Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 194 of 204
Found at i:57369242 original size:26 final size:26
Alignment explanation
Indices: 57369213--57369274 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
57369203 GTATGATTTT
* *
57369213 TGTACATATTTACAT-ATCTATATGTA
1 TGTACATATTT-CATAATATATATATA
**
57369239 TGTATTTATTTCATAATATATATATA
1 TGTACATATTTCATAATATATATATA
*
57369265 TTTACATATT
1 TGTACATATT
57369275 CTTCATTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (26 bp):
TGTACATATTTCATAATATATATATA
Found at i:57369311 original size:13 final size:13
Alignment explanation
Indices: 57369290--57369319 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57369280 TTTTTTTAAA
57369290 ATATCTATTTTAT
1 ATATCTATTTTAT
*
57369303 ATATGTATTTTAT
1 ATATCTATTTTAT
57369316 ATAT
1 ATAT
57369320 TATGATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (13 bp):
ATATCTATTTTAT
Found at i:57369980 original size:110 final size:109
Alignment explanation
Indices: 57369782--57370068 Score: 470
Period size: 110 Copynumber: 2.6 Consensus size: 109
57369772 TCAAAAAAGG
*
57369782 AAAATATTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
57369847 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATAG-CCTTC
65 GGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATAGCCCTTC
*
57369891 TTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACATGCCCTAAGGTGC
1 --AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGC
*
57369956 TGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCCTTC
64 TGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATAGCCCTTC
* *
57370002 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
57370066 GGT
66 GGT
57370069 TTAGATGTCT
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
108 21 0.13
109 43 0.26
110 94 0.56
111 9 0.05
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATAGCCCTTC
Found at i:57371938 original size:9 final size:9
Alignment explanation
Indices: 57371924--57371973 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
57371914 CATTTAAATA
57371924 AATAATTAT
1 AATAATTAT
57371933 AATAATTAT
1 AATAATTAT
57371942 AATAATTAT
1 AATAATTAT
57371951 -ATACA-TAT
1 AATA-ATTAT
*
57371959 AATATTTAT
1 AATAATTAT
57371968 ATATAA
1 A-ATAA
57371974 CTTAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 6 0.17
9 26 0.74
10 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:57379698 original size:20 final size:20
Alignment explanation
Indices: 57379675--57379714 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
57379665 CTTTTTTGTC
57379675 GTGATTTTTAAATTTTATTA
1 GTGATTTTTAAATTTTATTA
57379695 GTGATTTTTAAATTTTATTA
1 GTGATTTTTAAATTTTATTA
57379715 ATTTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
GTGATTTTTAAATTTTATTA
Found at i:57383416 original size:21 final size:23
Alignment explanation
Indices: 57383381--57383422 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
57383371 TGTTTCCCAA
*
57383381 TATTTATTATATATTTATATTAT
1 TATTTATTATATATTCATATTAT
57383404 TATTT-TT-TATATTCATATT
1 TATTTATTATATATTCATATT
57383423 CATGTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTATTATATATTCATATTAT
Found at i:57398495 original size:25 final size:22
Alignment explanation
Indices: 57398453--57398503 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
57398443 TATATATTAA
* *
57398453 ATATTTTTTTATTTTTAATCAAAT
1 ATATATTTTTATTATTAA--AAAT
57398477 ATATATTTTTATATATTAAAAAT
1 ATATATTTTTAT-TATTAAAAAT
57398500 ATAT
1 ATAT
57398504 TTTAATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 11 0.46
25 5 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATATTTTTATTATTAAAAAT
Found at i:57402484 original size:2 final size:2
Alignment explanation
Indices: 57402477--57402544 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
57402467 CCAAACCTTA
57402477 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
57402519 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
57402545 TTATGTGAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57403329 original size:24 final size:23
Alignment explanation
Indices: 57403296--57403340 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
57403286 AACATTTTAA
57403296 TAAATGAAAAAAAATATTAAATAT
1 TAAATGAAAAAAAATA-TAAATAT
* *
57403320 TAAATTAAAAATAATATAAAT
1 TAAATGAAAAAAAATATAAAT
57403341 GTTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAATGAAAAAAAATATAAATAT
Found at i:57403581 original size:2 final size:2
Alignment explanation
Indices: 57403574--57403615 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
57403564 AGCTTAATTA
57403574 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
57403616 CATTTATGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57408794 original size:18 final size:18
Alignment explanation
Indices: 57408752--57408785 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57408742 AGAAGTTGTG
57408752 ATAATTACACATTTAAAA
1 ATAATTACACATTTAAAA
*
57408770 ATAATTAGA-ATTTAAA
1 ATAATTACACATTTAAA
57408786 TTATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATTACACATTTAAAA
Found at i:57414551 original size:298 final size:296
Alignment explanation
Indices: 57413895--57415059 Score: 1203
Period size: 297 Copynumber: 3.9 Consensus size: 296
57413885 TTCTTTTTGA
* * * * *
57413895 GTTTTACTAAATTGGTGTCACCCTCAATTGGGTCACCAACTCAGTTAGGAAATTATGAGAATGT-
1 GTTTTACTAAGTTGGTGTCACCCTCAATCGGGTCACCAACTCAATTAGGAAATTATAAAAATGTC
* * ** ** * *
57413959 TTTTCTGTAATTAAAATAAGTTGTACCGTTTGAGGGTATTTTA-AATGTTCATTTTAAGAAAAAC
66 CTTTC-GTAATTAAAATAAGTTATACTATTTGAGGGTATTTTAGTCTTTTCATTTTAACAAAAAC
* * ** ** *
57414023 CAATTAAAATATGCATATGATAAGATTTGAATACATGCCAATT-AATTTAATAAAACTTTAAATT
130 AAATTAAAATATGCATATGATGAGATTTGAACCCACACCAATTGAA-TTAA-AAACCTTTAAATT
* * * * * *
57414087 TACCATTTAACCAAAGCTTCGTTTTAATGTATTTTATAATCGTGTT-TTTTAATATGCACAAGTT
193 TACCACTCAACCAAAGCTTCATTTTAATATATTTTATAAT-TTTTTATTTTAATATGCACAAGTT
* * *
57414151 ATTATCTCCATTAGTTGTATA-AATATACTATTTGTTAAGT
257 ATTATCTCCACTAGTTGTATACACT-TACTATTTATTAAGT
* * * * * *
57414191 ATTTTACTAAGTTGGTGTC-CTCCTCAACCAGGTCACCAACTCGATCAAGAAATTATAAAAATGT
1 GTTTTACTAAGTTGGTGTCAC-CCTCAATCGGGTCACCAACTCAATTAGGAAATTATAAAAATGT
** *
57414255 TATTTCGTAATTAAAATAAGTTATACTGTTTGAGGGTATTTTAGTCTTTTCATTTTAACAAAAAC
65 CCTTTCGTAATTAAAATAAGTTATACTATTTGAGGGTATTTTAGTCTTTTCATTTTAACAAAAAC
*
57414320 AAATTAAAATATGCATATGATGAGATTTGAACCCACACCAATTGGATCTAAAAACCTTTAAATTT
130 AAATTAAAATATGCATATGATGAGATTTGAACCCACACCAATTGAAT-TAAAAACCTTTAAATTT
* ** * *
57414385 ATCACTCAACCAAAATTTTATTTTAATATATTTTATACATTTTTTATTTTAATATGCGCACA-TT
194 ACCACTCAACCAAAGCTTCATTTTAATATATTTTATA-ATTTTTTATTTTAATATGCACA-AGTT
57414449 ATTATCTCCACTAGTTGTATACACTTACTATTTATTAAGT
257 ATTATCTCCACTAGTTGTATACACTTACTATTTATTAAGT
* * *
57414489 GTTTTAC-AATGTTGGTGTCACCCTCGATCGGGTCACCAAATCAATTAGGAAATTACAAAAATG-
1 GTTTTACTAA-GTTGGTGTCACCCTCAATCGGGTCACCAACTCAATTAGGAAATTATAAAAATGT
* * *
57414552 CCCTTCATAATTAAAATAATTTATACTATTTGA-GGTCATTTTAGTCTTTTCATTTTAACAAAAA
65 CCTTTCGTAATTAAAATAAGTTATACTATTTGAGGGT-ATTTTAGTCTTTTCATTTTAACAAAAA
* * * * * * * *
57414616 CAAATTAAAATAAGCATATGGTGGGATTTGAACCCACCCCAATTAAATTAGTAAA-GTATAAATT
129 CAAATTAAAATATGCATATGATGAGATTTGAACCCACACCAATTGAATTA-AAAACCTTTAAA-T
* * * * *
57414680 TATACCACTTAAAC-AAGTCTTTATTTTAATATATTTTATACA-TTTTTATTTTAATATACAAAA
192 T-TACCACTCAACCAAAG-CTTCATTTTAATATATTTTATA-ATTTTTTATTTTAATATGCACAA
* * *
57414743 GTTATTATCTCCAGTAGTTGTATATCTATCCTTACCA-TTATTAATT
254 GTTATTATCTCCACTAGTTGTATA-C-A--CTTACTATTTATTAAGT
* * * * * *
57414789 GTTTTACTAAGTTGGTGTCACCCACATTTGGGTCACCAACTCAGTTAGAAAATTATAAAAATGCC
1 GTTTTACTAAGTTGGTGTCACCCTCAATCGGGTCACCAACTCAATTAGGAAATTATAAAAATGTC
* *
57414854 CTTTCGTAATTAAAATAAGTTATACTATTTAACAGTAGCTATTTTAGTCTTTTCATTTTAACAAA
66 CTTTCGTAATTAAAATAAGTTATACTATTT--GAG--GGTATTTTAGTCTTTTCATTTTAACAAA
** *
57414919 AACAAATTAAAATATGCATACAAT-AGGATTTGAACCCACACTAATTGAGA-TAGCAAAACC-TT
127 AACAAATTAAAATATGCATATGATGA-GATTTGAACCCACACCAATTGA-ATTA--AAAACCTTT
* * * * * * *
57414981 AATTTTACCATTCAACCAAAGCTTCATTTTATTCTAATTTATAAATTTTCATTTTAATATGCACA
188 AAATTTACCACTCAACCAAAGCTTCATTTTAATATATTTTATAATTTTTTATTTTAATATGCACA
57415046 AGTTATTATCTCCA
253 AGTTATTATCTCCA
57415060 TTACTTTTAT
Statistics
Matches: 724, Mismatches: 111, Indels: 60
0.81 0.12 0.07
Matches are distributed among these distances:
295 1 0.00
296 97 0.13
297 248 0.34
298 137 0.19
299 5 0.01
300 60 0.08
301 36 0.05
303 2 0.00
304 58 0.08
305 71 0.10
306 9 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (296 bp):
GTTTTACTAAGTTGGTGTCACCCTCAATCGGGTCACCAACTCAATTAGGAAATTATAAAAATGTC
CTTTCGTAATTAAAATAAGTTATACTATTTGAGGGTATTTTAGTCTTTTCATTTTAACAAAAACA
AATTAAAATATGCATATGATGAGATTTGAACCCACACCAATTGAATTAAAAACCTTTAAATTTAC
CACTCAACCAAAGCTTCATTTTAATATATTTTATAATTTTTTATTTTAATATGCACAAGTTATTA
TCTCCACTAGTTGTATACACTTACTATTTATTAAGT
Found at i:57426554 original size:19 final size:19
Alignment explanation
Indices: 57426530--57426571 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
57426520 GTGATGTATT
57426530 TAAACAAGGCATCCATTAA
1 TAAACAAGGCATCCATTAA
57426549 TAAACAAGGCATCCATTAA
1 TAAACAAGGCATCCATTAA
57426568 TAAA
1 TAAA
57426572 GGAACTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (19 bp):
TAAACAAGGCATCCATTAA
Found at i:57431917 original size:2 final size:2
Alignment explanation
Indices: 57431910--57431934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57431900 TTACATTATG
