Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008577.1 Hibiscus syriacus cultivar Beakdansim tig00111506_pilon, 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: 1329373
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1189150 original size:112 final size:112
Alignment explanation
Indices: 1189021--1189250 Score: 435
Period size: 112 Copynumber: 2.1 Consensus size: 112
1189011 TAAGACCAGA
*
1189021 CTTTGTCAACTGCATAAAGGTAATTCATATATTAAAGTAAAAGATTTCACATTGGTAAATTTCAA
1 CTTTGGCAACTGCATAAAGGTAATTCATATATTAAAGTAAAAGATTTCACATTGGTAAATTTCAA
1189086 AGCCACCAAATAAC-CTGGTGGGTTTGAATATGAAAACTTTAGTTTTT
66 AGCCACCAAATAACTC-GGTGGGTTTGAATATGAAAACTTTAGTTTTT
1189133 CTTTGGCAACTGCATAAAGGTAATTCATATATTAAAGTAAAAGATTTCACATTGGTAAATTTCAA
1 CTTTGGCAACTGCATAAAGGTAATTCATATATTAAAGTAAAAGATTTCACATTGGTAAATTTCAA
1189198 AGCCACCAAATAACTCGGTGGGTTTGAATATGAAAACTTTAGTTTTT
66 AGCCACCAAATAACTCGGTGGGTTTGAATATGAAAACTTTAGTTTTT
1189245 CTTTGG
1 CTTTGG
1189251 TTTTAGAAAA
Statistics
Matches: 116, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
112 115 0.99
113 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (112 bp):
CTTTGGCAACTGCATAAAGGTAATTCATATATTAAAGTAAAAGATTTCACATTGGTAAATTTCAA
AGCCACCAAATAACTCGGTGGGTTTGAATATGAAAACTTTAGTTTTT
Found at i:1189791 original size:28 final size:28
Alignment explanation
Indices: 1189760--1189813 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1189750 ATTAACATAG
1189760 AATAATAAATTATAATTTATTATTGAAA
1 AATAATAAATTATAATTTATTATTGAAA
*
1189788 AATAATAATTTATAATTTATTATTGA
1 AATAATAAATTATAATTTATTATTGA
1189814 CGTGATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
AATAATAAATTATAATTTATTATTGAAA
Found at i:1192119 original size:17 final size:17
Alignment explanation
Indices: 1192089--1192139 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1192079 TAAAATAATA
1192089 ATTAATTA-TAAAATATT
1 ATTAATTATTAAAAT-TT
*
1192106 ATT-TTTATTAAAATTT
1 ATTAATTATTAAAATTT
1192122 -TTAATTATTAAAATTT
1 ATTAATTATTAAAATTT
1192138 AT
1 AT
1192140 AAAATGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 17 0.59
17 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAATTATTAAAATTT
Found at i:1207146 original size:19 final size:19
Alignment explanation
Indices: 1207122--1207159 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1207112 TCAGAAAATG
1207122 TCCGGAGGTTTAATGGTCA
1 TCCGGAGGTTTAATGGTCA
1207141 TCCGGAGGTTTAATGGTCA
1 TCCGGAGGTTTAATGGTCA
1207160 AGGGACACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (19 bp):
TCCGGAGGTTTAATGGTCA
Found at i:1211833 original size:14 final size:14
Alignment explanation
Indices: 1211811--1211840 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1211801 AGTAGCGGTA
1211811 ACAACCTTCATTTC
1 ACAACCTTCATTTC
*
1211825 ACAATCTTCATTTC
1 ACAACCTTCATTTC
1211839 AC
1 AC
1211841 TGTCTCAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (14 bp):
ACAACCTTCATTTC
Found at i:1214324 original size:16 final size:13
Alignment explanation
Indices: 1214292--1214330 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1214282 TTGATTTTTT
1214292 TAATATTTCTAAA
1 TAATATTTCTAAA
1214305 TAATATTTCTAAA
1 TAATATTTCTAAA
*
1214318 TAATAATTCTAAA
1 TAATATTTCTAAA
1214331 AATCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATATTTCTAAA
Found at i:1214358 original size:32 final size:30
Alignment explanation
Indices: 1214322--1214380 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1214312 TCTAAATAAT
1214322 AATTCTAAAAATCATTTTTTAAAAATATAGAG
1 AATTC-AAAAATCA-TTTTTAAAAATATAGAG
* * *
1214354 AATTCATAAATTATTTTTAAAATTATA
1 AATTCAAAAATCATTTTTAAAAATATA
1214381 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.54
31 6 0.25
32 5 0.21
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (30 bp):
AATTCAAAAATCATTTTTAAAAATATAGAG
Found at i:1214904 original size:11 final size:11
Alignment explanation
Indices: 1214890--1214914 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1214880 CTTTACTCTA
1214890 AATTTAAATAT
1 AATTTAAATAT
1214901 AATTTAAATAT
1 AATTTAAATAT
1214912 AAT
1 AAT
1214915 ACATGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATAT
Found at i:1215104 original size:20 final size:21
Alignment explanation
Indices: 1215079--1215118 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1215069 TAAAAATATA
*
1215079 ATATTAAT-TAAAAGTATCTG
1 ATATTAATATAAAAATATCTG
*
1215099 ATATTATTATAAAAATATCT
1 ATATTAATATAAAAATATCT
1215119 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTAATATAAAAATATCTG
Found at i:1225039 original size:54 final size:54
Alignment explanation
Indices: 1224968--1225070 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
1224958 AATAAAATAA
* *
1224968 AAAAAGTGTAGCACTTAACACGTACATACACCCGTGTAAGTATGTACATCTCTC
1 AAAAAGTATAGCACTTAACACATACATACACCCGTGTAAGTATGTACATCTCTC
* ** * * *
1225022 AAAAAGTATAGTACTTAACACATATGTATATCGGTGTAAGTATGTACAT
1 AAAAAGTATAGCACTTAACACATACATACACCCGTGTAAGTATGTACAT
1225071 TTGTCAATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (54 bp):
