Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 76 of 145
Found at i:25167034 original size:7 final size:7
Alignment explanation
Indices: 25167016--25167076 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
25167006 GTGTTGCCAT
*
25167016 TTTAAGG
1 TTTATGG
25167023 TTTATGG
1 TTTATGG
*
25167030 ATTATGGG
1 TTTAT-GG
*
25167038 TTTAGGG
1 TTTATGG
*
25167045 ATTATGG
1 TTTATGG
*
25167052 GTTATGG
1 TTTATGG
25167059 TTTATGG
1 TTTATGG
25167066 TTTATGG
1 TTTATGG
25167073 TTTA
1 TTTA
25167077 AAGGTTGGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 40 0.89
8 5 0.11
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
TTTATGG
Found at i:25167041 original size:15 final size:15
Alignment explanation
Indices: 25167021--25167072 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
25167011 GCCATTTTAA
25167021 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
25167036 GGTTTAGGGATTATG
1 GGTTTATGGATTATG
*
25167051 GG-TTATGGTTTAT-
1 GGTTTATGGATTATG
25167064 GGTTTATGG
1 GGTTTATGG
25167073 TTTAAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 2 0.06
14 15 0.45
15 16 0.48
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:25167157 original size:20 final size:21
Alignment explanation
Indices: 25167124--25167162 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
25167114 GGTTTATGGT
*
25167124 TTTACGGTTTTAGGGTTTAAA
1 TTTACGGTTTTAGGATTTAAA
25167145 TTTACGG-TTTAGGATTTA
1 TTTACGGTTTTAGGATTTA
25167163 GATTAACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (21 bp):
TTTACGGTTTTAGGATTTAAA
Found at i:25178283 original size:20 final size:20
Alignment explanation
Indices: 25178250--25178289 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25178240 AAATATTTTC
** *
25178250 AGTAAATCGTTTTCTAGAAA
1 AGTAAATCACTTTCCAGAAA
25178270 AGTAAATCACTTTCCAGAAA
1 AGTAAATCACTTTCCAGAAA
25178290 TTATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTAAATCACTTTCCAGAAA
Found at i:25179743 original size:9 final size:9
Alignment explanation
Indices: 25179729--25179759 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25179719 GTTAAACGAA
25179729 TCGAGTTAT
1 TCGAGTTAT
*
25179738 TCGAGTTAA
1 TCGAGTTAT
25179747 TCGAGTTAT
1 TCGAGTTAT
25179756 TCGA
1 TCGA
25179760 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:25181167 original size:23 final size:24
Alignment explanation
Indices: 25181137--25181189 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
25181127 GCCTGGCCCG
*
25181137 ATTTT-AAATAAACACAA-AAAAAT
1 ATTTTAAAATAAA-AAAATAAAAAT
25181160 ATTTTAAAAATAAAAAAATAAAAAT
1 ATTTT-AAAATAAAAAAATAAAAAT
25181185 ATTTT
1 ATTTT
25181190 TAAAGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 3 0.12
25 18 0.69
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTTTAAAATAAAAAAATAAAAAT
Found at i:25183357 original size:69 final size:67
Alignment explanation
Indices: 25183260--25183391 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 67
25183250 TCCGAATAAG
** *
25183260 AAAAGACAAAACTACATCGTTTTGATAAATGTTCACCTTTTCTAAATTAAAAGTCAAAATCATTA
1 AAAAGACAAAACTACATCGTTTTGATAAATGTTCA-CTCAT-TAAATTAAAAGGCAAAATCATTA
25183325 AGTT
64 AGTT
* *
25183329 AAAAGACAAAACTACGA-CGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAATCATTA
1 AAAAGACAAAACTAC-ATCGTTTTGATAAATGTTCACTCATTAAATTAAAAGGCAAAATCATTA
25183392 TATTGTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 21 0.37
68 3 0.05
69 32 0.56
70 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (67 bp):
AAAAGACAAAACTACATCGTTTTGATAAATGTTCACTCATTAAATTAAAAGGCAAAATCATTAAG
TT
Found at i:25212697 original size:16 final size:17
Alignment explanation
Indices: 25212672--25212709 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
25212662 TCTTGTCCTT
* *
25212672 ATCCCCATCC-ACTTCC
1 ATCCCAATCCAACTACC
25212688 ATCCCAATCCAACTACC
1 ATCCCAATCCAACTACC
25212705 ATCCC
1 ATCCC
25212710 TATAGTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (17 bp):
ATCCCAATCCAACTACC
Found at i:25213988 original size:102 final size:103
Alignment explanation
Indices: 25213861--25214065 Score: 387
Period size: 102 Copynumber: 2.0 Consensus size: 103
25213851 TAGGACTAGG
25213861 ATTTTCAAATAAAAAAGGATAATATGCTAAAAAAAAGCCCTTAAACTATTATATCTCATCTTGTT
1 ATTTTCAAATAAAAAAGGATAATATGCTAAAAAAAAGCCCTTAAACTATTATATCTCATCTTGTT
25213926 TTGAAAAAACTCTTATGTTATTTTT-ATCCATGAAAGCT
66 TTGAAAAAACTCTTATGTTATTTTTAAT-CATGAAAGCT
25213964 ATTTTCAAAT-AAAAAGGATAATATGCTAAAAAAAAGCCCTTAAACTATTATATCTCATCTTGTT
1 ATTTTCAAATAAAAAAGGATAATATGCTAAAAAAAAGCCCTTAAACTATTATATCTCATCTTGTT
25214028 TTGAAAAAACTCTTATGTTATTTTTAATCATGAAAGCT
66 TTGAAAAAACTCTTATGTTATTTTTAATCATGAAAGCT
25214066 TTTGATTTTA
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
102 89 0.88
103 12 0.12
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (103 bp):
ATTTTCAAATAAAAAAGGATAATATGCTAAAAAAAAGCCCTTAAACTATTATATCTCATCTTGTT
TTGAAAAAACTCTTATGTTATTTTTAATCATGAAAGCT
Found at i:25215654 original size:16 final size:17
Alignment explanation
Indices: 25215618--25215655 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
25215608 GAAGACTATA
* *
25215618 GGGATGGTAGTTGGATT
1 GGGATGGAAGTTGGATG
25215635 GGGATGGAAG-TGGATG
1 GGGATGGAAGTTGGATG
25215651 GGGAT
1 GGGAT
25215656 AAGGACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (17 bp):
GGGATGGAAGTTGGATG
Found at i:25216719 original size:14 final size:15
Alignment explanation
Indices: 25216700--25216731 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25216690 GTGGTTATAG
25216700 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
25216714 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
25216729 TTA
1 TTA
