Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002514.1 Kokia drynarioides strain JFW-HI SEQ_114680, 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: 53548
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:1202 original size:111 final size:112
Alignment explanation
Indices: 1079--1303 Score: 425
Period size: 112 Copynumber: 2.0 Consensus size: 112
1069 AACACATTTT
*
1079 AATCTGAATATTGCAACAAGTAAATCATGT-AAAAAAAAACAAAAATTTATAACATTTATCGTTA
1 AATCTGAATATTGCAACAAGTAAATCATGTAAAAAAAAAACAAAAATTTATAACATTTATCGTCA
1143 AATAAAAAGACTCGATCATTTCAATCTCAAACACTCGAACAAAATAC
66 AATAAAAAGACTCGATCATTTCAATCTCAAACACTCGAACAAAATAC
*
1190 AATCTGAATATTGCAATAAGTAAATCATGTAAAAAAAAAACAAAAATTTATAACATTTATCGTCA
1 AATCTGAATATTGCAACAAGTAAATCATGTAAAAAAAAAACAAAAATTTATAACATTTATCGTCA
1255 AATAAAAAGACTCGATCATTTCAATCTCAAACACTCGAACAAAATAC
66 AATAAAAAGACTCGATCATTTCAATCTCAAACACTCGAACAAAATAC
1302 AA
1 AA
1304 AAAAGAAAAA
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 29 0.26
112 82 0.74
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (112 bp):
AATCTGAATATTGCAACAAGTAAATCATGTAAAAAAAAAACAAAAATTTATAACATTTATCGTCA
AATAAAAAGACTCGATCATTTCAATCTCAAACACTCGAACAAAATAC
Found at i:1749 original size:16 final size:16
Alignment explanation
Indices: 1725--1792 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
1715 TATTTTATTA
*
1725 AATTGTATTTAATAAT
1 AATTATATTTAATAAT
*
1741 AATTATA-TTAAAATAT
1 AATTATATTTAATA-AT
* ** *
1757 AATTAAATTTTTTATT
1 AATTATATTTAATAAT
1773 AAATTATATTTAATAAT
1 -AATTATATTTAATAAT
1790 AAT
1 AAT
1793 CTTATTAAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
15 5 0.13
16 18 0.47
17 15 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:2288 original size:29 final size:27
Alignment explanation
Indices: 2243--2324 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
2233 AATAAATAAA
2243 TAAAATTGTTT-AAAAAATTAAAAATATG
1 TAAAATT-TTTAAAAAAATTAAAAAT-TG
* *
2271 ATAGAATTTTTAAAAAAAATTTAAAATTG
1 -TAAAATTTTT-AAAAAAATTAAAAATTG
* *
2300 TAAAAATTTTAAAAATATATAAAAA
1 TAAAATTTTTAAAAAAAT-TAAAAA
2325 AGTTATTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.16
28 16 0.36
29 8 0.18
30 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (27 bp):
TAAAATTTTTAAAAAAATTAAAAATTG
Found at i:2309 original size:28 final size:30
Alignment explanation
Indices: 2254--2314 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
2244 AAAATTGTTT
* *
2254 AAAAAATTAAAAATATGATAGAATTTTTAA
1 AAAAAATTAAAAATATGATAAAAATTTTAA
*
2284 AAAAAATTTAAAAT-TG-TAAAAATTTTAA
1 AAAAAATTAAAAATATGATAAAAATTTTAA
2312 AAA
1 AAA
2315 TATATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.46
29 2 0.07
30 13 0.46
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAAATTAAAAATATGATAAAAATTTTAA
Found at i:13306 original size:80 final size:80
Alignment explanation
Indices: 13222--13406 Score: 243
Period size: 82 Copynumber: 2.3 Consensus size: 80
13212 AAAGACTAAG
* *
13222 AATTAAGAAAATAAAATAAAAGGATTTAA-T-TTTTAGAAAATTGAACAAAA-GA-AATTTTTTA
1 AATTAA-AAAATATAATAAAAGG--TTAATTGTTTTA-AAAATGGAACAAAAGGATAATTTTTTA
*
13283 AAAAGGAATAAAATGATTT
62 AAAAAGAATAAAATGATTT
*
