Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 38
Found at i:2968203 original size:139 final size:139
Alignment explanation
Indices: 2967953--2968245 Score: 487
Period size: 139 Copynumber: 2.1 Consensus size: 139
2967943 AAAATGAAAA
* *
2967953 GGGTTTGTTATCTGACTACTTGGTATTATAGGGGTCCTTGAAAGGTTATATCCCACACTTATATC
1 GGGTTTGTTATCTGACTACTTGGTATTATAGGGATCCTTGAAAAGTTATATCCCACACTTATATC
* * * * *
2968018 TGGAATTGTGTTGGGCATAGATGATTTAAGAAAAATGAAAAGTCGAAACAACATAATAGGTAGGG
66 CGGAATTGTGTTGGGCATAAACGAGTCAAGAAAAATGAAAAGTCGAAACAACATAATAGGTAGGG
2968083 CAATAATTT
131 CAATAATTT
*
2968092 GGGTTTGTTATCTGACTAGTTGGTATTATAGGGATCCTTGAAAAGTTATATCCCACACTTATATC
1 GGGTTTGTTATCTGACTACTTGGTATTATAGGGATCCTTGAAAAGTTATATCCCACACTTATATC
*
2968157 CGGAATTGTGTTGGGCATAAACGAGTCAAGAAAAATGAAAAGTCGAAACAACATAATATGTAGGG
66 CGGAATTGTGTTGGGCATAAACGAGTCAAGAAAAATGAAAAGTCGAAACAACATAATAGGTAGGG
2968222 CAATAATTT
131 CAATAATTT
* *
2968231 AGTTTTGTTATCTGA
1 GGGTTTGTTATCTGA
2968246 GTAATTGATA
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
139 143 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (139 bp):
GGGTTTGTTATCTGACTACTTGGTATTATAGGGATCCTTGAAAAGTTATATCCCACACTTATATC
CGGAATTGTGTTGGGCATAAACGAGTCAAGAAAAATGAAAAGTCGAAACAACATAATAGGTAGGG
CAATAATTT
Found at i:2970688 original size:29 final size:30
Alignment explanation
Indices: 2970626--2970684 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2970616 GTATAAATGC
**
2970626 TAATTAAGTACATAATGTAATAATTATTAA
1 TAATTAAGTACATAAAATAATAATTATTAA
*
2970656 TAATTAA-TACATAAAATATTAA-TATTAA
1 TAATTAAGTACATAAAATAATAATTATTAA
2970684 T
1 T
2970685 TAATCTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.27
29 12 0.46
30 7 0.27
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATTAAGTACATAAAATAATAATTATTAA
Found at i:2971912 original size:3 final size:3
Alignment explanation
Indices: 2971899--2971939 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2971889 ATGTAAAATT
*
2971899 ATA ACTA ATA ATA ATA ATA AT- ATA ATT ATA AT- ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2971940 TTTATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:2971929 original size:17 final size:18
Alignment explanation
Indices: 2971899--2971951 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
2971889 ATGTAAAATT
*
2971899 ATAACTAATAATAATAATA
1 ATAA-TAATTATAATAATA
2971918 AT-ATAATTATAAT-ATA
1 ATAATAATTATAATAATA
* *
2971934 ATAATATTTATTATAATA
1 ATAATAATTATAATAATA
2971952 TTTATAACGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 4 0.14
19 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATAATTATAATAATA
Found at i:2971931 original size:20 final size:21
Alignment explanation
Indices: 2971906--2971951 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
2971896 ATTATAACTA
2971906 ATAATAATAATAATA-TAATT
1 ATAATAATAATAATATTAATT
*
2971926 ATAAT-ATAATAATATTTATT
1 ATAATAATAATAATATTAATT
2971946 ATAATA
1 ATAATA
2971952 TTTATAACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAATAATAATATTAATT
Found at i:2976855 original size:23 final size:23
Alignment explanation
Indices: 2976837--2976897 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2976827 CTCATATAAA
*
2976837 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
2976860 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
2976883 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2976898 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:2977086 original size:103 final size:103
Alignment explanation
Indices: 2976913--2977439 Score: 982
Period size: 103 Copynumber: 5.1 Consensus size: 103
2976903 TAATGTCCAT
*
2976913 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2976978 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2977016 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2977081 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2977119 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2977184 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2977222 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
* *
2977287 GACTTCACACATATTCCAAAGAAAACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
2977325 AAGTACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTCTATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2977390 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2977428 AAGGACCACATA
1 AAGGACCACATA
2977440 GACCCTCGAC
Statistics
Matches: 411, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 411 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2978235 original size:20 final size:19
Alignment explanation
Indices: 2978198--2978241 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2978188 AACTCCTATA
*
2978198 ATCATTTCATATAATTTATT
1 ATCATATCATATAATTTA-T
**
2978218 ATCATATCATATGGTTTAT
1 ATCATATCATATAATTTAT
2978237 ATCAT
1 ATCAT
2978242 CATAACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
ATCATATCATATAATTTAT
Found at i:2978702 original size:21 final size:21
Alignment explanation
Indices: 2978678--2978721 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2978668 CCATGTTCGT
* * *
2978678 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2978699 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2978720 TT
1 TT
2978722 ACCCAGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2981933 original size:23 final size:23
Alignment explanation
Indices: 2981907--2981967 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2981897 CTCATATAAA
*
2981907 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
***
2981930 TGCACCGTAGTGCCGTGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
2981953 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
2981968 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:2982413 original size:94 final size:99
Alignment explanation
Indices: 2981983--2982492 Score: 740
Period size: 103 Copynumber: 5.1 Consensus size: 99
2981973 TAATGTCCAT
*
2981983 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCACACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
2982048 GACTTCACACATGTTCCAAAGAATACATATATGTCCCT
66 GACTTCACACATGTTCCAAAG---A-ATATATGTCCCG
*
2982086 AATGACCACATATCATTCCTTAAGAATCATATAC----A-TAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2982146 GACTTCACACATGTTCCAAAGAATACATATATGT-CCG
66 GACTTCACACATGTTCCAAAG---A-ATATATGTCCCG
*
2982183 AAAGACCACATATCATTCCTTAAG-ATCA-ATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2982246 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAG---A-ATATATGTCCCG
2982284 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2982349 GACTTCACACATGTTCCAAAG-A-ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATATATGTCCCG
*
2982381 AAGGA-C-CA-ATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTCTGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
2982443 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAG---A-ATATATGTCCCG
2982481 AAGGACCACATA
1 AAGGACCACATA
2982493 GACCCTCGAC
Statistics
Matches: 384, Mismatches: 6, Indels: 34
0.91 0.01 0.08
Matches are distributed among these distances:
94 74 0.19
95 6 0.02
96 5 0.01
97 40 0.10
98 59 0.15
99 3 0.01
100 74 0.19
101 27 0.07
102 6 0.02
103 90 0.23
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (99 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATATATGTCCCG
Found at i:2987183 original size:45 final size:45
Alignment explanation
Indices: 2987134--2987220 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
2987124 GAACATCGAA
* * *
2987134 TGCATTTTATGCATCGATGCATATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACATACCATGCATCGATACACTCAG
*
2987179 TGCATTTGATGCATCGATGCACATGCCATGCATCGATACACT
1 TGCATTTGATGCATCGATGCACATACCATGCATCGATACACT
2987221 TAGGCTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACATACCATGCATCGATACACTCAG
Found at i:2987351 original size:19 final size:18
Alignment explanation
Indices: 2987319--2987355 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2987309 GAATTTTACA
2987319 CTTGATGCACCGATGCAC
1 CTTGATGCACCGATGCAC
*
2987337 CTTGCATGCATCGATGCAC
1 CTTG-ATGCACCGATGCAC
2987356 TGACGCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (18 bp):
CTTGATGCACCGATGCAC
Found at i:2994720 original size:20 final size:20
Alignment explanation
Indices: 2994691--2994728 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2994681 TTTTAAAGTG
2994691 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
2994711 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
2994729 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2994797 original size:45 final size:44
Alignment explanation
Indices: 2994747--2994845 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 44
2994737 TGAACATAGA
* *
2994747 ATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTC
1 ATGCATTTTATGCATCGATGCACAAACCACGCATCGATGCACTC
*
2994791 AGTGCATTTGATGCATCGATGCACAAACCACGCATCGATGCACTC
1 A-TGCATTTTATGCATCGATGCACAAACCACGCATCGATGCACTC
2994836 ATGCTATTTT
1 ATGC-ATTTT
2994846 GAAACATCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 4 0.08
45 45 0.92
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (44 bp):
ATGCATTTTATGCATCGATGCACAAACCACGCATCGATGCACTC
Found at i:3003516 original size:35 final size:36
Alignment explanation
Indices: 3003441--3003516 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
3003431 GTGGTATAGC
*
3003441 GGATAGTTACAAGACAAAATTCATAGGACATATGCT