25216732 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:25218719 original size:222 final size:222
Alignment explanation
Indices: 25218333--25218777 Score: 890
Period size: 222 Copynumber: 2.0 Consensus size: 222
25218323 TGAAAAAATG
25218333 AGATTTTGTGAATTGATTTTGGCTTAAATAGCCAATTAAAACGGCGCCGTTTAAGGCCAGGGTTG
1 AGATTTTGTGAATTGATTTTGGCTTAAATAGCCAATTAAAACGGCGCCGTTTAAGGCCAGGGTTG
25218398 ACCCGGATCCGACCCAACCCAGCTTTAGGATCCGCGTGTTTTATATGGAGGGGCAAATTCGTTTT
66 ACCCGGATCCGACCCAACCCAGCTTTAGGATCCGCGTGTTTTATATGGAGGGGCAAATTCGTTTT
25218463 GACCCCTCCGCCTTTTTAATATATTTCTAATTAGGTTTGTTTTATTTTTTTTAAATTCGGTCTTT
131 GACCCCTCCGCCTTTTTAATATATTTCTAATTAGGTTTGTTTTATTTTTTTTAAATTCGGTCTTT
25218528 AATTTATTTTAAATTTCAATTTAATCC
196 AATTTATTTTAAATTTCAATTTAATCC
25218555 AGATTTTGTGAATTGATTTTGGCTTAAATAGCCAATTAAAACGGCGCCGTTTAAGGCCAGGGTTG
1 AGATTTTGTGAATTGATTTTGGCTTAAATAGCCAATTAAAACGGCGCCGTTTAAGGCCAGGGTTG
25218620 ACCCGGATCCGACCCAACCCAGCTTTAGGATCCGCGTGTTTTATATGGAGGGGCAAATTCGTTTT
66 ACCCGGATCCGACCCAACCCAGCTTTAGGATCCGCGTGTTTTATATGGAGGGGCAAATTCGTTTT
25218685 GACCCCTCCGCCTTTTTAATATATTTCTAATTAGGTTTGTTTTATTTTTTTTAAATTCGGTCTTT
131 GACCCCTCCGCCTTTTTAATATATTTCTAATTAGGTTTGTTTTATTTTTTTTAAATTCGGTCTTT
25218750 AATTTATTTTAAATTTCAATTTAATCC
196 AATTTATTTTAAATTTCAATTTAATCC
25218777 A
1 A
25218778 TTTGAGCGGC
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 223 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (222 bp):
AGATTTTGTGAATTGATTTTGGCTTAAATAGCCAATTAAAACGGCGCCGTTTAAGGCCAGGGTTG
ACCCGGATCCGACCCAACCCAGCTTTAGGATCCGCGTGTTTTATATGGAGGGGCAAATTCGTTTT
GACCCCTCCGCCTTTTTAATATATTTCTAATTAGGTTTGTTTTATTTTTTTTAAATTCGGTCTTT
AATTTATTTTAAATTTCAATTTAATCC
Found at i:25219073 original size:23 final size:25
Alignment explanation
Indices: 25219019--25219067 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
25219009 TACACATATA
25219019 TATATTTTTTAAACGAATATTTTCC
1 TATATTTTTTAAACGAATATTTTCC
* *
25219044 TATATTTTTTTAATGAATATTTTC
1 TATATTTTTTAAACGAATATTTTC
25219068 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TATATTTTTTAAACGAATATTTTCC
Found at i:25225063 original size:132 final size:132
Alignment explanation
Indices: 25224826--25225573 Score: 1410
Period size: 132 Copynumber: 5.7 Consensus size: 132
25224816 NNNNNNNNNN
25224826 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
25224891 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
66 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
25224956 CA
131 CA
25224958 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
25225023 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
66 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
25225088 CA
131 CA
25225090 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
25225155 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
66 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
25225220 CA
131 CA
25225222 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
25225287 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
66 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
25225352 CA
131 CA
25225354 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
25225419 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
66 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
25225484 CA
131 CA
* * *
25225486 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAATAGTGAAATAGATT
1 GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGACAACAGTGGAATAGACT
* * *
25225550 GGAGATTGTA-AGTTTTATCTCCCT
65 GAAGATTTTAGA-TCTTATCTCCCT
25225574 GCAGTTGCAG
Statistics
Matches: 608, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
131 1 0.00
132 605 1.00
133 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
GTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGACTG
AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCC
CA
Found at i:25226281 original size:24 final size:24
Alignment explanation
Indices: 25226249--25226297 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25226239 AGGGAAGAAA
*
25226249 CGACCTGAGTGGTGCCCAGACCCG
1 CGACCTGAGTGGTGCCCAGAACCG
25226273 CGACCTGAGTGGTGCCCAGAACCG
1 CGACCTGAGTGGTGCCCAGAACCG
25226297 C
1 C
25226298 CGTGAACGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.37, G:0.33, T:0.12
Consensus pattern (24 bp):
CGACCTGAGTGGTGCCCAGAACCG
Found at i:25229260 original size:71 final size:72
Alignment explanation
Indices: 25229185--25229327 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
25229175 CCGGTTAAGT
*
25229185 ATATAGAAATATCAAAT-AATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
25229249 AGTTGAA
66 AGTTGAA
**
25229256 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTGGGGTGTGCCTCATATTTTC
1 ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
25229321 AGTTGAA
66 AGTTGAA
25229328 TAGACGACGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 16 0.24
72 52 0.76
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (72 bp):
ATATAGAAATACCAAATAAATTTGAGTTGACATATTTAATAATGTAAGGTGTGCCTCATATTTTC
AGTTGAA
Found at i:25232463 original size:28 final size:28
Alignment explanation
Indices: 25232423--25232478 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
25232413 TTGTCTTCAC
25232423 ATCCATTTGATGTACCAACAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
*
25232451 ATCCATTTGATGTACCAGCAAATTGTGA
1 ATCCATTTGATGTACCAACAAATTGTGA
25232479 TTGAAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (28 bp):
ATCCATTTGATGTACCAACAAATTGTGA
Found at i:25236794 original size:35 final size:35
Alignment explanation
Indices: 25236748--25236819 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
25236738 ACCTTTAAAG
