Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 39
Found at i:2883007 original size:259 final size:258
Alignment explanation
Indices: 2882536--2883786 Score: 1849
Period size: 259 Copynumber: 4.8 Consensus size: 258
2882526 AAATAGCTCT
* * *
2882536 GAAGGACTTATCATCTTGTTCGAAAGACTGACAGATGACACGAAA-GATTTAATCATCATGCTTG
1 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAC-CCAAAGGATTTAATCATCATGCTCG
2882600 AAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTT
65 AAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTT
* * * * * *
2882665 GGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTT-TTAAAAATACTAAATAAGAAAATTTGTA
130 GGAAATCGCTTTCTTACTTTTC-AAAATTTCATTTTCTGAAAAA-ATTAAATGAGAAACTTTGAA
* * * *
2882729 AAT-AGTTTTCTCGTTTTTCAAATTATAATATGAAAGCATCTTTCCCAAAGGTCTTATAGATGGC
193 AATCA-CTTTCTCATTTTTCAAATTATAATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGC
2882793 CC
257 CC
*
2882795 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACTCAAAGGATTTAATCATCATGCTCGA
1 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGATTTAATCATCATGCTCGA
2882860 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* * *
2882925 GAAATCGCTTTCTTACTTTTCAAATTTTTCATTTTTTGAAAAAATTAAATGAAAAACTTTGAAAA
131 GAAATCGCTTTCTTACTTTTCAAA-ATTTCATTTTCTGAAAAAATTAAATGAGAAACTTTGAAAA
* *
2882990 TCACTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGTCC
195 TCACTTTCTCATTTTTCAAATTATAATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGCCC
* * * *
2883054 GAAGGACTTATCATCTTGCCCAAAAGACTGACAGATGACCCAAAGGGTTTAATCATCATGCTCAA
1 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGATTTAATCATCATGCTCGA
2883119 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* * *
2883184 GAAATCGCTTTCTTACTTTTTGAAATTTTCATTTTCT-AAAAATATTAAATGAGAAACTTTAAAA
131 GAAATCGCTTTCTTAC-TTTTCAAAATTTCATTTTCTGAAAAA-ATTAAATGAGAAACTTTGAAA
** * **
2883248 ATTGCTTTCTCATTTTTCAAATTATCATATGAAATTATCTTGCCCGAAGGTCTTATAGATGGCCC
194 ATCACTTTCTCATTTTTCAAATTATAATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGCCC
* * * * *
2883313 AAAGGACTTATCATCTTGCTCAAAAGACTGACAGATGACTCGAATGATTTAATCATCATGCTCGA
1 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGATTTAATCATCATGCTCGA
* * *
2883378 AAGACTTACTGATAGCCCGAAGGACTTACCAATTTTGGATATAGCTTACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* *
2883443 GAAATTGCTTTCTTTCTTTTCGAAAATTTCATTTTCTGAAAATAA-TAAATGAGAAACTTTGAAA
131 GAAATCGCTTTCTTACTTTTC-AAAATTTCATTTTCTGAAAA-AATTAAATGAGAAACTTTGAAA
* * *
2883507 ATCACTTTCTCATTTTTC-AA--AT--TATGAAAGAATCTTGCCTGAAGGTCTTATAGATGGCCT
194 ATCACTTTCTCATTTTTCAAATTATAATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGCCC
* *
2883567 GAAGGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCAAAGGATTTATTCATCATGCTCGA
1 GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGATTTAATCATCATGCTCGA
* *
2883632 AAGACTTACTAATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
*
2883697 GAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG-AAAATTCTAAATGAGAAACTTTGAAA
131 GAAATCGCTTTCTTACTTTTC-AAAATTTCATTTTCTGAAAAAAT-TAAATGAGAAACTTTGAAA
* * * *
2883761 ATCAATTTTTTATTGTTCAAATTATA
194 ATCACTTTCTCATTTTTCAAATTATA
2883787 TAAAAACAAC
Statistics
Matches: 904, Mismatches: 73, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
252 1 0.00
253 3 0.00
254 220 0.24
255 2 0.00
256 2 0.00
257 2 0.00
258 17 0.02
259 637 0.70
260 19 0.02
261 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (258 bp):
GAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGATTTAATCATCATGCTCGA
AAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
GAAATCGCTTTCTTACTTTTCAAAATTTCATTTTCTGAAAAAATTAAATGAGAAACTTTGAAAAT
CACTTTCTCATTTTTCAAATTATAATATGAAAGCATCTTGCCCGAAGGTCTTATAGATGGCCC
Found at i:2883655 original size:42 final size:41
Alignment explanation
Indices: 2883558--2883659 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 41
2883548 AAGGTCTTAT
*
2883558 AGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGATTGAC
1 AGATGGCCTGAAGGACTTATCATCATGCTCGAAAGATTGAC
* ** *
2883599 AGATGACCCAAAGGATTTATTCATCATGCTCGAAAGACTT-AC
1 AGATGGCCTGAAGGACTTA-TCATCATGCTCGAAAGA-TTGAC
2883641 TA-ATGGCCTGAAGGACTTA
1 -AGATGGCCTGAAGGACTTA
2883660 CCAATTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 15 0.31
42 31 0.63
43 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (41 bp):
AGATGGCCTGAAGGACTTATCATCATGCTCGAAAGATTGAC
Found at i:2889323 original size:54 final size:54
Alignment explanation
Indices: 2889239--2889635 Score: 483
Period size: 54 Copynumber: 7.4 Consensus size: 54
2889229 TTCGTTGAGA
* * * *
2889239 TGCACACGTAGTGCCAATACGGCCGTTCATCAACATATGATGAATTCTGTTGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* * * * * *
2889293 TGAACACATAGTGTCTATGCGGGCATTCATCAACATATGATGAATT-TAGTAGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGT
2889347 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGT
* ** * * **
2889401 TGTACACATAGTGTTTATACGATCGTTCATCAATATATGATGAATTCCATGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* * * **
2889455 TGCACGCATAGTGCCTATACGATCATTCATCAACATATGATGAATTCCATGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* * * *
2889509 TGCACCCATAGTGCCTATACGGCCGTTCATCAACATATGATAAATTTTGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* * *
2889563 TGAACACATAGTGCCTATATGGTTGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
**
2889617 TGCACTTATAGTGCCTATA
1 TGCACACATAGTGCCTATA
2889636 GTACACATAA
Statistics
Matches: 295, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
53 1 0.00
54 294 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
Found at i:2896341 original size:54 final size:54
Alignment explanation
Indices: 2896270--2896592 Score: 450
Period size: 54 Copynumber: 6.0 Consensus size: 54
2896260 GATGCAAACG
* * * *
2896270 TAGTGCCAATACGGTCGTTCATAAACATATGATGAATTTTTTAGGTTGCACACA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACA
* * * **
2896324 TAGTGCCTATACAGTCGTTCATCAACATATGATG-ATTTCCGTGAGTTATACACA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-TGTGGGTTGCACACA
* *
2896378 TAGTGCCTATACGGTCGTTCATCAACATATAATGAATTCTGTGGGTTGCACACA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACA
* * *
2896432 TAGTGCCTATATGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACCCA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACA
* * * *
2896486 TAGTGCATATATGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACG
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACA
* *
2896540 TAGTGCCTATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACAC
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACAC
2896593 CAAATGTAAC
Statistics
Matches: 239, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
53 4 0.02
54 232 0.97
55 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGCACACA
Found at i:2897042 original size:95 final size:95
Alignment explanation
Indices: 2896894--2897092 Score: 244
Period size: 95 Copynumber: 2.1 Consensus size: 95
2896884 CCCTACCATG
* * * * *
2896894 GTATTGATACTTATATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTAC-TTTT
1 GTATCGATACTCATATACTATAGTACTGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
* *
2896958 TGGAATCCATGATATTGATACCTTTCTC-TCA
66 T-GAATCAATGATATCGATACCTTTCTCAT-A
* *
2896989 GTATCGATACTCATATACTATAGTAAC-GATACTCCATTAT-GGTATCGATACCATTTCTGCATT
1 GTATCGATACTCATATACTATAGT-ACTGATACTCCATT-TCAGTATCGATACCATTTCTACATT
*
2897052 CTTGAATCAATGGTATCGATACCTTTCTCATA
64 CTTGAATCAATGATATCGATACCTTTCTCATA
2897084 GTATCGATA
1 GTATCGATA
2897093 TACACATCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
95 82 0.91
96 8 0.09
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (95 bp):
GTATCGATACTCATATACTATAGTACTGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
TGAATCAATGATATCGATACCTTTCTCATA
Found at i:2901889 original size:23 final size:22
Alignment explanation
Indices: 2901841--2901889 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
2901831 TGGGCATCCA
* ** *
2901841 AAAATATATTTTTAATTTTAAT
1 AAAATATAATTTTAATTAAAAC
2901863 AAAATATTAATTTTAATTAAAAC
1 AAAATA-TAATTTTAATTAAAAC
2901886 AAAA
1 AAAA
2901890 ATTTTACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATAATTTTAATTAAAAC
Found at i:2904555 original size:13 final size:14
Alignment explanation
Indices: 2904537--2904565 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2904527 CAAAAACAAG
2904537 AAAATTAAAA-TAA
1 AAAATTAAAATTAA
2904550 AAAATTAAAATTAA
1 AAAATTAAAATTAA
2904564 AA
1 AA
2904566 TAATATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATTAAAATTAA
Found at i:2904577 original size:19 final size:19
Alignment explanation
Indices: 2904537--2904578 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2904527 CAAAAACAAG
*
2904537 AAAATTAAAATAAAAAATT
1 AAAATTAAAATAAAAAAGT
* *
2904556 AAAATTAAAATAATATAGT
1 AAAATTAAAATAAAAAAGT
2904575 AAAA
1 AAAA
2904579 GAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATTAAAATAAAAAAGT
Found at i:2906654 original size:20 final size:20
Alignment explanation