1 GGATAGTTACAAGACAAAATTCATAGGACATACGCT
*
3003477 -GATAGTTACAAGACAAAATTCATAGGAGATACG-T
1 GGATAGTTACAAGACAAAATTCATAGGACATACGCT
3003511 GGATAG
1 GGATAG
3003517 ATATGCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (36 bp):
GGATAGTTACAAGACAAAATTCATAGGACATACGCT
Found at i:3004297 original size:19 final size:19
Alignment explanation
Indices: 3004273--3004310 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3004263 GTTTTCTTTA
3004273 TCTCTCTCTATCTCTATAT
1 TCTCTCTCTATCTCTATAT
*
3004292 TCTCTCTCTCTCTCTATAT
1 TCTCTCTCTATCTCTATAT
3004311 ATATATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.34, G:0.00, T:0.53
Consensus pattern (19 bp):
TCTCTCTCTATCTCTATAT
Found at i:3004299 original size:21 final size:21
Alignment explanation
Indices: 3004273--3004312 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3004263 GTTTTCTTTA
*
3004273 TCTCTCTCTATCTCTATATTC
1 TCTCTCTCTATCTATATATTC
*
3004294 TCTCTCTCTCTCTATATAT
1 TCTCTCTCTATCTATATAT
3004313 ATATATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTCTCTCTATCTATATATTC
Found at i:3017480 original size:26 final size:25
Alignment explanation
Indices: 3017451--3017531 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
3017441 TTAATTTAAA
*
3017451 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTAAGTAGTTAT-CTTAT
* *
3017477 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTAAGTAGTT-ATCTT-AT
*
3017502 CTAAACTACTCAGTAGTTATCTTTAT
1 CTAAACTACTAAGTAGTTATC-TTAT
3017528 CTAA
1 CTAA
3017532 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (25 bp):
CTAAACTACTAAGTAGTTATCTTAT
Found at i:3017493 original size:25 final size:24
Alignment explanation
Indices: 3017465--3017545 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
3017455 ACTACTTAGT
3017465 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
3017490 AGTTAAT-TTAAACTAAAC-TACTCAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
3017515 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
3017541 AGTTA
1 AGTTA
3017546 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:3017517 original size:51 final size:51
Alignment explanation
Indices: 3017441--3017582 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 51
3017431 GAACAAGTAT
*
3017441 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTAAGTAGTTATCCTTATCTAACTTTCTAAGAG
* *
3017492 TTAATTTAAACTAAACTACTCAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTAAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * *
3017543 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTAAGTAGTTATCCTTATCTA
3017583 TCGCATAACC
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 53 0.66
52 27 0.34
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTAAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:3018880 original size:16 final size:16
Alignment explanation
Indices: 3018859--3018889 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3018849 ATAAAGATAT
*
3018859 TTTTTAAATTATATTC
1 TTTTTAAATCATATTC
3018875 TTTTTAAATCATATT
1 TTTTTAAATCATATT
3018890 AAATCAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAAATCATATTC
Found at i:3021740 original size:21 final size:23
Alignment explanation
Indices: 3021697--3021754 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
3021687 TAACCATTTT
3021697 TTTTGAAAAATAATTAAATATTA
1 TTTTGAAAAATAATTAAATATTA
*
3021720 TTTT-AAAAATAGTTATAATTATT-
1 TTTTGAAAAATAATTA-AA-TATTA
3021743 TATTTGAAAAAT
1 T-TTTGAAAAAT
3021755 TAGCGGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 10 0.33
23 7 0.23
24 7 0.23
25 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TTTTGAAAAATAATTAAATATTA
Found at i:3021742 original size:24 final size:23
Alignment explanation
Indices: 3021692--3021754 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
3021682 GGTCATAACC
*
3021692 ATTTTTTTTGAAAAATAATTAAAT
1 ATTTATTTT-AAAAATAATTAAAT
*
3021716 A-TTATTTTAAAAATAGTTATAATT
1 ATTTATTTTAAAAATAATTA-AA-T
*
3021740 ATTTATTTGAAAAAT
1 ATTTATTTTAAAAAT
3021755 TAGCGGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 10 0.30
23 8 0.24
24 3 0.09
25 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATTTATTTTAAAAATAATTAAAT
Found at i:3024174 original size:3 final size:3
Alignment explanation
Indices: 3024108--3024161 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
3024098 ATGTAAATTA
*
3024108 AAT AAA AAT AAT AA- ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3024153 AAT AAT AAT
1 AAT AAT AAT
3024162 GTAGTTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 45 0.96
4 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3024665 original size:51 final size:51
Alignment explanation
Indices: 3024538--3024667 Score: 162
Period size: 48 Copynumber: 2.6 Consensus size: 51
3024528 AGGTCTGGTC
* * *
3024538 AGGG-GATGACACGGTTCCTATGCGATGAGGACGATATGCTATCTTTAGGG
1 AGGGTGATAACACGGTTCCTATGCGATGAGGACGATAGGCCATCTTTAGGG
* *
3024588 A---TGATAACACGGTTCCTACGTGATGAGGACGGA-AGGCCATCTTTAGGG
1 AGGGTGATAACACGGTTCCTATGCGATGAGGAC-GATAGGCCATCTTTAGGG
*
3024636 AGGGTGATAACACGGTTCTTATGCGATGAGGA
1 AGGGTGATAACACGGTTCCTATGCGATGAGGA
3024668 TGGCTAGTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
48 39 0.58
49 2 0.03
50 1 0.01
51 25 0.37
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (51 bp):
AGGGTGATAACACGGTTCCTATGCGATGAGGACGATAGGCCATCTTTAGGG
Found at i:3024765 original size:181 final size:182
Alignment explanation
Indices: 3024440--3024770 Score: 468
Period size: 181 Copynumber: 1.8 Consensus size: 182
3024430 GAAGAGTTCT
* *
3024440 GGCCATCTTTAGGAAGGGTGATAACACAGTTCCTACGCGATGAGGATGACTATTTATCTAGGGTT
1 GGCCATCTTTAGGAAGGGTGATAACACAGTTCCTACGCGATGAGGATGACTAGTTATCTAGGGGT
* ** * *
3024505 GACATGGCTCATACGTGATGAAGAGGTCTGGTCAGGGGATGACACGGTTCCTATGCGATGAGGAC
66 GACACGAATCATACGTGATGAAGAGGTCTGGTCAGGGGATGACACGATTCCTACGCGATGAGGAC
* * *
3024570 GATATGCTATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACGGAA
131 GATAGGCCATCTTTAAGGATGATAACACGGTTCCTACGTGATGAGGACGGAA
* * * * *
3024622 GGCCATCTTTAGGGAGGGTGATAACACGGTTCTTATGCGATGAGGATGGCTAGTTATC-AGGGGT
1 GGCCATCTTTAGGAAGGGTGATAACACAGTTCCTACGCGATGAGGATGACTAGTTATCTAGGGGT
* * * *
3024686 GACACGAATCCTACGTGATGAGGAGGTCTGGTCTGGGGATGACACGATTCCTACGCGATGATGAC
66 GACACGAATCATACGTGATGAAGAGGTCTGGTCAGGGGATGACACGATTCCTACGCGATGAGGAC
3024751 -AGTAGGCCATCTTTAAGGAT
131 GA-TAGGCCATCTTTAAGGAT
3024771 TTTGGTTTCA
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
180 1 0.01
181 76 0.59
182 52 0.40
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (182 bp):
GGCCATCTTTAGGAAGGGTGATAACACAGTTCCTACGCGATGAGGATGACTAGTTATCTAGGGGT
GACACGAATCATACGTGATGAAGAGGTCTGGTCAGGGGATGACACGATTCCTACGCGATGAGGAC
GATAGGCCATCTTTAAGGATGATAACACGGTTCCTACGTGATGAGGACGGAA
Found at i:3024936 original size:62 final size:62
Alignment explanation
Indices: 3024866--3025212 Score: 349
Period size: 62 Copynumber: 5.5 Consensus size: 62
3024856 TCAAATATGT
* ** ** *
3024866 AAATTTTGTTTCCAGTGAAACAGTCTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACG
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACA
* * *
3024928 AAATTTTGTTTCAAATGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAAATGTATCAAGAGAGA
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAGA--TTTTT-TCAAAAGAAACTGTCTC-A-AGAGA
3024993 CA
61 CA
* * * * * *
3024995 AAACTTTGCTTCCAGAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTATCAAGAGATA
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACA
* * *
3025057 AAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTATCTTAAGAGAGAC
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAGA-TTTTT-TCAAAAGAAACTGTC-TCA-AGAGAC
3025122 A
62 A
* * * * * * * *
3025123 AAACTTTATTTCCAAAGAAATAGACTCAAAGA-TTTTTCAAAAGAAATTGTCTCGAGATACA
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACA
*
3025184 AAA-TTTGTTTCAAGAGAAAC-AACTCAAAG
1 AAATTTTGTTTCAAAAGAAACAAACTCAAAG
3025213 GATACTAATA
Statistics
Matches: 239, Mismatches: 37, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
59 8 0.03
60 13 0.05
61 9 0.04
62 63 0.26
63 20 0.08
64 37 0.15
65 22 0.09
66 34 0.14
67 33 0.14
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (62 bp):
AAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACA
Found at i:3025023 original size:129 final size:125
Alignment explanation
Indices: 3024870--3025212 Score: 467
Period size: 129 Copynumber: 2.7 Consensus size: 125
3024860 ATATGTAAAT
* *
3024870 TTTGTTTCCAGTGAAACAGTCTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACGAAATTTT
1 TTTGTTTCCAGAGAAACAGACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAC-AAATTTT
3024935 GTTTCAAATGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAAATGTATC-AAGAGAGACAAAAC
65 GTTTCAAA-GAAACAAACTCAAAGA-TTTTTTCTCAAAAG-AAAT-TATCTAAGAGAGACAAAAC
* * * *
3024999 TTTGCTTCCAGAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTATCAAGAGATAAAATTTT
1 TTTGTTTCCAGAGAAACAGACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGA-CAAATTTT
3025064 GTTTCAAAAGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTATCTTAAGAGAGACAAAAC
65 GTTTC-AAAGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTATC-TAAGAGAGACAAAAC
* * * * * * *
3025127 TTTATTTCCAAAGAAATAGACTCAAAGA-TTTTTCAAAAGAAATTGTCTCGAGATACAAAATTTG
1 TTTGTTTCCAGAGAAACAGACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACAAATTTTG
3025191 TTTCAAGAGAAAC-AACTCAAAG
66 TTTCAA-AGAAACAAACTCAAAG
3025213 GATACTAATA