25236748 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
1 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
25236783 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
1 TTGAAATCCACATTCTCTCAAACATCTACAATTTC
25236818 TT
1 TT
25236820 CAATTATGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (35 bp):
TTGAAATCCACATTCTCTCAAACATCTACAATTTC
Found at i:25246748 original size:58 final size:58
Alignment explanation
Indices: 25246654--25246769 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
25246644 TGTGGCGTTA
*
25246654 GCTATACCTTTGGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
1 GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
* * * * *
25246712 GCTATACCTTTAGTTGCTTTCTTGTTAGATAGTGGGTCAAGGTTTATTTGCTGATTTC
1 GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
25246770 ATTTTTTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (58 bp):
GCTATACCTTTAGTTCCTATCTCGTTAGATAATGGGTCAAGGTTTATTTACTGATTTC
Found at i:25251808 original size:41 final size:41
Alignment explanation
Indices: 25251762--25251916 Score: 258
Period size: 41 Copynumber: 3.8 Consensus size: 41
25251752 TTAAATAGAT
* * * *
25251762 TCACCGGCACTTAGTCTGTTAGACTTA-AAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAA-CTTGATTCAGA
25251803 TCACCGGCACTTAGCCTGCTAGGCTTATAACTTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACTTGATTCAGA
25251844 TCACCGGCACTTAGCCTGCTAGGCTTATAACTTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACTTGATTCAGA
25251885 TCACCGGCACTTAGCCTGCTAGGCTTATAACT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACT
25251917 ATTTCATCGA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 107 0.98
42 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACTTGATTCAGA
Found at i:25252345 original size:77 final size:77
Alignment explanation
Indices: 25252242--25252456 Score: 231
Period size: 77 Copynumber: 2.8 Consensus size: 77
25252232 TACATTTAAC
* *
25252242 ATTCGAATCT-CACATATACCTATATAATTTCATA-TCCCATTTCAATACAAGAACTTATACATG
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACA-TTCAATACAAGAACTTATACATG
* * *
25252305 TACATATATACAT
65 CACACACATACAT
* * * * *
25252318 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAATACAAGTACTTATACTTGC
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAGAACTTATACATGC
* *
25252383 ATACACATGCAT
66 ACACACATACAT
* * * * *
25252395 ATTCGAATTTA-ACATATACATATATAATTTCATACTTATACTCAATATAAGCAA-TTATACAT
1 ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAG-AACTTATACAT
25252457 ATGTATACAT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
76 52 0.45
77 61 0.53
78 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (77 bp):
ATTCGAATCTACACATATACATATATAATTTCATACTCACATTCAATACAAGAACTTATACATGC
ACACACATACAT
Found at i:25252467 original size:76 final size:74
Alignment explanation
Indices: 25252242--25252496 Score: 230
Period size: 76 Copynumber: 3.4 Consensus size: 74
25252232 TACATTTAAC
* * **
25252242 ATTCGAATCTCACATATACCTATATAATTTCATATCCCAT-TTCAATACAAGAACTTATACA-TG
1 ATTCGAATCTAACATATACATATATAATTTCATA-CTTATATTCAATACAAGAA-TTATACATTG
* *
25252305 TACATATATACAT
64 T--ATACATGCAT
* * * *
25252318 ATTCGAATCTACATATATACATATATAATTTTATACTTACATTCAATACAAGTACTTATAC-TTG
1 ATTCGAATCTA-ACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACATTG
*
25252382 CATACACATGCAT
64 --TATACATGCAT
* * *
25252395 ATTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACATATG
1 ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAG-AATTATACAT-TG
*
25252460 TATACATGCTT
64 TATACATGCAT
* *
25252471 ATTCG-ATCCAAACATATACAAATATA
1 ATTCGAAT-CTAACATATACATATATA
25252497 TTATACATAT
Statistics
Matches: 146, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
75 2 0.01
76 83 0.57
77 57 0.39
78 3 0.02
79 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (74 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTTATATTCAATACAAGAATTATACATTGTA
TACATGCAT
Found at i:25255115 original size:51 final size:51
Alignment explanation
Indices: 25255051--25255151 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
25255041 CGATGCCTAA
* * *
25255051 CAGGTTTAATGCCGGTGAATTATTTCAGACTTTATGTCTAGCAGGCTTTAG
1 CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTAG
*
25255102 CAGGCTTAATGCCGGTGAATTATTTTAAACTTTATGACTAGCAGGCTTTA
1 CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTA
25255152 TGCCGGTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (51 bp):
CAGGCTTAATGCCGGTGAATTATTTCAAACTTTATGACTAGCAGGCTTTAG
Found at i:25256479 original size:43 final size:44
Alignment explanation
Indices: 25256419--25256504 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 44
25256409 TCATGGATAT
25256419 TTTTATTTATTTATTTATTGAATTGATGTAATAATACATAACTA
1 TTTTATTTATTTATTTATTGAATTGATGTAATAATACATAACTA
*
25256463 TTTT-TTTATTTTTTTATTGAATTGATGTAATAATACATAACT
1 TTTTATTTATTTATTTATTGAATTGATGTAATAATACATAACT
25256505 CTTGCTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 37 0.90
44 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (44 bp):
TTTTATTTATTTATTTATTGAATTGATGTAATAATACATAACTA
Found at i:25256520 original size:43 final size:43
Alignment explanation
Indices: 25256432--25256524 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
25256422 TATTTATTTA
** * *
25256432 TTTATTGAATTGATGTAATAATACATAACTATTTTTTTATTTT
1 TTTATTGAATTGATGTAATAATACATAACTATTGCTTAATATT
*
25256475 TTTATTGAATTGATGTAATAATACATAACTCTTGCTTAATATT
1 TTTATTGAATTGATGTAATAATACATAACTATTGCTTAATATT
25256518 TTTATTG
1 TTTATTG
25256525 TACATTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (43 bp):
TTTATTGAATTGATGTAATAATACATAACTATTGCTTAATATT
