTATATAAAAA
1 TAATGTTAAAAGTTTTAAGATTATAAATAGAAACAGACATTATATAAAAA
* * *
63315 TAATGTTAAAAGTTTTGAGATTATAAATAGGAACATACATTATATAAAAA
1 TAATGTTAAAAGTTTTAAGATTATAAATAGAAACAGACATTATATAAAAA
* *
63365 AAAT-TTTAAAGTTT
1 TAATGTTAAAAGTTT
63379 GCTTGGGACA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 9 0.15
50 50 0.85
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (50 bp):
TAATGTTAAAAGTTTTAAGATTATAAATAGAAACAGACATTATATAAAAA
Found at i:68824 original size:24 final size:23
Alignment explanation
Indices: 68795--68873 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
68785 TAACCATTTA
68795 AAAATAATAAAAATATAAGCTATT
1 AAAATAATAAAAATATAA-CTATT
68819 AAAATAAT-AAAAT-T-AC-ATT
1 AAAATAATAAAAATATAACTATT
* * * *
68838 TATATTATAAAGATATAAACTATT
1 AAAATAATAAAAATAT-AACTATT
68862 AAAATAATAAAA
1 AAAATAATAAAA
68874 TTACATTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
19 8 0.19
20 5 0.12
21 2 0.05
22 1 0.02
23 7 0.17
24 19 0.45
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAATAATAAAAATATAACTATT
Found at i:68855 original size:43 final size:43
Alignment explanation
Indices: 68801--68888 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
68791 TTTAAAAATA
*
68801 ATAAAAATATAAGCTATTAAAATAATAAAATTACATTTATATT
1 ATAAAAATATAAACTATTAAAATAATAAAATTACATTTATATT
*
68844 ATAAAGATATAAACTATTAAAATAATAAAATTACATTTATATT
1 ATAAAAATATAAACTATTAAAATAATAAAATTACATTTATATT
68887 AT
1 AT
68889 CGTAAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (43 bp):
ATAAAAATATAAACTATTAAAATAATAAAATTACATTTATATT
Found at i:69584 original size:55 final size:55
Alignment explanation
Indices: 69500--69610 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
69490 AGCACATTCT
69500 TCCCAACTGGCCAAAAGGATAAACAAAGTCAAATCATGGCTTGACAATTTTTAGA
1 TCCCAACTGGCCAAAAGGATAAACAAAGTCAAATCATGGCTTGACAATTTTTAGA
69555 TCCCAACTGGCCAAAAGGATAAACAAAGTCAAATCATGGCTTGACAATTTTTAGA
1 TCCCAACTGGCCAAAAGGATAAACAAAGTCAAATCATGGCTTGACAATTTTTAGA
69610 T
1 T
69611 AATAATGGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (55 bp):
TCCCAACTGGCCAAAAGGATAAACAAAGTCAAATCATGGCTTGACAATTTTTAGA
Found at i:70421 original size:17 final size:17
Alignment explanation
Indices: 70398--70454 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
70388 CCCTTTTTTT
70398 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
70415 GATTTATTTTTAATTTA
1 AATTTATTTTAAATTTA
* *
70432 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
70449 AATTTA
1 AATTTA
70455 ATTCCAAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:70447 original size:28 final size:28
Alignment explanation
Indices: 70393--70457 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
70383 TTGGACCCTT
** *
70393 TTTTTAATTTATTTTAAATTTAGATTTA
1 TTTTTAATTTAAATTAAATTTAAATTTA
70421 TTTTTAATTTAAATT-AATCTTAAATTTA
1 TTTTTAATTTAAATTAAAT-TTAAATTTA
**
70449 AATTTAATT
1 TTTTTAATT
70458 CCAAAGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTTAATTTAAATTAAATTTAAATTTA
Found at i:72267 original size:30 final size:30
Alignment explanation
Indices: 72233--72629 Score: 276
Period size: 30 Copynumber: 13.7 Consensus size: 30
72223 GAGGTCCCCG
72233 AACTTCCCAAAATCCCATTTTTAACCTCGA
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
* * *
72263 AACTTCCAAAAATTCCATTTTTACCCTCG-
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
* *
72292 AACTTCCCCAAAATCCCATTTTTACCCTTG-
1 AACTT-CCCAAAATCCCATTTTTAACCTCGA
* *
72322 AACTTCCCTAAAATCCCATTTTTTACCCCGA
1 AACTTCCC-AAAATCCCATTTTTAACCTCGA
* * *