Statistics
Matches: 192, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
125 11 0.06
126 21 0.11
127 27 0.14
128 51 0.27
129 79 0.41
130 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (125 bp):
TTTGTTTCCAGAGAAACAGACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGACAAATTTTG
TTTCAAAGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTATCTAAGAGAGACAAAAC
Found at i:3025323 original size:32 final size:32
Alignment explanation
Indices: 3025282--3025351 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
3025272 TTTATATCAA
*
3025282 GATGTTGAATCCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
*
3025314 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
3025346 GATGTT
1 GATGTT
3025352 TCTTGCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:3027056 original size:20 final size:20
Alignment explanation
Indices: 3027002--3027062 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3026992 AGATACATAC
*
3027002 AATGTTTCAAGGTCGAAAAG
1 AATGTTTCAAGGTCTAAAAG
*
3027022 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTAAAAG
* *
3027042 AATGTTTTAAGGTCTTAAAG
1 AATGTTTCAAGGTCTAAAAG
3027062 A
1 A
3027063 GAGGGAATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCTAAAAG
Found at i:3029230 original size:21 final size:21
Alignment explanation
Indices: 3029205--3029244 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3029195 ATTTTGTTTG
3029205 AAAACAATTAAT-ATTATTTTA
1 AAAACAATT-ATGATTATTTTA
*
3029226 AAAACAGTTATGATTATTT
1 AAAACAATTATGATTATTT
3029245 ATTTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAACAATTATGATTATTTTA
Found at i:3030453 original size:202 final size:202
Alignment explanation
Indices: 3030128--3030526 Score: 798
Period size: 202 Copynumber: 2.0 Consensus size: 202
3030118 TACCAAAAAT
3030128 AAGCATTTAAGGGACCAAAATATGATTAACAGAAATTTGAAGGTCTAAACAGTAATAAAAAAGCA
1 AAGCATTTAAGGGACCAAAATATGATTAACAGAAATTTGAAGGTCTAAACAGTAATAAAAAAGCA
3030193 TAACCAAGATCGGAAATATTACAAAATACAGGTACTGGAAATGAAAAAACCCCATAACTAATAAA
66 TAACCAAGATCGGAAATATTACAAAATACAGGTACTGGAAATGAAAAAACCCCATAACTAATAAA
3030258 GGACTAAAATAGAATAAAAGTAAAACATACATGAAAAATTCAGGGTTTAACCCAAAATACAGAAT
131 GGACTAAAATAGAATAAAAGTAAAACATACATGAAAAATTCAGGGTTTAACCCAAAATACAGAAT
3030323 AAAAGTA
196 AAAAGTA
3030330 AAGCATTTAAGGGACCAAAATATGATTAACAGAAATTTGAAGGTCTAAACAGTAATAAAAAAGCA
1 AAGCATTTAAGGGACCAAAATATGATTAACAGAAATTTGAAGGTCTAAACAGTAATAAAAAAGCA
3030395 TAACCAAGATCGGAAATATTACAAAATACAGGTACTGGAAATGAAAAAACCCCATAACTAATAAA
66 TAACCAAGATCGGAAATATTACAAAATACAGGTACTGGAAATGAAAAAACCCCATAACTAATAAA
3030460 GGACTAAAATAGAATAAAAGTAAAACATACATGAAAAATTCAGGGTTTAACCCAAAATACAGAAT
131 GGACTAAAATAGAATAAAAGTAAAACATACATGAAAAATTCAGGGTTTAACCCAAAATACAGAAT
3030525 AA
196 AA
3030527 TGATCAAAAT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 197 1.00
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.20
Consensus pattern (202 bp):
AAGCATTTAAGGGACCAAAATATGATTAACAGAAATTTGAAGGTCTAAACAGTAATAAAAAAGCA
TAACCAAGATCGGAAATATTACAAAATACAGGTACTGGAAATGAAAAAACCCCATAACTAATAAA
GGACTAAAATAGAATAAAAGTAAAACATACATGAAAAATTCAGGGTTTAACCCAAAATACAGAAT
AAAAGTA
Found at i:3038901 original size:86 final size:87
Alignment explanation
Indices: 3038752--3038941 Score: 278
Period size: 86 Copynumber: 2.2 Consensus size: 87
3038742 TAGATAAATG
* * * *
3038752 CCTT-CCCCTGAACTTGAGGGGATGTTTCTATATGGATTATTGGTGGATCCACCTCGGTAGAGAT
1 CCTTCCCCCTGAACTTGAGGGGATATTTCCATATGGATTATTGGTGGACCCACATCGGTAGAGAT
**
3038816 TGTAAGTAGTAGCTGATGAA-T
66 CATAAGTAGTAGCTGATGAATT
3038837 CCTTCCCCCTGAACTTGAGGGGATATTTCCATATGGATTATTGGTGGACCCACATCGGTAGAGAT
1 CCTTCCCCCTGAACTTGAGGGGATATTTCCATATGGATTATTGGTGGACCCACATCGGTAGAGAT
*
3038902 CATAAGTAGTAGTTGATGAATT
66 CATAAGTAGTAGCTGATGAATT
*
3038924 CC-TCCCCATTGAACTTGA
1 CCTTCCCC-CTGAACTTGA
3038942 TGGCATGCCA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
85 4 0.04
86 78 0.83
87 12 0.13
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (87 bp):
CCTTCCCCCTGAACTTGAGGGGATATTTCCATATGGATTATTGGTGGACCCACATCGGTAGAGAT
CATAAGTAGTAGCTGATGAATT
Found at i:3042044 original size:171 final size:169
Alignment explanation
Indices: 3041537--3042240 Score: 502
Period size: 168 Copynumber: 4.2 Consensus size: 169
3041527 AGTTATTATG
* * * * * * * *
3041537 ATGAATAGTTCCCCGTAA-GGAAACATTATCTGTGCATATAACTGAAT-ACAAAATACAGAGAAT
1 ATGAATAGTTCCCCG-AAGGGGAACATCATATATGCATATAATTGACTGA-AAAACACAAAGAAT
* * * * * * * * *
3041600 CTCTAACAAAAAAAGGAAGGCTCGTCCTACAGGAAG--TGTTTCACGTTTTGTAGGGAAACTGTG
64 CTCT-A-ATAAAAAGGAAGACTCGTCCTACAAGAAGCAT-TTTCACATTTTGCAGAGAATCTCTA
* * * * * * * * **
3041663 CTATGTCATAGTGTCTAATCCTATCAGACGTGAGAGTTATTGTG
126 CTATGTCATAGTGTATCATCCCATCAAACATGAAAGGTGTTGAC
* * ** * *
3041707 ATGAATAGTTCCCCAAAGGGGAACATCATCTATGCATATAATTGACTG-AAAATGCATATAATCT
1 ATGAATAGTTCCCCGAAGGGGAACATCATATATGCATATAATTGACTGAAAAACACAAAGAATCT
* * * * * ** * * * * * * * * *
3041771 ATGACAAAAGGGAAGGCTTTTTCTATAGGAATCACTTTCACA------AG-GAATTGTTTTCCAT
66 CTAATAAAAAGGAAGACTCGTCCTACAAGAAGCATTTTCACATTTTGCAGAGAA-TCTCTACTAT
* * *
3041829 GTCATAGTGTCTCATCCCATCAAACATGAGAGGAGTTGAC
130 GTCATAGTGTATCATCCCATCAAACATGAAAGGTGTTGAC
* * *
3041869 ATGAATAGTTCCCCGAAGGGGAACATCATATATGCATTTAATTGACTGAAAAATACAAAGAATGT
1 ATGAATAGTTCCCCGAAGGGGAACATCATATATGCATATAATTGACTGAAAAACACAAAGAATCT
* * * * *
3041934 TTAATAAAAAAGGGAATACTCGTCCTACAAGAAGC-TCTTTCACATTTTGTAGGGAATCTTTACT
66 CTAAT-AAAAA-GGAAGACTCGTCCTACAAGAAGCAT-TTTCACATTTTGCAGAGAATCTCTACT
*
3041998 ATGTCATAGTGTATCATCCCATCAAACATGAAAGGTGGTGAC
128 ATGTCATAGTGTATCATCCCATCAAACATGAAAGGTGTTGAC
* * * * *
3042040 ATGAATAGTTCCCCGAA-GGAAACATCATTTGTGCATATAATTGACTGAAAAACATAGAGAATCT
1 ATGAATAGTTCCCCGAAGGGGAACATCATATATGCATATAATTGACTGAAAAACACAAAGAATCT
* * * *
3042104 CTAATAAAAAGGAAGGCTTGTCCTACAAGAAGCATTTTCACCTTTTGCAGAGAATCTCTGCTATG
66 CTAATAAAAAGGAAGACTCGTCCTACAAGAAGCATTTTCACATTTTGCAGAGAATCTCTACTATG
* * * * *
3042169 TCATAATG-ACCCATCGCATCAAACGTGAAAGGTGTTAAC
131 TCATAGTGTA-TCATCCCATCAAACATGAAAGGTGTTGAC
* * * *
3042208 ATTAATATTTCCTCGAAGGGGAACATTATATAT
1 ATGAATAGTTCCCCGAAGGGGAACATCATATAT
3042241 TTTTTTGTTC
Statistics
Matches: 424, Mismatches: 91, Indels: 39
0.77 0.16 0.07
Matches are distributed among these distances:
161 3 0.01
162 83 0.20
163 14 0.03
164 4 0.01
165 22 0.05
167 23 0.05
168 96 0.23
169 33 0.08
170 81 0.19
171 62 0.15
172 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (169 bp):
ATGAATAGTTCCCCGAAGGGGAACATCATATATGCATATAATTGACTGAAAAACACAAAGAATCT
CTAATAAAAAGGAAGACTCGTCCTACAAGAAGCATTTTCACATTTTGCAGAGAATCTCTACTATG
TCATAGTGTATCATCCCATCAAACATGAAAGGTGTTGAC
Found at i:3044444 original size:23 final size:23
Alignment explanation
Indices: 3044410--3044461 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
3044400 GAGTCGATGG
3044410 TTCTACGCGGTCCTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
* * *
3044433 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAA
3044456 TTCTAC
1 TTCTAC
3044462 ACAGCACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAA
Found at i:3051577 original size:57 final size:57
Alignment explanation
Indices: 3051484--3051598 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3051474 GTACTGAGCA
*
3051484 TTGGAATGCTCTTAATCATTTACTTCGATACCTTAAAGGTACAATAAATTATGAACT
1 TTGGAATGCTCTTAATCATTTACTTAGATACCTTAAAGGTACAATAAATTATGAACT
* *
3051541 TTGGAATGCTCTTAATCGTTTACTTAGATACGTTAAAGGTACAATAAATTATGAACT
1 TTGGAATGCTCTTAATCATTTACTTAGATACCTTAAAGGTACAATAAATTATGAACT
3051598 T
1 T
3051599 AAATTCTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (57 bp):
TTGGAATGCTCTTAATCATTTACTTAGATACCTTAAAGGTACAATAAATTATGAACT
Found at i:3054352 original size:2 final size:2
Alignment explanation
Indices: 3054347--3054373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3054337 CTATGCATGA
3054347 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3054374 AATTAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3054649 original size:7 final size:7
Alignment explanation
Indices: 3054637--3054697 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
3054627 CGTAGTTGAC
3054637 AAGGCGG
1 AAGGCGG
3054644 AAGGCGG
1 AAGGCGG
3054651 AAGGCGG
1 AAGGCGG
3054658 AAGGCGG
1 AAGGCGG
3054665 AAGGCGG
1 AAGGCGG
3054672 AAGGCGG
1 AAGGCGG
3054679 AAGGCGG
1 AAGGCGG
3054686 AAGGCGG
1 AAGGCGG
3054693 AAGGC
1 AAGGC
3054698 ATTACAAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.30, C:0.15, G:0.56, T:0.00
Consensus pattern (7 bp):
AAGGCGG
Found at i:3059386 original size:25 final size:25
Alignment explanation
Indices: 3059338--3059387 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3059328 TGGTTAACTC
*
3059338 TTTTATGAGATTTACAGCAGTATGA
1 TTTTATGAGATTTACAGCACTATGA
3059363 TTTTATGAGATTTACTAG-ACTATGA
1 TTTTATGAGATTTAC-AGCACTATGA
3059388 CTTGTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (25 bp):
TTTTATGAGATTTACAGCACTATGA
Found at i:3061397 original size:25 final size:25
Alignment explanation
Indices: 3061369--3061422 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
3061359 ATTTTTTATT
3061369 TTTTATAT-TAATTATATATATAATA
1 TTTTATATAT-ATTATATATATAATA
*
3061394 TTTTATATATTTTATATATATAATA
1 TTTTATATATATTATATATATAATA
3061419 TTTT
1 TTTT
3061423 TGGGTTCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTATATATATTATATATATAATA
Found at i:3061452 original size:19 final size:21
Alignment explanation
Indices: 3061412--3061452 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3061402 ATTTTATATA