Found at i:25262501 original size:87 final size:87
Alignment explanation
Indices: 25262296--25262501 Score: 288
Period size: 87 Copynumber: 2.4 Consensus size: 87
25262286 AAAAACACAA
* * * *
25262296 GTTTTTGAGAAAAGAATCAATGGAAAAGAAGACATTTTTTTGTCTTTAAAATTATAGGTTTTCTT
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
*
25262361 TTTTCAGTTCTCAAAAATCATG
66 TTTTCAGTTCACAAAAATCATG
* *
25262383 GTTTTTAAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATCTAGGTTTT-TT
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
* ***
25262447 TTTTCAGTTCACTAGGTTCAATG
66 TTTTCAGTTCACAAAAATC-ATG
*
25262470 GTTTTTGAGATAAGAATCAATGGAGAAGAAGG
1 GTTTTTGAGAAAAGAATCAATGGAGAAGAAGG
25262502 TTTGAATTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
86 16 0.15
87 89 0.85
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (87 bp):
GTTTTTGAGAAAAGAATCAATGGAGAAGAAGGCATTTTTTTGCCTTTAAAAATATAGGTTTTCTT
TTTTCAGTTCACAAAAATCATG
Found at i:25265021 original size:21 final size:21
Alignment explanation
Indices: 25264980--25265035 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
25264970 GTGGAAATCT
* *
25264980 CACACACCCGTGTGGCTAAGG
1 CACACAGCCGTGTGGCCAAGG
* *
25265001 GACACAGCCGTGTGTCCAAGG
1 CACACAGCCGTGTGGCCAAGG
25265022 CACAC-GCCTGTGTG
1 CACACAGCC-GTGTG
25265036 AAAATTGACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.16
Consensus pattern (21 bp):
CACACAGCCGTGTGGCCAAGG
Found at i:25265148 original size:12 final size:13
Alignment explanation
Indices: 25265122--25265154 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25265112 TTTCACACAG
25265122 CCGTGTGGACCAC
1 CCGTGTGGACCAC
25265135 CCGTGTGG-CCAC
1 CCGTGTGGACCAC
*
25265147 CCATGTGG
1 CCGTGTGG
25265155 TCACGAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.36, G:0.33, T:0.18
Consensus pattern (13 bp):
CCGTGTGGACCAC
Found at i:25268499 original size:20 final size:20
Alignment explanation
Indices: 25268462--25268502 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25268452 TAAAAAGACA
* *
25268462 TATAATTATTCATCTAATAT
1 TATAAATATTCAACTAATAT
*
25268482 TATAAATATTCAAGTAATAT
1 TATAAATATTCAACTAATAT
25268502 T
1 T
25268503 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAAATATTCAACTAATAT
Found at i:25273008 original size:36 final size:36
Alignment explanation
Indices: 25272961--25273032 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
25272951 GATTAAATAT
25272961 AAAATATTTAAGGACATTCCAATTTAAATTTCGTGA
1 AAAATATTTAAGGACATTCCAATTTAAATTTCGTGA
25272997 AAAATATTTAAGGACATTCCAATTTAAATTTCGTGA
1 AAAATATTTAAGGACATTCCAATTTAAATTTCGTGA
25273033 TTTTTGGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAATATTTAAGGACATTCCAATTTAAATTTCGTGA
Found at i:25279876 original size:14 final size:15
Alignment explanation
Indices: 25279854--25279882 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25279844 GGCTGGAGAG
25279854 TGAGTATATGAGATA
1 TGAGTATATGAGATA
25279869 TGAG-ATATGAGATA
1 TGAGTATATGAGATA
25279883 GAGCTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (15 bp):
TGAGTATATGAGATA
Found at i:25286404 original size:25 final size:24
Alignment explanation
Indices: 25286376--25286572 Score: 121
Period size: 25 Copynumber: 8.0 Consensus size: 24
25286366 ATCTCGTTAT
*
25286376 ATGGCTCTCACGAGCTTCCCGATTA
1 ATGGCTCTCATGAGCTTCCCGA-TA
* * *
25286401 ATGGTTCTCTTGAGCTTTCC-ATA
1 ATGGCTCTCATGAGCTTCCCGATA
* *
25286424 TATGGCTCGTAATAAGCTTCCCGATA
1 -ATGGCTC-TCATGAGCTTCCCGATA
*
25286450 ATTGGCTCTCATGAGCTTCCTGATTA
1 A-TGGCTCTCATGAGCTTCCCGA-TA
*
25286476 ATGGATCTC-TGGAGC-TCCCGATA
1 ATGGCTCTCAT-GAGCTTCCCGATA
* * * * *
25286499 TTGGGTCACATGAGCTTCCCGGTT
1 ATGGCTCTCATGAGCTTCCCGATA
* * ** *
25286523 ATGACCTCTTATGAGCTTTTCGTTA
1 ATG-GCTCTCATGAGCTTCCCGATA
* *
25286548 CATAGCTCACATGAGCTTCCCGATA
1 -ATGGCTCTCATGAGCTTCCCGATA
25286573 TATATATGGC
Statistics
Matches: 127, Mismatches: 35, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
23 14 0.11
24 22 0.17
25 77 0.61
26 14 0.11
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (24 bp):
ATGGCTCTCATGAGCTTCCCGATA
Found at i:25289344 original size:54 final size:54
Alignment explanation
Indices: 25289262--25289382 Score: 233
Period size: 54 Copynumber: 2.2 Consensus size: 54
25289252 TCCCTCTCTT
*
25289262 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTC
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
25289316 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
1 CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
25289370 CTAATTCAACTAG
1 CTAATTCAACTAG
25289383 GGTTCCTCTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.45
Consensus pattern (54 bp):
CTAATTCAACTAGAAGATTGATTTTTCTATTAAATAAGTATTATTTGTATTCTA
Found at i:25289525 original size:20 final size:19
Alignment explanation
Indices: 25289486--25289525 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
25289476 AAATAGTGAG
* *
25289486 AATTTATTTTCTAAGTATA
1 AATTTATTTTCCAAGAATA
25289505 AATTCTATTTTCCAAGAATA
1 AATT-TATTTTCCAAGAATA
25289525 A
1 A
25289526 TAATTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTTATTTTCCAAGAATA
Found at i:25289553 original size:2 final size:2
Alignment explanation
Indices: 25289546--25289611 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
25289536 AGTTTCTATA
25289546 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25289588 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
25289612 TTTTTTTTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25296474 original size:20 final size:20
Alignment explanation
Indices: 25296451--25296513 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
25296441 TATCAAAGTA
25296451 CAATCAGGGGCACGTATGTG