57431910 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 T
57431935 TTCTTCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57436265 original size:4 final size:4
Alignment explanation
Indices: 57436256--57436292 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
57436246 CAAAAATGGG
57436256 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AGAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A-AAT AAA
57436293 GGCTGGGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:57445406 original size:5 final size:5
Alignment explanation
Indices: 57445389--57445454 Score: 96
Period size: 5 Copynumber: 13.2 Consensus size: 5
57445379 TTTCATTCTG
* * * *
57445389 ATCAT ATCTT ATCAT ATCAT AACGT ATCAT AACAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
57445439 ATCAT ATCAT ATCAT A
1 ATCAT ATCAT ATCAT A
57445455 ACATGTCCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (5 bp):
ATCAT
Found at i:57445599 original size:23 final size:22
Alignment explanation
Indices: 57445569--57445623 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
57445559 TGTAACACCC
*
57445569 TAAGAATTTGAGTGTTGTTTGT
1 TAAGAATTTGAGTGCTGTTTGT
57445591 TCAAGAATTTGAGTGCTGTTTGT
1 T-AAGAATTTGAGTGCTGTTTGT
57445614 TAA-AATTTGA
1 TAAGAATTTGA
57445624 TATAGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 7 0.23
22 3 0.10
23 21 0.68
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (22 bp):
TAAGAATTTGAGTGCTGTTTGT
Found at i:57451396 original size:17 final size:16
Alignment explanation
Indices: 57451368--57451419 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
57451358 CTTCATATAT
*
57451368 TTTCACTTCTTTTTCC
1 TTTCATTTCTTTTTCC
*
57451384 TTTCATATTCTTTTTCA
1 TTTCAT-TTCTTTTTCC
*
57451401 TTTCATTTCTCTTTCC
1 TTTCATTTCTTTTTCC
57451417 TTT
1 TTT
57451420 GTTTTCCCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCATTTCTTTTTCC
Found at i:57454717 original size:29 final size:30
Alignment explanation
Indices: 57454678--57454735 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
57454668 AACCTTTCCC
*
57454678 CTTAGCTTTTATGGCTAAACTAGAACCCTT
1 CTTAGCTTTTATGGCTAAACTAAAACCCTT
*
57454708 CTTAG-TTTTATGGCTTAACTAAAACCCT
1 CTTAGCTTTTATGGCTAAACTAAAACCCT
57454736 CCTAATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (30 bp):
CTTAGCTTTTATGGCTAAACTAAAACCCTT
Found at i:57460348 original size:18 final size:19
Alignment explanation
Indices: 57460304--57460350 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
57460294 AGACCTCTCC
*
57460304 AAATATTTTTTTATTTTTA
1 AAATATATTTTTATTTTTA
*
57460323 AAAAATATTTTTA-TTTTA
1 AAATATATTTTTATTTTTA
*
57460341 ATATATATTT
1 AAATATATTT
57460351 ACTACTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AAATATATTTTTATTTTTA
Found at i:57462690 original size:2 final size:2
Alignment explanation
Indices: 57462666--57462735 Score: 97
Period size: 2 Copynumber: 35.0 Consensus size: 2
57462656 TCATATCCAA
* * *
57462666 AT AT AC AT AT AG AT AT AT GT AT AT A- AGT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
57462708 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
57462736 CGGACACAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 58 0.97
3 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:57474423 original size:16 final size:17
Alignment explanation
Indices: 57474396--57474428 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
57474386 GGTCCAATGA
57474396 TTAAAAATTATTAAAAT
1 TTAAAAATTATTAAAAT
57474413 TTAAAAA-TATTAAAAT
1 TTAAAAATTATTAAAAT
57474429 AGAGTTTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATTATTAAAAT
Found at i:57478742 original size:27 final size:25
Alignment explanation
Indices: 57478691--57478738 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
57478681 AATGTACGTA
57478691 TTTTTGAAATATTAATGGTATATTT
1 TTTTTGAAATATTAATGGTATATTT
57478716 TTTTGTGAAA-ATTAATGGTATAT
1 TTTT-TGAAATATTAATGGTATAT
57478739 ATTTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (25 bp):
TTTTTGAAATATTAATGGTATATTT
Found at i:57478753 original size:27 final size:25
Alignment explanation
Indices: 57478695--57478747 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
57478685 TACGTATTTT
**
57478695 TGAAATATTAATGGTATATTTTTTTG
1 TGAAA-ATTAATGGTATATTTTAATG
57478721 TGAAAATTAATGGTATATATTTAATG
1 TGAAAATTAATGGTATAT-TTTAATG
57478747 T
1 T
57478748 ATAAAAGCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (25 bp):
TGAAAATTAATGGTATATTTTAATG
Found at i:57483284 original size:24 final size:24
Alignment explanation
Indices: 57483257--57483373 Score: 82
Period size: 24 Copynumber: 4.7 Consensus size: 24
57483247 AAGGAGAGGG
57483257 AAAGAAGAAGAAAGAAAGAAAGAA
1 AAAGAAGAAGAAAGAAAGAAAGAA
*
57483281 AAAGAAAGAAAATGAAAGGAGAGGAAAGAA
1 AAAG-AAG--AA-GAAA-GA-AAGAAAGAA
* *
57483311 AAA-AAAAAGAAGGAAAGAAAAGGAA
1 AAAGAAGAAGAAAGAAAG-AAA-GAA
*
57483336 AGGAGAAGAAGAAA-AAAGAAAGAA
1 A-AAGAAGAAGAAAGAAAGAAAGAA
57483360 AAA-AAG--GAAAGAAA
1 AAAGAAGAAGAAAGAAA
57483374 AGGAAAGGAG
Statistics
Matches: 74, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
20 4 0.05
21 3 0.04
22 3 0.04
23 3 0.04
24 13 0.18
25 13 0.18
26 7 0.09
27 9 0.12
28 6 0.08
29 2 0.03
30 11 0.15
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (24 bp):
AAAGAAGAAGAAAGAAAGAAAGAA
Found at i:57483308 original size:34 final size:34
Alignment explanation
Indices: 57483257--57483380 Score: 109
Period size: 34 Copynumber: 3.7 Consensus size: 34
57483247 AAGGAGAGGG
57483257 AAAGAAGAA-GAAA-GAAAGAAAGAAAAAGAAAGA
1 AAAGAA-AAGGAAAGGAAAGAAAGAAAAAGAAAGA
* * *
57483290 AAATG-AAAGGAGAGGAAAGAAA-AAAAAAAGAAGG
1 AAA-GAAAAGGAAAGGAAAGAAAGAAAAAGA-AAGA
57483324 AAAGAAAAGGAAAGGAGAAG-AAGAAAAAAGAAAG-
1 AAAGAAAAGGAAAGGA-AAGAAAG-AAAAAGAAAGA
*
57483358 AAA-AAAAGGAAAGAAAAGGAAAG
1 AAAGAAAAGGAAAGGAAA-GAAAG
57483381 GAGAAGAGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
32 4 0.05
33 26 0.35
34 33 0.44
35 6 0.08
36 6 0.08
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (34 bp):
AAAGAAAAGGAAAGGAAAGAAAGAAAAAGAAAGA
Found at i:57483367 original size:43 final size:43
Alignment explanation
Indices: 57483258--57483387 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 43
57483248 AGGAGAGGGA
* * *
57483258 AAGAAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAATGAAAGGAG
1 AAGAAGAAAAAAGAAAGAAA-AAAAGGAAAGAAAAGGAAAGGAG
*
57483302 -AG--GAAAGAAA-AAA-AAAAGAAGGAAAGAAAAGGAAAGGAG
1 AAGAAGAAA-AAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAG
57483341 AAGAAGAAAAAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAG
1 AAGAAGAAAAAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAG
57483384 AAGA
1 AAGA
57483388 GGGGAGGAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
39 20 0.27
40 5 0.07
41 9 0.12
42 10 0.13
43 31 0.41
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (43 bp):
AAGAAGAAAAAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAG
Found at i:57483374 original size:10 final size:10
Alignment explanation
Indices: 57483255--57483380 Score: 84
Period size: 10 Copynumber: 12.6 Consensus size: 10
57483245 AGAAGGAGAG
57483255 GGAAAGAAGAA
1 GGAAAGAA-AA
57483266 -GAAAG-AAA
1 GGAAAGAAAA
57483274 -GAAAGAAAA
1 GGAAAGAAAA
*
57483283 AGAAAGAAAA
1 GGAAAGAAAA
* * *
57483293 TGAAAGGAGA
1 GGAAAGAAAA
57483303 GGAAAGAAAA
1 GGAAAGAAAA
*
57483313 --AAAAAAGAA
1 GGAAAGAA-AA
57483322 GGAAAGAAAA
1 GGAAAGAAAA
57483332 GGAAAGGAGAAGA
1 GGAAA-GA-AA-A
* *
57483345 AGAAAAAAGAA
1 GGAAAGAA-AA
*
57483356 AGAAA-AAAA
1 GGAAAGAAAA
57483365 GGAAAGAAAA
1 GGAAAGAAAA
57483375 GGAAAG
1 GGAAAG
57483381 GAGAAGAGGG
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
8 12 0.13
9 12 0.13
10 47 0.50
11 14 0.15
12 4 0.04
13 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (10 bp):
GGAAAGAAAA
Found at i:57483701 original size:30 final size:30
Alignment explanation
Indices: 57483667--57483730 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
57483657 ATATGTTTAA
57483667 GAAAACATAAAATACAAAAAGAAAAAAACG
1 GAAAACATAAAATACAAAAAGAAAAAAACG
57483697 GAAAACATAAAATACAAAAAGAAAAAAACG
1 GAAAACATAAAATACAAAAAGAAAAAAACG
57483727 GAAA
1 GAAA
57483731 TTGTATATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.73, C:0.09, G:0.11, T:0.06
Consensus pattern (30 bp):
GAAAACATAAAATACAAAAAGAAAAAAACG
Found at i:57483972 original size:8 final size:8
Alignment explanation
Indices: 57483959--57483997 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
57483949 CTGAAATAAT
57483959 ATAAAATA
1 ATAAAATA
57483967 ATAAAATA
1 ATAAAATA
**
57483975 CGAAAATA
1 ATAAAATA
*
57483983 ATAAAATT
1 ATAAAATA
57483991 ATAAAAT
1 ATAAAAT
57483998 TAGAAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (8 bp):
ATAAAATA
Found at i:57483996 original size:16 final size:15
Alignment explanation
Indices: 57483956--57483997 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
57483946 GTACTGAAAT
57483956 AATATAAAATAATAA
1 AATATAAAATAATAA
*
57483971 AATACGAAAATAATAA
1 AATA-TAAAATAATAA
57483987 AATTATAAAAT
1 AA-TATAAAAT
57483998 TAGAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.74
17 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:57484118 original size:182 final size:182
Alignment explanation
Indices: 57483811--57484167 Score: 597
Period size: 182 Copynumber: 2.0 Consensus size: 182
57483801 GAAATAAAGA
* * *
57483811 AAAATTATAAAATATTAAATTTTTTAAAATAATAAAATGCGAAGAAAAAAATATGAAGAAATGGC