3061412 TATAATATTTTTGGGTTCGGG
1 TATAATATTTTTGGGTTCGGG
3061433 TATAATA-TTTTGGG-TCGGG
1 TATAATATTTTTGGGTTCGGG
3061452 T
1 T
3061453 TCGGGGACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.20, C:0.05, G:0.29, T:0.46
Consensus pattern (21 bp):
TATAATATTTTTGGGTTCGGG
Found at i:3069411 original size:68 final size:68
Alignment explanation
Indices: 3069285--3069430 Score: 220
Period size: 68 Copynumber: 2.1 Consensus size: 68
3069275 TACATGAACT
* * * * * *
3069285 TCACATTTCATGACATTCAAAATCATACTTATCATGAACCAAATTACATCCTTGACACACAATAC
1 TCACATATCATGACATTCAAAAGCATACTTATCATGAACCAAACTACAGCATTAACACACAATAC
3069350 TAA
66 TAA
*
3069353 TCACATATCATGACATTCAAAAGCATACTTATCATGAATCAAACTACAGCATTAACACACAATAC
1 TCACATATCATGACATTCAAAAGCATACTTATCATGAACCAAACTACAGCATTAACACACAATAC
*
3069418 TTA
66 TAA
3069421 TCACATATCA
1 TCACATATCA
3069431 ATATGCATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (68 bp):
TCACATATCATGACATTCAAAAGCATACTTATCATGAACCAAACTACAGCATTAACACACAATAC
TAA
Found at i:3074103 original size:2 final size:2
Alignment explanation
Indices: 3074096--3074132 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3074086 ATGGATTGCT
3074096 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
3074133 TTAGTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3074193 original size:2 final size:2
Alignment explanation
Indices: 3074186--3074223 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3074176 TTAATTTACA
3074186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3074224 GAAATGACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3074423 original size:2 final size:2
Alignment explanation
Indices: 3074416--3074513 Score: 196
Period size: 2 Copynumber: 49.0 Consensus size: 2
3074406 TCAGCTAATT
3074416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3074458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3074500 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3074514 CGAAATACAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3074690 original size:85 final size:85
Alignment explanation
Indices: 3074526--3074693 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
3074516 AAATACAATC
* * **
3074526 ATGACACACGAATGTATGTCATCTTCATTTATGACGAGGGCTTCAATGACACGCAATGTAAATCA
1 ATGACACACAAATGTATGTCATCTTCATTTATGAAGAGGGCTTCAATGACACGCAATACAAATCA
* **
3074591 TACATGCGTGTCATAAATTT
66 TAAATGCGCATCATAAATTT
* * * * ***
3074611 ATGACACACAAATGTGTGTCATCTTCATTTATGAAGGGGGCTTCAATGACGCTCAATACGCGTCA
1 ATGACACACAAATGTATGTCATCTTCATTTATGAAGAGGGCTTCAATGACACGCAATACAAATCA
*
3074676 TAAATGGGCATCATAAAT
66 TAAATGCGCATCATAAAT
3074694 GTGTCATAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (85 bp):
ATGACACACAAATGTATGTCATCTTCATTTATGAAGAGGGCTTCAATGACACGCAATACAAATCA
TAAATGCGCATCATAAATTT
Found at i:3074712 original size:13 final size:13
Alignment explanation
Indices: 3074669--3074714 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
3074659 ACGCTCAATA
3074669 CGCGTCATAAATG
1 CGCGTCATAAATG
* *
3074682 GGCATCATAAAT-
1 CGCGTCATAAATG
*
3074694 -GTGTCATAAATG
1 CGCGTCATAAATG
3074706 CGCGTCATA
1 CGCGTCATA
3074715 GATTTATGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (13 bp):
CGCGTCATAAATG
Found at i:3076029 original size:41 final size:41
Alignment explanation
Indices: 3075982--3076070 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
3075972 CCTATTTATA
* * **
3075982 GGGTATCAATATTATTCTTTGGGTATTGAT-ACCTAAGGATG
1 GGGTATCAATATTATTATTCGGGTATCAATAACC-AAGGATG
* * *
3076023 GGGTATCGATATTGTTATTCGGGTATCAATAACCAAGGGTG
1 GGGTATCAATATTATTATTCGGGTATCAATAACCAAGGATG
3076064 GGGTATC
1 GGGTATC
3076071 GATACTAGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 37 0.93
42 3 0.08
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (41 bp):
GGGTATCAATATTATTATTCGGGTATCAATAACCAAGGATG
Found at i:3088188 original size:21 final size:21
Alignment explanation
Indices: 3088149--3088188 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3088139 CGATGAAATG
* *
3088149 TTTGAACTATTATTTTGGTTA
1 TTTGAACTATGATTATGGTTA
*
3088170 TTTGAATTATGATTATGGT
1 TTTGAACTATGATTATGGT
3088189 GGTGTTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (21 bp):
TTTGAACTATGATTATGGTTA
Found at i:3091216 original size:41 final size:41
Alignment explanation
Indices: 3091164--3091253 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
3091154 ACCCTATTTA
*
3091164 TAGGGTATCGATATTATTCTTCGAGTATCAATACCCAAGGG
1 TAGGGTATCGATATTATTATTCGAGTATCAATACCCAAGGG
* * *
3091205 TAGGGTATCGATATTGTTATTTGGGTATCAATACCCAAGGG
1 TAGGGTATCGATATTATTATTCGAGTATCAATACCCAAGGG
*
3091246 TGGGGTAT
1 TAGGGTAT
3091254 TGGTACCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (41 bp):
TAGGGTATCGATATTATTATTCGAGTATCAATACCCAAGGG
Found at i:3096289 original size:29 final size:29
Alignment explanation
Indices: 3096257--3096388 Score: 171
Period size: 29 Copynumber: 4.6 Consensus size: 29
3096247 AAATATCACT
*
3096257 TTTTTTAAAATAATTCCCAGAATGTCATC
1 TTTTTAAAAATAATTCCCAGAATGTCATC
* *
3096286 -TTTTAAAAATAATTCCCAAAATGTCACC
1 TTTTTAAAAATAATTCCCAGAATGTCATC
*
3096314 TTTTTAAAAATATTTCCCAGAATGTCA-C
1 TTTTTAAAAATAATTCCCAGAATGTCATC
*
3096342 ATTTTTCAAAATAATTCCCAGAATGTCAAT-
1 -TTTTTAAAAATAATTCCCAGAATGTC-ATC
*
3096372 TTTTTCAAAATAATTCC
1 TTTTTAAAAATAATTCC
3096389 TAAAATATCA
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
28 26 0.28
29 65 0.71
30 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTTAAAAATAATTCCCAGAATGTCATC
Found at i:3096360 original size:58 final size:57
Alignment explanation
Indices: 3096235--3096388 Score: 195
Period size: 57 Copynumber: 2.7 Consensus size: 57
3096225 AGTCCACATT
* * *
3096235 AAAA-AATTCTCAAAATATCACTTTTTTTAAAATAATTCCCAGAATGTCATCTTTTA
1 AAAATAATTCCCAAAATGTCACTTTTTTAAAAATAATTCCCAGAATGTCATCTTTTA
* * *
3096291 AAAATAATTCCCAAAATGTCACCTTTTTAAAAATATTTCCCAGAATGTCA-CATTTTTC
1 AAAATAATTCCCAAAATGTCACTTTTTTAAAAATAATTCCCAGAATGTCATC--TTTTA
* * *
3096349 AAAATAATTCCCAGAATGTCAATTTTTTCAAAATAATTCC
1 AAAATAATTCCCAAAATGTCACTTTTTTAAAAATAATTCC
3096389 TAAAATATCA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 5 0.06
57 40 0.48
58 39 0.46
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (57 bp):
AAAATAATTCCCAAAATGTCACTTTTTTAAAAATAATTCCCAGAATGTCATCTTTTA
Found at i:3096434 original size:17 final size:17
Alignment explanation
Indices: 3096400--3096457 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
3096390 AAAATATCAC
3096400 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTC-GGTCAA
3096418 CGGGTCGGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
*
3096435 CGGGTCAGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
3096452 CGGGTC
1 CGGGTC
3096458 AACCTGGTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
17 28 0.72
18 11 0.28
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCGGTCAA
Found at i:3096478 original size:19 final size:19
Alignment explanation
Indices: 3096454--3096494 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3096444 TCGGTCAACG
**
3096454 GGTCAACCTGGTTCAGACC
1 GGTCAACCAAGTTCAGACC
3096473 GGTCAACCAAGTTCAGACC
1 GGTCAACCAAGTTCAGACC
3096492 GGT
1 GGT
3096495 TTGGATCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAACCAAGTTCAGACC
Found at i:3097960 original size:10 final size:9
Alignment explanation
Indices: 3097925--3098004 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
3097915 GCTGCTGGAA
*
3097925 ACCGGTTTA
1 ACCGGTTTG
*
3097934 ACCGGTTTTCA
1 ACCGG-TTT-G
3097945 ACCGGTTCTG
1 ACCGGTT-TG
3097955 ACCGGTTTG
1 ACCGGTTTG
*
3097964 ACCGGTTTCA
1 ACCGGTTT-G
*
3097974 ACCGGTTCG
1 ACCGGTTTG
3097983 AACCGGTTTG
1 -ACCGGTTTG
*
3097993 ACCGGTCTG
1 ACCGGTTTG
3098002 ACC
1 ACC
3098005 CGACCCGACC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
9 26 0.43
10 27 0.45
11 7 0.12
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3097987 original size:29 final size:30
Alignment explanation
Indices: 3097924--3097998 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
3097914 GGCTGCTGGA
*
3097924 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
3097955 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
3097983 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
3097999 CTGACCCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:3098011 original size:5 final size:5
Alignment explanation
Indices: 3098001--3098058 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3097991 TGACCGGTCT
* *
3098001 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
3098050 GACCC GACC
1 GACCC GACC
3098059 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:3098027 original size:22 final size:22
Alignment explanation
Indices: 3098001--3098065 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
3097991 TGACCGGTCT
3098001 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3098023 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3098045 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
3098066 GTTGACTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:3104864 original size:29 final size:30
Alignment explanation
Indices: 3104801--3104877 Score: 122
Period size: 29 Copynumber: 2.6 Consensus size: 30
3104791 GGCTGCTGGA
*
3104801 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
3104832 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
3104860 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCGGTTT
3104878 GACCGGTCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 30 0.68
30 13 0.30
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:3104889 original size:9 final size:9
Alignment explanation
Indices: 3104802--3104890 Score: 88
Period size: 9 Copynumber: 9.3 Consensus size: 9
3104792 GCTGCTGGAA
*
3104802 ACCGGTTTA
1 ACCGGTTTG
*
3104811 ACCGGTTTTCA
1 ACCGG-TTT-G
3104822 ACCGGTTCTG
1 ACCGGTT-TG
3104832 ACCGGTTTG
1 ACCGGTTTG
*
3104841 ACCGGTTTCA
1 ACCGGTTT-G
*
3104851 ACCGGTTCG
1 ACCGGTTTG
3104860 AACCGGTTTG
1 -ACCGGTTTG
3104870 ACCGGTTTG
1 ACCGGTTTG
*
3104879 ACCGGTCTG
1 ACCGGTTTG
3104888 ACC
1 ACC
3104891 CGACCCGACC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
9 35 0.51
10 27 0.39
11 7 0.10
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3104897 original size:5 final size:5
Alignment explanation
Indices: 3104887--3104944 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3104877 TGACCGGTCT
* *
3104887 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
3104936 GACCC GACC
1 GACCC GACC
3104945 GTTGACAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:3104913 original size:22 final size:22
Alignment explanation
Indices: 3104887--3104950 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
3104877 TGACCGGTCT
3104887 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3104909 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3104931 GACCCGACCCGACCGTTGAC
1 GACCCGACCCGACCGTTGAC
3104951 AGTTGACCGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:3104957 original size:7 final size:7
Alignment explanation
Indices: 3104941--3104971 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3104931 GACCCGACCC
3104941 GACCGTT
1 GACCGTT
*
3104948 GACAGTT
1 GACCGTT
3104955 GACCGTT
1 GACCGTT
3104962 GACCGTT
1 GACCGTT
3104969 GAC
1 GAC
3104972 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:3112070 original size:32 final size:31
Alignment explanation
Indices: 3112034--3112110 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3112024 CGGGGTCATG
*
3112034 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
3112066 GGGCCTACCCGAGAATGATCTCAGTGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3112097 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3112111 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3113026 original size:29 final size:29
Alignment explanation
Indices: 3112979--3113137 Score: 227
Period size: 29 Copynumber: 5.6 Consensus size: 29
3112969 ATAGTCCACA
3112979 TTCAAAAT--TTCCCAAAATGTCACATTT
1 TTCAAAATAATTCCCAAAATGTCACATTT
*
3113006 TTCAAAATAATTCCCAGAATGTCA-ACTTT
1 TTCAAAATAATTCCCAAAATGTCACA-TTT
3113035 TTCAAAATAATTCCCAAAATGTCACA-TT
1 TTCAAAATAATTCCCAAAATGTCACATTT
* * *
3113063 TTCTAAAATAATTCCTAGAATGTCACTTTT
1 TTC-AAAATAATTCCCAAAATGTCACATTT
*
3113093 TTCAAAATAATTCCCAAAATGTCACCTTT
1 TTCAAAATAATTCCCAAAATGTCACATTT
3113122 TTCAAAATAATTCCCA
1 TTCAAAATAATTCCCA
3113138 CCGTTCGCAT
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
27 8 0.07
28 6 0.05
29 98 0.83
30 6 0.05
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCAAAATAATTCCCAAAATGTCACATTT
Found at i:3113057 original size:58 final size:58
Alignment explanation
Indices: 3112979--3113137 Score: 254
Period size: 58 Copynumber: 2.8 Consensus size: 58
3112969 ATAGTCCACA
3112979 TTCAAAAT--TTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCAAC-TTT
1 TTCAAAATAATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTC-ACTTTT
*
3113035 TTCAAAATAATTCCCAAAATGTCACA-TTTTCTAAAATAATTCCTAGAATGTCACTTTT
1 TTCAAAATAATTCCCAAAATGTCACATTTTTC-AAAATAATTCCCAGAATGTCACTTTT
*
3113093 TTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATAATTCCCA
1 TTCAAAATAATTCCCAAAATGTCACATTTTTCAAAATAATTCCCA
3113138 CCGTTCGCAT
Statistics
Matches: 95, Mismatches: 3, Indels: 8
0.90 0.03 0.08
Matches are distributed among these distances:
56 8 0.08
57 7 0.07
58 75 0.79
59 5 0.05
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (58 bp):
TTCAAAATAATTCCCAAAATGTCACATTTTTCAAAATAATTCCCAGAATGTCACTTTT
Found at i:3119684 original size:41 final size:41
Alignment explanation
Indices: 3119639--3119978 Score: 150
Period size: 41 Copynumber: 8.3 Consensus size: 41
3119629 TCCTAATATA
* * *
3119639 TAGTGGCGTTTTTGGGAAATCGCCACTACAAACACATACTT
1 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACACATACTT
* * * * ** * *
3119680 TAGTGGCATTTATGTTACAAACGCCGCTATATCCAAATA-TA
1 TAGTGGCGTTTTTGTGA-AAACGCCGCTACAAACACATACTT
* *
3119721 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACGCGTACTT
1 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACACATACTT
* * * * * ** * *
3119762 TAGTGGCATTTATGTAAAAAACGTCG-TGATATCCAGATA-TA
1 TAGTGGCGTTTTTGT-GAAAACGCCGCT-ACAAACACATACTT
* ** * *
3119803 TAGTGGCGTTTTTGTGAAAACACTACTA-AAAAATCGTACTT
1 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACA-CATACTT
* ** * * * ** * *
3119844 TAGTGGCGTTTATGAAAAAATGCTGCTATAGCCAAATA-TA
1 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACACATACTT
* * * **
3119884 TAGTGGCGTTTTAGTGTAAATGCCGCTACAAACATGTACTT
1 TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACACATACTT
* * * * * * **
3119925 TAATGGTGTTTGTGTAAAAAATGCCGCTATAAATGCATACTT
1 TAGTGGCGTTTTTGT-GAAAACGCCGCTACAAACACATACTT
3119967 TAGTGGCGTTTT
1 TAGTGGCGTTTT
3119979 AGAAAAAACG
Statistics
Matches: 206, Mismatches: 83, Indels: 19
0.67 0.27 0.06
Matches are distributed among these distances:
39 2 0.01
40 51 0.25
41 95 0.46
42 58 0.28
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (41 bp):
TAGTGGCGTTTTTGTGAAAACGCCGCTACAAACACATACTT
Found at i:3119720 original size:82 final size:82
Alignment explanation
Indices: 3119616--3119955 Score: 362
Period size: 82 Copynumber: 4.2 Consensus size: 82
3119606 TTTTTTAGAC
* * * * *
3119616 AAACGCCACGATATCCTAATATATAGTGGCGTTTTTGGGAAATCGCCACTACAAACACATACTTT
1 AAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGGGAAAACGCCACTACAAACACGTACTTT
* *
3119681 AGTGGCATTTATGTTAC
66 AGTGGCATTTATGTAAA
* * *
3119698 AAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTACAAACGCGTACTTT
1 AAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGGGAAAACGCCACTACAAACACGTACTTT
3119763 AGTGGCATTTATGTAAA
66 AGTGGCATTTATGTAAA
* * * * * *
3119780 AAACGTCG-TGATATCCAGATATATAGTGGCGTTTTTGTGAAAACACTACTA-AAAAATCGTACT
1 AAACGCCGCT-ATATCCAAATATATAGTGGCGTTTTTGGGAAAACGCCACTACAAACA-CGTACT
*
3119843 TTAGTGGCGTTTATG-AAA
64 TTAGTGGCATTTATGTAAA
* * * * * * * * *
3119861 AAATGCTGCTATAGCCAAATATATAGTGGCGTTTTAGTGTAAATGCCGCTACAAACATGTACTTT
1 AAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGGGAAAACGCCACTACAAACACGTACTTT
* ** *
3119926 AATGGTGTTTGTGTAAA
66 AGTGGCATTTATGTAAA
*
3119943 AAATGCCGCTATA
1 AAACGCCGCTATA
3119956 AATGCATACT
Statistics
Matches: 218, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
81 62 0.28
82 156 0.72
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGGGAAAACGCCACTACAAACACGTACTTT
AGTGGCATTTATGTAAA
Found at i:3119925 original size:163 final size:164
Alignment explanation
Indices: 3119625--3119945 Score: 414
Period size: 163 Copynumber: 2.0 Consensus size: 164
3119615 CAAACGCCAC
* * *
3119625 GATATCCTAATATATAGTGGCGTTTTTGGGAAATCGCCACTACAAACACATACTTTAGTGGCATT
1 GATATCCTAATATATAGTGGCGTTTTTGGGAAAACACCACTACAAAAACATACTTTAGTGGCATT
* * * * *
3119690 TATGTTACAAACGCCGCTATATCCAAATATATAGTGGCGTTTTTGTGAAAACGCCGCTACAAACG
66 TATGTAAAAAACGCCGCTATAGCCAAATATATAGTGGCGTTTTAGTGAAAACGCCGCTACAAACA
*
3119755 CGTACTTTAGTGGCATTTATGTAAAAAACGTCGT
131 CGTACTTTAATGGCATTTATGTAAAAAACGTCGT
* * * *
3119789 GATATCC-AGATATATAGTGGCGTTTTTGTGAAAACACTACTA-AAAAATCGTACTTTAGTGGCG
1 GATATCCTA-ATATATAGTGGCGTTTTTGGGAAAACACCACTACAAAAA-CATACTTTAGTGGCA
* * * *
3119852 TTTATG-AAAAAATGCTGCTATAGCCAAATATATAGTGGCGTTTTAGTGTAAATGCCGCTACAAA
64 TTTATGTAAAAAACGCCGCTATAGCCAAATATATAGTGGCGTTTTAGTGAAAACGCCGCTACAAA
* ** *
3119916 CATGTACTTTAATGGTGTTTGTGTAAAAAA
129 CACGTACTTTAATGGCATTTATGTAAAAAA
3119946 TGCCGCTATA
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
163 79 0.59
164 55 0.41
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (164 bp):
GATATCCTAATATATAGTGGCGTTTTTGGGAAAACACCACTACAAAAACATACTTTAGTGGCATT
TATGTAAAAAACGCCGCTATAGCCAAATATATAGTGGCGTTTTAGTGAAAACGCCGCTACAAACA
CGTACTTTAATGGCATTTATGTAAAAAACGTCGT
Found at i:3127355 original size:2 final size:2
Alignment explanation
Indices: 3127348--3127397 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3127338 AAATAGGGGA
3127348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3127390 AT AT AT AT
1 AT AT AT AT
3127398 TCATCGATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3127511 original size:2 final size:2
Alignment explanation
Indices: 3127504--3127541 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3127494 AAATAGGGGA
3127504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3127542 GCGAGAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3127524 original size:156 final size:156
Alignment explanation
Indices: 3127240--3127541 Score: 595
Period size: 156 Copynumber: 1.9 Consensus size: 156
3127230 TCATTGTCAC
*
3127240 ATTCATCGATTTCCCCGAGACACTTGAGCTGCTCAAAATAGATCTATGGGTCATAATCATCATTG
1 ATTCATCGATTTCCCCGAGACACTTGAGCTGCTCAAAATAGATCTATGGGTCATAATAATCATTG
3127305 TCCACATCATTAATATCCAAAGACCTGAAAGGAAAATAGGGGAATATATATATATATATATATAT
66 TCCACATCATTAATATCCAAAGACCTGAAAGGAAAATAGGGGAATATATATATATATATATATAT
3127370 ATATATATATATATATATATATATAT
131 ATATATATATATATATATATATATAT