13302 AATTAAAAAACATAATAAAAAGGTTAATTGTTTTAAAAATGGAACAAAAGGATTAATTTTTTAAA
1 AATTAAAAAATATAAT-AAAAGGTTAATTGTTTTAAAAATGGAACAAAAGGA-TAATTTTTTAAA
13367 AAAGAATAAAATGATTT
64 AAAGAATAAAATGATTT
13384 AATTAAAAGAATATAATAAAAGG
1 AATTAAAA-AATATAATAAAAGG
13407 GCTAAATTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
78 4 0.04
79 22 0.24
80 19 0.20
82 41 0.44
83 7 0.08
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (80 bp):
AATTAAAAAATATAATAAAAGGTTAATTGTTTTAAAAATGGAACAAAAGGATAATTTTTTAAAAA
AGAATAAAATGATTT
Found at i:13385 original size:28 final size:29
Alignment explanation
Indices: 13274--13387 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 29
13264 GAACAAAAGA
*
13274 AATTTTTTAAAAA-GGAATAAAATGATTT
1 AATTTTTTAAAAACAGAATAAAATGATTT
* * * *
13302 AA---TTAAAAAACATAATAAAAAG-GTT
1 AATTTTTTAAAAACAGAATAAAATGATTT
** * *
13327 AATTGTTTTAAAAATGGAACAAAAGGA-TT
1 AATT-TTTTAAAAACAGAATAAAATGATTT
13356 AATTTTTTAAAAA-AGAATAAAATGATTT
1 AATTTTTTAAAAACAGAATAAAATGATTT
13384 AATT
1 AATT
13388 AAAAGAATAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
25 11 0.17
26 8 0.12
27 9 0.14
28 17 0.26
29 20 0.31
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.34
Consensus pattern (29 bp):
AATTTTTTAAAAACAGAATAAAATGATTT
Found at i:14435 original size:2 final size:2
Alignment explanation
Indices: 14428--14452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14418 ATAAAAGAAT
14428 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
14453 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15939 original size:18 final size:17
Alignment explanation
Indices: 15909--15942 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
15899 TTTAAAAAAT
15909 AAAAACAAAAAAAATTA
1 AAAAACAAAAAAAATTA
*
15926 AAAAACTAAGAAAAATT
1 AAAAAC-AAAAAAAATT
15943 GAAGCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAACAAAAAAAATTA
Found at i:21874 original size:50 final size:49
Alignment explanation
Indices: 21666--21876 Score: 201
Period size: 49 Copynumber: 4.3 Consensus size: 49
21656 TAGGAAATGT
* ** * * *
21666 CGAATCATATACCCTAGAAGACATGAAGGGAAAGATTGAAGCCGCAACGA
1 CGAATCTTATACCCTAG-AGATGTGAAGGGAAAGATTAAAGCCACAACAA
* * * * ** *
21716 CAAATCTTATACCCTAAAGATGTGGAGGGAAA-AGTTGAAGCGTCAACAT
1 CGAATCTTATACCCTAGAGATGTGAAGGGAAAGA-TTAAAGCCACAACAA
* *
21765 TGAACCTTATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACAA
1 CGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACAA
* ***
21814 CGAATCTTATACCCTAGAGATGT-AGAGGGAAAGGTTTAAAGCCACAATGG
1 CGAATCTTATACCCTAGAGATGTGA-AGGGAAA-GATTAAAGCCACAACAA
21864 CGAATCTTATACC
1 CGAATCTTATACC
21877 ATGAAGATGA
Statistics
Matches: 132, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.02
49 89 0.67
50 41 0.31
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (49 bp):
CGAATCTTATACCCTAGAGATGTGAAGGGAAAGATTAAAGCCACAACAA
Found at i:22263 original size:94 final size:94
Alignment explanation
Indices: 22183--22680 Score: 452
Period size: 94 Copynumber: 5.4 Consensus size: 94
22173 TAAGAGATCA
* *
22183 CAATGTCCCCTGAGGTTACAATGGAGTGGAGTGTAGCGCCAAAATCTTATACCCCTGAGTTGCAG
1 CAATGT-CCCTGAGGTTACAATGGAGTGGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAG
* *
22248 TGGGTTAGATTAAAACAATGAAGCAAAACT
65 TGGGTCAGATTAAAACAATGAAGCAGAACT
* * * ** * *
22278 CAACGTCCTTAAGGTTACAGA-GGAGTGGAGTGAGAG-TTC-AAATCTCAT-CTTCCTG-GT-G-
1 CAATGTCCCTGAGGTTACA-ATGGAGTGGAGTGA-AGCGCCAAAATCTTATAC-CCCTGAGTCGC
* * *
22336 AGGTATAGAGAAGTGAG-TTAAAAC-ATGTAGCAGATCT
63 A-G--T-G-G--GTCAGATTAAAACAATGAAGCAGAACT
* * *
22373 CAATGTCCCTGAGGTTATAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGT
1 CAATGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGT
* * *
22438 GGGTCGGATGAAAATAATGAAGCAGAACT
66 GGGTCAGATTAAAACAATGAAGCAGAACT
* * *
22467 CAATGTCCTTGAGGTTACAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGT
1 CAATGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGT
* * * *
22532 GGGTCGGATGAAAATAATGAAGCAGAGCT
66 GGGTCAGATTAAAACAATGAAGCAGAACT
* * * *
22561 CAACGTCCCTGA-G------TGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGTAGT
1 CAATGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGT
* * * *
22619 GGGTCGGATGAAAATAATGAAGCAGAGCT
66 GGGTCAGATTAAAACAATGAAGCAGAACT
* *
22648 CAACGTCCCTGAGGTTACAGTGGAGTGGAGTGA
1 CAATGTCCCTGAGGTTACAATGGAGTGGAGTGA
22681 GTTTTTAGAT
Statistics
Matches: 341, Mismatches: 36, Indels: 53
0.79 0.08 0.12
Matches are distributed among these distances:
87 84 0.25
88 1 0.00
90 1 0.00
91 2 0.01
92 6 0.02
93 19 0.06
94 151 0.44
95 47 0.14
96 20 0.06
97 7 0.02
98 2 0.01
99 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (94 bp):
CAATGTCCCTGAGGTTACAATGGAGTGGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGT
GGGTCAGATTAAAACAATGAAGCAGAACT
Found at i:22398 original size:95 final size:95
Alignment explanation
Indices: 22084--22405 Score: 300
Period size: 95 Copynumber: 3.4 Consensus size: 95
22074 ATAAGTAACG
* * *
22084 GATCTCAATGTCCCTGAGGTTACAGT-GAGTGGAGTGAGACTTCAAATCCCATCTTCTTGGTGAG
1 GATCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGGTGAG
* *
22148 GTACAGAGAAGTGAGTCAAAACAGGTAAG-A
66 GTACAGAGAAGTGAGTTAAAACATGT-AGCA
* * * * * *
22178 GATCACAATGTCCCCTGAGGTTACAATGGAGTGGAGTGTAGCG-CCAAAATCTTATAC--CC--C
1 GATCTCAATGT-CCCTGAGGTTACAGTGGAGTGGAGTG-AGAGTTC-AAATCTCAT-CTTCCTGG
* * * * * *
22238 TGAGTTGCAGTG-GGTTAGATTAAAACAATGAAGCA
62 TGAGGTACAGAGAAGTGAG-TTAAAAC-ATGTAGCA
* * * * * *
22273 AAACTCAACGTCCTTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGGTGAG
1 GATCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGGTGAG
*
22338 GTATAGAGAAGTGAGTTAAAACATGTAGCA
66 GTACAGAGAAGTGAGTTAAAACATGTAGCA
*
22368 GATCTCAATGTCCCTGAGGTTATAGTGGAGTGGAGTGA
1 GATCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGA
22406 AGCGCTAAAA
Statistics
Matches: 171, Mismatches: 43, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
92 1 0.01
93 15 0.09
94 52 0.30
95 62 0.36
96 27 0.16
97 13 0.08
98 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (95 bp):
GATCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGGTGAG
GTACAGAGAAGTGAGTTAAAACATGTAGCA
Found at i:22439 original size:189 final size:189
Alignment explanation
Indices: 22087--22892 Score: 818
Period size: 189 Copynumber: 4.3 Consensus size: 189
22077 AGTAACGGAT
* * * *