1 AAAATTAGAAAATATGAAATTTTTTAAAATAATAAAATGCGAAGAAAAAAATACGAAGAAATGGC
* * *
57483876 TGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTTAGAAATAATTAATACAAATATTTCAAAC
66 CGAAGTAAAAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAAC
*
57483941 AAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATAAAATTAT
131 AAAATGTACTGAAATAATACAAAATAATAAAATACGAAAATAATAAAATTAT
* * * * * *
57483993 AAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGTGGAGAAAAAAATACGAATAAATGGC
1 AAAATTAGAAAATATGAAATTTTTTAAAATAATAAAATGCGAAGAAAAAAATACGAAGAAATGGC
57484058 CGAAGTAAAAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAAC
66 CGAAGTAAAAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAAC
57484123 AAAATGTACTGAAATAATACAAAATAATAAAATACGAAAATAATA
131 AAAATGTACTGAAATAATACAAAATAATAAAATACGAAAATAATA
57484168 TTTTTTATTG
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 162 1.00
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (182 bp):
AAAATTAGAAAATATGAAATTTTTTAAAATAATAAAATGCGAAGAAAAAAATACGAAGAAATGGC
CGAAGTAAAAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAAC
AAAATGTACTGAAATAATACAAAATAATAAAATACGAAAATAATAAAATTAT
Found at i:57484164 original size:16 final size:15
Alignment explanation
Indices: 57484138--57484167 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
57484128 GTACTGAAAT
57484138 AATACAAAATAATAA
1 AATACAAAATAATAA
57484153 AATACGAAAATAATA
1 AATAC-AAAATAATA
57484168 TTTTTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (15 bp):
AATACAAAATAATAA
Found at i:57487116 original size:27 final size:27
Alignment explanation
Indices: 57487078--57487202 Score: 171
Period size: 27 Copynumber: 4.6 Consensus size: 27
57487068 ATAACACGAG
*
57487078 TGGTACCGCCTATGGGAAAGGCACCTT
1 TGGTGCCGCCTATGGGAAAGGCACCTT
*
57487105 TGGTGCCGCCTATAGGAAAGGCACCTT
1 TGGTGCCGCCTATGGGAAAGGCACCTT
* *
57487132 TGGTGCCGCCCAT-GGAAATGGCACCAT
1 TGGTGCCGCCTATGGGAAA-GGCACCTT
* *
57487159 CGGTGCCGCCTATGGGAAAGGCACATT
1 TGGTGCCGCCTATGGGAAAGGCACCTT
*
57487186 TGGTGCCGCTTATGGGA
1 TGGTGCCGCCTATGGGA
57487203 TACCCTCCAC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
26 5 0.06
27 76 0.88
28 5 0.06
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCTATGGGAAAGGCACCTT
Found at i:57488103 original size:13 final size:14
Alignment explanation
Indices: 57488085--57488115 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
57488075 TGGTATGAGT
57488085 TTATA-GGTTTTGG
1 TTATAGGGTTTTGG
57488098 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
57488112 TTAT
1 TTAT
57488116 GGGCAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:57488274 original size:24 final size:25
Alignment explanation
Indices: 57488247--57488294 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
57488237 AGAGGAAAGT
57488247 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
57488271 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
57488295 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:57495960 original size:25 final size:25
Alignment explanation
Indices: 57495932--57495982 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
57495922 CACTATAAGA
57495932 AGTCATTCAACAAAAGTTACATACT
1 AGTCATTCAACAAAAGTTACATACT
57495957 AGTCATTCAACAAAAGTTACATACT
1 AGTCATTCAACAAAAGTTACATACT
57495982 A
1 A
57495983 TTTCTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
AGTCATTCAACAAAAGTTACATACT
Found at i:57498032 original size:153 final size:152
Alignment explanation
Indices: 57497769--57498136 Score: 494
Period size: 153 Copynumber: 2.4 Consensus size: 152
57497759 ATATTCCACC
* * * *
57497769 TGATATTTCTGGTCTATCCTCTTTGCTA-TC-TCTTGATCTTAGTGGTAATAATTTCATCAGCAT
1 TGATATTTCTGGTCTATCCTCTTTG--AGTCATCTTAATCTTAATGGTAACAATTTCATCAGCAA
* *
57497832 ACCTGCATCTCTTACTCAACTCTCGAAGCTTGAAAATCTTTATTTGTCAAATTGCAACATGTGCA
64 ACCTGCATCTCTTACTCAACTCTCAAAGCTT-AAAATCTTTAATTGTCAAATTGCAACATGTGCA
* * *
57497897 CTTTTGGTGAAGCAGATACTCATCG
128 CTCTTGGTGAAGCAGATACTAATAG
*
57497922 TGATATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTAATGGTAACAATTTCATCAGTAAAC
1 TGATATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTAATGGTAACAATTTCATCAGCAAAC
* *
57497987 CTGCATCTCTTACTCGACTCTCAAAGCTT-AAGTCTCTTGAATTGTCAAATTGCAACATGTGCAC
66 CTGCATCTCTTACTCAACTCTCAAAGCTTAAAATCT-TT-AATTGTCAAATTGCAACATGTGCAC
57498051 TCTTGGTGAAGCAGATACTAATAG
129 TCTTGGTGAAGCAGATACTAATAG
* * * *
57498075 TGACATTTCTGGTCTATCCTCTTTGAGTTATCTTTATCTT--TGTTATATCAATTTCATCAGCA
1 TGATATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTAATGGTA-A-CAATTTCATCAGCA
57498137 TTCCTTCGGC
Statistics
Matches: 192, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
151 10 0.05
152 5 0.03
153 177 0.92
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (152 bp):
TGATATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTAATGGTAACAATTTCATCAGCAAAC
CTGCATCTCTTACTCAACTCTCAAAGCTTAAAATCTTTAATTGTCAAATTGCAACATGTGCACTC
TTGGTGAAGCAGATACTAATAG
Found at i:57498194 original size:153 final size:152
Alignment explanation
Indices: 57497773--57498186 Score: 444
Period size: 153 Copynumber: 2.7 Consensus size: 152
57497763 TCCACCTGAT
* * *
57497773 ATTTCTGGTCTATCCTCTTTGCTA-TC-TCTTGATCTTAGTGGTAATAATTTCATCAGCATACCT
1 ATTTCTGGTCTATCCTCTTTG--AGTCATCTTAATCTTA-TGGTAACAATTTCATCAGCAAACCT
* * * * *
57497836 GCATCTCTTACTCAACTCTCGAAGCTTGAAAATCT-TT-ATTTGTCAAATTGCAACATGTGCACT
63 GCAGCTCTGACTCAACTCTCAAAGC-T-CAAATCTCTTAAATTGTCAAATTGCAACATGTGCACT
* * * *
57497899 TTTGGTGAAGCAGATACTCATCGTGAT
126 CTTGGTGAAGCAGATACTAATAGTGAC
*
57497926 ATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTAATGGTAACAATTTCATCAGTAAACCTGC
1 ATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTT-ATGGTAACAATTTCATCAGCAAACCTGC
* * * * * *
57497991 ATCTCTTACTCGACTCTCAAAGCTTAAGTCTCTTGAATTGTCAAATTGCAACATGTGCACTCTTG
65 AGCTCTGACTCAACTCTCAAAGCTCAAATCTCTTAAATTGTCAAATTGCAACATGTGCACTCTTG
57498056 GTGAAGCAGATACTAATAGTGAC
130 GTGAAGCAGATACTAATAGTGAC
* * * ** *
57498079 ATTTCTGGTCTATCCTCTTTGAGTTATCTTTATCTT-TGTTATATCAATTTCATCAGCATTCCTT
1 ATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTATGGTA-A-CAATTTCATCAGCAAACCTG
* * * *
57498143 CGGCTCTGACTCAACTTTCCAGGCTCAAAT-TGCTTAAATTGTCA
64 CAGCTCTGACTCAACTCTCAAAGCTCAAATCT-CTTAAATTGTCA
57498187 GGTTGCAAGA
Statistics
Matches: 223, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
151 10 0.04
152 7 0.03
153 205 0.92
154 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (152 bp):
ATTTCTGGTCTATCCTCTTTGAGTCATCTTAATCTTATGGTAACAATTTCATCAGCAAACCTGCA
GCTCTGACTCAACTCTCAAAGCTCAAATCTCTTAAATTGTCAAATTGCAACATGTGCACTCTTGG
TGAAGCAGATACTAATAGTGAC
Found at i:57499732 original size:27 final size:25
Alignment explanation
Indices: 57499681--57499728 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
57499671 AATGTATGTA
57499681 TTTTTGAAATATTAATGGTATATTT
1 TTTTTGAAATATTAATGGTATATTT
57499706 TTTTGTGAAA-ATTAATGGTATAT
1 TTTT-TGAAATATTAATGGTATAT
57499729 ATTTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (25 bp):
TTTTTGAAATATTAATGGTATATTT
Found at i:57501451 original size:153 final size:153
Alignment explanation
Indices: 57501184--57501544 Score: 521
Period size: 153 Copynumber: 2.4 Consensus size: 153
57501174 GATATTCCAC
* * * *
57501184 GTGATATTTCTGGTCTATCCTGTTTG-GAAAAACTTGATCTTAGTGGTAACAATTTCATCAGCAT
1 GTGACATTTCTGGTCTATCCTCTTTGAG-ATATCTTGATCTTAGTGGTAACAATTTCATCAGCAT
*
57501248 ACCTGCATCTCTTACTCGACTCTCGAAGCTTGAAAATCTGACATTGTCAAATTGCAACATGTGCA
65 ACCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTGACATTGTCAAATTGCAACATGTGCA
*
57501313 CTTTTGGTGAAGCAGATACTCATA
130 CTCTTGGTGAAGCAGATACTCATA
*
57501337 GTGACATTTCTGGTCTATCCTCTTTGAGTTATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
1 GTGACATTTCTGGTCTATCCTCTTTGAGATATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
* *** * * *
57501402 CCTGCATCTCTTACTCGACTCTCAAAGCTTTATGTTCTTGTC-TTTTCAAATTGCAACGTGTGCA
66 CCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATC-TGACATTGTCAAATTGCAACATGTGCA
*
57501466 CTCTTGGTGAAGCAGATATTCATA
130 CTCTTGGTGAAGCAGATACTCATA
* *
57501490 GTGATC-TTTCTGGTCTATCCTCTTTGAGATATCTTTATCTTAGTGGTAAGAATTT
1 GTGA-CATTTCTGGTCTATCCTCTTTGAGATATCTTGATCTTAGTGGTAACAATTT
57501545 GTTCATTGTT
Statistics
Matches: 187, Mismatches: 18, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
153 182 0.97
154 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (153 bp):
GTGACATTTCTGGTCTATCCTCTTTGAGATATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
CCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTGACATTGTCAAATTGCAACATGTGCAC
TCTTGGTGAAGCAGATACTCATA
Found at i:57502776 original size:5 final size:5
Alignment explanation
Indices: 57502766--57502791 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57502756 TGAGTATTCG
57502766 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
57502792 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:57503450 original size:15 final size:17
Alignment explanation
Indices: 57503424--57503455 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57503414 GGGGAAAATA
57503424 AAAAGTTTTGAG-GAAT
1 AAAAGTTTTGAGCGAAT
57503440 AAAAG-TTTGAGCGAAT
1 AAAAGTTTTGAGCGAAT
57503456 GTAAATAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (17 bp):
AAAAGTTTTGAGCGAAT
Found at i:57503576 original size:31 final size:30
Alignment explanation
Indices: 57503541--57503600 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
57503531 GGAGGTGGGA
* *