Indices: 2906625--2906665 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2906615 AAATAGTTGG
*
2906625 TGCTTGATTCTGTTTGATAT
1 TGCTTGATTCTGCTTGATAT
*
2906645 TGCTTTATTCTGCTTGATAT
1 TGCTTGATTCTGCTTGATAT
2906665 T
1 T
2906666 TATAAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (20 bp):
TGCTTGATTCTGCTTGATAT
Found at i:2915224 original size:7 final size:7
Alignment explanation
Indices: 2915214--2915275 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
2915204 AATTTAACAT
2915214 TTAACCC
1 TTAACCC
2915221 TTAACCC
1 TTAACCC
2915228 -TAACCC
1 TTAACCC
* *
2915234 CTAACTCT
1 TTAAC-CC
2915242 TTAACCC
1 TTAACCC
2915249 -TAA-CC
1 TTAACCC
2915254 TCTAACGCC
1 T-TAAC-CC
2915263 TTAA-CC
1 TTAACCC
2915269 TTAACCC
1 TTAACCC
2915276 AAAATGATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
5 2 0.04
6 15 0.33
7 17 0.38
8 8 0.18
9 3 0.07
ACGTcount: A:0.29, C:0.42, G:0.02, T:0.27
Consensus pattern (7 bp):
TTAACCC
Found at i:2915247 original size:21 final size:21
Alignment explanation
Indices: 2915215--2915275 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2915205 ATTTAACATT
2915215 TAAC-CCTTAACCCTAACCCC
1 TAACGCCTTAACCCTAACCCC
* * *
2915235 TAACTCTTTAACCCTAACCTC
1 TAACGCCTTAACCCTAACCCC
*
2915256 TAACGCCTTAACCTTAACCC
1 TAACGCCTTAACCCTAACCC
2915276 AAAATGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.30, C:0.43, G:0.02, T:0.26
Consensus pattern (21 bp):
TAACGCCTTAACCCTAACCCC
Found at i:2915247 original size:28 final size:28
Alignment explanation
Indices: 2915208--2915275 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
2915198 TTCTGCAATT
*
2915208 TAACATTTAACCCTTAACC-CTAAC-CCC
1 TAACCTTTAACCC-TAACCTCTAACGCCC
*
2915235 TAACTCTTTAACCCTAACCTCTAACGCCT
1 TAAC-CTTTAACCCTAACCTCTAACGCCC
2915264 TAACC-TTAACCC
1 TAACCTTTAACCC
2915276 AAAATGATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 16 0.44
28 14 0.39
29 6 0.17
ACGTcount: A:0.31, C:0.40, G:0.01, T:0.28
Consensus pattern (28 bp):
TAACCTTTAACCCTAACCTCTAACGCCC
Found at i:2916970 original size:2 final size:2
Alignment explanation
Indices: 2916963--2917007 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2916953 ACATCAGCTG
2916963 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
2917005 AT A
1 AT A
2917008 AAAACTCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2919242 original size:127 final size:131
Alignment explanation
Indices: 2919058--2919311 Score: 365
Period size: 127 Copynumber: 1.9 Consensus size: 131
2919048 GTGGAATTAT
* * * *
2919058 ATTTTGCAGAGTATGTACAGAATGTGAAAATTATAATAGATTGAAGCAAATTAAAAATGTATAGT
1 ATTTTGCAGAGTATATACAGAATGTGAAAACTAAAATAGATTAAAGCAAATTAAAAATGTATA-T
* *
2919123 T-TTTGC-T-AATTTGAATTTTTGTTATTTAAGGTATAATTTTATGCAACTGTG-ACAAAATTAG
65 TATTTGCATGAATTTGAATATTTGTTATTTAAGGTATAATTTTATGCAACAGTGAACAAAATTAG
2919184 AA
130 AA
* *
2919186 ATTTT-CAGAGTATATACAGAATGTGAAAACTAAAATAGGTTAAAGCAAATTGAAAATGTATATT
1 ATTTTGCAGAGTATATACAGAATGTGAAAACTAAAATAGATTAAAGCAAATTAAAAATGTATATT
2919250 ATTTGCTAATGGAATTTGAATATTTGTTATTTAAGGTATAATTTTATGCAACAGTGAACAAA
66 ATTTGC--AT-GAATTTGAATATTTGTTATTTAAGGTATAATTTTATGCAACAGTGAACAAA
2919312 TAGAATTTTG
Statistics
Matches: 111, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
126 2 0.02
127 56 0.50
128 5 0.05
130 1 0.01
132 42 0.38
133 5 0.05
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (131 bp):
ATTTTGCAGAGTATATACAGAATGTGAAAACTAAAATAGATTAAAGCAAATTAAAAATGTATATT
ATTTGCATGAATTTGAATATTTGTTATTTAAGGTATAATTTTATGCAACAGTGAACAAAATTAGA
A
Found at i:2928875 original size:12 final size:12
Alignment explanation
Indices: 2928858--2928882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2928848 GATGAATCAG
2928858 AGGACATTGAGA
1 AGGACATTGAGA
2928870 AGGACATTGAGA
1 AGGACATTGAGA
2928882 A
1 A
2928883 TAGTTCCTCA
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:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
AGGACATTGAGA
Found at i:2940320 original size:18 final size:18
Alignment explanation
Indices: 2940284--2940381 Score: 55
Period size: 18 Copynumber: 5.6 Consensus size: 18
2940274 ATCAAATAAT
* *
2940284 ATATATTAAAAATATAATA
1 ATATA-TAAAATTAAAATA
*
2940303 ATA-ATACTAATTAAAATA
1 ATATATA-AAATTAAAATA
*
2940321 TTATATAAAATTAAAAT-
1 ATATATAAAATTAAAATA
* * *
2940338 ATATTTAAACAAT-AATTA
1 ATATATAAA-ATTAAAATA
2940356 A-A-ATAAAATTAAAACTA
1 ATATATAAAATTAAAA-TA
2940373 A-ATATAAAA
1 ATATATAAAA
2940382 AGTAATAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.03
16 6 0.10
17 17 0.28
18 29 0.48
19 6 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATAAAATTAAAATA
Found at i:2940356 original size:11 final size:11
Alignment explanation
Indices: 2940281--2940369 Score: 55
Period size: 11 Copynumber: 8.2 Consensus size: 11
2940271 TTAATCAAAT
2940281 AATATATATTAAA
1 AATATA-ATT-AA
2940294 AATATAA-TAA
1 AATATAATTAA
2940304 TAATACTAATT-A
1 -AATA-TAATTAA
2940316 AA-AT-ATT-A
1 AATATAATTAA
* *
2940324 TATAAAATTAA
1 AATATAATTAA
*
2940335 AATATATTTAA
1 AATATAATTAA
2940346 ACA-ATAATTAA
1 A-ATATAATTAA
*
2940357 AATAAAATTAA
1 AATATAATTAA
2940368 AA
1 AA
2940370 CTAAATATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 7 0.11
11 34 0.56
12 6 0.10
13 7 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAATTAA
Found at i:2941642 original size:3 final size:3
Alignment explanation
Indices: 2941636--2941696 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
2941626 AATAATTATT
*
2941636 TAA TAA TAA TAA T-A TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
2941681 TATT TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA
2941697 CAAATTTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.88
4 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2941674 original size:22 final size:22
Alignment explanation
Indices: 2941642--2941696 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
2941632 TATTTAATAA
2941642 TAATAAT-ATAATAATAATATT
1 TAATAATAATAATAATAATATT
2941663 TAATAATAATAATAATAATATT
1 TAATAATAATAATAATAATATT
2941685 TAATAATAATAA
1 TAATAATAATAA
2941697 CAAATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAATAATAATAATAATATT
Found at i:2942014 original size:76 final size:76
Alignment explanation
Indices: 2941827--2942854 Score: 1867
Period size: 76 Copynumber: 13.5 Consensus size: 76
2941817 GATGGAAATG
* * * * *
2941827 TTTGAAAATATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
2941892 TCCCGAAGGCTTTT
65 TCCCGAAGGC--TT
* *
2941906 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2941971 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2941982 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942047 CCCGAAGGCTT
66 CCCGAAGGCTT
2942058 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942123 CCCGAAGGCTT
66 CCCGAAGGCTT
2942134 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942199 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2942210 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942275 CCCGAAGGCTT
66 CCCGAAGGCTT
2942286 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942351 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2942362 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942427 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2942438 TTTGGAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942503 CCCGAAGGCTT
66 CCCGAAGGCTT
2942514 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942579 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
2942590 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942655 CCCGAAGGCTTT
66 CCCGAAGGC-TT
2942667 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942732 CCCGAAGGCTT
66 CCCGAAGGCTT
2942743 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2942808 CCCGAAGGCTT
66 CCCGAAGGCTT
2942819 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2942855 GGGAAATAGT
Statistics
Matches: 923, Mismatches: 25, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
76 782 0.85
77 73 0.08
78 29 0.03
79 39 0.04
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2943557 original size:22 final size:22
Alignment explanation
Indices: 2943529--2943584 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
2943519 CATAAAGCTT
2943529 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2943551 TCATCTTTTAAAAAGATAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
2943574 TCATCTTTGAA
1 TCATCTTTGAA
2943585 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2948437 original size:2 final size:2
Alignment explanation
Indices: 2948430--2948457 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2948420 ACAACAAAGG
2948430 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
2948458 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2950720 original size:21 final size:21
Alignment explanation
Indices: 2950696--2950736 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2950686 TAAAAAGTAA
2950696 AAATACAAAATGAAAATGCAC
1 AAATACAAAATGAAAATGCAC
*
2950717 AAATACAAAATGTAAATGCA
1 AAATACAAAATGAAAATGCA