22087 CTCAATGTCCCTGAGGTTACAGT-GAGTGGAGTGAGACTTCAAATCCCATCTTCTTGGTGAGGTA
1 CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTGGTGAGGTA
* * * *
22151 CAGAGAAGTGAGTCAAAACAGGTAAG-AGATCACAATGTCCCCTGAGGTTACAATGGAGTGGAGT
66 CAGAGAAGTGAGTCAAAACAGGT-AGCAGATCTCAACGT-CCCTGAGGTTATAGTGGAGTGGAGT
* * ** * * *
22215 GTAGCGCCAAAATCTTATACCCCTGAGTTGCAGTGGGTTAGATTAAAACAATGAAGCAAAA
129 GAAGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGAA
* * *
22276 CTCAACGTCCTTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGGTGAGGTA
1 CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTGGTGAGGTA
* * * *
22341 TAGAGAAGTGAGTTAAAACATGTAGCAGATCTCAATGTCCCTGAGGTTATAGTGGAGTGGAGTGA
66 CAGAGAAGTGAGTCAAAACAGGTAGCAGATCTCAACGTCCCTGAGGTTATAGTGGAGTGGAGTGA
*
22406 AGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGAA
131 AGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGAA
* * * * * * *
22465 CTCAATGTCCTTGAGGTTACAGTGGAGTGGAGTGA-AGCGCTAAAATCTTATAC--CC--CTGA-
1 CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGA-C-TTCAAATCTCAT-CTTCCTGGTGAG
* * * * * * * *
22524 GTCGCAGTG-GGTCG-GATGAAAATAATGAAGCAGAGCTCAACGTCCCT---G----AGTGGAGT
63 GT-ACAGAGAAGT-GAG-TCAAAA-CAGGTAGCAGATCTCAACGTCCCTGAGGTTATAGTGGAGT
* * *
22580 GAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGTAGTGGGTCGGATGAAAATAATGAAGCAGA
124 GGAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGA
*
22645 G
189 A
* ** * * * *
22646 CTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGTTTTTAGATCCCATCTTCCTTGTGAGGTA
1 CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTGGTGAGGTA
* * * * * * *
22711 CAGAAAAGTGGGTCAAAACAGGTAGCAGATCTCAACATCCTTGATGTTATAGTGGAGTGGAATAA
66 CAGAGAAGTGAGTCAAAACAGGTAGCAGATCTCAACGTCCCTGAGGTTATAGTGGAGTGGAGTGA
* * * *
22776 AGCGCCACAATCTTATACCCCTGAATTGCAGTGGGTCGGATGAAAATAATGAAGCAGAG
131 AGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGAA
* * * * *
22835 CTCAATGTCCCTAAGGTTATAGTGGAGTGGAGTGAAACTTCAAAATCTCGTCGTCCTG
1 CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGACTTC-AAATCTCATCTTCCTG
22893 AGACTACGAG
Statistics
Matches: 510, Mismatches: 82, Indels: 49
0.80 0.13 0.08
Matches are distributed among these distances:
179 1 0.00
180 7 0.01
181 106 0.21
182 18 0.04
183 12 0.02
184 5 0.01
185 2 0.00
186 5 0.01
187 12 0.02
188 21 0.04
189 231 0.45
190 89 0.17
191 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (189 bp):
CTCAACGTCCCTAAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTGGTGAGGTA
CAGAGAAGTGAGTCAAAACAGGTAGCAGATCTCAACGTCCCTGAGGTTATAGTGGAGTGGAGTGA
AGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGAA
Found at i:22630 original size:87 final size:87
Alignment explanation
Indices: 22485--22660 Score: 334
Period size: 87 Copynumber: 2.0 Consensus size: 87
22475 TTGAGGTTAC
*
22485 AGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAAT
1 AGTGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAAT
22550 GAAGCAGAGCTCAACGTCCCTG
66 GAAGCAGAGCTCAACGTCCCTG
*
22572 AGTGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGTAGTGGGTCGGATGAAAATAAT
1 AGTGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAAT
22637 GAAGCAGAGCTCAACGTCCCTG