72353 AACTTCCAAAAATTCTA-TTTTAACACTCG-
1 AACTTCCCAAAATCCCATTTTTAAC-CTCGA
*
72382 AACTCCCCAAAATCCCA-TTTT----T-G-
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
* * * *
72405 -AC--CCCAAAAATTCTATTTTTACCCT-TA
1 AACTTCCC-AAAATCCCATTTTTAACCTCGA
* * * * *
72432 AACTCCCTAAAATCCCATTTTTGACCCCAA
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
** * *
72462 AACTTCTAAAAATTCCATTTTT-ACCCCG-
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
*
72490 AACTTCCCAAAATCCCATTTTTGACCTCGA
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
* * * *
72520 AACTTCCAAAAATTCCGTTTTTACCCTC-A
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
* ** *
72549 AACTTCCCCAAAACCCCA-TTTGGACCCCGA
1 AACTT-CCCAAAATCCCATTTTTAACCTCGA
* * * *
72579 AACTTCCAAAAATTCCATTTTT-ACCCCAA
1 AACTTCCCAAAATCCCATTTTTAACCTCGA
72608 AACTTCCCAAAATCCCATTTTT
1 AACTTCCCAAAATCCCATTTTT
72630 GACCCCAAAA
Statistics
Matches: 289, Mismatches: 58, Indels: 41
0.74 0.15 0.11
Matches are distributed among these distances:
20 3 0.01
21 7 0.02
22 6 0.02
23 1 0.00
24 1 0.00
26 1 0.00
28 21 0.07
29 102 0.35
30 140 0.48
31 7 0.02
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.31
Consensus pattern (30 bp):
AACTTCCCAAAATCCCATTTTTAACCTCGA
Found at i:72397 original size:59 final size:58
Alignment explanation
Indices: 72228--72642 Score: 379
Period size: 59 Copynumber: 7.2 Consensus size: 58
72218 CCCTTGAGGT
* * * * *
72228 CCCCG-AACTTCCCAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTT-A
1 CCCCGAAACTTCCAAAAATTCCATTTTT-ACCTCG-AACTCCCCAAAATCCCATTTTTGA
* * * * *
72286 CCCTCG-AACTTCCCCAAAATCCCATTTTTACCCTTGAACTTCCCTAAAATCCCATTTTTTA
1 CCC-CGAAACTT-CCAAAAATTCCATTTTTA-CCTCGAAC-TCCCCAAAATCCCATTTTTGA
* *
72347 CCCCGAAACTTCCAAAAATTCTATTTTAACACTCGAACTCCCCAAAATCCCATTTTTGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTAC-CTCGAACTCCCCAAAATCCCATTTTTGA
* ** *
72406 ---C----C--CCAAAAATTCTATTTTTACCCTTAAACTCCCTAAAATCCCATTTTTGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA-CCTCGAACTCCCCAAAATCCCATTTTTGA
* * * *
72456 CCCCAAAACTTCTAAAAATTCCATTTTTACCCCGAACTTCCCAAAATCCCATTTTTGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTACCTCGAACTCCCCAAAATCCCATTTTTGA
* * * * *
72514 CCTCGAAACTTCCAAAAATTCCGTTTTTACCCTCAAACTTCCCCAAAACCCCA-TTTGGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTA-CCTCGAAC-TCCCCAAAATCCCATTTTTGA
* * *
72573 CCCCGAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCCAAAATCCCATTTTTGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTACCTC-GAACTCCCCAAAATCCCATTTTTGA
*
72632 CCCCAAAACTT
1 CCCCGAAACTT
72643 ACGAAGGTTA
Statistics
Matches: 298, Mismatches: 38, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
50 42 0.14
51 1 0.00
52 1 0.00
53 1 0.00
56 1 0.00
57 1 0.00
58 67 0.22
59 104 0.35
60 71 0.24
61 9 0.03
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.31
Consensus pattern (58 bp):
CCCCGAAACTTCCAAAAATTCCATTTTTACCTCGAACTCCCCAAAATCCCATTTTTGA
Found at i:72436 original size:50 final size:50
Alignment explanation
Indices: 72358--72469 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 50
72348 CCCGAAACTT
*
72358 CCAAAAATTCTATTTTAACACTCGAACTCCCCAAAATCCCATTTTTGACC
1 CCAAAAATTCTATTTTAACACTCAAACTCCCCAAAATCCCATTTTTGACC
* * * *
72408 CCAAAAATTCTATTTTTACCCTTAAACTCCCTAAAATCCCATTTTTGACC
1 CCAAAAATTCTATTTTAACACTCAAACTCCCCAAAATCCCATTTTTGACC
*
72458 CCAAAACTTCTA
1 CCAAAAATTCTA
72470 AAAATTCCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (50 bp):
CCAAAAATTCTATTTTAACACTCAAACTCCCCAAAATCCCATTTTTGACC
Done.