1 CAATCAGGGGCACGTATGTG
* * *
25296471 CAATCAGGGGTACCG-AAGTA
1 CAATCAGGGGCA-CGTATGTG
*
25296491 CAATCAGGGGCACATATGTG
1 CAATCAGGGGCACGTATGTG
25296511 CAA
1 CAA
25296514 ACATTCAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.91
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.17
Consensus pattern (20 bp):
CAATCAGGGGCACGTATGTG
Found at i:25296491 original size:40 final size:40
Alignment explanation
Indices: 25296436--25296513 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
25296426 AAATGCGTTT
* *
25296436 AGGGGTATCAAAGTACAATCAGGGGCACGTATGTGCAATC
1 AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAATC
*
25296476 AGGGGTACCGAAGTACAATCAGGGGCACATATGTGCAA
1 AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAA
25296514 ACATTCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (40 bp):
AGGGGTACCAAAGTACAATCAGGGGCACATATGTGCAATC
Found at i:25303797 original size:20 final size:20
Alignment explanation
Indices: 25303774--25303886 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
25303764 GGGTATCGAA
25303774 GTACAAACAGGGGCACACAT
1 GTACAAACAGGGGCACACAT
* * *
25303794 GTACAAACAAGGGTAC-CGAA
1 GTACAAACAGGGGCACAC-AT
* **
25303814 GAACAAACAGGGGCACTTAT
1 GTACAAACAGGGGCACACAT
* * *
25303834 GTGCGAACAGGGGTACTA-AT
1 GTACAAACAGGGGCAC-ACAT
* **
25303854 GTACAGACAGGGGCACGTAT
1 GTACAAACAGGGGCACACAT
*
25303874 GTACAATCAGGGG
1 GTACAAACAGGGG
25303887 TACCGAAGTA
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 68 0.99
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.14
Consensus pattern (20 bp):
GTACAAACAGGGGCACACAT
Found at i:25303814 original size:40 final size:40
Alignment explanation
Indices: 25303762--25303915 Score: 175
Period size: 40 Copynumber: 3.9 Consensus size: 40
25303752 AAATGCGTTT
* *
25303762 AGGGGTATCGAAGTACAAACAGGGGCACACATGTACAAAC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
* * * * *
25303802 AAGGGTACCGAAGAACAAACAGGGGCACTTATGTGCGAAC
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
* * * *
25303842 AGGGGTA-CTAATGTACAGACAGGGGCACGTATGTACAATC
1 AGGGGTACCGAA-GTACAAACAGGGGCACATATGTACAAAC
* *
25303882 AGGGGTACCGAAGTACAATCAGGGACACATATGT
1 AGGGGTACCGAAGTACAAACAGGGGCACATATGT
25303916 GCAGACATTC
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
39 3 0.03
40 86 0.93
41 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAACAGGGGCACATATGTACAAAC
Found at i:25306575 original size:15 final size:15
Alignment explanation
Indices: 25306552--25306582 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25306542 ATATTTTTTC
*
25306552 TTTTGAAAAATAATT
1 TTTTAAAAAATAATT
25306567 TTTTAAAAAATAATT
1 TTTTAAAAAATAATT
25306582 T
1 T
25306583 ATGAGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATAATT
Found at i:25312828 original size:40 final size:39
Alignment explanation
Indices: 25312739--25312841 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 39
25312729 CGTGATTCAG
* **
25312739 GTGGATCAGCTCTTATGATCTTCTGTTGGCGTGTTTCGA
1 GTGGATCAGCTCTTATGAGCTTCTGTTGGCGCATTTCGA
* * * *
25312778 GTGAACCAGCTCTTATGAGCTTTTGTTTGGCGCATTTCTA
1 GTGGATCAGCTCTTATGAGCTTCTG-TTGGCGCATTTCGA
* *
25312818 TTGGATCAGCTCTTATAAGCTTCT
1 GTGGATCAGCTCTTATGAGCTTCT
25312842 ATTTGGTGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
39 21 0.41
40 30 0.59
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (39 bp):
GTGGATCAGCTCTTATGAGCTTCTGTTGGCGCATTTCGA
Found at i:25313726 original size:103 final size:103
Alignment explanation
Indices: 25313547--25313756 Score: 402
Period size: 103 Copynumber: 2.0 Consensus size: 103
25313537 GTTTAATGTT
*
25313547 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTGATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
25313612 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
25313650 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
1 TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
*
25313715 GTTGATGGTTATGTAGTTGATAAATCTTGAGGTATTGG
66 GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
25313753 TATA
1 TATA
25313757 GGTTTATATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (103 bp):
TATAAAATACTATTAAGTTAGGAATGAAAAATATATATGATGTTAATAGACTTACTCATTTATGA
GTTGATGGTTATGTAGTTGATAAATCTTAAGGTATTGG
Found at i:25316722 original size:25 final size:24
Alignment explanation
Indices: 25316694--25316758 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
25316684 TTGTACATTG
25316694 TACTGACAACACTGTAGATAGTGTA
1 TACTGA-AACACTGTAGATAGTGTA
*
25316719 TACTGAAAACACTATAGATAGTGTA
1 TACTG-AAACACTGTAGATAGTGTA
25316744 TACTGAAA-ACTGTAG
1 TACTGAAACACTGTAG
25316759 CAAAATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 6 0.16
24 3 0.08
25 27 0.73
26 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
TACTGAAACACTGTAGATAGTGTA
Found at i:25320539 original size:35 final size:35
Alignment explanation
Indices: 25320500--25320569 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
25320490 GTGGATCGAT
25320500 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
1 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
25320535 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
1 TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
25320570 GACTTTTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
TGATCAAGTTTGCTCACTTCATCCCGGTAAGGACA
Found at i:25321459 original size:28 final size:28
Alignment explanation
Indices: 25321411--25321467 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
25321401 CTATTCCCTT
* *
25321411 AGTGAAGGTTCTACCGTGTAAAGGTAGC
1 AGTGAAGGTTCTACCGCGTAAAGATAGC
**
25321439 AGTGAAGGTTCTGTCGCGTAAAGATAGC
1 AGTGAAGGTTCTACCGCGTAAAGATAGC
25321467 A
1 A