66 GAAGCAGAGCTCAACGTCCCTG
22659 AG
1 AG
22661 GTTACAGTGG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.21
Consensus pattern (87 bp):
AGTGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAAT
GAAGCAGAGCTCAACGTCCCTG
Found at i:22699 original size:370 final size:370
Alignment explanation
Indices: 22204--22870 Score: 983
Period size: 370 Copynumber: 1.8 Consensus size: 370
22194 GAGGTTACAA
* * * * *
22204 TGGAGTGGAGTGTAGCGCCAAAATCTTATACCCCTGAGTTGCAGTGGGTTAGATTAAAACAATGA
1 TGGAGTGAAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCAGATGAAAACAATGA
* *
22269 AGCAAAACTCAACGTCCTTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCTCATCTTCCTGG
66 AGCAAAACTCAACGTCCCTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCCCATCTTCCTGG
* * * * **
22334 TGAGGTATAGAGAAGTGAGTTAAAACATGTAGCAGATCTCAATGTCCCTGAGGTTATAGTGGAGT
131 TGAGGTACAGAAAAGTGAGTCAAAACAGGTAGCAGATCTCAACATCCCTGAGGTTATAGTGGAGT
* * * *
22399 GGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGCAGTGGGTCGGATGAAAATAATGAAGCAGA
196 GGAATAAAGCGCCAAAATCTTATACCCCTGAATCGCAGTGGGTCGGATGAAAATAATGAAGCAGA
* *
22464 ACTCAATGTCCTTGAGGTTACAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGC
261 ACTCAATGTCCCTAAGGTTACAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGC
22529 AGTGGGTCGGATGAAAATAATGAAGCAGAGCTCAACGTCCCTGAG
326 AGTGGGTCGGATGAAAATAATGAAGCAGAGCTCAACGTCCCTGAG
* * * *
22574 TGGAGTGAAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGTAGTGGGTCGGATGAAAATAATGA
1 TGGAGTGAAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCAGATGAAAACAATGA
* * * * ** * * *
22639 AGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGTTTTTAGATCCCATCTTCCTTG
66 AGCAAAACTCAACGTCCCTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCCCATCTTCCTGG
* * *
22704 TGAGGTACAGAAAAGTGGGTCAAAACAGGTAGCAGATCTCAACATCCTTGATGTTATAGTGGAGT
131 TGAGGTACAGAAAAGTGAGTCAAAACAGGTAGCAGATCTCAACATCCCTGAGGTTATAGTGGAGT
* *
22769 GGAATAAAGCGCCACAATCTTATACCCCTGAATTGCAGTGGGTCGGATGAAAATAATGAAGCAGA
196 GGAATAAAGCGCCAAAATCTTATACCCCTGAATCGCAGTGGGTCGGATGAAAATAATGAAGCAGA
* *
22834 GCTCAATGTCCCTAAGGTTATAGTGGAGTGGAGTGAA
261 ACTCAATGTCCCTAAGGTTACAGTGGAGTGGAGTGAA
22871 ACTTCAAAAT
Statistics
Matches: 258, Mismatches: 39, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
370 258 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (370 bp):
TGGAGTGAAGTGAAGCGCCAAAATCTTATACCCCTGAGTCGCAGTGGGTCAGATGAAAACAATGA
AGCAAAACTCAACGTCCCTAAGGTTACAGAGGAGTGGAGTGAGAGTTCAAATCCCATCTTCCTGG
TGAGGTACAGAAAAGTGAGTCAAAACAGGTAGCAGATCTCAACATCCCTGAGGTTATAGTGGAGT
GGAATAAAGCGCCAAAATCTTATACCCCTGAATCGCAGTGGGTCGGATGAAAATAATGAAGCAGA
ACTCAATGTCCCTAAGGTTACAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTGAGTCGC
AGTGGGTCGGATGAAAATAATGAAGCAGAGCTCAACGTCCCTGAG
Found at i:22854 original size:94 final size:94
Alignment explanation
Indices: 22364--22870 Score: 500
Period size: 94 Copynumber: 5.5 Consensus size: 94
22354 TAAAACATGT
* * *
22364 AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTG
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAAGCGCTAAAATCTTATACCCCTG
22429 AGTCGCAGTGGGTCGGATGAAAATAATGA