2950737 TGTATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AAATACAAAATGAAAATGCAC
Found at i:2953655 original size:11 final size:11
Alignment explanation
Indices: 2953594--2953679 Score: 53
Period size: 11 Copynumber: 8.2 Consensus size: 11
2953584 TTAATCAAAT
2953594 AATATATATTAA
1 AATATA-ATTAA
2953606 AA-ATAA-TAA
1 AATATAATTAA
2953615 TAATACTAATT-A
1 -AATA-TAATTAA
2953627 AA-AT-ATT-A
1 AATATAATTAA
*
2953635 TATA-AATTAA
1 AATATAATTAA
*
2953645 AATATATTTAA
1 AATATAATTAA
2953656 ACA-ATAATTAA
1 A-ATATAATTAA
*
2953667 AATAAAATTAA
1 AATATAATTAA
2953678 AA
1 AA
2953680 CTAAATATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
8 5 0.08
9 8 0.14
10 9 0.15
11 29 0.49
12 7 0.12
13 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAATTAA
Found at i:2954952 original size:3 final size:3
Alignment explanation
Indices: 2954946--2955015 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
2954936 AATAATTATT
*
2954946 TAA TAA TAA TAA TAA T-A TAA TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
2954991 TAA TAA TAA TATT TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA
2955016 CAAATTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2954993 original size:28 final size:30
Alignment explanation
Indices: 2954935--2955015 Score: 139
Period size: 28 Copynumber: 2.7 Consensus size: 30
2954925 TTTGGGTTTG
2954935 TAATAATTATTTAATAATAATAATAATATAA
1 TAATAA-TATTTAATAATAATAATAATATAA
2954966 TAATAATATTTAATAATAATAAT-A-ATAA
1 TAATAATATTTAATAATAATAATAATATAA
2954994 TAATAATATTTAATAATAATAA
1 TAATAATATTTAATAATAATAA
2955016 CAAATTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.52
29 1 0.02
30 17 0.34
31 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATAATATTTAATAATAATAATAATATAA
Found at i:2956714 original size:20 final size:20
Alignment explanation
Indices: 2956675--2956715 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2956665 TTGAATGGGA
*
2956675 AAAAAGAAAAGAAAATGAAG
1 AAAAAGAAAAGAAAAGGAAG
2956695 AAAAA-AAAAGAAAGAGGAAG
1 AAAAAGAAAAGAAA-AGGAAG
2956715 A
1 A
2956716 TTTGGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAGGAAG
Found at i:2959107 original size:2 final size:2
Alignment explanation
Indices: 2959053--2959091 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2959043 TTCGTCTCAG
* * *
2959053 TA TA TG TA TG TA TG 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
2959092 GGCTTAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2959168 original size:29 final size:29
Alignment explanation
Indices: 2959131--2959190 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
2959121 ATGTCTATTT
* *
2959131 TTTCAGTTTAGTGTTTAATGTTTATTTCG
1 TTTCAGTTTAGTGTTTAATGTTCATTCCG
2959160 TTTCAGTTTAGTGTTTAATGTTCATTCCG
1 TTTCAGTTTAGTGTTTAATGTTCATTCCG
2959189 TT
1 TT
2959191 ACTCAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (29 bp):
TTTCAGTTTAGTGTTTAATGTTCATTCCG
Found at i:2959931 original size:6 final size:7
Alignment explanation
Indices: 2959915--2959947 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2959905 TTTAATTGCG
2959915 AAAATTA
1 AAAATTA
2959922 AAAATT-
1 AAAATTA
2959928 AAAATTA
1 AAAATTA
2959935 AAAATTA
1 AAAATTA
2959942 AAAATT
1 AAAATT
2959948 CAATTCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTA
Found at i:2959931 original size:13 final size:13
Alignment explanation
Indices: 2959915--2959944 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2959905 TTTAATTGCG
2959915 AAAATTAAAAATT
1 AAAATTAAAAATT
2959928 AAAATTAAAAATT
1 AAAATTAAAAATT
2959941 AAAA
1 AAAA
2959945 ATTCAATTCG
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:2960056 original size:37 final size:35
Alignment explanation
Indices: 2960017--2960096 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
2960007 GATAAAATTA
* *
2960017 ATAATAATAAATGAAA-ATAA-AACATATAAAAAAT
1 ATAATAATAAATCAAAGA-AATAAAATATAAAAAAT
*
2960051 ATAATAATAAATCAAAGAAATAAAATATAAGAAAT
1 ATAATAATAAATCAAAGAAATAAAATATAAAAAAT
*
2960086 A-AATAAAAAAT
1 ATAATAATAAAT
2960097 ATAATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 26 0.65
35 14 0.35
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (35 bp):
ATAATAATAAATCAAAGAAATAAAATATAAAAAAT
Found at i:2960359 original size:24 final size:22
Alignment explanation
Indices: 2960332--2960379 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2960322 AAATGAGAAT
*
2960332 AAATTAAAGCGTATAACATGCAAA
1 AAATTAAA-CATATAA-ATGCAAA
*
2960356 AAATTAAACATATAAATTCAAA
1 AAATTAAACATATAAATGCAAA
2960378 AA
1 AA
2960380 TTCAAATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 6 0.27
24 8 0.36
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.23
Consensus pattern (22 bp):
AAATTAAACATATAAATGCAAA
Found at i:2962571 original size:35 final size:35
Alignment explanation
Indices: 2962531--2962626 Score: 149
Period size: 35 Copynumber: 2.7 Consensus size: 35
2962521 GTCGGAAAAC
2962531 GGTTTTTTTTTATGTTTCAAGAGAAACAATTTCAAA
1 GGTTTTTTTTT-TGTTTCAAGAGAAACAATTTCAAA
* **
2962567 -GTTTTTTTTGTGTTTCAAGAGAAATGATTTCAAA
1 GGTTTTTTTTTTGTTTCAAGAGAAACAATTTCAAA
2962601 GGTTTTTTTTTTGTTTCAAGAGAAAC
1 GGTTTTTTTTTTGTTTCAAGAGAAAC
2962627 TGTCTCAAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 22 0.41
35 32 0.59
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (35 bp):
GGTTTTTTTTTTGTTTCAAGAGAAACAATTTCAAA
Found at i:2962573 original size:34 final size:35
Alignment explanation
Indices: 2962534--2962626 Score: 143
Period size: 34 Copynumber: 2.7 Consensus size: 35
2962524 GGAAAACGGT
2962534 TTTTTTTTATGTTTCAAGAGAAACAATTTCAAA-G
1 TTTTTTTTATGTTTCAAGAGAAACAATTTCAAAGG
* **
2962568 TTTTTTTTGTGTTTCAAGAGAAATGATTTCAAAGG
1 TTTTTTTTATGTTTCAAGAGAAACAATTTCAAAGG
*
2962603 TTTTTTTTTTGTTTCAAGAGAAAC
1 TTTTTTTTATGTTTCAAGAGAAAC
2962627 TGTCTCAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 30 0.57
35 23 0.43
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (35 bp):
TTTTTTTTATGTTTCAAGAGAAACAATTTCAAAGG
Found at i:2962699 original size:36 final size:36
Alignment explanation
Indices: 2962610--2962969 Score: 474
Period size: 36 Copynumber: 10.2 Consensus size: 36
2962600 AGGTTTTTTT
2962610 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2962646 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2962683 TTTGTTTCAAGAGAAAC-GTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2962718 CTTAGTTCCAATAGAAAATGTCTCAAGAGAGA-GAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2962754 TTTGTTTCAAG-GAAAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
2962783 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
2962819 TTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2962855 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2962891 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
**
2962927 TTTGTTTCAAGAGAAACCATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2962963 TTTGTTT
1 TTTGTTT
2962970 AATGTAAAAC
Statistics
Matches: 286, Mismatches: 22, Indels: 31
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.06
30 2 0.01
31 1 0.00
32 4 0.01
33 1 0.00
34 2 0.01
35 32 0.11
36 175 0.61
37 49 0.17
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2962803 original size:136 final size:141
Alignment explanation
Indices: 2962610--2962969 Score: 457
Period size: 136 Copynumber: 2.5 Consensus size: 141
2962600 AGGTTTTTTT
*
2962610 TTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAGGA-AAACTATCTCAAGAGAG---AAA-TTTGTTTCAAGGGAAACTGTCTCAAGA
* * *
2962674 GAGACAAAATTTGTTTCAAGAGAAAC-GTCTCAAGAGAGACAAAACTTAGTTCCAATAGAAAATG
61 GAGACAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAA-TTAGTTCCAAGAGAAAATG
*
2962738 TCTCAAGAGAGA-GAAA
125 TCTCAAGAGAGACAAAA
*
2962754 TTTGTTTCAAGGAAAACATAT-TC-A-A-AG-ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TTTGTTTCAAGGAAAAC-TATCTCAAGAGAGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * *
2962814 CAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCA
65 CAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTAGTTCCAAGAGAAAATGTCTCA
2962879 AGAGAGACAAAA
130 AGAGAGACAAAA
* * **
2962891 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACCATCTCAAGAGA
1 TTTGTTTCAAGGAAAACTATCTCAAGAGAG---AAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
2962956 GACAAAATTTGTTT
63 GACAAAATTTGTTT
2962970 AATGTAAAAC
Statistics
Matches: 190, Mismatches: 14, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
136 81 0.43
137 40 0.21
138 1 0.01
139 1 0.01
140 2 0.01
141 2 0.01
142 1 0.01
143 1 0.01
144 57 0.30
145 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (141 bp):
TTTGTTTCAAGGAAAACTATCTCAAGAGAGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
AAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTAGTTCCAAGAGAAAATGTCTCAA
GAGAGACAAAA
Found at i:2962830 original size:21 final size:21
Alignment explanation
Indices: 2962804--2962940 Score: 85
Period size: 21 Copynumber: 7.4 Consensus size: 21
2962794 GGAAACTGTC
2962804 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
2962825 TC---A-AGA-AAAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