AAAAAGTATAGCACTTAACACATACATACACCCGTGTAAGTATGTACATCTCTC
Found at i:1230927 original size:13 final size:13
Alignment explanation
Indices: 1230899--1230928 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1230889 AAATCACAGA
1230899 TTTTTTAAATATT
1 TTTTTTAAATATT
1230912 TTTTATTAAATATT
1 TTTT-TTAAATATT
1230926 TTT
1 TTT
1230929 GATATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTAAATATT
Found at i:1235030 original size:13 final size:13
Alignment explanation
Indices: 1235012--1235041 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1235002 CAGTGGTACA
1235012 CATTAAATCTTAT
1 CATTAAATCTTAT
1235025 CATTAAATCTTAT
1 CATTAAATCTTAT
1235038 CATT
1 CATT
1235042 TTTAAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (13 bp):
CATTAAATCTTAT
Found at i:1239225 original size:12 final size:12
Alignment explanation
Indices: 1239208--1239241 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1239198 TTATTGATGG
1239208 GGCTGAGAGGAA
1 GGCTGAGAGGAA
1239220 GGCTGAGAGGAA
1 GGCTGAGAGGAA
1239232 GGCTGTAGAG
1 GGCTG-AGAG
1239242 TCATATGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.29, C:0.09, G:0.50, T:0.12
Consensus pattern (12 bp):
GGCTGAGAGGAA
Found at i:1266648 original size:60 final size:60
Alignment explanation
Indices: 1266542--1266671 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
1266532 GGTGACTACA
* * * *
1266542 TTGTAACTTTTAATAGTCGAAGAACTCAACAAAGTAACTCCTTATAATTAGAGGACCATT
1 TTGTAACTTTTAATAATCAAAGAACTCAACAAAATAACTCCTTATAATCAGAGGACCATT
* *
1266602 TTGTAACTTTTAATAATCAAA-AGACTTAACAAAATAA-TAACC-TATAATCAGATGACCATT
1 TTGTAACTTTTAATAATCAAAGA-ACTCAACAAAATAACT--CCTTATAATCAGAGGACCATT
1266662 TATGT-ACTTT
1 T-TGTAACTTT
1266672 ACCTATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
59 2 0.03
60 53 0.88
61 5 0.08
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (60 bp):
TTGTAACTTTTAATAATCAAAGAACTCAACAAAATAACTCCTTATAATCAGAGGACCATT
Found at i:1277735 original size:21 final size:21
Alignment explanation
Indices: 1277693--1277735 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277683 TATCTTATAA
* *
1277693 TATTTTATAATAATAATTAAT
1 TATTTAATAATAATAATAAAT
1277714 TATTTAATAA-AATATATAAAT
1 TATTTAATAATAATA-ATAAAT
1277735 T
1 T
1277736 TAGCCCTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTTAATAATAATAATAAAT
Found at i:1282281 original size:22 final size:20
Alignment explanation
Indices: 1282247--1282294 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1282237 TTGAGTAAGT
1282247 TTTGATAAGTTAT-TTTGATAA
1 TTTGATAAGTTATGTTT--TAA
*
1282268 TTTGAGTATGTTATGTTTTAA
1 TTTGA-TAAGTTATGTTTTAA
1282289 TTTGAT
1 TTTGAT
1282295 TGATGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 13 0.54
22 7 0.29
23 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (20 bp):
TTTGATAAGTTATGTTTTAA
Found at i:1290088 original size:23 final size:23
Alignment explanation
Indices: 1290044--1290089 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1290034 ACTAGCTTTA
* *
1290044 TGAGTTCATGACCTATTCATTTG
1 TGAGTTCATGACCAATTAATTTG
1290067 TGAGTTCAT-AGCCAATTAATTTG
1 TGAGTTCATGA-CCAATTAATTTG
1290090 CCATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (23 bp):
TGAGTTCATGACCAATTAATTTG
Found at i:1290999 original size:23 final size:23
Alignment explanation
Indices: 1290968--1291011 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1290958 AAACAAACAT
*
1290968 GAGTATTTTTTAACTTAAAATAA
1 GAGTATTTTTTAACTAAAAATAA
*
1290991 GAGTTTTTTTTAACTAAAAAT
1 GAGTATTTTTTAACTAAAAAT
1291012 GAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (23 bp):
GAGTATTTTTTAACTAAAAATAA
Found at i:1291465 original size:21 final size:22
Alignment explanation
Indices: 1291440--1291480 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1291430 AAAAGCGTCG
*
1291440 TAATTTTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
1291461 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
1291481 TAATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:1304887 original size:20 final size:20
Alignment explanation
Indices: 1304864--1304915 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1304854 AACGCGATCC
1304864 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1304884 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1304904 CCAAAATCGCAA
1 CCAGAATCGCAA
1304916 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1304996 original size:20 final size:20
Alignment explanation
Indices: 1304971--1305164 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1304961 GATTTTCCAT
* *
1304971 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1304991 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1305011 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1305031 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1305051 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1305071 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1305091 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1305111 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1305132 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1305152 AATCGCAACGCGA