66 AGTCGCAGTGGGTCGGATGAAAATAATGA
* * * * *
22458 AGCAGAACTCAATGTCCTTGAGGTTACAGTGGAGTGGAGTGAAGCGCTAAAATCTTATACCCCTG
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAAGCGCTAAAATCTTATACCCCTG
22523 AGTCGCAGTGGGTCGGATGAAAATAATGA
66 AGTCGCAGTGGGTCGGATGAAAATAATGA
22552 AGCAGAGCTCAACGTCCCT---G----AGTGGAGT-GAAGTGAAGCGCTAAAATCTTATACCCCT
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAA-TGAAGCGCTAAAATCTTATACCCCT
*
22609 GAGTCGTAGTGGGTCGGATGAAAATAATGA
65 GAGTCGCAGTGGGTCGGATGAAAATAATGA
* * *** * * **
22639 AGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG-AGTTTTTAGATCCCAT-CTTCCT
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAAGCGCTAAAATCTTATAC--CC-
* * *** * * * * *
22702 TGTGAGGT-ACAGAAAAGT-GGGTCAAAA-CAGGT
63 -CTGA-GTCGCAG-TGGGTCGGATGAAAATAATGA
* * * * * * *
22734 AGCAGATCTCAACATCCTTGATGTTATAGTGGAGTGGAATAAAGCGCCACAATCTTATACCCCTG
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAAGCGCTAAAATCTTATACCCCTG
* *
22799 AATTGCAGTGGGTCGGATGAAAATAATGA
66 AGTCGCAGTGGGTCGGATGAAAATAATGA
* * *
22828 AGCAGAGCTCAATGTCCCTAAGGTTATAGTGGAGTGGAGTGAA
1 AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAA
22871 ACTTCAAAAT
Statistics
Matches: 331, Mismatches: 62, Indels: 40
0.76 0.14 0.09
Matches are distributed among these distances:
86 2 0.01
87 81 0.24
90 1 0.00
91 1 0.00
92 4 0.01
93 22 0.07
94 156 0.47
95 40 0.12
96 19 0.06
97 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (94 bp):
AGCAGAGCTCAACGTCCCTGAGGTTATAGTGGAGTGGAATGAAGCGCTAAAATCTTATACCCCTG
AGTCGCAGTGGGTCGGATGAAAATAATGA
Found at i:24680 original size:32 final size:32
Alignment explanation
Indices: 24635--24711 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
24625 ATTTATTCTA
*
24635 TTTTTTAAAATTAAATCCTTCTATTTCTATT-
1 TTTTTTAAAATTAAACCCTTCTATTTCTATTC
* *
24666 TTTTGTTAAAATTAAACCCTTTTATTTTTATTC
1 TTTT-TTAAAATTAAACCCTTCTATTTCTATTC
*
24699 CTTTTTAAAATTA
1 TTTTTTAAAATTA
24712 CCCTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.10
32 33 0.82
33 3 0.08
ACGTcount: A:0.30, C:0.12, G:0.01, T:0.57
Consensus pattern (32 bp):
TTTTTTAAAATTAAACCCTTCTATTTCTATTC
Found at i:24694 original size:27 final size:26
Alignment explanation
Indices: 24611--24694 Score: 62
Period size: 32 Copynumber: 3.0 Consensus size: 26
24601 GGTTTTCCCC
* *
24611 TTTAAAATT-TACCCATTTATTCTATTT
1 TTTAAAATTAAACCCTTTTATT-T-TTT
24638 TTTAAAATTAAATCCTTCTATTTCTATTTTTT
1 TTTAAAATTAAA-CC--C--TTT-TATTTTTT
*
24670 GTTAAAATTAAACCCTTTTATTTTT
1 TTTAAAATTAAACCCTTTTATTTTT
24695 ATTCCTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
26 7 0.15
27 12 0.26
28 1 0.02
29 3 0.06
31 3 0.06
32 14 0.30
33 3 0.06
34 4 0.09
ACGTcount: A:0.30, C:0.13, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTAAAATTAAACCCTTTTATTTTTT
Found at i:29205 original size:24 final size:21
Alignment explanation
Indices: 29178--29233 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
29168 CTTACCATAG
29178 TACGCCATAAGACGACACACAGAA
1 TACGCCATAAGACGA-ACA-A-AA
* *
29202 TACGCCATTAAGGCTAACAAAA
1 TACGCCA-TAAGACGAACAAAA
29224 TACGCCATAA
1 TACGCCATAA
29234 AGTCTAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.10