57503541 TGGGAAGGAAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGGAAATAAAAATTTTAGGAGAAAAG
* *
57503572 TGGGAGGGAGTAAAAATTTTAGGAGAAAA
1 TGGGAGGAAATAAAAATTTTAGGAGAAAA
57503601 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (30 bp):
TGGGAGGAAATAAAAATTTTAGGAGAAAAG
Found at i:57518676 original size:24 final size:25
Alignment explanation
Indices: 57518649--57518708 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
57518639 AAAGAGAAAT
* *
57518649 GTATGTATTTTTGA-AATATTAATG
1 GTATATATTTTTGAGAAAATTAATG
*
57518673 GTATATTTTTTTTGAGAAAATTAATG
1 GTATA-TATTTTTGAGAAAATTAATG
57518699 GTATATATTT
1 GTATATATTT
57518709 AATGTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 12 0.40
26 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (25 bp):
GTATATATTTTTGAGAAAATTAATG
Found at i:57518708 original size:28 final size:25
Alignment explanation
Indices: 57518656--57518704 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
57518646 AATGTATGTA
*
57518656 TTTTTGAAATATTAATGGTATATTT
1 TTTTTGAAAAATTAATGGTATATTT
57518681 TTTTTGAGAAAATTAATGGTATAT
1 TTTTTGA-AAAATTAATGGTATAT
57518705 ATTTAATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (25 bp):
TTTTTGAAAAATTAATGGTATATTT
Found at i:57520442 original size:153 final size:153
Alignment explanation
Indices: 57520156--57520471 Score: 444
Period size: 153 Copynumber: 2.1 Consensus size: 153
57520146 AGATATTCCA
57520156 TCATCAGCATACCTGCATCTCTTACTCGACTCTCGAAGATTGCAAATCTTATATTGTCAAATTGC
1 TCATCAGCATACCTGCATCTCTTACTCGACTCTCGAAGATTGCAAATCTTATATTGTCAAATTGC
* * *
57520221 AACATGTGCACTTTTGGTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCTTTGAGTTA
66 AACATGTGCACTCTTGGTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCCTTGAGTCA
* *
57520286 TCTTAATGTTAGTGGTAACAATT
131 TCTTAATCTTAGTGGTAACAAGT
* *
57520309 TCATCAGCATACCTGCATCTCTTACTCGACTCTC-AATGCTT-CATGAA-CTTGA-CTTGTCAAA
1 TCATCAGCATACCTGCATCTCTTACTCGACTCTCGAA-GATTGCA--AATCTT-ATATTGTCAAA
* * * *
57520370 TTGCAACGTGTGCACTCTTGGTGTAGCAGATATTCATAGTGATCTTTCTGGTCTATCCTCCTTGA
62 TTGCAACATGTGCACTCTTGGTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCCTTGA
*
57520435 -TACATCTTGATCTTAGTGGTAACAAGT
127 GT-CATCTTAATCTTAGTGGTAACAAGT
57520462 TCATCAGCAT
1 TCATCAGCAT
57520472 TCCTTTGGCT
Statistics
Matches: 146, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
152 5 0.03
153 138 0.95
154 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (153 bp):
TCATCAGCATACCTGCATCTCTTACTCGACTCTCGAAGATTGCAAATCTTATATTGTCAAATTGC
AACATGTGCACTCTTGGTGAAGCAGATACTCATAGTGATATTTCTGGTCTATCCTCCTTGAGTCA
TCTTAATCTTAGTGGTAACAAGT
Found at i:57528950 original size:9 final size:9
Alignment explanation
Indices: 57528936--57528963 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57528926 TGAGTTTTCG
57528936 AATTCGAAT
1 AATTCGAAT
57528945 AATTCGAAT
1 AATTCGAAT
57528954 AATTCGAAT
1 AATTCGAAT
57528963 A
1 A
57528964 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57529212 original size:30 final size:31
Alignment explanation
Indices: 57529176--57529235 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
57529166 AAACCTTTTA
*
57529176 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
57529206 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
57529236 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:57529479 original size:17 final size:17
Alignment explanation
Indices: 57529459--57529541 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
57529449 ATTTATATCT
57529459 ATTATTTATATTATTAA
1 ATTATTTATATTATTAA
* *
57529476 ATTAAATTTCACATT-TTAT
1 ATT--ATTT-ATATTATTAA
*
57529495 ATTATTTATATTATTGA
1 ATTATTTATATTATTAA
*
57529512 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTAA
57529530 A-TATTTATATTA
1 ATTATTTATATTA
57529542 AAATTGAGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 23 0.43
18 8 0.15
19 11 0.20
20 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTAA
Found at i:57532886 original size:14 final size:14
Alignment explanation
Indices: 57532858--57532891 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
57532848 ATAGAACTAG
57532858 AGAAAA-AAAGAAA
1 AGAAAAGAAAGAAA
*
57532871 AGAAAAGAAAGCAA
1 AGAAAAGAAAGAAA
57532885 AGAAAAG
1 AGAAAAG
57532892 TGAAGAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAGAAA
Found at i:57536690 original size:12 final size:13
Alignment explanation
Indices: 57536675--57536703 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
57536665 TGTAATGTTA
57536675 TTATATAATT-TG
1 TTATATAATTATG
57536687 TTATATAATTATG
1 TTATATAATTATG
57536700 TTAT
1 TTAT
57536704 TATACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TTATATAATTATG
Found at i:57536846 original size:47 final size:47
Alignment explanation
Indices: 57536777--57536875 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
57536767 TAATAAAAAC
57536777 TTTTAAATAGGTATAATGACAAAAAAATGTTCTTAGCATTTATAAGA
1 TTTTAAATAGGTATAATGACAAAAAAATGTTCTTAGCATTTATAAGA
57536824 TTTTAAATAGGTATAATGACAAAAAAATGTTCTTAGCATTTATAAGA
1 TTTTAAATAGGTATAATGACAAAAAAATGTTCTTAGCATTTATAAGA
57536871 TTTTA
1 TTTTA
57536876 TTTTGAGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (47 bp):
TTTTAAATAGGTATAATGACAAAAAAATGTTCTTAGCATTTATAAGA
Found at i:57540817 original size:42 final size:42
Alignment explanation
Indices: 57540756--57540837 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
57540746 TGTCCCTAAA
* * *
57540756 TTTCCTTTTGTCTTTAATTTAGTCCCTACAAGATGAAAAACC
1 TTTCCTTTTATCTTCAATTTAGTCCCTACAAGACGAAAAACC
57540798 TTTCCTTTTATCTTCAATTTAGTCCCTACAAGACGAAAAA
1 TTTCCTTTTATCTTCAATTTAGTCCCTACAAGACGAAAAA
57540838 TCATAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (42 bp):
TTTCCTTTTATCTTCAATTTAGTCCCTACAAGACGAAAAACC
Found at i:57541125 original size:25 final size:25
Alignment explanation
Indices: 57541091--57541141 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
57541081 ATCTATGTAA
57541091 ACTTATTTGCTTATGAGATATAATC
1 ACTTATTTGCTTATGAGATATAATC
57541116 ACTTATTTGCTTATGAGATATAATC
1 ACTTATTTGCTTATGAGATATAATC
57541141 A
1 A
57541142 TTCTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (25 bp):
ACTTATTTGCTTATGAGATATAATC
Found at i:57552787 original size:44 final size:44
Alignment explanation
Indices: 57552704--57552790 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
57552694 AAGCCTTACT
* * * * *
57552704 TCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTATTAATCCTATC
1 TCCCGGAAGTTGCAGTGGAGCAGACTAAAACGATGAATCCTATC
* *
57552748 TCCCGGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTAT
1 TCCCGGAAGTTGCAGTGGAGCAGACTAAAACGATGAATCCTAT
57552791 ACCTTTAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
TCCCGGAAGTTGCAGTGGAGCAGACTAAAACGATGAATCCTATC
Found at i:57554027 original size:36 final size:36
Alignment explanation
Indices: 57553980--57554062 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
57553970 TACTTATACA
57553980 ACGTCGTTTTGACATTAGGGGGCAGGTGCCAAAACG
1 ACGTCGTTTTGACATTAGGGGGCAGGTGCCAAAACG
57554016 ACGTCGTTTTGACATTAGGGGGCAGGTGCCAAAACG
1 ACGTCGTTTTGACATTAGGGGGCAGGTGCCAAAACG
57554052 ACGTCGTTTTG
1 ACGTCGTTTTG
57554063 GCCCTGACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (36 bp):
ACGTCGTTTTGACATTAGGGGGCAGGTGCCAAAACG
Found at i:57562610 original size:43 final size:43
Alignment explanation
Indices: 57562555--57562689 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 43
57562545 TGCTGGAAAA
*
57562555 CTTTA-CGGCGCTTTTAGTGA-AAAAGCCACTATAATTCTTGAC
1 CTTTAGCGGCGCTTTTA-TGACAAAAGCCACTATAAGTCTTGAC
* * * * *
57562597 CTTTAGCGACGC-TTTATTACAAATGCCGCTATAAGTCTTGGC
1 CTTTAGCGGCGCTTTTATGACAAAAGCCACTATAAGTCTTGAC
* * * * * *
57562639 CTTTAGCGGCGCTTTTTTTACAAACGCCGCTAGAAGTCTTGGC
1 CTTTAGCGGCGCTTTTATGACAAAAGCCACTATAAGTCTTGAC
57562682 CTTTAGCG
1 CTTTAGCG
57562690 ACGTTTGACA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 38 0.47
43 40 0.50
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTATGACAAAAGCCACTATAAGTCTTGAC
Found at i:57562629 original size:42 final size:43
Alignment explanation
Indices: 57562583--57562692 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
57562573 GAAAAAGCCA
* * *
57562583 CTATAATTCTTGACCTTTAGCGACGC-TTTATTACAAATGCCG
1 CTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAACGCCG
* *
57562625 CTATAAGTCTTGGCCTTTAGCGGCGCTTTTTTTACAAACGCCG
1 CTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAACGCCG
*
57562668 CTAGAAGTCTTGGCCTTTAGCGACG
1 CTATAAGTCTTGGCCTTTAGCGACG
57562693 TTTGACAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
42 23 0.38
43 37 0.62
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (43 bp):
CTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAACGCCG
Found at i:57563137 original size:21 final size:21
Alignment explanation
Indices: 57563113--57563171 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
57563103 ATTTTGCTCT
* * *
57563113 GCCTCCCTCGTTGTTGCCGTC
1 GCCTCCCTCGCTGCTGCCGCC
*
57563134 GCCTCCCTCACTGCTGCCGCC
1 GCCTCCCTCGCTGCTGCCGCC
57563155 GCCTCCCTCGCTGCTGC
1 GCCTCCCTCGCTGCTGC
57563172 ATCTGCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.02, C:0.51, G:0.22, T:0.25
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCGCC
Found at i:57563578 original size:13 final size:14
Alignment explanation
Indices: 57563552--57563580 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
57563542 ACTAACGACG
57563552 AATTAAACCATTAT
1 AATTAAACCATTAT
57563566 AATTAAA-CATTAT
1 AATTAAACCATTAT