1 AATCGCAACGCGA
1305165 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1305016 original size:40 final size:39
Alignment explanation
Indices: 1304967--1305164 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1304957 TTGCGATTTT
* ** *
1304967 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1305005 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1305046 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1305086 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1305125 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1305165 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1305054 original size:60 final size:60
Alignment explanation
Indices: 1304971--1305163 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1304961 GATTTTCCAT
* ** * *
1304971 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1305031 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1305091 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1305152 AATCGCAACGCG
1 AATCGCAACGCG
1305164 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1305583 original size:33 final size:33
Alignment explanation
Indices: 1305544--1305614 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1305534 TTCACTTAGA
*
1305544 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1305577 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1305610 TTTCA
1 TTTCA
1305615 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1305754 original size:14 final size:14
Alignment explanation
Indices: 1305735--1305789 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1305725 AGAATGACTG
1305735 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1305749 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1305768 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1305782 TCGCAACG
1 TCGCAACG
1305790 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1305772 original size:33 final size:33
Alignment explanation
Indices: 1305735--1305805 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1305725 AGAATGACTG
**
1305735 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1305768 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1305801 TCGCA
1 TCGCA
1305806 TTGCGATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1305853 original size:33 final size:33
Alignment explanation
Indices: 1305806--1305919 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
1305796 CAAAATCGCA
* *
1305806 TTGCGA-TTTCATTTCGCGTTACGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1305838 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1305871 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1305904 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1305920 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 6 0.08
33 69 0.92
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1305860 original size:19 final size:18
Alignment explanation
Indices: 1305801--1305897 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
1305791 GAAACCAAAA
*
1305801 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
1305819 TCGCGTTACGA-TTC-TG
1 TCGCGTTGCGATTTCATT
1305835 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
1305852 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
1305866 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
1305885 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1305898 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 17 0.27
15 1 0.02
16 7 0.11
17 8 0.13
18 9 0.15
19 20 0.32
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:1305874 original size:14 final size:14
Alignment explanation
Indices: 1305855--1305911 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1305845 TTTCATTTCG
1305855 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1305869 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1305886 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1305902 CGTTGCGATT
1 CGTTGCGATT
1305912 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1307912 original size:92 final size:93
Alignment explanation
Indices: 1307617--1308085 Score: 885
Period size: 92 Copynumber: 5.1 Consensus size: 93
1307607 TAGATTGCTT
*
1307617 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1307682 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1307710 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTC-TTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1307773 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1307801 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1307866 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1307893 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1307957 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1307985 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA-TGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1308049 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1308077 AGTAAATTT