3127396 ATTCATCGATTTCCCCGAGACACTTGAGCTGCTCAAAATAGATCTATGGGTCATAATAATCATTG
1 ATTCATCGATTTCCCCGAGACACTTGAGCTGCTCAAAATAGATCTATGGGTCATAATAATCATTG
3127461 TCCACATCATTAATATCCAAAGACCTGAAAGGAAAATAGGGGAATATATATATATATATATATAT
66 TCCACATCATTAATATCCAAAGACCTGAAAGGAAAATAGGGGAATATATATATATATATATATAT
3127526 ATATATATATATATAT
131 ATATATATATATATAT
3127542 GCGAGAGTAA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 145 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (156 bp):
ATTCATCGATTTCCCCGAGACACTTGAGCTGCTCAAAATAGATCTATGGGTCATAATAATCATTG
TCCACATCATTAATATCCAAAGACCTGAAAGGAAAATAGGGGAATATATATATATATATATATAT
ATATATATATATATATATATATATAT
Found at i:3130609 original size:16 final size:16
Alignment explanation
Indices: 3130588--3130628 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
3130578 TTGTCTTTAT
3130588 TTGATCTTTCAACTAC
1 TTGATCTTTCAACTAC
3130604 TTGATCTTTCAACTAC
1 TTGATCTTTCAACTAC
3130620 TTGATCTTT
1 TTGATCTTT
3130629 TCCTCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (16 bp):
TTGATCTTTCAACTAC
Found at i:3130742 original size:24 final size:24
Alignment explanation
Indices: 3130715--3130764 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3130705 TTACAAAGAG
3130715 TTGTGCTTTCACAGCAGAAGAAGC
1 TTGTGCTTTCACAGCAGAAGAAGC
** *
3130739 TTGTGCTTTTGCAGCAGATGAAGC
1 TTGTGCTTTCACAGCAGAAGAAGC
3130763 TT
1 TT
3130765 CTACTTTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (24 bp):
TTGTGCTTTCACAGCAGAAGAAGC
Found at i:3130771 original size:24 final size:24
Alignment explanation
Indices: 3130726--3130802 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
3130716 TGTGCTTTCA
* * *
3130726 CAGCAGAAGAAGCTTGTGCTTTTG
1 CAGCAGATGAAGCTTCTACTTTTG
3130750 CAGCAGATGAAGCTTCTACTTTTG
1 CAGCAGATGAAGCTTCTACTTTTG
* * *
3130774 CAACAGATGAAACTTTTACTTTTG
1 CAGCAGATGAAGCTTCTACTTTTG
*
3130798 TAGCA
1 CAGCA
3130803 AACGAGTCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (24 bp):
CAGCAGATGAAGCTTCTACTTTTG
Found at i:3132463 original size:16 final size:15
Alignment explanation
Indices: 3132442--3132474 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3132432 TAAAAATTCC
3132442 TACCCCACATGATATT
1 TACCCCACATGAT-TT
3132458 TACCCCACATGATTT
1 TACCCCACATGATTT
3132473 TA
1 TA
3132475 TTCTTACCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (15 bp):
TACCCCACATGATTT
Found at i:3134807 original size:22 final size:22
Alignment explanation
Indices: 3134786--3134862 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 22
3134776 TATGTAAATA
3134786 AATAAATATATAAT-GAATAAT
1 AATAAATATATAATAGAATAAT
*
3134807 AATAATATTATTATAATATAATAAT
1 AATAA-A-TA-TATAATAGAATAAT
**
3134832 AAT-AATATATAATATCATAAT
1 AATAAATATATAATAGAATAAT
3134853 -AT-AATATATA
1 AATAAATATATA
3134863 CAACAACAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
20 10 0.20
21 18 0.36
22 3 0.06
23 3 0.06
24 7 0.14
25 9 0.18
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
AATAAATATATAATAGAATAAT
Found at i:3134809 original size:3 final size:3
Alignment explanation
Indices: 3134790--3134858 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
3134780 TAAATAAATA
* *
3134790 AAT ATAT AAT GAAT AAT AAT AAT -AT TAT TAT AAT -AT AAT AAT AAT
1 AAT A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3134835 AAT ATAT AAT -AT CAT AAT -AT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT A
3134859 TATACAACAA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
2 8 0.14
3 40 0.70
4 9 0.16
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:3134810 original size:25 final size:21
Alignment explanation
Indices: 3134790--3134862 Score: 94
Period size: 22 Copynumber: 3.4 Consensus size: 21
3134780 TAAATAAATA
3134790 AATATATAATGAATAATAATAAT
1 AATATATAAT--ATAATAATAAT
*
3134813 ATTATTATAATATAATAATAAT
1 AATA-TATAATATAATAATAAT
*
3134835 AATATATAATATCATAAT-AT
1 AATATATAATATAATAATAAT
3134855 AATATATA
1 AATATATA
3134863 CAACAACAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.22
21 13 0.28
22 14 0.30
23 3 0.07
24 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
AATATATAATATAATAATAAT
Found at i:3134826 original size:29 final size:29
Alignment explanation
Indices: 3134793--3134858 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
3134783 ATAAATAAAT
* *
3134793 ATATAATGAATAATAATA-ATATTATTATA
1 ATATAAT-AATAATAATATATAATATCATA
3134822 ATATAATAATAATAATATATAATATCATA
1 ATATAATAATAATAATATATAATATCATA
3134851 ATATAATA
1 ATATAATA
3134859 TATACAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
ATATAATAATAATAATATATAATATCATA
Found at i:3134832 original size:8 final size:8
Alignment explanation
Indices: 3134801--3134862 Score: 60
Period size: 8 Copynumber: 8.1 Consensus size: 8
3134791 ATATATAATG
3134801 AATAATAAT
1 AATAAT-AT
*
3134810 AATATTAT
1 AATAATAT
*
3134818 TATAATAT
1 AATAATAT
3134826 AAT-A-AT
1 AATAATAT
3134832 AATAATAT
1 AATAATAT
3134840 -ATAATAT
1 AATAATAT
*
3134847 CATAATAT
1 AATAATAT
3134855 AAT-ATAT
1 AATAATAT
3134862 A
1 A
3134863 CAACAACAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 5 0.11
7 14 0.31
8 21 0.47
9 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
AATAATAT
Found at i:3134870 original size:3 final size:3
Alignment explanation
Indices: 3134862--3134889 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3134852 TATAATATAT
3134862 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
3134890 AACCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3139320 original size:2 final size:2
Alignment explanation
Indices: 3139309--3139446 Score: 77
Period size: 2 Copynumber: 74.0 Consensus size: 2
3139299 CGGTGGAAAC
3139309 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
3139350 TA -A AA TA TA GA -A TA CTA TA TA AA TA -A TA TA GA -A TG TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3139389 TA -A TA AA TGA CA TA TA -A TA AA TA TA -A TA TA -A TA TA TA -A
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3139427 TA TA TA -A AA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3139447 GTAGCGTATA
Statistics
Matches: 106, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
1 13 0.12
2 88 0.83
3 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (2 bp):
TA
Found at i:3139426 original size:7 final size:7
Alignment explanation
Indices: 3139309--3139446 Score: 104
Period size: 7 Copynumber: 19.6 Consensus size: 7
3139299 CGGTGGAAAC
3139309 TATAATA
1 TATAATA
3139316 TAT-ATA
1 TATAATA
3139322 TAT-ATA
1 TATAATA
3139328 TATATATA
1 TATA-ATA
*
3139336 TATACTA
1 TATAATA
3139343 TATAATA
1 TATAATA
*
3139350 TAAAATA
1 TATAATA
*
3139357 TAGAATA
1 TATAATA
3139364 CTAT-ATA
1 -TATAATA
*
3139371 AATAATA
1 TATAATA
*
3139378 TAGAATGTA
1 TATAA--TA
3139387 TATAATA
1 TATAATA
* * *
3139394 AATGACA
1 TATAATA
3139401 TATAATA
1 TATAATA
*
3139408 AAT-ATAA
1 TATAAT-A
3139415 TATAATA
1 TATAATA
3139422 TATAATA
1 TATAATA
*
3139429 TATAAAA
1 TATAATA
*
3139436 TATATTA
1 TATAATA
3139443 TATA
1 TATA
3139447 GTAGCGTATA
Statistics
Matches: 103, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
6 16 0.16
7 70 0.68
8 11 0.11
9 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (7 bp):
TATAATA
Found at i:3139434 original size:39 final size:39
Alignment explanation
Indices: 3139309--3139434 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 39
3139299 CGGTGGAAAC
* * *
3139309 TATAATATATATATATATATATATATATATACTATATAATA
1 TATAATATATAAATACATATA-ATAAATATA-TATATAATA
* *
3139350 TA-AA-ATATAGAATAC-TAT-ATAAATA-ATATAGAATG
1 TATAATATATA-AATACATATAATAAATATATATATAATA
3139385 TAT-ATA-ATAAATGACATATAATAAATATA-ATATAATA
1 TATAATATATAAAT-ACATATAATAAATATATATATAATA
3139422 TATAATATATAAA
1 TATAATATATAAA
3139435 ATATATTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
34 3 0.04
35 15 0.22
36 5 0.07
37 22 0.32
38 4 0.06
39 13 0.19
40 5 0.07
41 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.38
Consensus pattern (39 bp):
TATAATATATAAATACATATAATAAATATATATATAATA
Found at i:3139828 original size:2 final size:2
Alignment explanation
Indices: 3139821--3139859 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3139811 TGTATGTATG
3139821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3139860 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3144516 original size:13 final size:15
Alignment explanation
Indices: 3144486--3144517 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3144476 AGTGAGTGAA
3144486 AGAAAAATATACGAG
1 AGAAAAATATACGAG
3144501 AGAAAAA-ATA-GAG
1 AGAAAAATATACGAG
3144514 AGAA
1 AGAA
3144518 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.03, G:0.22, T:0.09
Consensus pattern (15 bp):
AGAAAAATATACGAG
Found at i:3147097 original size:72 final size:72
Alignment explanation
Indices: 3147012--3147158 Score: 190
Period size: 72 Copynumber: 2.0 Consensus size: 72
3147002 TTTGATATTT
* * * *
3147012 TTTTAGTCTCATTTAAATTGTATACCATCAA-AGTCTTCTTTTGGACTGA-GTTTTCAATGGATT
1 TTTTAGTCTCATTTAAACTGTACACCATCAAGA-CCTTCTTTT-GAATGAGGTTTTCAATGGATT
3147075 TTCATCTTC
64 TTCATCTTC
* * * *
3147084 TTTTGGTCTCATTTAAACTGTACAGCGTCAAGACCTTCTTTTGAATTAGGTTTTCAATGGATTTT
1 TTTTAGTCTCATTTAAACTGTACACCATCAAGACCTTCTTTTGAATGAGGTTTTCAATGGATTTT
3147149 CATCTTC
66 CATCTTC
3147156 TTT
1 TTT
3147159 AGGCCTCCAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
71 4 0.06
72 60 0.92
73 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (72 bp):
TTTTAGTCTCATTTAAACTGTACACCATCAAGACCTTCTTTTGAATGAGGTTTTCAATGGATTTT