57563579 AA
1 AA
57563581 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:57563603 original size:17 final size:19
Alignment explanation
Indices: 57563577--57563615 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
57563567 ATTAAACATT
*
57563577 ATAAATATTTA-TAA-TAA
1 ATAAAAATTTATTAAGTAA
57563594 ATAAAAATTTATTAAGTAA
1 ATAAAAATTTATTAAGTAA
57563613 ATA
1 ATA
57563616 TACCATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAAAATTTATTAAGTAA
Found at i:57572428 original size:42 final size:43
Alignment explanation
Indices: 57572382--57572495 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
57572372 TAGTGAAAAA
* *
57572382 GCCGCTATAATTCTTGGCCTTTAGCGACGC-TTTATTACAAAT
1 GCCGCTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAAC
* * *
57572424 GCCGCTATAAGTCTTGGCATTTAGCGGCGCTTTTTTTACAAAC
1 GCCGCTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAAC
*
57572467 GCCGCTAGAAGTCTTGGCCTTTAGCGACG
1 GCCGCTATAAGTCTTGGCCTTTAGCGACG
57572496 TTTGACAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 27 0.43
43 36 0.57
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (43 bp):
GCCGCTATAAGTCTTGGCCTTTAGCGACGCTTTTATTACAAAC
Found at i:57573426 original size:13 final size:14
Alignment explanation
Indices: 57573400--57573428 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
57573390 ACTAACGACG
57573400 AATTAAACCATTAT
1 AATTAAACCATTAT
57573414 AATTAAA-CATTAT
1 AATTAAACCATTAT
57573427 AA
1 AA
57573429 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:57573451 original size:17 final size:19
Alignment explanation
Indices: 57573425--57573463 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
57573415 ATTAAACATT
*
57573425 ATAAATATTTA-TAA-TAA
1 ATAAAAATTTATTAAGTAA
57573442 ATAAAAATTTATTAAGTAA
1 ATAAAAATTTATTAAGTAA
57573461 ATA
1 ATA
57573464 TACCATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAAAATTTATTAAGTAA
Found at i:57576369 original size:16 final size:16
Alignment explanation
Indices: 57576363--57576568 Score: 182
Period size: 16 Copynumber: 13.1 Consensus size: 16
57576353 TATTATGTAA
57576363 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
57576379 ATTATGTGAGTTATGT
1 ATTATGTAAGTTATGT
*
57576395 AAGTTGTGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
*
57576411 AAGTTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
* *
57576429 ATTATGTAAGCTGTGT
1 ATTATGTAAGTTATGT
*
57576445 ATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
57576461 ATTATG-AA---A-G-
1 ATTATGTAAGTTATGT
*
57576471 -TTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
57576486 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
57576502 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
57576518 AAGTTGTGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
*
57576534 AAGTTATATAAGTTATGT
1 -A-TTATGTAAGTTATGT
57576552 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
57576568 A
1 A
57576569 AGTTGTGTAT
Statistics
Matches: 162, Mismatches: 13, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.03
10 2 0.01
11 1 0.01
14 1 0.01
15 2 0.01
16 122 0.75
17 8 0.05
18 21 0.13
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:57576376 original size:25 final size:25
Alignment explanation
Indices: 57576348--57576580 Score: 280
Period size: 25 Copynumber: 9.4 Consensus size: 25
57576338 TGATATAAAT
*
57576348 TTATGTATTATGTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
57576373 TTATGTATTATGTGAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
57576398 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* * *
57576423 TTGTGTATTATGTAAGCTGTGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
* *
57576446 TTATGTAAGTTGTGT-A-TTATGAAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
57576471 TTATGTAAGTTGTGT-A-TTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
57576496 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
57576521 TTGTGTATTATGTAAGTTATATAAG
1 TTATGTATTATGTAAGTTATGTAAG
57576546 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
57576571 TTGTGTATTA
1 TTATGTATTA
57576581 CGTATGTTGA
Statistics
Matches: 184, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
23 13 0.07
24 6 0.03
25 165 0.90
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:57576394 original size:41 final size:41
Alignment explanation
Indices: 57576363--57576568 Score: 235
Period size: 41 Copynumber: 5.0 Consensus size: 41
57576353 TATTATGTAA
*
57576363 ATTATGTAAGTTATGT-A-TTATGTGAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGT
* * *
57576404 ATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGCTGTGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGT
* * *
57576445 ATTATGTAAGTTGTGT-A-TTATGAAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATG-TA-TTATGTAAGTTATGT
*
57576486 ATTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTATGT
*
57576527 ATTATGTAAGTTATATAAGTTATGTATTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGT
57576568 A
1 A
57576569 AGTTGTGTAT
Statistics
Matches: 148, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
39 4 0.03
40 2 0.01
41 127 0.86
42 4 0.03
43 11 0.07
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (41 bp):
ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGT
Found at i:57577724 original size:26 final size:25
Alignment explanation
Indices: 57577685--57577736 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
57577675 ATGATATATA
*
57577685 TATATATAAGATAAAATAAATAATG
1 TATATAAAAGATAAAATAAATAATG
* *
57577710 TATATAAAAGTATAAGATAAGTAATG
1 TATATAAAAG-ATAAAATAAATAATG
57577736 T
1 T
57577737 GAAGGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (25 bp):
TATATAAAAGATAAAATAAATAATG
Found at i:57579385 original size:9 final size:9
Alignment explanation
Indices: 57579371--57579446 Score: 56
Period size: 9 Copynumber: 9.0 Consensus size: 9
57579361 GGACCAATTT
57579371 TGTAAGTTA
1 TGTAAGTTA
*
57579380 TGTAAGTTG
1 TGTAAGTTA
57579389 TGT-A-TTA
1 TGTAAGTTA
*
57579396 --TAGGGTTA
1 TGTA-AGTTA
57579404 TGTAAGTTA
1 TGTAAGTTA
*
57579413 TGTAAGTTG
1 TGTAAGTTA
*
57579422 TGT-A-TAA
1 TGTAAGTTA
*
57579429 TGTAAATTA
1 TGTAAGTTA
57579438 TGTAAGTTA
1 TGTAAGTTA
57579447 AGCATTATGA
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
5 1 0.02
7 6 0.12
8 6 0.12
9 36 0.71
10 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:57583071 original size:25 final size:26
Alignment explanation
Indices: 57583042--57583098 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
57583032 AAAAGAGAAA
*
57583042 TGTATATATTTTG-AAATATTAATGG
1 TGTATATATTTTGTAAAGATTAATGG
* *
57583067 TGTAT-TTTTTTGTGAAGATTAATGG
1 TGTATATATTTTGTAAAGATTAATGG
*
57583092 TATATAT
1 TGTATAT
57583099 TTAATGTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.23
25 19 0.73
26 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.51
Consensus pattern (26 bp):
TGTATATATTTTGTAAAGATTAATGG
Found at i:57587089 original size:53 final size:46
Alignment explanation
Indices: 57587008--57587322 Score: 347
Period size: 46 Copynumber: 6.6 Consensus size: 46
57586998 TGCGTATGAT
* *
57587008 CACTT-ATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTCATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
* * *
57587052 CACTTATCACTTTCCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CAC-T-TCA---T-CACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCTAC
57587105 CACTT-ATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA-GCTAC
* *
57587151 CACTTATCACTTTCCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CAC-T-TCA---T-CACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
57587204 CACTT-ATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTAC
1 CACTTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA-GCTAC
57587250 CAC-TCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTCATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
*
57587296 CACTT-ATCACTTTGTTACTTGATCAGA
1 CACTTCATCACTTTGTCACTTGATCAGA
57587323 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 10, Indels: 44
0.82 0.03 0.15
Matches are distributed among these distances:
44 3 0.01
45 7 0.03
46 135 0.57
47 7 0.03
48 1 0.00
49 1 0.00
50 3 0.01
51 5 0.02
52 8 0.03
53 65 0.27
54 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:57587137 original size:99 final size:99
Alignment explanation
Indices: 57587006--57587322 Score: 483
Period size: 99 Copynumber: 3.3 Consensus size: 99
57586996 CTTGCGTATG
* *
57587006 ATCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTGAA-GCTATCACTTATCACTTTCCA
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AACGCTACCACTTATCACTTTCCA
**
57587068 CTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCT
65 CTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCT
*
57587103 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTCCAC
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTACCACTTATCACTTTCCAC
57587168 TTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCT
66 TTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCT
57587202 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTACCAC---TCA---T-CAC
1 ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTACCACTTATCACTTTCCAC
*
57587260 TTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
66 TTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCT
* *
57587294 ACCACTTATCACTTTGTTACTTGATCAGA
1 ATCACTTATCACTTTGTCACTTGATCAGA