1 AGTAAATTT
1308086 ATCCATTCAA
Statistics
Matches: 369, Mismatches: 3, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
91 119 0.32
92 188 0.51
93 62 0.17
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1308169 original size:19 final size:19
Alignment explanation
Indices: 1308129--1308257 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1308119 TAGTTTACTT
* *
1308129 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1308149 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1308168 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1308187 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1308201 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1308220 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1308234 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1308253 TCGCA
1 TCGCA
1308258 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1308208 original size:33 final size:32
Alignment explanation
Indices: 1308165--1308257 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1308155 CGCGAAACCA
**
1308165 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1308197 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1308230 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1308258 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1308255 original size:52 final size:52
Alignment explanation
Indices: 1308129--1308257 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1308119 TAGTTTACTT
**
1308129 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1308181 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1308234 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1308258 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1308275 original size:19 final size:19
Alignment explanation
Indices: 1308253--1308387 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1308243 GAAACCAAAA
*
1308253 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1308272 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1308288 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1308305 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1308321 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1308338 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1308357 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1308377 TCGTGTTGCGA
1 TCGCGTTGCGA
1308388 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1308294 original size:14 final size:14
Alignment explanation
Indices: 1308275--1308331 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1308265 TTTCATTTCG
1308275 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1308289 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1308306 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1308322 CGTTGCGATT
1 CGTTGCGATT
1308332 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1308300 original size:33 final size:33
Alignment explanation
Indices: 1308258--1308350 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1308248 CAAAATCGCA
*
1308258 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1308291 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1308324 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1308351 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1310311 original size:14 final size:14
Alignment explanation
Indices: 1310292--1310325 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1310282 GTTTAATTGA
1310292 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
*
1310306 TTGTAAAAGTTGAT
1 TTGTAAAAGATGAT
1310320 TTGTAA
1 TTGTAA
1310326 TTGATGCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:1310442 original size:19 final size:19
Alignment explanation
Indices: 1310426--1310526 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
1310416 CAAAATGACT
1310426 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1310445 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1310463 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1310477 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1310496 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1310516 ATCGCAATGCG
1 ATCGCAATGCG
1310527 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
16 4 0.05
18 10 0.14
19 30 0.41
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1310579 original size:19 final size:19
Alignment explanation
Indices: 1310555--1310846 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
1310545 GATTATCTCG
1310555 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310574 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