25321468 CTGAGGAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.25
Consensus pattern (28 bp):
AGTGAAGGTTCTACCGCGTAAAGATAGC
Found at i:25324202 original size:35 final size:35
Alignment explanation
Indices: 25324156--25324225 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
25324146 ATTGAGTTTG
25324156 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
1 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
*
25324191 AGGTGCCTTTTGGCATATTTGTTGTATGGATAAAT
1 AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
25324226 GACCTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (35 bp):
AGGTGCCTTTTGGCATATTGGTTGTATGGATAAAT
Found at i:25330433 original size:7 final size:7
Alignment explanation
Indices: 25330421--25330446 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25330411 AATTGCTAAA
25330421 TGATATG
1 TGATATG
25330428 TGATATG
1 TGATATG
25330435 TGATATG
1 TGATATG
25330442 TGATA
1 TGATA
25330447 CGAAATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TGATATG
Found at i:25336615 original size:34 final size:34
Alignment explanation
Indices: 25336556--25336630 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
25336546 TTCATATAAC
* *
25336556 AAATCAAGTATTTCATGTAGCTTATAAACCATGT
1 AAATCATGTATTTCATGTAACTTATAAACCATGT
* * *
25336590 AAATCATGTATTTCATGTAATTTATAATCTATGT
1 AAATCATGTATTTCATGTAACTTATAAACCATGT
*
25336624 GAATCAT
1 AAATCAT
25336631 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (34 bp):
AAATCATGTATTTCATGTAACTTATAAACCATGT
Found at i:25336836 original size:22 final size:22
Alignment explanation
Indices: 25336806--25336861 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
25336796 TCAGCTGGTA
*
25336806 AACGGTAAGCTCTATCGAGCTG
1 AACGATAAGCTCTATCGAGCTG
25336828 AACGATAAGCTCTATCGAGCTG
1 AACGATAAGCTCTATCGAGCTG
25336850 AACGATAAGCTC
1 AACGATAAGCTC
25336862 CGTAAAGCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (22 bp):
AACGATAAGCTCTATCGAGCTG
Found at i:25336870 original size:22 final size:22
Alignment explanation
Indices: 25336823--25336873 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
25336813 AGCTCTATCG
* **
25336823 AGCTGAACGATAAGCTCTATCG
1 AGCTGAACGATAAGCTCCATAA
*
25336845 AGCTGAACGATAAGCTCCGTAA
1 AGCTGAACGATAAGCTCCATAA
25336867 AGCTGAA
1 AGCTGAA
25336874 ATGGTCAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (22 bp):
AGCTGAACGATAAGCTCCATAA
Found at i:25344126 original size:34 final size:34
Alignment explanation
Indices: 25344079--25344156 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
25344069 AAATGATCCG
* *
25344079 TGTAAGTCATGTATTTTATGCAACTTATAAACCA
1 TGTAAATCATGTATTTCATGCAACTTATAAACCA
* * * * *
25344113 TGTAAATCGTGTATTTCATGTAATTTATAATCCT
1 TGTAAATCATGTATTTCATGCAACTTATAAACCA
25344147 TGTAAATCAT
1 TGTAAATCAT
25344157 ATAACTCTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
TGTAAATCATGTATTTCATGCAACTTATAAACCA
Found at i:25344418 original size:23 final size:23
Alignment explanation
Indices: 25344331--25344437 Score: 87
Period size: 23 Copynumber: 4.7 Consensus size: 23
25344321 TTCAGCTGGT
*
25344331 AAACGGTAAGCTC-TATCGAGCT-
1 AAACGGTAAGCTCATA-AGAGCTA
* *
25344353 GAATGGTAAGCTCCAT-AGAGCTA
1 AAACGGTAAGCT-CATAAGAGCTA
* *
25344376 AAACGGTAAGATCCGT-AGAGCTA
1 AAACGGTAAGCT-CATAAGAGCTA
* *
25344399 AAACGGTAACCTCATAAGAGCTG
1 AAACGGTAAGCTCATAAGAGCTA
*
25344422 AAATGGTAAGCTCATA
1 AAACGGTAAGCTCATA
25344438 CAAGGTGTAG
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.25
23 50 0.74
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (23 bp):
AAACGGTAAGCTCATAAGAGCTA
Found at i:25346084 original size:27 final size:27
Alignment explanation
Indices: 25346054--25346141 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
25346044 AAGGCATTTC
* * *
25346054 TTTCAGAGTTAACCACAAGGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
25346081 TTTCAAAGTTAGCCACAAAGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
*
25346108 TTTCATAGTTAGCCACAAAGGCTTCCT
1 TTTCAAAGTTAGCCACAAAGGCTTCCT
*
25346135 CTTCAAA
1 TTTCAAA
25346142 CATTTTTATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (27 bp):
TTTCAAAGTTAGCCACAAAGGCTTCCT
Found at i:25348035 original size:17 final size:17
Alignment explanation
Indices: 25348005--25348037 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25347995 ACAAAGAACG
25348005 AATAAAAATCATAAATA
1 AATAAAAATCATAAATA
25348022 AATAAGAAAT-ATAAAT
1 AATAA-AAATCATAAAT
25348038 TATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AATAAAAATCATAAATA
Found at i:25349264 original size:12 final size:13
Alignment explanation
Indices: 25349241--25349270 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
25349231 AATCTCAGAC
25349241 ATACCTTGATTCT
1 ATACCTTGATTCT
25349254 ATACC-TGATTCT
1 ATACCTTGATTCT
25349266 ATACC
1 ATACC
25349271 ATACATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (13 bp):
ATACCTTGATTCT
Found at i:25356112 original size:28 final size:28
Alignment explanation
Indices: 25356058--25356148 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 28
25356048 TATTCAGTAT
* *
25356058 CAGT-ACAGTGTGGGCC-TAGCCCGATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
25356084 CAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* * *
25356112 CAGTAATAGTGT-GGCCTTAGCTCAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
25356139 CAGTAACAAT
1 CAGTAACAAT
25356149 ATAGTGCCCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
26 4 0.07
27 33 0.59
28 19 0.34
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:25356495 original size:27 final size:27
Alignment explanation
Indices: 25356463--25356523 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