CATCTTC
Found at i:3150151 original size:17 final size:17
Alignment explanation
Indices: 3150131--3150163 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3150121 ACTTTGACTG
*
3150131 TTGACTTGCGTTGACCA
1 TTGACTGGCGTTGACCA
3150148 TTGACTGGCGTTGACC
1 TTGACTGGCGTTGACC
3150164 GAAACTTTGA
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:0.15, C:0.24, G:0.27, T:0.33
Consensus pattern (17 bp):
TTGACTGGCGTTGACCA
Found at i:3152576 original size:24 final size:24
Alignment explanation
Indices: 3152544--3152602 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
3152534 TGATATGAAA
3152544 TCTGTTCTGATTCCTAACCTGGAT
1 TCTGTTCTGATTCCTAACCTGGAT
3152568 TCTGTTCTGATTCCTAACCTGGAT
1 TCTGTTCTGATTCCTAACCTGGAT
*
3152592 TCTTTTCTGAT
1 TCTGTTCTGAT
3152603 ATCTGATCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (24 bp):
TCTGTTCTGATTCCTAACCTGGAT
Found at i:3153619 original size:41 final size:41
Alignment explanation
Indices: 3153590--3153795 Score: 387
Period size: 41 Copynumber: 5.0 Consensus size: 41
3153580 CGCGAACTTG
3153590 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
3153631 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
3153672 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
3153713 G-CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
3153753 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
3153794 GA
1 GA
3153796 TTTACATATT
Statistics
Matches: 161, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
40 39 0.24
41 122 0.76
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:3153754 original size:81 final size:82
Alignment explanation
Indices: 3153590--3153795 Score: 396
Period size: 81 Copynumber: 2.5 Consensus size: 82
3153580 CGCGAACTTG
*
3153590 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
3153655 ATCGCAATGCGATAGTC
66 ATCGCAATGCGATAGTC
3153672 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCG-CTATCGCAATGCGAATATGTAA
1 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
3153736 ATCGCAATGCGATAGTC
66 ATCGCAATGCGATAGTC
3153753 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCGA
1 GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCGA
3153796 TTTACATATT
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
81 81 0.66
82 41 0.34
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (82 bp):
GACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
ATCGCAATGCGATAGTC
Found at i:3153856 original size:68 final size:62
Alignment explanation
Indices: 3153736--3153918 Score: 171
Period size: 68 Copynumber: 2.9 Consensus size: 62
3153726 GAATATGTAA
* * * *
3153736 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTA-A-A-TCGTAATGCGATAGTCGATT
1 ATCGCATTGCGATAGTCGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCG---
3153798 TACAT
60 -AC-T
*
3153803 ATTCGCATTGTGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGACT
*
3153866 ATCGCATTGCGAT--T-TACATATTCGCATTGCGATTTACATATTCGCATTGCGAT
1 ATCGCATTGCGATAGTCGAC-TA-TCGCATTGCGATTTACATATTCGCATTGCGAT
3153919 TTACATATTC
Statistics
Matches: 103, Mismatches: 7, Indels: 18
0.80 0.05 0.14
Matches are distributed among these distances:
59 2 0.02
60 3 0.03
61 32 0.31
62 11 0.11
63 2 0.02
64 2 0.02
65 2 0.02
66 2 0.02
67 4 0.04
68 43 0.42
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (62 bp):
ATCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGACT
Found at i:3153958 original size:40 final size:41
Alignment explanation
Indices: 3153793--3153938 Score: 235
Period size: 41 Copynumber: 3.6 Consensus size: 41
3153783 ATGCGATAGT
*
3153793 CGATTTACATATTCGCATTGTGATAGTCGACTATCGCATTG
1 CGATTTACATATTCGCATTGCGATAGTCGACTATCGCATTG
3153834 CGATTTACATATTCGCATTGCGATAGTCGACTATCGCATTG
1 CGATTTACATATTCGCATTGCGATAGTCGACTATCGCATTG
*
3153875 CGATTTACATATTCGCATTGCGAT--T-TACATATTCGCATTG
1 CGATTTACATATTCGCATTGCGATAGTCGAC-TA-TCGCATTG
3153915 CGATTTACATATTCGCATTGCGAT
1 CGATTTACATATTCGCATTGCGAT
3153939 TTACATATTC
Statistics
Matches: 101, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 32 0.32
41 64 0.63
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (41 bp):
CGATTTACATATTCGCATTGCGATAGTCGACTATCGCATTG
Found at i:3153978 original size:21 final size:20
Alignment explanation
Indices: 3153793--3153958 Score: 214
Period size: 20 Copynumber: 8.2 Consensus size: 20
3153783 ATGCGATAGT
3153793 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
* *
3153813 TGATAGT-CGACTA-TCGCATTG
1 CGAT-TTAC-A-TATTCGCATTG
3153834 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
*
3153854 CGATAGT-CGACTA-TCGCATTG
1 CGAT-TTAC-A-TATTCGCATTG
3153875 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
3153895 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
3153915 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
*
3153935 CGATTTACATATTCACATTG
1 CGATTTACATATTCGCATTG
3153955 CGAT
1 CGAT
3153959 AGTCCAAGTT
Statistics
Matches: 129, Mismatches: 7, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.03
20 92 0.71
21 29 0.22
22 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
CGATTTACATATTCGCATTG
Found at i:3153988 original size:21 final size:21
Alignment explanation
Indices: 3153845--3153999 Score: 85
Period size: 20 Copynumber: 7.6 Consensus size: 21
3153835 GATTTACATA
* *
3153845 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
3153865 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
* *
3153886 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
* *
3153906 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
* *
3153926 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
3153946 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3153967 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
3153988 TTCGCGTTGCGA
1 TTCGCATTGCGA
3154000 ATCTGGAAAC
Statistics
Matches: 122, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
20 74 0.61
21 47 0.39
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3154197 original size:18 final size:18
Alignment explanation
Indices: 3154174--3154211 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3154164 ATTTATATGG
3154174 TATAAAAAATAAAATATT
1 TATAAAAAATAAAATATT
3154192 TATAAAAAATAAAATATT
1 TATAAAAAATAAAATATT
3154210 TA
1 TA
3154212 GGCAAGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAAAAATAAAATATT
Found at i:3155519 original size:33 final size:34
Alignment explanation
Indices: 3155469--3155534 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
3155459 TGTTTACAAT
3155469 ATATATATATATATCTTGGGAAATAACAAATTGC
1 ATATATATATATATCTTGGGAAATAACAAATTGC
*
3155503 ATATAT-TATATCTCTTGGGAAATAACAAATTG
1 ATATATATATATATCTTGGGAAATAACAAATTG
3155535 TTTGAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (34 bp):
ATATATATATATATCTTGGGAAATAACAAATTGC
Found at i:3155860 original size:21 final size:22
Alignment explanation
Indices: 3155815--3155860 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3155805 TTTACCCTAA
**
3155815 AAATCAAATTCCATTTAAATGT
1 AAATCAAATTCCAAATAAATGT
*
3155837 AAATCAAATT-CAAATAAGTGT
1 AAATCAAATTCCAAATAAATGT
3155858 AAA
1 AAA
3155861 GCTAAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
AAATCAAATTCCAAATAAATGT
Found at i:3155880 original size:14 final size:14
Alignment explanation
Indices: 3155861--3155890 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3155851 TAAGTGTAAA
3155861 GCTAAGAACAGATG
1 GCTAAGAACAGATG
3155875 GCTAAGAACAGATG
1 GCTAAGAACAGATG
3155889 GC
1 GC
3155891 AAGGCGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (14 bp):
GCTAAGAACAGATG
Found at i:3159522 original size:50 final size:50
Alignment explanation
Indices: 3159462--3159562 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
3159452 TATTTATTCT
*
3159462 TCACGTTTATATTTTCGTCATCCAATTACATTTTCTTTCTAAATAATTAC
1 TCACGGTTATATTTTCGTCATCCAATTACATTTTCTTTCTAAATAATTAC
3159512 TCACGGTTATATTTTCGTCATCCAATTACATTTTCTTTCTAAATAATTAC
1 TCACGGTTATATTTTCGTCATCCAATTACATTTTCTTTCTAAATAATTAC
3159562 T
1 T
3159563 AAATTTAAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (50 bp):
TCACGGTTATATTTTCGTCATCCAATTACATTTTCTTTCTAAATAATTAC
Found at i:3159685 original size:18 final size:18
Alignment explanation
Indices: 3159657--3159712 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
3159647 TATACGTTTA
3159657 ATTTATAATAATAAATAAT
1 ATTT-TAATAATAAATAAT
3159676 ATTTTAATAATAAATAAT
1 ATTTTAATAATAAATAAT
** *
3159694 ATCATAACAATAAATAAT
1 ATTTTAATAATAAATAAT
3159712 A
1 A
3159713 GCATAACGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 30 0.88
19 4 0.12
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTTAATAATAAATAAT
Found at i:3159717 original size:18 final size:18
Alignment explanation
Indices: 3159661--3159719 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
3159651 CGTTTAATTT
* *
3159661 ATAATAATAAATAATATT
1 ATAACAATAAATAATATC
* *
3159679 TTAATAATAAATAATATC
1 ATAACAATAAATAATATC
*
3159697 ATAACAATAAATAATAGC
1 ATAACAATAAATAATATC
3159715 ATAAC
1 ATAAC
3159720 GTATATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAACAATAAATAATATC
Found at i:3160422 original size:57 final size:57
Alignment explanation
Indices: 3160353--3160903 Score: 967
Period size: 57 Copynumber: 9.7 Consensus size: 57
3160343 GTCATTGCGT
* *
3160353 CTATTTTCGATAATTAGTGTAAACAAAATCTCACCTTTATAGTAATACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
* *