57587323 AGTACTCAAA
Statistics
Matches: 209, Mismatches: 8, Indels: 11
0.92 0.04 0.05
Matches are distributed among these distances:
92 63 0.30
93 1 0.00
96 3 0.01
97 12 0.06
98 7 0.03
99 123 0.59
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (99 bp):
ATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTACCACTTATCACTTTCCAC
TTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCT
Found at i:57588873 original size:18 final size:18
Alignment explanation
Indices: 57588850--57588886 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
57588840 ATTCAATTCT
57588850 TTCAATAAAATCAGCATA
1 TTCAATAAAATCAGCATA
57588868 TTCAATAAAATCAGCATA
1 TTCAATAAAATCAGCATA
57588886 T
1 T
57588887 GAACAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (18 bp):
TTCAATAAAATCAGCATA
Found at i:57591761 original size:26 final size:23
Alignment explanation
Indices: 57591713--57591772 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 23
57591703 GAAAAAGAAA
57591713 TTTAAAATCAACTATATACAAAACAAT
1 TTTAAAAT--ACTATATAC-AAA-AAT
* *
57591740 TTTAGAAATACTATGTATAAAAAT
1 TTTA-AAATACTATATACAAAAAT
57591764 TTTAAAATA
1 TTTAAAATA
57591773 AATAATATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 5 0.17
24 7 0.23
25 3 0.10
26 7 0.23
27 4 0.13
28 4 0.13
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (23 bp):
TTTAAAATACTATATACAAAAAT
Found at i:57594565 original size:30 final size:29
Alignment explanation
Indices: 57594521--57594604 Score: 123
Period size: 31 Copynumber: 2.8 Consensus size: 29
57594511 ATATAATAAA
*
57594521 AATTTTTTTTATTTTTTTATTTTTAAAAT
1 AATTTTTTTAATTTTTTTATTTTTAAAAT
57594550 AATTTTTTTAAATTTTTTTTATTTTTAAAAT
1 AATTTTTTT-AA-TTTTTTTATTTTTAAAAT
* *
57594581 ACTTTTTTTAATTTTTTAATTTTT
1 AATTTTTTTAATTTTTTTATTTTT
57594605 TTGGTGTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 21 0.42
30 3 0.06
31 26 0.52
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (29 bp):
AATTTTTTTAATTTTTTTATTTTTAAAAT
Found at i:57606714 original size:42 final size:42
Alignment explanation
Indices: 57606620--57606702 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
57606610 AAGCTCGAGC
** *
57606620 TCAAGTTCGA-TCTTGAGTATGAAAATTGATAAACAAGTTTAA
1 TCAAGTTCGAGT-TTGAGTACAAAAATTGATAAACAAGCTTAA
*
57606662 TCAAGTTCGAGTTTGAGTACAAAAATTGATAAATAAGCTTA
1 TCAAGTTCGAGTTTGAGTACAAAAATTGATAAACAAGCTTA
57606703 TTTGAATTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.33
Consensus pattern (42 bp):
TCAAGTTCGAGTTTGAGTACAAAAATTGATAAACAAGCTTAA
Found at i:57608111 original size:28 final size:28
Alignment explanation
Indices: 57608071--57608127 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
57608061 GGAAATAAAG
57608071 TAAGAATTAACTCATCATTTTAACTTAT
1 TAAGAATTAACTCATCATTTTAACTTAT
57608099 TAAGAATTAACTCATCATTTTAACTTAT
1 TAAGAATTAACTCATCATTTTAACTTAT
57608127 T
1 T
57608128 TTCATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.44
Consensus pattern (28 bp):
TAAGAATTAACTCATCATTTTAACTTAT
Found at i:57612987 original size:23 final size:23
Alignment explanation
Indices: 57612961--57613022 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
57612951 TCAAAAGAGA
*
57612961 AATGTATGTATTTT-TGAAATATT
1 AATGTATATATTTTGTGAAA-ATT
*
57612984 AATGGTATATTTTTTTGTGAAAATT
1 AAT-GTATA-TATTTTGTGAAAATT
57613009 AATGCTATATATTT
1 AATG-TATATATTT
57613023 AATGTACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 3 0.09
24 9 0.28
25 15 0.47
26 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (23 bp):
AATGTATATATTTTGTGAAAATT
Found at i:57612999 original size:25 final size:25
Alignment explanation
Indices: 57612971--57613018 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
57612961 AATGTATGTA
*
57612971 TTTT-TGAAATATTAATGGTATATTT
1 TTTTGTGAAA-ATTAATGCTATATTT
57612996 TTTTGTGAAAATTAATGCTATAT
1 TTTTGTGAAAATTAATGCTATAT
57613019 ATTTAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTTGTGAAAATTAATGCTATATTT
Found at i:57619845 original size:26 final size:22
Alignment explanation
Indices: 57619793--57619835 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
57619783 TTGGTTCTTT
57619793 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
57619815 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
57619836 ACTATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:57624532 original size:9 final size:9
Alignment explanation
Indices: 57624518--57624545 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57624508 TTTTGTTACA
57624518 ACAATTAAT
1 ACAATTAAT
57624527 ACAATTAAT
1 ACAATTAAT
57624536 ACAATTAAT
1 ACAATTAAT
57624545 A
1 A
57624546 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:57624567 original size:68 final size:66
Alignment explanation
Indices: 57624488--57624629 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
57624478 TCAAGTTTGT
*
57624488 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
57624553 AAA
64 AAA
57624556 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
57624621 T
66 A
57624622 TTTACTAA
1 TTTACTAA
57624630 CAATTAAATT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:57624648 original size:59 final size:66
Alignment explanation
Indices: 57624488--57624651 Score: 198
Period size: 68 Copynumber: 2.5 Consensus size: 66
57624478 TCAAGTTTGT
* *
57624488 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGAATTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
57624553 AAA
64 AAA
*
57624556 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGAATTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
57624619 AAT
64 AAA
*
57624622 TTTACTAA-C-AA-TTA-AATTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGAATTTATACAACAATTA
57624652 GTTTTAATTT
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
59 9 0.10
61 5 0.05
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.30
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGAATTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:57624657 original size:16 final size:16
Alignment explanation
Indices: 57624618--57624659 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
57624608 AATAATTTGA
*
57624618 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
57624634 TAAATTTAATAACAAT
1 TAATTTTAATAACAAT
*
57624650 TAGTTTTAAT
1 TAATTTTAAT
57624660 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:57624658 original size:22 final size:22
Alignment explanation
Indices: 57624633--57624687 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
57624623 TTACTAACAA
* * * *
57624633 TTAAATTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
57624655 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
57624677 TTAATTTTAAT
1 TTAATTTTAAT
57624688 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:57630921 original size:20 final size:20
Alignment explanation
Indices: 57630898--57630960 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
57630888 CAAAAAATAA
57630898 AAAATATATTTTTAAAAATT
1 AAAATATATTTTTAAAAATT
57630918 -AAA-ATA---TTAAAAATTT
1 AAAATATATTTTTAAAAA-TT
* *
57630934 AAAAAATATTTTTAAAATTT
1 AAAATATATTTTTAAAAATT
57630954 AAAATAT
1 AAAATAT
57630961 TAATTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 3 0.09
18 6 0.17
19 3 0.09
20 8 0.23
21 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATATTTTTAAAAATT
Found at i:57630943 original size:36 final size:37
Alignment explanation
Indices: 57630879--57630963 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 37
57630869 AATTTATTTT
57630879 TTAAAAT-TTCAAAAAATAAAAAATATATTTTTAAAAA
1 TTAAAATATT-AAAAAATAAAAAATATATTTTTAAAAA
* * *
57630916 TTAAAATATTAAAAATTTAAAAA-ATATTTTTAAAAT
1 TTAAAATATTAAAAAATAAAAAATATATTTTTAAAAA
57630952 TTAAAATATTAA
1 TTAAAATATTAA
57630964 TTAAATACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 24 0.55
37 18 0.41
38 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (37 bp):
TTAAAATATTAAAAAATAAAAAATATATTTTTAAAAA
Found at i:57630958 original size:18 final size:18
Alignment explanation
Indices: 57630903--57630961 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
57630893 AATAAAAAAT
*
57630903 ATATTTTTAAAAATTAAA
1 ATATTTTTAAAATTTAAA
*
57630921 ATA--TTAAAAATTTAAAAA
1 ATATTTTTAAAATTT--AAA
57630939 ATATTTTTAAAATTTAAA
1 ATATTTTTAAAATTTAAA
57630957 ATATT
1 ATATT
57630962 AATTAAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 8 0.24
18 17 0.50
20 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTTTAAAATTTAAA
Found at i:57630969 original size:18 final size:18
Alignment explanation
Indices: 57630916--57630969 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
57630906 TTTTTAAAAA
57630916 TTAAAATATTAA--AAAT
1 TTAAAATATTAATTAAAT
*
57630932 TTAAAAAATATT-TTTAAAAT
1 TT--AAAATATTAATT-AAAT
57630952 TTAAAATATTAATTAAAT
1 TTAAAATATTAATTAAAT
57630970 ACTAACATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 2 0.07
18 20 0.67
19 2 0.07
20 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATATTAATTAAAT
Found at i:57635971 original size:39 final size:39
Alignment explanation
Indices: 57635915--57635997 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
57635905 TCAAGGAAAA
*
57635915 GGTTTGATATTACTATGCCTGGAAGTGAAATCCCAGAAT
1 GGTTTGATATTACTATGCCCGGAAGTGAAATCCCAGAAT
* * *
57635954 GGTTTGATATTATTATGCCCGGAAGTGGAATCTCAGAAT
1 GGTTTGATATTACTATGCCCGGAAGTGAAATCCCAGAAT
57635993 GGTTT
1 GGTTT
57635998 AGCCAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (39 bp):