1310592 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1310606 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310625 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310644 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310663 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310682 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1310701 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1310720 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1310734 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1310753 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1310772 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1310786 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1310806 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1310820 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1310839 TTGCGATT
1 TTGCGATT
1310847 GTATTTTCCG
Statistics
Matches: 243, Mismatches: 8, Indels: 44
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.12
16 26 0.11
17 17 0.07
18 15 0.06
19 144 0.59
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1310760 original size:52 final size:52
Alignment explanation
Indices: 1310574--1310818 Score: 313
Period size: 52 Copynumber: 4.6 Consensus size: 52
1310564 TCATTTCGCA
*
1310574 TTGCGATTTTCA-TTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
1310623 CATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
1310680 CATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1310734 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1310786 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCAT
1310819 GTTGGGATTT
Statistics
Matches: 183, Mismatches: 4, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
51 12 0.07
52 77 0.42
53 17 0.09
54 7 0.04
55 8 0.04
57 62 0.34
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1313139 original size:12 final size:12
Alignment explanation
Indices: 1313122--1313146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1313112 TCTTCGGGGA
1313122 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1313134 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1313146 C
1 C
1313147 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1314069 original size:20 final size:20
Alignment explanation
Indices: 1314041--1314389 Score: 427
Period size: 20 Copynumber: 17.4 Consensus size: 20
1314031 AAATTTAAGT
* * * *
1314041 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1314061 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1314081 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
1314101 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1314121 GTTACGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1314141 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1314161 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1314181 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1314201 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1314221 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
1314241 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1314261 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1314281 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1314301 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1314321 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1314341 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1314361 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1314381 GTTGCGATT
1 GTTGCGATT
1314390 ATGGAAAATC
Statistics
Matches: 289, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.01
20 280 0.97
21 5 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1317411 original size:15 final size:15
Alignment explanation
Indices: 1317336--1317421 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 15
1317326 TGAATGACAT
*
1317336 AATAAAAAATA-ATA
1 AATAAATAATATATA
*
1317350 AATTAATAATATA-A
1 AATAAATAATATATA
* *
1317364 TATTAA-AATATTATA
1 AATAAATAATA-TATA
* *
1317379 AATATAGTAAAAATATA
1 AATA-AAT-AATATATA
1317396 ACAT-AATAATATATA
1 A-ATAAATAATATATA
1317411 AATAAATAATA
1 AATAAATAATA
1317422 CGAATTTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
13 4 0.07
14 19 0.35
15 19 0.35
16 3 0.05
17 5 0.09
18 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (15 bp):
AATAAATAATATATA
Found at i:1317810 original size:31 final size:30
Alignment explanation
Indices: 1317747--1317812 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
1317737 TAACATTTAT
**
1317747 TCAAATAATATTTTATCTAAAATTTAAAGA
1 TCAAATAATATTTTATCTAAAATCCAAAGA
* **
1317777 TCAAATTAATATTTTATCTAAAGTCCAGGGA
1 TCAAA-TAATATTTTATCTAAAATCCAAAGA
1317808 TCAAA
1 TCAAA
1317813 CTAAAACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (30 bp):
TCAAATAATATTTTATCTAAAATCCAAAGA
Found at i:1326715 original size:23 final size:22
Alignment explanation
Indices: 1326689--1326755 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
1326679 CACCACAGCT
1326689 CGTATAAATGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
* * *
1326712 CGTAGAATTGCACCGTAGTGCCG
1 CGTA-AAATGCACCGAAGTGCCA
* *
1326735 CGTAGAATGCACCGAATTGCC
1 CGTAAAATGCACCGAAGTGCC
1326756 TATAATATGT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Done.