22 9 0.31
23 1 0.03
24 10 0.34
25 6 0.21
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.14
Consensus pattern (21 bp):
TACGCCATAAGACGAACAAAA
Found at i:29228 original size:22 final size:22
Alignment explanation
Indices: 29200--29260 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
29190 CGACACACAG
*
29200 AATACGCCATTAAGGCTAACAA
1 AATACGCCATAAAGGCTAACAA
* *
29222 AATACGCCATAAAGTCTAACAG
1 AATACGCCATAAAGGCTAACAA
* * *
29244 ACTACGTCTTAAAGGCT
1 AATACGCCATAAAGGCT
29261 GATAGAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (22 bp):
AATACGCCATAAAGGCTAACAA
Found at i:33992 original size:22 final size:20
Alignment explanation
Indices: 33957--33996 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
33947 ATCGAAAATT
33957 TCTTTCTTTTTGTTTCTTCC
1 TCTTTCTTTTTGTTTCTTCC
33977 TCTTTCTCATTTTGTTTCTT
1 TCTTTCT--TTTTGTTTCTT
33997 TTTCAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.03, C:0.23, G:0.05, T:0.70
Consensus pattern (20 bp):
TCTTTCTTTTTGTTTCTTCC
Found at i:37714 original size:27 final size:27
Alignment explanation
Indices: 37663--37719 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
37653 AAAGGAATTT
37663 CTTTGTGGCAAACTCTAAAGGGAATGC
1 CTTTGTGGCAAACTCTAAAGGGAATGC
*
37690 CTTTGTGGCAAACTCTGAAA-TGAATGC
1 CTTTGTGGCAAACTCT-AAAGGGAATGC
37717 CTT
1 CTT
37720 GACGGCGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (27 bp):
CTTTGTGGCAAACTCTAAAGGGAATGC
Found at i:39209 original size:21 final size:21
Alignment explanation
Indices: 39164--39238 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
39154 TAATGTAGAA
** *
39164 TTCTACCGATACAAGGGATAG
1 TTCTACCGATACAAGTAATAC
*
39185 TTCTACCGATACAAGTAACAC
1 TTCTACCGATACAAGTAATAC
** * *
39206 TTCTATTGATACAAGTCATGC
1 TTCTACCGATACAAGTAATAC
39227 TTCTACCGATAC
1 TTCTACCGATAC
39239 CAAAAACTCC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGTAATAC
Found at i:46543 original size:21 final size:21
Alignment explanation
Indices: 46495--46547 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
46485 TAGTGTAGAA
* *
46495 TTCTACCGATACAAGTGACAC
1 TTCTACCGATACAAATCACAC
* **
46516 TTTTACCGATACAAATCATGC
1 TTCTACCGATACAAATCACAC
46537 TTCTACC-ATAC
1 TTCTACCGATAC
46548 CAAAAACTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAATCACAC
Found at i:49550 original size:20 final size:22
Alignment explanation
Indices: 49503--49561 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
49493 CACAAAGTAG
* *
49503 TGAGAATGAGAATT-TATTTTC
1 TGAGAATTATAATTCTATTTTC
*
49524 TTAGAA-TA-AATTCTATTTTC
1 TGAGAATTATAATTCTATTTTC
*
49544 TGGGAATTATAATTCTAT
1 TGAGAATTATAATTCTAT
49562 CGGTTTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 7 0.23
22 8 0.26
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (22 bp):
TGAGAATTATAATTCTATTTTC
Found at i:52394 original size:11 final size:11
Alignment explanation
Indices: 52378--52404 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52368 AACATAAAGT
52378 ATGTTAATATC
1 ATGTTAATATC
52389 ATGTTAATATC
1 ATGTTAATATC
52400 ATGTT
1 ATGTT
52405 TAGGCCCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (11 bp):
ATGTTAATATC
Done.