GGTTTGATATTACTATGCCCGGAAGTGAAATCCCAGAAT
Found at i:57637739 original size:33 final size:33
Alignment explanation
Indices: 57637697--57637760 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
57637687 GAAATCAAAA
57637697 ATTTTAATAGTTTATATATTTATAATTTTTATC
1 ATTTTAATAGTTTATATATTTATAATTTTTATC
57637730 ATTTTAATAGTTTATATATTTATAATTTTTA
1 ATTTTAATAGTTTATATATTTATAATTTTTA
57637761 AAAGATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (33 bp):
ATTTTAATAGTTTATATATTTATAATTTTTATC
Found at i:57638052 original size:15 final size:15
Alignment explanation
Indices: 57638026--57638063 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
57638016 TTATTTAATT
*
57638026 TTTTTTATATTTTTA
1 TTTTTTATATTTGTA
57638041 GTTTTTTA-ATTTGTA
1 -TTTTTTATATTTGTA
57638056 TTTTTTAT
1 TTTTTTAT
57638064 CAAATCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTTTATATTTGTA
Found at i:57644524 original size:2 final size:2
Alignment explanation
Indices: 57644519--57644543 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57644509 TTAATTTTAT
57644519 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 T
57644544 TAACTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57650607 original size:19 final size:19
Alignment explanation
Indices: 57650583--57650685 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
57650573 TTGCAGCACC
*
57650583 AATTTTTAAAAAAAACGAA
1 AATTTTTAAAAAACACGAA
* *
57650602 AATTTTT--GAAACATGAGA
1 AATTTTTAAAAAACACGA-A
* *
57650620 AATTTTTTTAAAAACACAAA
1 AA-TTTTTAAAAAACACGAA
*
57650640 AATTTTT--GAAACACGAA
1 AATTTTTAAAAAACACGAA
57650657 AA-TTTTAAAAAACACGAA
1 AATTTTTAAAAAACACGAA
57650675 AATTTTTAAAA
1 AATTTTTAAAA
57650686 CACAGCAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
16 4 0.06
17 16 0.24
18 14 0.21
19 25 0.37
20 3 0.04
21 6 0.09
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (19 bp):
AATTTTTAAAAAACACGAA
Found at i:57650622 original size:18 final size:16
Alignment explanation
Indices: 57650594--57650731 Score: 73
Period size: 17 Copynumber: 8.0 Consensus size: 16
57650584 ATTTTTAAAA
57650594 AAAAC-GAAAATTTTT
1 AAAACAGAAAATTTTT
*
57650609 GAAACATGAGAAATTTTTTT
1 AAAACA-GA-AAA--TTTTT
*
57650629 AAAAACACAAAAATTTTT
1 -AAAACA-GAAAATTTTT
* *
57650647 GAAACACGAAAATTTTAA
1 AAAACA-GAAAATTTT-T
57650665 AAAACACGAAAATTTTT
1 AAAACA-GAAAATTTTT
* *
57650682 AAAACACAGCAATTTTT
1 AAAACAGA-AAATTTTT
* *
57650699 GAAACACGATAATTTTT
1 AAAACA-GAAAATTTTT
*
57650716 CAAAACA-CAAATTTTT
1 -AAAACAGAAAATTTTT
57650732 TTAAAGAACA
Statistics
Matches: 96, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
15 4 0.04
16 8 0.08
17 41 0.43
18 29 0.30
20 8 0.08
21 6 0.06
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (16 bp):
AAAACAGAAAATTTTT
Found at i:57650696 original size:35 final size:35
Alignment explanation
Indices: 57650586--57650724 Score: 129
Period size: 35 Copynumber: 3.9 Consensus size: 35
57650576 CAGCACCAAT
* * *
57650586 TTTTAAAAAAAACGAAAATTTTTGAAACATGAGAAA
1 TTTTAAAAAACACGAAAATTTTTAAAACA-CAGAAA
* * *
57650622 TTTTTTTAAAAACACAAAAATTTTTGAAACAC-GAAAA
1 --TTTTAAAAAACACGAAAATTTTTAAAACACAG-AAA
*
57650659 TTTTAAAAAACACGAAAATTTTTAAAACACAGCAA
1 TTTTAAAAAACACGAAAATTTTTAAAACACAGAAA
** *
57650694 TTTT-TGAAACACGATAATTTTTCAAAACACA
1 TTTTAAAAAACACGAAAATTTTT-AAAACACA
57650725 AATTTTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
34 15 0.17
35 41 0.47
36 2 0.02
37 3 0.03
38 26 0.30
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (35 bp):
TTTTAAAAAACACGAAAATTTTTAAAACACAGAAA
Found at i:57650903 original size:35 final size:35
Alignment explanation
Indices: 57650631--57650984 Score: 165
Period size: 35 Copynumber: 10.2 Consensus size: 35
57650621 ATTTTTTTAA
* * **
57650631 AAACACAAAAATTTTTG-AAACACGAAAATTTTAAA
1 AAACACGAAAATTTTTGAAAACACGAAGATTTT-TG
*
57650666 AAACACGAAAATTTTT-AAAACACAGCA-ATTTTTG
1 AAACACGAAAATTTTTGAAAACAC-GAAGATTTTTG
* * * ** *
57650700 AAACACGATAATTTTTCAAAACACAAATTTTTTTAA
1 AAACACGAAAATTTTTGAAAACACGAAGATTTTT-G
* * * * **
57650736 AGAACATGACAATTTGTG-AAACAC-TAGAGTCATTG
1 A-AACACGAAAATTTTTGAAAACACGAAGA-TTTTTG
* * * * * *
57650771 AAAACACGGAAATTTGTGAAAAAACAAAAATTTATG
1 -AAACACGAAAATTTTTGAAAACACGAAGATTTTTG
*** *
57650807 AAACAC-AGAAATTTAAAAAAAAAC-ACAGATTTTTG
1 AAACACGA-AAATTTTTGAAAACACGA-AGATTTTTG
57650842 AAACACCG-AAATTTTTGAAAACACGAAGATTTTTG
1 AAACA-CGAAAATTTTTGAAAACACGAAGATTTTTG
* ** *
57650877 AAACACGAAAATTTTTGAAAATACGAATTTTTTTT
1 AAACACGAAAATTTTTGAAAACACGAAGATTTTTG
* **
57650912 AAATAC-AGAAATTTTT--AAACACGGGGATTTTTG
1 AAACACGA-AAATTTTTGAAAACACGAAGATTTTTG
* * ** ** *
57650945 AAACATG-GAATTTTTTTAAACGTGAAAATTTTTG
1 AAACACGAAAATTTTTGAAAACACGAAGATTTTTG
57650979 AAACAC
1 AAACAC
57650985 AATTTTTTTT
Statistics
Matches: 241, Mismatches: 58, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
32 7 0.03
33 15 0.06
34 37 0.15
35 145 0.60
36 23 0.10
37 14 0.06
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (35 bp):
AAACACGAAAATTTTTGAAAACACGAAGATTTTTG
Found at i:57650908 original size:17 final size:17
Alignment explanation
Indices: 57650624--57650927 Score: 142
Period size: 17 Copynumber: 17.3 Consensus size: 17
57650614 ATGAGAAATT
* *
57650624 TTTTTAAAAACACAAAAA
1 TTTTTGAAAACAC-GAAA
57650642 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
**
57650659 TTTTAAAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
57650677 TTTTT-AAAACACAGCAA
1 TTTTTGAAAACAC-GAAA
57650694 TTTTTG-AAACACGATAA
1 TTTTTGAAAACACGA-AA
*
57650711 TTTTTCAAAACAC-AAA
1 TTTTTGAAAACACGAAA
* *
57650727 TTTTTTTAAAGAACATGACAA
1 --TTTTTGAA-AACACGA-AA
* * *
57650748 TTTGTG-AAACACTAGAG
1 TTTTTGAAAACACGA-AA
**
57650765 TCATTGAAAACACGGAAA
1 TTTTTGAAAACAC-GAAA
* * *
57650783 TTTGTGAAAAAACAAAAA
1 TTTTTGAAAACAC-GAAA
*
57650801 TTTATG-AAACACAGAAA
1 TTTTTGAAAACAC-GAAA
*** *
57650818 TTTAAAAAAAAACAC-AGA
1 TTT--TTGAAAACACGAAA
57650836 TTTTTG-AAACACCGAAA
1 TTTTTGAAAACA-CGAAA
57650853 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
57650871 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
* *
57650888 TTTTTGAAAATACGAATT
1 TTTTTGAAAACACGAA-A
*
57650906 TTTTTTAAATACA-GAAA
1 TTTTTGAAA-ACACGAAA
57650923 TTTTT
1 TTTTT
57650928 AAACACGGGG
Statistics
Matches: 220, Mismatches: 42, Indels: 49
0.71 0.14 0.16
Matches are distributed among these distances:
15 5 0.02
16 4 0.02
17 95 0.43
18 95 0.43
19 12 0.05
20 7 0.03
21 2 0.01
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:57650959 original size:17 final size:17
Alignment explanation
Indices: 57650938--57650983 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
57650928 AAACACGGGG
*
57650938 ATTTTTGAAACATGGAA
1 ATTTTTGAAACATGAAA
* * *
57650955 TTTTTTTAAACGTGAAA
1 ATTTTTGAAACATGAAA
57650972 ATTTTTGAAACA
1 ATTTTTGAAACA
57650984 CAATTTTTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (17 bp):
ATTTTTGAAACATGAAA
Found at i:57651473 original size:8 final size:8
Alignment explanation
Indices: 57651460--57651495 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
57651450 AATTGAACCC
57651460 TTTTCTTT
1 TTTTCTTT
57651468 TTTTC-TT
1 TTTTCTTT
57651475 TTTTC--T
1 TTTTCTTT
57651481 TTTTCTTT
1 TTTTCTTT
57651489 TTTTCTT
1 TTTTCTT
57651496 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 7 0.27
8 13 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTCTTT
Found at i:57651483 original size:13 final size:13
Alignment explanation
Indices: 57651467--57651491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57651457 CCCTTTTCTT
57651467 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
57651480 TTTTTCTTTTTT
1 TTTTTCTTTTTT
57651492 TCTTCCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:57651504 original size:21 final size:21
Alignment explanation
Indices: 57651460--57651507 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
57651450 AATTGAACCC
*
57651460 TTTTCTTTTTTTCTTTTTTCT
1 TTTTCTTTTTTTCTTCTTTCT
57651481 TTTTCTTTTTTTCTTCCTTT-T
1 TTTTCTTTTTTTCTT-CTTTCT
57651502 TTTTCT
1 TTTTCT
57651508 GCTGCTGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTCTTTTTTTCTTCTTTCT
Found at i:57651690 original size:18 final size:16
Alignment explanation
Indices: 57651669--57651707 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
57651659 TTTTGCTGTT
57651669 TGCTGTTTTTTTAGGGGC
1 TGCTGTTTTTTT--GGGC
*
57651687 TGCTCTTTTTTTGGGC
1 TGCTGTTTTTTTGGGC
57651703 TGCTG
1 TGCTG
57651708 GGCTGCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.51
Consensus pattern (16 bp):
TGCTGTTTTTTTGGGC
Found at i:57651806 original size:22 final size:22
Alignment explanation
Indices: 57651779--57651862 Score: 123
Period size: 22 Copynumber: 3.8 Consensus size: 22
57651769 CGGGTCGACC
**
57651779 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAAA
* * *
57651801 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
57651823 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
57651845 CATGAGAGCTTAGTACGT
1 CATGAGAGCTTAGTACGT
57651863 GCTTTTTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:57652538 original size:30 final size:28
Alignment explanation
Indices: 57652436--57652573 Score: 109
Period size: 30 Copynumber: 4.7 Consensus size: 28
57652426 AAATATGGGC
* *
57652436 CAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAATGTAAATT-TTGAAAGTTT-GGGGT
* ***
57652466 CAAAGTG-AAATTTTTAGAAAGTCTAAAGGT
1 CAAAATGTAAA-TTTT-GAAAGT-TTGGGGT
*
57652496 CGAAATGT-AATTTTAGAAAGTTTTGGGGT