3160410 CTATTTTTGATAATTAGCGTAAACAAAATCTCACCTTTATAGTAATACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
*
3160467 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTAATACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
*
3160524 CTATTTTCGATAATTAGCATAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
3160581 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
*
3160638 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGT
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
*
3160695 CTATTTTCGATAATTAGCGTAAACAAAATCTCACATTTATAGTACTACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
*
3160752 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCGTGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
* * *
3160809 CTATTTTCGATAATTAGCATAAACAAAATCTTACCTTTATAGTAATACTTATCATGA
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
* * *
3160866 CTATTTTTGATAATTAGTGTAAACAAAAGCTCACCTTT
1 CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTT
3160904 GTACTGTTGA
Statistics
Matches: 474, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 474 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (57 bp):
CTATTTTCGATAATTAGCGTAAACAAAATCTCACCTTTATAGTACTACTTATCATGA
Found at i:3166379 original size:48 final size:49
Alignment explanation
Indices: 3166285--3166400 Score: 153
Period size: 48 Copynumber: 2.4 Consensus size: 49
3166275 CTACATATCA
*
3166285 GTAAATCAAAAGTTTACAAATTTTGAATGAAACTGAATCAAATGTTATG
1 GTAAACCAAAAGTTTACAAATTTTGAATGAAACTGAATCAAATGTTATG
* * * * *
3166334 GTAAACCATAAGTTTATAAATTTT-TATGAAATTGAATCACATGTTATG
1 GTAAACCAAAAGTTTACAAATTTTGAATGAAACTGAATCAAATGTTATG
* *
3166382 GTAAACTAGAAGTTTACAA
1 GTAAACCAAAAGTTTACAA
3166401 GTTTGAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
48 37 0.64
49 21 0.36
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (49 bp):
GTAAACCAAAAGTTTACAAATTTTGAATGAAACTGAATCAAATGTTATG
Found at i:3167083 original size:2 final size:2
Alignment explanation
Indices: 3167076--3167110 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3167066 TGAAGTAGAT
3167076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3167111 GTCTCACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3168732 original size:17 final size:17
Alignment explanation
Indices: 3168710--3168746 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3168700 TCGACCCGAC
*
3168710 CCGTTGACCAGCGTTGA
1 CCGTTGACCAGCATTGA
*
3168727 CCGTTGACCGGCATTGA
1 CCGTTGACCAGCATTGA
3168744 CCG
1 CCG
3168747 ACCATTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (17 bp):
CCGTTGACCAGCATTGA
Found at i:3171719 original size:87 final size:89
Alignment explanation
Indices: 3171571--3171909 Score: 468
Period size: 90 Copynumber: 3.8 Consensus size: 89
3171561 GACCTAAGGG
* *
3171571 ACCTAAGGATACCCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTCGGTTGGTTCCCTTTTG
1 ACCTAAGGATATCCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTG
3171636 CTGTGTGCTTAGGTAACCCTACGA
66 CTGTGTGCTTAGGTAACCCTACGA
* * * *
3171660 ACCTAATGATA-CCTTGGGTAGACTCACAGG-CCCAAGGCATATCCTTAGGTTAGTTCCCTTTTG
1 ACCTAAGGATATCCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTG
3171723 CTGTGTGCTTAGGTAACCCTAC-A
66 CTGTGTGCTTAGGTAACCCTACGA
* * *
3171746 GATCTAAGGATATCATTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTT
1 -ACCTAAGGATATC-CTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTT
* *
3171811 TGATGTGTGCTTAGGTAACCCTACGG
64 TGCTGTGTGCTTAGGTAACCCTACGA
* * * * * *
3171837 ACCTAAGGATATCCTTGGGTTAGGTTCAAAGGCCCCATGGTATATCCTTATGTTGGCTCCCCTTT
1 ACCTAAGGATATCCTTGGG-TAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGG-TTCCCTTT
3171902 TGCTGTGT
64 TGCTGTGT
3171910 AATGAGGGTA
Statistics
Matches: 219, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.00
87 62 0.28
88 18 0.08
89 29 0.13
90 95 0.43
91 14 0.06
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (89 bp):
ACCTAAGGATATCCTTGGGTAGGCTCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTG
CTGTGTGCTTAGGTAACCCTACGA
Found at i:3177046 original size:89 final size:89
Alignment explanation
Indices: 3176816--3177179 Score: 471
Period size: 89 Copynumber: 4.1 Consensus size: 89
3176806 GATAAGACCT
* * * * * *
3176816 TACGGACCTAAGGATACCCTTGGGTAGGCTCATGGACCCTAAGACATATCCTTCGGTTGGTTCCT
1 TACGGACCTAAGGATATCCTTGGGTAGGCTCATAGACCCCAAGATATATCCTTAGGTTGGTTCCC
3176881 TTTTGCTGTGTGCTTAGGTAACCC
66 TTTTGCTGTGTGCTTAGGTAACCC
* * * *
3176905 TACTGACCTAAGGATA-CCTTGGGTAGACTCATAGGCCCCAAGGTATATCCTTAGGTTGGTTCCC
1 TACGGACCTAAGGATATCCTTGGGTAGGCTCATAGACCCCAAGATATATCCTTAGGTTGGTTCCC
*
3176969 TTTTGCTGTGTACTTAGGTAACCC
66 TTTTGCTGTGTGCTTAGGTAACCC
* * *
3176993 TACGGATCTAAGGATATCCTTGGGTAGGCCCATTGACCCCAAGATATATCCTTAGGTTGGTTCCC
1 TACGGACCTAAGGATATCCTTGGGTAGGCTCATAGACCCCAAGATATATCCTTAGGTTGGTTCCC
*
3177058 TTTTGTTGTGTGCTTAGGTAACCC
66 TTTTGCTGTGTGCTTAGGTAACCC
* * * * * *
3177082 TACAGACCTAAGGATATCCTTGGGGTAGGTTTATAGGCCCCAAGGTATATCCTTAGGTTGGATCC
1 TACGGACCTAAGGATATCCTT-GGGTAGGCTCATAGACCCCAAGATATATCCTTAGGTTGG-TTC
* *
3177147 CCTTTT-CGGTGTGCTGAGGGTAAGCCC
64 CCTTTTGCTGTGTGCTTA-GGTAA-CCC
3177174 TACGGA
1 TACGGA
3177180 TGCAGTTCTA
Statistics
Matches: 238, Mismatches: 32, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
88 77 0.32
89 99 0.42
90 41 0.17
91 13 0.05
92 8 0.03
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (89 bp):
TACGGACCTAAGGATATCCTTGGGTAGGCTCATAGACCCCAAGATATATCCTTAGGTTGGTTCCC
TTTTGCTGTGTGCTTAGGTAACCC
Found at i:3186820 original size:11 final size:11
Alignment explanation
Indices: 3186804--3186828 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3186794 CTACTTATCT
3186804 TTTATTTACTA
1 TTTATTTACTA
3186815 TTTATTTACTA
1 TTTATTTACTA
3186826 TTT
1 TTT
3186829 TTACCATTTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTTACTA
Found at i:3193215 original size:21 final size:20
Alignment explanation
Indices: 3193189--3193232 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3193179 TAACTTTTTC
3193189 TTTTCTCTTTAATTTTTAACT
1 TTTTCTCTTTAA-TTTTAACT
* *
3193210 TTTTCTTTTTCATTTTAACT
1 TTTTCTCTTTAATTTTAACT
3193230 TTT
1 TTT
3193233 ACTTTATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCTCTTTAATTTTAACT
Found at i:3193236 original size:26 final size:26
Alignment explanation
Indices: 3193176--3193237 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
3193166 CCCTCCCTTT
*
3193176 TTTTAACTTTTTCTTTTCTCTTTAAT
1 TTTTAACTTTTTCTTTTCTCTTTAAC
3193202 TTTTAACTTTTTCTTTT-TCATTTTAAC
1 TTTTAACTTTTTCTTTTCTC--TTTAAC
3193229 TTTT-ACTTT
1 TTTTAACTTT
3193238 ATCTCTCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 2 0.06
26 22 0.67
27 9 0.27
ACGTcount: A:0.16, C:0.15, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTAACTTTTTCTTTTCTCTTTAAC
Found at i:3193248 original size:26 final size:27
Alignment explanation
Indices: 3193196--3193250 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
3193186 TTCTTTTCTC
* * * *
3193196 TTTAATTTTTAACTTTTTCTTTTTCAT
1 TTTAACTTTTAACTTTATCTCTCTCAT
3193223 TTTAACTTTT-ACTTTATCTCTCTCAT
1 TTTAACTTTTAACTTTATCTCTCTCAT
3193249 TT
1 TT
3193251 ATTCATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTAACTTTTAACTTTATCTCTCTCAT
Found at i:3194645 original size:21 final size:21
Alignment explanation
Indices: 3194621--3194669 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3194611 GGTATCTCAC
3194621 TTGCATTCATTCTCATTTAGT
1 TTGCATTCATTCTCATTTAGT
*
3194642 TTGCATTCATTCTTATTTAGT
1 TTGCATTCATTCTCATTTAGT
3194663 TTGCATT
1 TTGCATT
3194670 TCTTTGCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (21 bp):
TTGCATTCATTCTCATTTAGT
Found at i:3208010 original size:2 final size:2
Alignment explanation
Indices: 3208003--3208034 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3207993 GGAATCCAAA
3208003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3208035 GGGATGGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3208321 original size:22 final size:23
Alignment explanation
Indices: 3208288--3208330 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3208278 ACTCTAACTC
*
3208288 TAAAAAATTATTTTATTATGACT
1 TAAAAAATTATTTAATTATGACT
3208311 TAAAAAA-TATTTAATTATGA
1 TAAAAAATTATTTAATTATGA
3208331 GTTATAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
TAAAAAATTATTTAATTATGACT
Found at i:3222023 original size:18 final size:18
Alignment explanation
Indices: 3222000--3222039 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3221990 GCTATACAAG
3222000 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
3222018 TGTGACTATTCCAAGACT
1 TGTGACTATTCCAAGACT
3222036 TGTG
1 TGTG
3222040 CCTAGTCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (18 bp):
TGTGACTATTCCAAGACT
Found at i:3222948 original size:8 final size:8
Alignment explanation
Indices: 3222935--3222968 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
3222925 CCCGCAACGA
3222935 TTAATATG
1 TTAATATG
3222943 TTAATATG
1 TTAATATG
3222951 TTAATATG
1 TTAATATG
3222959 TTAATATG
1 TTAATATG
3222967 TT
1 TT
3222969 TTTCAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (8 bp):
TTAATATG
Found at i:3228716 original size:16 final size:15
Alignment explanation
Indices: 3228687--3228730 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3228677 TATGATTATT
3228687 TAAATATTTAAAAAAA
1 TAAAT-TTTAAAAAAA
*
3228703 TAAATTTTATAAAATA
1 TAAATTTTA-AAAAAA
*
3228719 TATATTTTAAAA
1 TAAATTTTAAAA
3228731 CTATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTTTAAAAAAA
Done.