25356453 TGATCTCCTA
*
25356463 GAGGTATAATAGTTATTTTACCCTATG
1 GAGGTATAATAGTCATTTTACCCTATG
* ** * *
25356490 GGGGTATTTTGGTCATTTTACCTTATG
1 GAGGTATAATAGTCATTTTACCCTATG
25356517 GAGGTAT
1 GAGGTAT
25356524 TTTGATCATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (27 bp):
GAGGTATAATAGTCATTTTACCCTATG
Found at i:25356524 original size:27 final size:27
Alignment explanation
Indices: 25356477--25356562 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
25356467 TATAATAGTT
*
25356477 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCTTATGGGGGTATTTTGGTC
* *
25356504 ATTTTACCTTATGGAGGTATTTTGATC
1 ATTTTACCTTATGGGGGTATTTTGGTC
* *
25356531 ATTTTACCTTATGGGGGTCTTTCGGTC
1 ATTTTACCTTATGGGGGTATTTTGGTC
25356558 -TTTTA
1 ATTTTA
25356563 TTGACCCCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
26 5 0.10
27 47 0.90
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (27 bp):
ATTTTACCTTATGGGGGTATTTTGGTC
Found at i:25356819 original size:19 final size:19
Alignment explanation
Indices: 25356795--25356832 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25356785 CAGCCCATAC
*
25356795 GGCCCATTTCGGCCAACGT
1 GGCCCATTACGGCCAACGT
*
25356814 GGCCCATTACGGCCTACGT
1 GGCCCATTACGGCCAACGT
25356833 CCATGGAATT
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:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (19 bp):
GGCCCATTACGGCCAACGT
Found at i:25360474 original size:52 final size:52
Alignment explanation
Indices: 25360396--25360503 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
25360386 TTTCAAGGAT
25360396 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
1 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
25360448 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
1 CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
25360500 CAAC
1 CAAC
25360504 TAAAACTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.24
Consensus pattern (52 bp):
CAACCTTAATTCCCTCGGTAGATACCACATGACCCAAAAATGTCACTTCTCG
Found at i:25363838 original size:28 final size:28
Alignment explanation
Indices: 25363788--25363860 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
25363778 GTATTAGTAC
* *
25363788 AGTGTGGGCC-TAGCCCGATACAGTAAA
1 AGTGTGGGCCTTAGCCCAACACAGTAAA
* *
25363815 ATTGTGGGCCTTAGCCCAACACAGTAAT
1 AGTGTGGGCCTTAGCCCAACACAGTAAA
*
25363843 AGTAT-GGCCTTAGCCCAA
1 AGTGTGGGCCTTAGCCCAA
25363861 TACAATAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAACACAGTAAA
Found at i:25363872 original size:27 final size:27
Alignment explanation
Indices: 25363821--25363873 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
25363811 TAAAATTGTG
*
25363821 GGCCTTAGCCCAACACAGTAATAGTAT
1 GGCCTTAGCCCAACACAATAATAGTAT
* *
25363848 GGCCTTAGCCCAATACAATAGTAGTA
1 GGCCTTAGCCCAACACAATAATAGTA
25363874 CAGTGCCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (27 bp):
GGCCTTAGCCCAACACAATAATAGTAT
Found at i:25364004 original size:26 final size:26
Alignment explanation
Indices: 25363975--25364025 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
25363965 AACACACCAA
25363975 TATCGAAACAAAGCTGCCAGTAATAG
1 TATCGAAACAAAGCTGCCAGTAATAG
* ***
25364001 TATCGCAGTGAAGCTGCCAGTAATA
1 TATCGAAACAAAGCTGCCAGTAATA
25364026 ATATATGTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
TATCGAAACAAAGCTGCCAGTAATAG
Found at i:25364244 original size:27 final size:27
Alignment explanation
Indices: 25364214--25364272 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
25364204 ATCTCCTAGA
*
25364214 GGTATAACAGTCATTTTACCCTATGTG
1 GGTATAACAGTCATTTTACCCTATGGG
** *
25364241 GGTATTTCGGTCATTTTACCCTATGGG
1 GGTATAACAGTCATTTTACCCTATGGG
25364268 GGTAT
1 GGTAT
25364273 TTTGATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GGTATAACAGTCATTTTACCCTATGGG
Found at i:25364273 original size:27 final size:27
Alignment explanation
Indices: 25364223--25364311 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
25364213 AGGTATAACA
* *
25364223 GTCATTTTACCCTATGTGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTTG
*
25364250 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
* *
25364277 ATAATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTTG
25364304 GTC-TTTTA
1 GTCATTTTA
25364312 ATGATCGCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 5 0.09
27 50 0.91
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTTG
Found at i:25383190 original size:17 final size:17
Alignment explanation
Indices: 25383139--25383190 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
25383129 ATGGAAACAT
* *
25383139 AATCTTCGAGGATATGC
1 AATCTTAGAAGATATGC
*
25383156 AATCTTATATATGATATGC
1 AATCTTAGA-A-GATATGC
25383175 AATCTTAGAAGATATG
1 AATCTTAGAAGATATG
25383191 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
19 15 0.52
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (17 bp):
AATCTTAGAAGATATGC
Found at i:25383209 original size:22 final size:23
Alignment explanation
Indices: 25383179--25383224 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
25383169 ATATGCAATC
25383179 TTAGAAGATATGATTTTGTA-ATA
1 TTAGAAGATATGA-TTTGTAGATA
*
25383202 TTAG-AGATTTGATTTGTAGATA
1 TTAGAAGATATGATTTGTAGATA
25383224 T
1 T
25383225 CTTTTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (23 bp):
TTAGAAGATATGATTTGTAGATA
Found at i:25384046 original size:28 final size:27
Alignment explanation
Indices: 25384007--25384075 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
25383997 TGATTCACTG
* *
25384007 CAAAGGCATTTTCTTTCAGATTTAGCCA
1 CAAAGGC-TTTTTTTTCAGAGTTAGCCA
*
25384035 CAAAGGCTTTTTTTTCATAGTTAGCCA
1 CAAAGGCTTTTTTTTCAGAGTTAGCCA
*
25384062 CAAAGGCTTCTTTT