*
2962840 TAAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
2962861 TC-A-AGAG---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
2962876 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
2962897 TC-A-AG-G--AAAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
2962912 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
2962933 TCAAGAGA
1 TCAAGAGA
2962941 AACCATCTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 36
0.63 0.10 0.27
Matches are distributed among these distances:
15 14 0.17
16 13 0.15
17 9 0.11
18 4 0.05
19 9 0.11
20 13 0.15
21 22 0.26
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:2962981 original size:209 final size:209
Alignment explanation
Indices: 2962610--2962993 Score: 605
Period size: 209 Copynumber: 1.8 Consensus size: 209
2962600 AGGTTTTTTT
* * *
2962610 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
* **
2962675 AGACAAAATTTGTTTCAAGAGAAACGTCTCAAGAGAGACAAAACTTAGTTCCAATAGAAAATGTC
66 AGACAAAATTTGTTTCAAGAGAAACGTCTCAAGAGAGACAAAACTTAGTTCCAAGAGAAAACATC
*
2962740 TCAAGAGAGAGAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
131 TCAAGAGAGAAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
2962805 CAAGAGAGACAAAA
196 CAAGAGAGACAAAA
2962819 TTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
* * *
2962883 AGACAAAATTTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACCA
66 AGACAAAATTTGTTTCAAGAG-AAAC-GTCTCAAGAGAGACAAAACTTAGTTCCAAGAGAAAACA
*
2962946 TCTCAAGAGAGACAAAATTTGTTT-AATGTAAAACATATTCAAAGATTT
129 TCTCAAGAGAGA-AAAATTTGTTTCAA-GGAAAACATATTCAAAGATTT
2962994 CATTTTGAGT
Statistics
Matches: 160, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
207 1 0.01
208 77 0.48
209 82 0.51
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (209 bp):
TTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
AGACAAAATTTGTTTCAAGAGAAACGTCTCAAGAGAGACAAAACTTAGTTCCAAGAGAAAACATC
TCAAGAGAGAAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
CAAGAGAGACAAAA
Found at i:2966116 original size:39 final size:39
Alignment explanation
Indices: 2966024--2966128 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
2966014 AATGAAAAAT
* *
2966024 CCTACCC-CACATGATATCTACCCCACATGCTTATTATG
1 CCTACCCAAACATGATATCTATCCCACATGCTTATTATG
** * *
2966062 CCTACCCGGACATGATATCTATCCCGCATGCTTATTATT
1 CCTACCCAAACATGATATCTATCCCACATGCTTATTATG
* * *
2966101 CCTGCCCAAATATGATCTCTATCCCACA
1 CCTACCCAAACATGATATCTATCCCACA
2966129 AGTTGATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 7 0.12
39 49 0.88
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.30
Consensus pattern (39 bp):
CCTACCCAAACATGATATCTATCCCACATGCTTATTATG
Found at i:2967095 original size:17 final size:18
Alignment explanation
Indices: 2967041--2967140 Score: 78
Period size: 18 Copynumber: 5.3 Consensus size: 18
2967031 AAAATGTTAG
*
2967041 ATAATAATAATAATAATAA
1 ATAAAAATAA-AATAATAA
*
2967060 ATAAAAATAAAACATATAA
1 ATAAAAATAAAATA-ATAA
*
2967079 A-AAAAATAGAATAATAA
1 ATAAAAATAAAATAATAA
2967096 ATCAAAGAAATAAAAT-ATAA
1 AT--AA-AAATAAAATAATAA
* *
2967116 GTAATAAATAAAAAAATATA
1 ATAA-AAATAAAATAATA-A
2967136 ATAAA
1 ATAAA
2967141 TAAAGTCCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
17 5 0.08
18 23 0.35
19 18 0.28
20 11 0.17
21 8 0.12
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAAATAATAA
Found at i:2967110 original size:26 final size:24
Alignment explanation
Indices: 2967077--2967143 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
2967067 TAAAACATAT
2967077 AAAA-AAAATAGAATAATAAATCAAA
1 AAAATAAAATA-AATAATAAAT-AAA
*
2967102 GAAATAAAATATAAGTAATAAATAAA
1 AAAATAAAATA-AA-TAATAAATAAA
*
2967128 AAAATATAATAAATAA
1 AAAATAAAATAAATAA
2967144 AGTCCTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.08
25 5 0.14
26 20 0.56
27 8 0.22
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAATAAAATAAATAATAAATAAA
Found at i:2967683 original size:25 final size:25
Alignment explanation
Indices: 2967627--2967693 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
2967617 AGTAATAATA
* *
2967627 GTAAAAAAATAAATAAAATATGTAT
1 GTAAAAAAATAAATAAAAAATGGAT
2967652 GTAAAAAATATAAATAAATAAATGGAT
1 GTAAAAAA-ATAAATAAA-AAATGGAT
2967679 -TAAAATAAA-AAATAA
1 GTAAAA-AAATAAATAA
2967694 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 14 0.38
26 15 0.41
27 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (25 bp):
GTAAAAAAATAAATAAAAAATGGAT
Found at i:2972820 original size:65 final size:65
Alignment explanation
Indices: 2972711--2972837 Score: 209
Period size: 65 Copynumber: 2.0 Consensus size: 65
2972701 AGTGAACAAG
*
2972711 TACAAATCACTCATATAACTCATATACCTTTGTGGTGCATGAGGTGGAATGATAATTGAATAAAA
1 TACAAATCACTCATATAACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATAAAA
* * * *
2972776 TACATATCACTCATATGACTCATGTACCTATGTGGTGCATGAGGTGGAGTGATAATTGAATA
1 TACAAATCACTCATATAACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATA
2972838 CTGCAAAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (65 bp):
TACAAATCACTCATATAACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATAAAA
Found at i:2972850 original size:65 final size:65
Alignment explanation
Indices: 2972716--2972857 Score: 187
Period size: 65 Copynumber: 2.2 Consensus size: 65
2972706 ACAAGTACAA
* * * * *
2972716 ATCACTCATATAACTCATATACCTTTGTGGTGCATGAGGTGGAATGATAATTGAATAAAATACAT
1 ATCACTCATATGACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATAAAACAAAG
* * ***
2972781 ATCACTCATATGACTCATGTACCTATGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCAAAG
1 ATCACTCATATGACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATAAAACAAAG
2972846 ATCACTCA-ATGA
1 ATCACTCATATGA
2972858 GAATAGAGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 4 0.06
65 63 0.94
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (65 bp):
ATCACTCATATGACTCATATACCTATGTGGTGCATGAGGTGGAATGATAATTGAATAAAACAAAG
Found at i:2973029 original size:16 final size:17
Alignment explanation
Indices: 2973007--2973044 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2972997 ATAATGTAAT
2973007 AAAAGAAAATA-TACAG
1 AAAAGAAAATAGTACAG
* *
2973023 TAAAGAAATTAGTACAG
1 AAAAGAAAATAGTACAG
2973040 AAAAG
1 AAAAG
2973045 GAACAATACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.16, T:0.16
Consensus pattern (17 bp):
AAAAGAAAATAGTACAG
Found at i:2973077 original size:17 final size:17
Alignment explanation
Indices: 2973041--2973097 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
2973031 TTAGTACAGA
* **
2973041 AAAGGAACAATACAATG
1 AAAGGAACAATATAGGG
*
2973058 AAAGGAACGATATAGGG
1 AAAGGAACAATATAGGG
* * *
2973075 AAAAGAATAATATAGTG
1 AAAGGAACAATATAGGG
2973092 AAAGGA
1 AAAGGA
2973098 TTGGTACAAG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.56, C:0.05, G:0.25, T:0.14
Consensus pattern (17 bp):
AAAGGAACAATATAGGG
Found at i:2975960 original size:23 final size:23
Alignment explanation
Indices: 2975925--2975991 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
2975915 AATGAAATGA
*
2975925 AATAAGTAAATAA-ATGGATAA-AT
1 AATAAATAAATAATAT--ATAATAT
*
2975948 AATAAATATATAATATATAATAT
1 AATAAATAAATAATATATAATAT
*
2975971 AATAAAT-AATACTA-ATAATAT
1 AATAAATAAATAATATATAATAT
2975992 GTATGTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 7 0.18
22 9 0.24
23 20 0.53
24 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (23 bp):
AATAAATAAATAATATATAATAT
Found at i:2976103 original size:2 final size:2
Alignment explanation
Indices: 2976096--2976122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2976086 TTTAAAAAGT
2976096 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 T
2976123 TCAAAATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2976150 original size:20 final size:21
Alignment explanation
Indices: 2976127--2976168 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2976117 ATATATTCAA
2976127 AATA-ATATGTTTTAAAAAAC
1 AATACATATGTTTTAAAAAAC
*
2976147 AATACTATATGTTTTCAAAAAC
1 AATAC-ATATGTTTTAAAAAAC
2976169 TATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
AATACATATGTTTTAAAAAAC
Found at i:2976202 original size:2 final size:2
Alignment explanation
Indices: 2976195--2976267 Score: 121
Period size: 2 Copynumber: 36.0 Consensus size: 2
2976185 TTGAAATTAT
2976195 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
2976237 TA TA TA TA TA TA T- TA TCA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA
2976268 ATGTAATAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.01
2 63 0.93
3 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2989630 original size:4 final size:4
Alignment explanation
Indices: 2989611--2989677 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
2989601 GGACTTGGAC
* * **
2989611 ATAA ATAA A-AA TTAA ATAAA ATAA GTAA ATAA ATGG ATAA AT-A ATAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
2989658 ATAT AT-A ATATA ATAA ATAA
1 ATAA ATAA ATA-A ATAA ATAA
2989678 TACTAATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
3 7 0.15
4 33 0.69