1 CAAAATGTAAATTTT-GAAAG-TTTGGGGT
*
57652525 TAAAATGTAAATTTTGGAAAAGTTTGGGGT
1 CAAAATGTAAATTTT-G-AAAGTTTGGGGT
57652555 CAAAATGTAAATTTTGAAA
1 CAAAATGTAAATTTTGAAA
57652574 AGTACAGGGG
Statistics
Matches: 86, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
28 3 0.03
29 25 0.29
30 53 0.62
31 5 0.06
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (28 bp):
CAAAATGTAAATTTTGAAAGTTTGGGGT
Found at i:57652584 original size:30 final size:30
Alignment explanation
Indices: 57652520--57652595 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
57652510 AGAAAGTTTT
**
57652520 GGGGTTAAAATGTAAATTTTGGAAAAGTTT
1 GGGGTTAAAATGTAAATTTTGGAAAAGTCA
*
57652550 GGGGTCAAAATGTAAATTTT-GAAAAGTACA
1 GGGGTTAAAATGTAAATTTTGGAAAAGT-CA
*
57652580 GGGGTTAAAATATAAA
1 GGGGTTAAAATGTAAA
57652596 AAAAACTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 7 0.17
30 33 0.82
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (30 bp):
GGGGTTAAAATGTAAATTTTGGAAAAGTCA
Found at i:57664289 original size:15 final size:15
Alignment explanation
Indices: 57664269--57664299 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57664259 TTGGTGTAAT
57664269 ATAGGCTATGATATA
1 ATAGGCTATGATATA
57664284 ATAGGCTATGATATA
1 ATAGGCTATGATATA
57664299 A
1 A
57664300 CCAACATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
ATAGGCTATGATATA
Found at i:57669330 original size:19 final size:19
Alignment explanation
Indices: 57669306--57669352 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
57669296 AATATTTTAT
57669306 ATTATTTATTTT-TAATATA
1 ATTATTTATTTTATAAT-TA
*
57669325 ATTATTCTTTTTTATAATTA
1 ATTATT-TATTTTATAATTA
*
57669345 ATTTTTTA
1 ATTATTTA
57669353 AACTATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATTTATTTTATAATTA
Found at i:57669349 original size:32 final size:32
Alignment explanation
Indices: 57669290--57669350 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
57669280 AATGATATTC
* *
57669290 ATAATTAATATTTTATATTATTTATTTTTAAT
1 ATAATTAATATTTTATATAATTAATTTTTAAT
* * *
57669322 ATAATTATTCTTTTTTATAATTAATTTTT
1 ATAATTAATATTTTATATAATTAATTTTT
57669351 TAAACTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (32 bp):
ATAATTAATATTTTATATAATTAATTTTTAAT
Found at i:57669351 original size:16 final size:16
Alignment explanation
Indices: 57669290--57669352 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
57669280 AATGATATTC
*
57669290 ATAATTAATATTTTAT
1 ATAATTAATTTTTTAT
* * *
57669306 ATTATTTATTTTTAAT
1 ATAATTAATTTTTTAT
*
57669322 ATAATT-ATTCTTTTTT
1 ATAATTAATT-TTTTAT
57669338 ATAATTAATTTTTTA
1 ATAATTAATTTTTTA
57669353 AACTATAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 3 0.08
16 31 0.84
17 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATAATTAATTTTTTAT
Found at i:57670451 original size:2 final size:2
Alignment explanation
Indices: 57670444--57670494 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
57670434 CTCCAAATGC
57670444 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
57670486 AT AT AT AT A
1 AT AT AT AT A
57670495 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57670865 original size:9 final size:9
Alignment explanation
Indices: 57670851--57671160 Score: 239
Period size: 9 Copynumber: 34.7 Consensus size: 9
57670841 TATTATGTAC
57670851 TAAGTTATG
1 TAAGTTATG
*
57670860 TAAGTTGTG
1 TAAGTTATG
57670869 T-A-TTATG
1 TAAGTTATG
*
57670876 TGAGTTATG
1 TAAGTTATG
*
57670885 TGAGTTATG
1 TAAGTTATG
*
57670894 TAAGTTATT
1 TAAGTTATG
57670903 TAA-TATATG
1 TAAGT-TATG
57670912 TAAGTTATG
1 TAAGTTATG
57670921 TAAGTTATG
1 TAAGTTATG
* *
57670930 TAGGCTATG
1 TAAGTTATG
*
57670939 T-A-TTATC
1 TAAGTTATG
* *
57670946 TAAATAATG
1 TAAGTTATG
*
57670955 TAAGTTAGG
1 TAAGTTATG
* *
57670964 GAGGTTATG
1 TAAGTTATG
57670973 T-A-TTATG
1 TAAGTTATG
*
57670980 TAAGTTATT
1 TAAGTTATG
57670989 TAAGTTATG
1 TAAGTTATG
*
57670998 TAAGTTATT
1 TAAGTTATG
*
57671007 TAATTTATG
1 TAAGTTATG
57671016 TAAGTTATG
1 TAAGTTATG
57671025 TAAGTTATG
1 TAAGTTATG
57671034 TAAGTTATG
1 TAAGTTATG
*
57671043 TAAGTTATT
1 TAAGTTATG
*
57671052 TAATTTATG
1 TAAGTTATG
57671061 TAAGTTATTTAG
1 TAAGTTA--T-G
* *
57671073 AAAAAATTATG
1 --TAAGTTATG
57671084 TAAGTTATG
1 TAAGTTATG
57671093 TACTAAGTTATG
1 ---TAAGTTATG
57671105 T-A-TTATG
1 TAAGTTATG
* *
57671112 TAAATAATG
1 TAAGTTATG
57671121 TAAGTTA-G
1 TAAGTTATG
* *
57671129 GAAGGTTATT
1 TAA-GTTATG
57671139 TAAGTTATG
1 TAAGTTATG
57671148 T-A-TTATG
1 TAAGTTATG
57671155 TAAGTT
1 TAAGTT
57671161 TATATATAAG
Statistics
Matches: 238, Mismatches: 41, Indels: 44
0.74 0.13 0.14
Matches are distributed among these distances:
7 27 0.11
8 12 0.05
9 178 0.75
10 3 0.01
11 2 0.01
12 11 0.05
14 5 0.02
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:57671172 original size:12 final size:14
Alignment explanation
Indices: 57671139--57671262 Score: 63
Period size: 12 Copynumber: 9.1 Consensus size: 14
57671129 GAAGGTTATT
*
57671139 TAAGTTATGTATTATG
1 TAAGTTATG-A-TATA
57671155 TAAGTT-T-ATATA
1 TAAGTTATGATATA
57671167 TAAGTTATGATATA
1 TAAGTTATGATATA
*
57671181 T-A-TTATTGATAAATT
1 TAAGTTA-TGAT--ATA
57671196 TAAGTTAT-ATAT-
1 TAAGTTATGATATA
* *
57671208 T--G-TATGTTATT
1 TAAGTTATGATATA
*
57671219 TAAGTTATGTATTATG
1 TAAGTTATG-A-TATA
57671235 TAAGTT-T-ATATA
1 TAAGTTATGATATA
57671247 TAAGTTATGATATA
1 TAAGTTATGATATA
57671261 TA
1 TA
57671263 TTATTGATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
9 3 0.03
10 4 0.05
11 1 0.01
12 22 0.26
13 12 0.14
14 17 0.20
15 7 0.08
16 17 0.20
17 3 0.03
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TAAGTTATGATATA
Found at i:57671172 original size:28 final size:28
Alignment explanation
Indices: 57671139--57671255 Score: 106
Period size: 28 Copynumber: 4.3 Consensus size: 28
57671129 GAAGGTTATT
57671139 TAAGTTATGTATTATGTAAGTTTATATA
1 TAAGTTATGTATTATGTAAGTTTATATA
* *
57671167 TAAGTTATGATATATAT-T-A-TTGATAAATT
1 TAAGTTATG-TAT-TATGTAAGTT--TATATA
* *
57671196 TAAGTTATATA-T-TGTATG-TTAT-T-
1 TAAGTTATGTATTATGTAAGTTTATATA
57671219 TAAGTTATGTATTATGTAAGTTTATATA
1 TAAGTTATGTATTATGTAAGTTTATATA
57671247 TAAGTTATG
1 TAAGTTATG
57671256 ATATATATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
23 10 0.14
24 2 0.03
25 8 0.11
26 6 0.09
27 4 0.06
28 21 0.30
29 16 0.23
30 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (28 bp):
TAAGTTATGTATTATGTAAGTTTATATA
Found at i:57671205 original size:40 final size:41
Alignment explanation
Indices: 57671155--57671281 Score: 138
Period size: 40 Copynumber: 3.1 Consensus size: 41
57671145 ATGTATTATG
57671155 TAAGTTTATATATAAGTTATGATATATATTATTGATAAATT
1 TAAGTTTATATATAAGTTATGATATATATTATTGATAAATT
* * * * *
57671196 TAAG-TTATATAT-TG-TATGTTATTTAAGTTA-TG-TATTATG
1 TAAGTTTATATATAAGTTATGATATAT-A-TTATTGATA-AATT
57671235 TAAGTTTATATATAAGTTATGATATATATTATTGATAAATT
1 TAAGTTTATATATAAGTTATGATATATATTATTGATAAATT
*
57671276 TGAGTT
1 TAAGTT
57671282 ATGTAAGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
38 10 0.15
39 10 0.15
40 22 0.33
41 15 0.22
42 10 0.15
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (41 bp):
TAAGTTTATATATAAGTTATGATATATATTATTGATAAATT
Found at i:57671227 original size:80 final size:80
Alignment explanation
Indices: 57671133--57671283 Score: 293
Period size: 80 Copynumber: 1.9 Consensus size: 80
57671123 AGTTAGGAAG
57671133 GTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATATATTATTGATAAATTTA
1 GTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATATATTATTGATAAATTTA
57671198 AGTTATATATTGTAT
66 AGTTATATATTGTAT
*
57671213 GTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATATATTATTGATAAATTTG
1 GTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATATATTATTGATAAATTTA
57671278 AGTTAT
66 AGTTAT
57671284 GTAAGTTTTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (80 bp):
GTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATATATTATTGATAAATTTA
AGTTATATATTGTAT
Found at i:57673092 original size:25 final size:24
Alignment explanation
Indices: 57673016--57673167 Score: 188
Period size: 25 Copynumber: 6.3 Consensus size: 24
57673006 CACTAATGAA
*
57673016 CAGAGAGCACTAAAGTGCT-ATA-
1 CAGAGAGCACTAACGTGCTAATAT
*
57673038 CAGAGAGCAC-AGATGTGCTAA-A-
1 CAGAGAGCACTA-ACGTGCTAATAT
*
57673060 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTAACGTGCT-AATAT
*
57673085 CAGAGAGCACCAACGTGCTAATAGT
1 CAGAGAGCACTAACGTGCTAATA-T
57673110 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAAT-AT
57673135 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAAT-AT
57673160 CAGAGAGC
1 CAGAGAGC
57673168 GCGCTAAAGT
Statistics
Matches: 116, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.28
23 3 0.03
24 5 0.04
25 73 0.63
26 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTAATAT
Found at i:57674214 original size:11 final size:11
Alignment explanation
Indices: 57674198--57674223 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57674188 TCTTTCTTTC
57674198 TTTCTCCCCTG
1 TTTCTCCCCTG
57674209 TTTCTCCCCTG
1 TTTCTCCCCTG
57674220 TTTC
1 TTTC
57674224 GTTTCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:57674304 original size:16 final size:16
Alignment explanation
Indices: 57674285--57674321 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
57674275 TATATATTTA
57674285 TATAATAATATAATAT
1 TATAATAATATAATAT
57674301 TATAATAATATAATAT
1 TATAATAATATAATAT
*
57674317 AATAA
1 TATAA
57674322 CTTACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Done.