5 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:2989665 original size:23 final size:23
Alignment explanation
Indices: 2989612--2989686 Score: 55
Period size: 23 Copynumber: 3.1 Consensus size: 23
2989602 GACTTGGACA
*
2989612 TAAATAA-AAATTAAATAAAATAA
1 TAAATAATAAA-TAAATAATATAA
**
2989635 GTAAATAAATGGATAAATAATA-AA
1 -TAAAT-AATAAATAAATAATATAA
*
2989659 TATATAATATAATAAATAATACTAA
1 TAAATAATA-AATAAATAATA-TAA
2989684 TAA
1 TAA
2989687 TATGTATGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.08
23 14 0.36
24 7 0.18
25 14 0.36
26 1 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAATAATAAATAAATAATATAA
Found at i:2989686 original size:16 final size:17
Alignment explanation
Indices: 2989650--2989688 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2989640 TAAATGGATA
2989650 AATAATAAATATATAAT
1 AATAATAAATATATAAT
*
2989667 -ATAATAAATA-ATACT
1 AATAATAAATATATAAT
2989682 AATAATA
1 AATAATA
2989689 TGTATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAAATATATAAT
Found at i:2989795 original size:37 final size:38
Alignment explanation
Indices: 2989754--2989882 Score: 129
Period size: 40 Copynumber: 3.3 Consensus size: 38
2989744 TTTCAAAGAT
*
2989754 TATATATTATATATGTTTTC-AAAAACCGTTTAAAAAC
1 TATATATTATATATATTTTCAAAAAACCGTTTAAAAAC
* **
2989791 TATATATATATATATATATTCAAAATAATATGTTTTCAAAAAC
1 TATATAT-TATATATATTTTCAAAA-AA-CCG-TTT-AAAAAC
* *
2989834 --TATATTATATATATTTTCAAAAAACCATTTTAAAAAA
1 TATATATTATATATATTTTCAAAAAACC-GTTTAAAAAC
2989871 TATATATTATAT
1 TATATATTATAT
2989883 GTTTTCAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
37 12 0.16
38 14 0.19
39 15 0.20
40 18 0.24
41 6 0.08
42 3 0.04
43 6 0.08
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (38 bp):
TATATATTATATATATTTTCAAAAAACCGTTTAAAAAC
Found at i:2989796 original size:80 final size:79
Alignment explanation
Indices: 2989709--2989882 Score: 201
Period size: 80 Copynumber: 2.2 Consensus size: 79
2989699 AAAACTATAT
* * * *
2989709 AATATATATTGTATTTCAAAAACAATATAATATGTTTTCAAAGATTA-TATATTATATATGTTTT
1 AATATATATTATATAT-AAAAACAAAATAATATGTTTTCAAA-A--ACTATATTATATATATTTT
2989773 C-AAAAACC-GTTTAAAA
62 CAAAAAACCAGTTTAAAA
* * **
2989789 ACTATATATATATATATATATTCAAAATAATATGTTTTCAAAAACTATATTATATATATTTTCAA
1 AATATATAT-TATATATAAAAACAAAATAATATGTTTTCAAAAACTATATTATATATATTTTCAA
*
2989854 AAAACCATTTTAAAA
65 AAAACCAGTTTAAAA
2989869 AATATATATTATAT
1 AATATATATTATAT
2989883 GTTTTCAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
77 1 0.01
78 17 0.21
79 13 0.16
80 44 0.55
81 5 0.06
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (79 bp):
AATATATATTATATATAAAAACAAAATAATATGTTTTCAAAAACTATATTATATATATTTTCAAA
AAACCAGTTTAAAA
Found at i:2989898 original size:14 final size:14
Alignment explanation
Indices: 2989879--2989908 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2989869 AATATATATT
2989879 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
2989893 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
2989907 AT
1 AT
2989909 TATACTATAT
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:2989907 original size:38 final size:39
Alignment explanation
Indices: 2989737--2989918 Score: 153
Period size: 37 Copynumber: 4.7 Consensus size: 39
2989727 AAAACAATAT
* * *
2989737 AATATGTTTTCAAAGATTATATATTATATATGTTTTCAAA
1 AATATGTTTTCAAAAAATATATA-TATATATATTTTCAAA
** *
2989777 AA-CCG-TTT-AAAAACTATATATATATATATATATTCAAAA
1 AATATGTTTTCAAAAA--ATATATATATATATATTTTC-AAA
*
2989816 TAATATGTTTTCAAAAACTATAT-TATATATATTTTCAAA
1 -AATATGTTTTCAAAAAATATATATATATATATTTTCAAA
** *
2989855 AA-ACCATTTT-AAAAAATATATAT-TATATGTTTTCAAA
1 AATA-TGTTTTCAAAAAATATATATATATATATTTTCAAA
*
2989892 AATATGTTTTCAAAAATTATACTATAT
1 AATATGTTTTCAAAAAATATA-TATAT
2989919 TTTCAAAAAC
Statistics
Matches: 112, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
37 34 0.30
38 31 0.28
39 16 0.14
40 17 0.15
41 6 0.05
42 3 0.03
43 5 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (39 bp):
AATATGTTTTCAAAAAATATATATATATATATTTTCAAA
Found at i:2989916 original size:80 final size:81
Alignment explanation
Indices: 2989735--2989919 Score: 219
Period size: 80 Copynumber: 2.4 Consensus size: 81
2989725 CAAAAACAAT
* *
2989735 ATAATATGTTTTCAAAGAT-TA-TATATTATATATGTTTTCAAAAACCGTTTAAAAACTATATAT
1 ATAATATGTTTTCAAAAATATACTATATTATATATATTTTCAAAAACCGTTTAAAAAC-ATATAT
2989798 ATATATATATATTCAAA
65 ATATATATATATTCAAA
*
2989815 ATAATATGTTTTC--AAA-A-ACTATATTATATATATTTTCAAAAAACCATTTTAAAAA-ATATA
1 ATAATATGTTTTCAAAAATATACTATATTATATATATTTTC-AAAAACC-GTTTAAAAACATATA
* *
2989875 TAT-TATATGTTTTC-AA
64 TATATATATATATTCAAA
2989891 A-AATATGTTTTCAAAAATTATACTATATT
1 ATAATATGTTTTCAAAAA-TATACTATATT
2989920 TTCAAAAACT
Statistics
Matches: 91, Mismatches: 5, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
75 11 0.12
76 3 0.03
77 13 0.14
78 27 0.30
79 8 0.09
80 29 0.32
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (81 bp):
ATAATATGTTTTCAAAAATATACTATATTATATATATTTTCAAAAACCGTTTAAAAACATATATA
TATATATATATTCAAA
Found at i:2989936 original size:19 final size:19
Alignment explanation
Indices: 2989893--2989938 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
2989883 GTTTTCAAAA
* *
2989893 ATATGTTTTCAAAAATTAT
1 ATATATTTTCAAAAACTAT
2989912 ACTATATTTTCAAAAACTAT
1 A-TATATTTTCAAAAACTAT
2989932 ATATATT
1 ATATATT
2989939 ATATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATTTTCAAAAACTAT
Found at i:2989969 original size:12 final size:12
Alignment explanation
Indices: 2989929--2989983 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
2989919 TTTCAAAAAC
2989929 TATATA-TATTA
1 TATATATTATTA
2989940 TATAT-TT-TTGA
1 TATATATTATT-A
*
2989951 AAT-TATTATTA
1 TATATATTATTA
*
2989962 TATATATTATCA
1 TATATATTATTA
2989974 TATATATTAT
1 TATATATTAT
2989984 ATAATGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.08
11 14 0.39
12 19 0.53
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TATATATTATTA
Found at i:2998076 original size:35 final size:35
Alignment explanation
Indices: 2998003--2998077 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2997993 CGTCACGTCC
* **
2998003 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAAGAACCGCCA
*
2998038 AGTAAGGCCCTGAGCACACAGCCGAAGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAAGAACCGCCA
2998073 AGTAA
1 AGTAA
2998078 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAAGAACCGCCA
Found at i:2998183 original size:24 final size:24
Alignment explanation
Indices: 2998156--2998246 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2998146 CATAATTCAA
*
2998156 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
2998180 GTCATGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
2998204 ATCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
2998227 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
2998247 TCAAATTTGA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:3004635 original size:35 final size:35
Alignment explanation
Indices: 3004562--3004636 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
3004552 CGTCACGTCC
* **
3004562 AGTAAGGCCCTGAGCACATAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
3004597 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
3004632 AGTAA
1 AGTAA
3004637 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:3004741 original size:24 final size:24
Alignment explanation
Indices: 3004714--3004797 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
3004704 CATAATTCAA
3004714 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
3004738 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
*
3004762 GTCAA-TATCATATAAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
*
3004785 GTCAGGTATCATA
1 GTCAAGTATCATA
3004798 ACATAATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.38
24 33 0.62
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:3013234 original size:42 final size:42
Alignment explanation
Indices: 3013110--3013245 Score: 123
Period size: 42 Copynumber: 3.2 Consensus size: 42
3013100 GCATCCCAAG
* * * *
3013110 GCGGCATTGTAATAACAAACACCACTAATGTGT-ACCTCTACT
1 GCGGCATTTTAATAACAAACGCCACTAAGGT-TCACCTCTATT
* * * * * * *
3013152 GTGGCGTTTCAACAAAAAACGCCACTAAGGTACGA-ATCTATT
1 GCGGCATTTTAATAACAAACGCCACTAAGGTTC-ACCTCTATT
* *
3013194 GCGGCGTTTTAATACCAAACGCCACTAAGGTTCACCTCTATT
1 GCGGCATTTTAATAACAAACGCCACTAAGGTTCACCTCTATT
3013236 GCGGCATTTT
1 GCGGCATTTT
3013246 TGATAAAAAA
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
GCGGCATTTTAATAACAAACGCCACTAAGGTTCACCTCTATT
Found at i:3016779 original size:22 final size:21
Alignment explanation
Indices: 3016753--3016818 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
3016743 TGATCATTTA
3016753 TATAAATACTCATTATATATT
1 TATAAATACTCATTATATATT
* * * *
3016774 TGATAATCTAAT-ATTATTAAATA
1 T-ATAA-ATACTCATTA-TATATT
3016797 TATAAATACTCATTATATATT
1 TATAAATACTCATTATATATT
3016818 T
1 T
3016819 TACTATCTCG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
21 9 0.27
22 16 0.48
23 8 0.24
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAAATACTCATTATATATT
Found at i:3016898 original size:40 final size:40
Alignment explanation
Indices: 3016845--3016920 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3016835 TATTTTAAAA
* *
3016845 AAAATTAGCTGACCCTTATTCCTATATGTAATGGGGAAAT
1 AAAATTAGCTGACCCTCATTCCCATATGTAATGGGGAAAT
*
3016885 AAAATTAGTTGACCCTCATTCCCATATGTAATGGGG
1 AAAATTAGCTGACCCTCATTCCCATATGTAATGGGG
3016921 TAAGGGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (40 bp):
AAAATTAGCTGACCCTCATTCCCATATGTAATGGGGAAAT
Found at i:3026183 original size:31 final size:32
Alignment explanation
Indices: 3026144--3026236 Score: 131
Period size: 31 Copynumber: 3.0 Consensus size: 32
3026134 AATAATTTGG
3026144 CCATATGTCCAGAAGAACATAGGTAAAT-TGT
1 CCATATGTCCAGAAGAACATAGGTAAATCTGT
*
3026175 TCATATGTCCCA-AAGAACATAGGT-AATCTGT
1 CCATATGT-CCAGAAGAACATAGGTAAATCTGT
*
3026206 CCATATGTCCCGAAGAACATAGGT-AATCTGT
1 CCATATGTCCAGAAGAACATAGGTAAATCTGT
3026237 AACATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
30 5 0.09
31 48 0.86
32 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (32 bp):
CCATATGTCCAGAAGAACATAGGTAAATCTGT
Found at i:3026463 original size:31 final size:31
Alignment explanation
Indices: 3026425--3026530 Score: 178
Period size: 31 Copynumber: 3.5 Consensus size: 31
3026415 TCCATAGATT
*
3026425 CCGAAGAACCTAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
*
3026456 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
*
3026487 CCGAAGAACATAGGTAAACAATCTA-ATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
3026517 CCGAAGAACATAGG
1 CCGAAGAACATAGG
3026531 CATGCCAACT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
30 19 0.27
31 52 0.73
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCTATATGTC
Found at i:3031630 original size:9 final size:9
Alignment explanation
Indices: 3031608--3031638 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3031598 ATGGTTCCTT
3031608 CTTTTCTT-
1 CTTTTCTTG
3031616 CTTTTCTTG
1 CTTTTCTTG
3031625 CTTTTCTTG
1 CTTTTCTTG
3031634 CTTTT
1 CTTTT
3031639 GATATTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (9 bp):
CTTTTCTTG
Found at i:3035142 original size:25 final size:25
Alignment explanation
Indices: 3035112--3035167 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
3035102 ATATCATCGA
3035112 GCCAGTGCTTAAAAGCAACGACGAT
1 GCCAGTGCTTAAAAGCAACGACGAT
* *
3035137 GCCAGTGCTTGAAAGCAACGATGAT
1 GCCAGTGCTTAAAAGCAACGACGAT
3035162 GCCAGT
1 GCCAGT
3035168 AGACATCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (25 bp):
GCCAGTGCTTAAAAGCAACGACGAT
Found at i:3037407 original size:30 final size:31
Alignment explanation
Indices: 3037353--3037410 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3037343 TTGATCGAAT
*
3037353 GATCAAGGAGACCCTACGTCACGGTTGATTC
1 GATCAAGGAGACCCAACGTCACGGTTGATTC
3037384 GATCAAGGAGACCCAAC-TCACGGTTGA
1 GATCAAGGAGACCCAACGTCACGGTTGA
3037411 GCAGCAAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (31 bp):
GATCAAGGAGACCCAACGTCACGGTTGATTC
Found at i:3038962 original size:21 final size:20
Alignment explanation
Indices: 3038919--3038964 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3038909 TAAATATATC
*
3038919 TATATTTTAATCACATCATA
1 TATATTTTAACCACATCATA
* *
3038939 TATATTTTAACCGCATTTATA
1 TATATTTTAACCACA-TCATA
3038960 TATAT
1 TATAT
3038965 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATTTTAACCACATCATA
Found at i:3039692 original size:2 final size:2
Alignment explanation
Indices: 3039685--3039717 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3039675 GTCGAGACTA
3039685 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3039718 CCTAATAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3061419 original size:2 final size:2
Alignment explanation
Indices: 3061412--3061442 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3061402 CAAACTAAAA
3061412 AT AT 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 AT AT A
3061443 ATTCTTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3062439 original size:9 final size:9
Alignment explanation
Indices: 3062426--3062457 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3062416 AACTACAACT
*
3062426 AAATAAATT
1 AAATAAATA
3062435 AAATAAATA
1 AAATAAATA
3062444 AAATAAATA
1 AAATAAATA
3062453 AAATA
1 AAATA
3062458 TTAACAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAATAAATA
Found at i:3062443 original size:13 final size:13
Alignment explanation
Indices: 3062403--3062454 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
3062393 AATATTATAG
*
3062403 AAATTAAA-ATAT
1 AAATTAAATAAAT
*
3062415 AAACTACAACTAAAT
1 AAATTA-AA-TAAAT
3062430 AAATTAAATAAAT
1 AAATTAAATAAAT
*
3062443 AAAATAAATAAA
1 AAATTAAATAAA
3062455 ATATTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 5 0.15
13 18 0.55
14 2 0.06
15 8 0.24
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATTAAATAAAT
Found at i:3062586 original size:11 final size:11
Alignment explanation
Indices: 3062570--3062635 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 11
3062560 TTATAACTTT
3062570 AAAAATTAATA
1 AAAAATTAATA
3062581 AAAAATTAATATAA
1 AAAAATT-A-AT-A
3062595 TAAAAATTTAATA
1 -AAAAA-TTAATA
3062608 AAAAATTAATATAA
1 AAAAATT-A-AT-A
3062622 AAAAATTAATA
1 AAAAATTAATA
3062633 AAA
1 AAA
3062636 TAATAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
11 13 0.28
12 9 0.19
13 6 0.13
14 11 0.23
15 6 0.13
16 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTAATA
Found at i:3062595 original size:16 final size:16
Alignment explanation
Indices: 3062576--3062645 Score: 73
Period size: 14 Copynumber: 4.8 Consensus size: 16
3062566 CTTTAAAAAT
3062576 TAATAAAAAATTAATA
1 TAATAAAAAATTAATA
3062592 TAAT-AAAAA-T--T-
1 TAATAAAAAATTAATA
3062603 TAATAAAAAATTAATA
1 TAATAAAAAATTAATA
3062619 T-A-AAAAAATTAATA
1 TAATAAAAAATTAATA
* *
3062633 AAATAATAAATTA
1 TAATAAAAAATTA
3062646 TTAATTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 4 0.09
12 6 0.13
13 1 0.02
14 13 0.29
15 8 0.18
16 13 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAAAAAATTAATA
Found at i:3062600 original size:27 final size:25
Alignment explanation
Indices: 3062570--3062635 Score: 114
Period size: 27 Copynumber: 2.6 Consensus size: 25
3062560 TTATAACTTT
3062570 AAAAATTAATAAAAAATTAATATAA
1 AAAAATTAATAAAAAATTAATATAA
3062595 TAAAAATTTAATAAAAAATTAATATAA
1 -AAAAA-TTAATAAAAAATTAATATAA
3062622 AAAAATTAATAAAA
1 AAAAATTAATAAAA
3062636 TAATAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.23
26 10 0.26
27 20 0.51
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATTAATAAAAAATTAATATAA
Found at i:3062625 original size:14 final size:14
Alignment explanation
Indices: 3062580--3062632 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
3062570 AAAAATTAAT
3062580 AAAAAATTAATATA
1 AAAAAATTAATATA
*
3062594 ATAAAAATTTA-AT-
1 A-AAAAATTAATATA
3062607 AAAAAATTAATATA
1 AAAAAATTAATATA
3062621 AAAAAATTAATA
1 AAAAAATTAATA
3062633 AAATAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 15 0.44
15 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAATTAATATA
Found at i:3065758 original size:14 final size:13
Alignment explanation
Indices: 3065736--3065776 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
3065726 AAACAAGTAT
*
3065736 TAAAGAAAATAGAA
1 TAAATAAAATA-AA
3065750 TAAATAAAATAAA
1 TAAATAAAATAAA
3065763 TAAAATAAAATAAA
1 T-AAATAAAATAAA
3065777 ACAAAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:3065759 original size:5 final size:5
Alignment explanation
Indices: 3065741--3065782 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3065731 AGTATTAAAG
* *
3065741 AAAAT AGAAT -AAAT AAAAT -AAAT AAAAT AAAAT AAAAC AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3065783 ACCAACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.22
5 25 0.78
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3065760 original size:9 final size:9
Alignment explanation
Indices: 3065742--3065777 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3065732 GTATTAAAGA
*
3065742 AAATAGAAT
1 AAATAAAAT
3065751 AAATAAAAT
1 AAATAAAAT
3065760 AAATAAAAT
1 AAATAAAAT
3065769 AAAATAAAA
1 -AAATAAAA
3065778 CAAAAACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3066697 original size:29 final size:28
Alignment explanation
Indices: 3066658--3066716 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
3066648 TCAGGTATGT
*
3066658 TTCGTTTCTTCTTTTCTCTCTTTTTTTTTC
1 TTCGTTTCTTC--TTCTCTCTTATTTTTTC
3066688 TTCG-TTCTTCTTCTCTCTTATTTTTTC
1 TTCGTTTCTTCTTCTCTCTTATTTTTTC
3066715 TT
1 TT
3066717 TTCTTTCGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 18 0.64
29 6 0.21
30 4 0.14
ACGTcount: A:0.02, C:0.24, G:0.03, T:0.71
Consensus pattern (28 bp):
TTCGTTTCTTCTTCTCTCTTATTTTTTC
Found at i:3067302 original size:3 final size:3
Alignment explanation
Indices: 3067294--3067337 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
3067284 ATAAAATGAC
*
3067294 AAT AAT AAT AAT ATAT AAC AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3067338 ATAAAAATGG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3067343 original size:27 final size:27
Alignment explanation
Indices: 3067282--3067343 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
3067272 GTAATTTTAT
*
3067282 TAATAAAATGACAATAATAATAATATA
1 TAATAAAATAACAATAATAATAATATA
* *
3067309 TAACAAAATAATAATAATAATAATA-A
1 TAATAAAATAACAATAATAATAATATA
3067335 TAAATAAAA
1 T-AATAAAA
3067344 ATGGATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (27 bp):
TAATAAAATAACAATAATAATAATATA
Found at i:3067746 original size:40 final size:41
Alignment explanation
Indices: 3067629--3067746 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 41
3067619 TAGGAATGGT
* * *
3067629 GATAACTCGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGG
1 GATAACACGGTTCCTACGTGATGAGGACGACTGGTTA--TAGG
* * * * *
3067672 GTTAACGCGGCTCCTACGTGATGAGGAGGTCTGGTTA-AGG
1 GATAACACGGTTCCTACGTGATGAGGACGACTGGTTATAGG
* *
3067712 GATAACACGGTTCCTACGTGTTGAGGCCGACTGGT
1 GATAACACGGTTCCTACGTGATGAGGACGACTGGT
3067747 CATCTTTATT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 31 0.50
43 31 0.50
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.25
Consensus pattern (41 bp):
GATAACACGGTTCCTACGTGATGAGGACGACTGGTTATAGG
Found at i:3068814 original size:24 final size:24
Alignment explanation
Indices: 3068786--3068851 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
3068776 ATCTTGAACC
3068786 CTTCTTTATTTATTTTTTC-TTTTT
1 CTTCTTT-TTTATTTTTTCATTTTT
*
3068810 CTTCTTTTTCA-TTTTTCATTTTT
1 CTTCTTTTTTATTTTTTCATTTTT
*
3068833 CATTTTTTTTTCATTTTTT
1 C-TTCTTTTTT-ATTTTTT
3068852 TAAGTGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 6 0.17
23 9 0.26
24 14 0.40
25 1 0.03
26 5 0.14
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (24 bp):
CTTCTTTTTTATTTTTTCATTTTT
Found at i:3068824 original size:7 final size:7
Alignment explanation
Indices: 3068814--3068850 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3068804 CTTTTTCTTC
3068814 TTTTTCA
1 TTTTTCA
3068821 TTTTTCA
1 TTTTTCA
3068828 TTTTTCA
1 TTTTTCA
3068835 -TTTT--
1 TTTTTCA
3068839 TTTTTCA
1 TTTTTCA
3068846 TTTTT
1 TTTTT
3068851 TTAAGTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.15
6 4 0.15
7 19 0.70
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:3068849 original size:10 final size:11
Alignment explanation
Indices: 3068814--3068852 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
3068804 CTTTTTCTTC
3068814 TTTTTCATTTTT
1 TTTTTCA-TTTT
3068826 CATTTTTCATTTT
1 --TTTTTCATTTT
3068839 TTTTTCATTTT
1 TTTTTCATTTT
3068850 TTT
1 TTT
3068853 AAGTGTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.56
13 4 0.16
14 7 0.28
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:3076011 original size:30 final size:30
Alignment explanation
Indices: 3075949--3076016 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
3075939 TTAAACTTGA
* **
3075949 ATGCATATTATTGGTAATGTGTTATAAATG
1 ATGCATTTTATTGGTAATGCATTATAAATG
* * *
3075979 ATGCATTTTATTGGTGATGCATTGTAAGTG
1 ATGCATTTTATTGGTAATGCATTATAAATG
*
3076009 ATGAATTT
1 ATGCATTT
3076017 ATTTATGTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (30 bp):
ATGCATTTTATTGGTAATGCATTATAAATG
Found at i:3080393 original size:13 final size:13
Alignment explanation
Indices: 3080361--3080402 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
3080351 CCAAACAAGT
*
3080361 AATAAAGAAAATA
1 AATAAATAAAATA
3080374 GAATAAATAAAATA
1 -AATAAATAAAATA
3080388 AATAAATAAAATA
1 AATAAATAAAATA
3080401 AA
1 AA
3080403 ACAAAAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:3081320 original size:13 final size:13
Alignment explanation
Indices: 3081293--3081334 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3081283 CATCTCTTCC
*
3081293 TTTCTCTCTTTTT
1 TTTCTCTCTTATT
3081306 TTTCT-TCGTTATT
1 TTTCTCTC-TTATT
3081319 TTTCTCTCTTATT
1 TTTCTCTCTTATT
3081332 TTT
1 TTT
3081335 TCTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTCTCTCTTATT
Found at i:3081930 original size:21 final size:18
Alignment explanation
Indices: 3081904--3081962 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 18
3081894 GTAATTGTAT
3081904 TAATAAAATGACAATAATAA
1 TAATAAAAT-A-AATAATAA
3081924 TATATAACAAATAAATAATAA
1 TA-AT-A-AAATAAATAATAA
*
3081945 TAAT--AATAAATAAAAA
1 TAATAAAATAAATAATAA
3081961 TA
1 TA
3081963 GATAGAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 13 0.37
20 4 0.11
21 12 0.34
22 2 0.06
23 4 0.11
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (18 bp):
TAATAAAATAAATAATAA
Found at i:3081952 original size:16 final size:17
Alignment explanation
Indices: 3081919--3081962 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3081909 AAATGACAAT
3081919 AATAATATATAACAAATA
1 AATAATA-ATAACAAATA
*
3081937 AATAATAATAA-TAATA
1 AATAATAATAACAAATA
*
3081953 AATAAAAATA
1 AATAATAATA
3081963 GATAGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
17 4 0.17
18 7 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAACAAATA
Found at i:3086774 original size:21 final size:19
Alignment explanation
Indices: 3086737--3086776 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
3086727 ATGAATTTTG
*
3086737 GGTTGGTAGTATCGATACT
1 GGTTGGTAGTACCGATACT
3086756 GGTTGAGTAGGTACCGATACT
1 GGTTG-GTA-GTACCGATACT
3086777 ACAAGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.33
Consensus pattern (19 bp):
GGTTGGTAGTACCGATACT
Found at i:3086880 original size:21 final size:21
Alignment explanation
Indices: 3086828--3086888 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3086818 TTGTATGAAC
3086828 AGTATCGATACCATAAGGAAGG
1 AGTATCGATACCA-AAGGAAGG
* * *
3086850 AGTATTGATACCAATGTGGAGG
1 AGTATCGATACCAAAG-GAAGG
3086872 -GTATCGATACC-AAGGAA
1 AGTATCGATACCAAAGGAA
3086889 CATCGAAGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 12 0.38
22 16 0.50
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (21 bp):
AGTATCGATACCAAAGGAAGG
Found at i:3099797 original size:20 final size:20
Alignment explanation
Indices: 3099768--3099805 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3099758 AGAATCCTCA
*
3099768 GGGGGTATCGATTCCCCTGG
1 GGGGGAATCGATTCCCCTGG
*
3099788 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
3099806 TCAAAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGG
Found at i:3099818 original size:23 final size:23
Alignment explanation
Indices: 3099789--3099848 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3099779 TTCCCCTGGG
*
3099789 GGGGAATCGGTTCCCCTTCAAAA
1 GGGGAATCGATTCCCCTTCAAAA
*
3099812 GGGGAATCGATTCCCCTTC-AAG
1 GGGGAATCGATTCCCCTTCAAAA
*
3099834 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
3099849 TTTGCCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (23 bp):
GGGGAATCGATTCCCCTTCAAAA
Found at i:3105709 original size:6 final size:6
Alignment explanation
Indices: 3105698--3106137 Score: 659
Period size: 6 Copynumber: 73.0 Consensus size: 6
3105688 CACAAAATGC
*
3105698 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGCAT GTATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATG--T GCATGT
* * * * * * * *
3105748 GTATGT GTATGT GTATGT GAATGT GTATGT GTATGT GTATGT GTATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
* * *
3105796 GTATGT GGATGT GCATGT GGATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
3105844 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
3105892 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
3105940 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
3105988 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
3106036 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
1 GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT GCATGT
* * * * * *
3106084 GTATGT -CTATGT GTATGT GTATGT -CTATGT GTATGT GTATGT GTATGT
1 GCATGT GC-ATGT GCATGT GCATGT GC-ATGT GCATGT GCATGT GCATGT
*
3106132 GTATGT
1 GCATGT
3106138 ATATGTATGT
Statistics
Matches: 416, Mismatches: 12, Indels: 12
0.95 0.03 0.03
Matches are distributed among these distances:
6 411 0.99
8 5 0.01
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.37
Consensus pattern (6 bp):
GCATGT
Found at i:3107533 original size:23 final size:24
Alignment explanation
Indices: 3107506--3107551 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3107496 TCAAATGTAA
*
3107506 CTTATAATATTTGA-ATTTTTATC
1 CTTATAATATTTAATATTTTTATC
*
3107529 CTTATAATTTTTAATATTTTTAT
1 CTTATAATATTTAATATTTTTAT
3107552 ATAGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (24 bp):
CTTATAATATTTAATATTTTTATC
Found at i:3107705 original size:2 final size:2
Alignment explanation
Indices: 3107700--3107737 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3107690 CAAATAACAA
3107700 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
3107738 GCAGGTATCA
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:3111764 original size:28 final size:28
Alignment explanation
Indices: 3111712--3111765 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3111702 TCGATATTGT
*
3111712 TTTCAAGCACTAGCTCGATAACATAATA
1 TTTCAAGCACTAGCTCGACAACATAATA
* * *
3111740 TTTCAAGCATTGGCTCGACATCATAA
1 TTTCAAGCACTAGCTCGACAACATAA
3111766 ATGTAAACTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACAACATAATA
Found at i:3112754 original size:19 final size:19
Alignment explanation
Indices: 3112730--3112767 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3112720 TCTATTTTTA
3112730 TTTAATAAAAATAATATTT
1 TTTAATAAAAATAATATTT
* *
3112749 TTTAATAAATATATTATTT
1 TTTAATAAAAATAATATTT
3112768 CATGTCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATAAAAATAATATTT
Found at i:3123282 original size:61 final size:61
Alignment explanation
Indices: 3123197--3123320 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
3123187 TTGCAAAATT
* * *
3123197 ATCTCTACAACTGAAAATCGAAAAGTTGTAGAGATTCCAGAAATGGTTACATTTCTCCAAA
1 ATCTCTACAACTGAAAATCCAAAAGTTGTAGAGATTCCAAAAATGGATACATTTCTCCAAA
* *
3123258 ATCTCTACAATTGAAAATCCAAAAGTTGTAGAGATTCCAAAAATGGATACGTTTCTCCAAA
1 ATCTCTACAACTGAAAATCCAAAAGTTGTAGAGATTCCAAAAATGGATACATTTCTCCAAA
3123319 AT
1 AT
3123321 AATTGTCTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (61 bp):
ATCTCTACAACTGAAAATCCAAAAGTTGTAGAGATTCCAAAAATGGATACATTTCTCCAAA
Found at i:3131438 original size:123 final size:123
Alignment explanation
Indices: 3131293--3131543 Score: 475
Period size: 123 Copynumber: 2.0 Consensus size: 123
3131283 CTAAACAACA
3131293 AATATTCCAATAAACACATAACATACAAGAAAAAAAAGGTAAATAACAATTTTGGTTGTCTCAGG
1 AATATTCCAATAAACACATAACATACAAGAAAAAAAAGGTAAATAACAATTTTGGTTGTCTCAGG
3131358 TGACCAAAATGTAAAAACACGCTAAACTTAGAGAGATTAAACATCAATTAACCCAATC
66 TGACCAAAATGTAAAAACACGCTAAACTTAGAGAGATTAAACATCAATTAACCCAATC
*
3131416 AATATTCCAATAAACACATAACATACAAGAAAGAAAAGGTAAATAACAATTTTGGTTGTCTCAGG
1 AATATTCCAATAAACACATAACATACAAGAAAAAAAAGGTAAATAACAATTTTGGTTGTCTCAGG
* *
3131481 TGACCGAAATGTAAAAACACGCTAAACTTAGAGGGATTAAACATCAATTAACCCAATC
66 TGACCAAAATGTAAAAACACGCTAAACTTAGAGAGATTAAACATCAATTAACCCAATC
3131539 AATAT
1 AATAT
3131544 ATAACACGTA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (123 bp):
AATATTCCAATAAACACATAACATACAAGAAAAAAAAGGTAAATAACAATTTTGGTTGTCTCAGG
TGACCAAAATGTAAAAACACGCTAAACTTAGAGAGATTAAACATCAATTAACCCAATC
Found at i:3132615 original size:18 final size:18
Alignment explanation
Indices: 3132570--3132633 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 18
3132560 TTTGTCCTGT
3132570 AATAATAATA-ATAAATTAA
1 AATAA-AATAGATAAA-TAA
3132589 AATTAAAATAGATAAATAA
1 AA-TAAAATAGATAAATAA
3132608 AATAAAATAGATAAATAAA
1 AATAAAATAGATAAAT-AA
3132627 AATAAAA
1 AATAAAA
3132634 GAATCGGGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 14 0.33
19 20 0.48
20 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AATAAAATAGATAAATAA
Found at i:3133065 original size:132 final size:132
Alignment explanation
Indices: 3132806--3133349 Score: 675
Period size: 132 Copynumber: 4.2 Consensus size: 132
3132796 AGATATTTTT
* ** * *
3132806 GAAGATGAAATCT--AAAAA-GGGATCTGCTCTATTGCACTTCAGGGCAGATCAGATATGGAAAC
1 GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCAGGGTAGATCAGATATGGAAAC
* * * * *
3132868 GTTGATTCATTCCAATGCTCTTCAGGGAAGATTGAATCGAGGTAAATTTGTTCCACTTCTACTCA
66 GTTGATTCATTCCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGCTCCTCA
3132933 GG
131 GG
* * * * * *
3132935 GAAGATCAAATATGGAAAAAGGGGATCTACTCCGCTGCTATTCAGGGTAGATCAAATATGGAGAC
1 GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCAGGGTAGATCAGATATGGAAAC
* * * * *
3133000 GTTGATTCATTCCACTACTCTTCAGCGAAGATTGAATCGAAGTAGATTTGTTCCATTGCTCCTCA
66 GTTGATTCATTCCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGCTCCTCA
3133065 GG
131 GG
* * * *
3133067 GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCATGATAGATCAGATCTGGAAAT
1 GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCAGGGTAGATCAGATATGGAAAC
* * * * *
3133132 GTTGATTCATTCTACTGCTCTTCAGGGAAGATTTAATCGAGGCATATTTGTTCTACTGCTCATCA
66 GTTGATTCATTCCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGCTCCTCA
3133197 GG
131 GG
* * * * *
3133199 GAAGATCAAATCTAGAAAAAGGGGATCTGTTATGCTGCTCTTCAGGGTAGATTAGATCTGGAAAC
1 GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCAGGGTAGATCAGATATGGAAAC
* * * * * *
3133264 ATTGATTCATTACACTGCTTTTCAAGGAAGATTGAATCGAGGCAGATTTGTTACACTGCTTCTCA
66 GTTGATTCATTCCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGCTCCTC-
3133329 AGG
130 AGG
3133332 G-AGATCAAATCT-GAAAAA
1 GAAGATCAAATCTGGAAAAA
3133350 TTAAACATTA
Statistics
Matches: 354, Mismatches: 57, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
129 11 0.03
131 11 0.03
132 328 0.93
133 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (132 bp):
GAAGATCAAATCTGGAAAAAGGGGATCTGCTCTGCTGCTCTTCAGGGTAGATCAGATATGGAAAC
GTTGATTCATTCCACTGCTCTTCAGGGAAGATTGAATCGAGGCAGATTTGTTCCACTGCTCCTCA
GG
Found at i:3134627 original size:7 final size:7
Alignment explanation
Indices: 3134617--3134667 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
3134607 TTATTTATTA
3134617 TTCTTTT
1 TTCTTTT
3134624 TTCTTTCT
1 TTCTTT-T
3134632 TTCTTTT
1 TTCTTTT
3134639 TT-TTTT
1 TTCTTTT
*
3134645 CT-TTTT
1 TTCTTTT
*
3134651 TTCATTT
1 TTCTTTT
3134658 TTCATTTT
1 TTC-TTTT
3134666 TT
1 TT
3134668 ATTTCTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 10 0.27
7 15 0.41
8 12 0.32
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTCTTTT
Found at i:3134637 original size:15 final size:15
Alignment explanation
Indices: 3134617--3134652 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3134607 TTATTTATTA
3134617 TTCTTTTTTCTTTCT
1 TTCTTTTTTCTTTCT
*
3134632 TTCTTTTTTTTTTCT
1 TTCTTTTTTCTTTCT
3134647 TT-TTTT
1 TTCTTTT
3134653 CATTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTCTTTTTTCTTTCT
Found at i:3134644 original size:19 final size:20
Alignment explanation
Indices: 3134620--3134659 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3134610 TTTATTATTC
3134620 TTTTTTCTTTCTTTC-TTTT
1 TTTTTTCTTTCTTTCATTTT
*
3134639 TTTTTTCTTTTTTTCATTTT
1 TTTTTTCTTTCTTTCATTTT
3134659 T
1 T
3134660 CATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTTCTTTCATTTT
Found at i:3134658 original size:15 final size:14
Alignment explanation
Indices: 3134627--3134671 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
3134617 TTCTTTTTTC
*
3134627 TTTCTTTCTTTTTTT
1 TTTCTTT-TTTTATT
3134642 TTTCTTTTTTTCATT
1 TTTCTTTTTTT-ATT
*
3134657 TTTCATTTTTTATT
1 TTTCTTTTTTTATT
3134671 T
1 T
3134672 CTTTCCTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTTATT
Found at i:3145181 original size:20 final size:20
Alignment explanation
Indices: 3145154--3145192 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3145144 AACCAGTTTT
*
3145154 TTTTAAACCGG-ATAGTATA
1 TTTTAAAACGGAATAGTATA
3145173 TTTTAAAACGGAATAGTATA
1 TTTTAAAACGGAATAGTATA
3145193 ACCGGTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
TTTTAAAACGGAATAGTATA
Found at i:3154041 original size:18 final size:20
Alignment explanation
Indices: 3154014--3154057 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
3154004 TAATGAATAT
* *
3154014 AATGCTATGC-GAAAA-GTA
1 AATGCAATGCAGAAAATGAA
3154032 AATGCAATGCAGAAAATGAA
1 AATGCAATGCAGAAAATGAA
3154052 AATGCA
1 AATGCA
3154058 CAATGTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 5 0.23
20 8 0.36
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGCAATGCAGAAAATGAA
Found at i:3157100 original size:43 final size:44
Alignment explanation
Indices: 3157013--3157102 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 44
3157003 GTAAAAGTAG
* ** *
3157013 AAAACACATAATCACACAACACATTTAATGGTTAATTGACTTGC
1 AAAAAACATAATCACACAACACATTTAATGGTTAATCAAATTGC
*
3157057 AAAAAACA-AATCATCACAAC-TATTTAATGGTTAATCAAATTGC
1 AAAAAACATAATCA-CACAACACATTTAATGGTTAATCAAATTGC
3157100 AAA
1 AAA
3157103 CACAAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 27 0.68
44 13 0.32
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.27
Consensus pattern (44 bp):
AAAAAACATAATCACACAACACATTTAATGGTTAATCAAATTGC
Found at i:3159550 original size:20 final size:20
Alignment explanation
Indices: 3159525--3159574 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
3159515 CTTCTTCTTC
3159525 TATTTTTTTGTAAATACATA
1 TATTTTTTTGTAAATACATA
*
3159545 TATTTTTTCCCGTAAATACATA
1 TATTTTTT--TGTAAATACATA
3159567 T-TTTTTTT
1 TATTTTTTT
3159575 CCAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTTTTTTGTAAATACATA
Found at i:3159559 original size:22 final size:22
Alignment explanation
Indices: 3159534--3159576 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3159524 CTATTTTTTT
3159534 GTAAATACATATATTTTTTCCC
1 GTAAATACATATATTTTTTCCC
*
3159556 GTAAATACATATTTTTTTTCC
1 GTAAATACATATATTTTTTCC
3159577 AAACTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (22 bp):
GTAAATACATATATTTTTTCCC
Found at i:3160107 original size:3 final size:3
Alignment explanation
Indices: 3160099--3160136 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
3160089 ATTTGGCCTG
3160099 TAA TAA TAA TAA TAA TAAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
3160137 AATGGAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Done.