1 CAAAGGCTTTTTTT
25384076 ATTGACATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (27 bp):
CAAAGGCTTTTTTTTCAGAGTTAGCCA
Found at i:25386596 original size:61 final size:61
Alignment explanation
Indices: 25386500--25386633 Score: 187
Period size: 61 Copynumber: 2.2 Consensus size: 61
25386490 AAAGGATAGT
* * * *
25386500 CTTTGTGGAAAAACCTTGGATAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAAC
1 CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
* * * * *
25386561 TTTTGTGGCAAAACTTTGAACAGGAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAAC
1 CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
25386622 CTTTGTGGCAAA
1 CTTTGTGGCAAA
25386634 TCTCAGGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (61 bp):
CTTTGTGGCAAAACCTTGAACAGGAAAACCTTTGTGGCGAGTACTGAAAGTAAATGACAAC
Found at i:25386630 original size:32 final size:31
Alignment explanation
Indices: 25386526--25386630 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 31
25386516 TGGATAGGAA
* *
25386526 AACCTTTGTGGCGAGTACTGAAAGTAAATGGC
1 AACCTTTGTGGCGAGTACTG-ATGTAAATGAC
* ** * *
25386558 AACTTTTGTGGC-AAAACT-TTG-AACAGGA-
1 AACCTTTGTGGCGAGTACTGATGTAA-ATGAC
25386586 AAGCCTTTGTGGCGAGTACTGGATGTAAATGAC
1 AA-CCTTTGTGGCGAGTACT-GATGTAAATGAC
25386619 AACCTTTGTGGC
1 AACCTTTGTGGC
25386631 AAATCTCAGG
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
28 4 0.07
29 12 0.22
30 4 0.07
31 4 0.07
32 26 0.48
33 4 0.07
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
AACCTTTGTGGCGAGTACTGATGTAAATGAC
Found at i:25386651 original size:61 final size:61
Alignment explanation
Indices: 25386523--25386661 Score: 154
Period size: 61 Copynumber: 2.3 Consensus size: 61
25386513 CCTTGGATAG
* * * ** *
25386523 GAAAACCTTTGTGGCGAGTACTGAAAGTAAATGGCAACTTTTGTGGCAAAACTTTGAACAG
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
* * *
25386584 GAAAGCCTTTGTGGCGAGTACTGGATGTAAATGACAACCTTTGTGGCAAATCTCAGGAA-AC
1 GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACT-AGGAACAC
* **
25386645 GTAAGCCTAGGTGGCGA
1 GAAAGCCTTTGTGGCGA
25386662 ACCTCTACAA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 62 0.95
62 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCGAGTACTGAAAGTAAATGACAACCTTTGTGGCAAAACTAGGAACAC
Found at i:25406845 original size:28 final size:28
Alignment explanation
Indices: 25406814--25406893 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
25406804 TATTTTACAA
**
25406814 ATTTTACAGTTTTATCCCTATTTTTTTT
1 ATTTTACAGTTTTATCCCTATTTTTTAG
*
25406842 ATTTTACAATTTTA-CTCCTATTTTTTAG
1 ATTTTACAGTTTTATC-CCTATTTTTTAG
* *
25406870 ATTTTACAGTTTTGTTCCTATTTT
1 ATTTTACAGTTTTATCCCTATTTT
25406894 ACAAAAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.20, C:0.14, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTTACAGTTTTATCCCTATTTTTTAG
Found at i:25408659 original size:3 final size:3
Alignment explanation
Indices: 25408651--25408682 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
25408641 CTTGACTTTC
*
25408651 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25408683 ATGGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:25413162 original size:23 final size:23
Alignment explanation
Indices: 25413131--25413181 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
25413121 ACCTACTTTC
*
25413131 TTACTGTAGTAATTTTCAGGG-TA
1 TTACAGTAGTAATTTTC-GGGATA
25413154 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
25413177 TTACA
1 TTACA
25413182 CTTCACCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:25420268 original size:23 final size:23
Alignment explanation
Indices: 25420241--25420287 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
25420231 ACTATATCAG
* * *
25420241 TGAGAAATTCACTTATTGTGAAT
1 TGAGAAACTCACCTATTGAGAAT
*
25420264 TGAGATACTCACCTATTGAGAAT
1 TGAGAAACTCACCTATTGAGAAT
25420287 T
1 T
25420288 TATGTTGCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (23 bp):
TGAGAAACTCACCTATTGAGAAT
Found at i:25421877 original size:14 final size:14
Alignment explanation
Indices: 25421858--25421897 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25421848 TTGATTGCCA
25421858 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
25421872 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
25421886 GGAAAATGTTTT
1 GTAAAATGTTTT
25421898 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:25421913 original size:34 final size:35
Alignment explanation
Indices: 25421866--25421932 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
25421856 CAGTAAAATG
* *
25421866 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
25421900 TTTTCTGTGAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
25421933 CTGCTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:25423876 original size:54 final size:54
Alignment explanation
Indices: 25423806--25423980 Score: 138
Period size: 54 Copynumber: 3.4 Consensus size: 54
25423796 TTTCCCTGGC
*
25423806 GTTGTAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
* * * ** * * * *
25423860 GTTGTAGTGGAGCAGATTGAAGC--C--ACCA--GC----CTTATTTCCCTAG-C
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCT-TCTTGAA
*
25423904 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
* * *
25423958 GTTACAGTGGAGCAGATTTAAGC
1 GTTGCAGTGGAACAGATTAAAGC
25423981 CACCAACCTT
Statistics
Matches: 88, Mismatches: 21, Indels: 24
0.66 0.16 0.18
Matches are distributed among these distances:
44 26 0.30
45 3 0.03
46 1 0.01
48 4 0.05
50 4 0.05
52 1 0.01
53 2 0.02
54 47 0.53
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (54 bp):
GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAA
Found at i:25423918 original size:98 final size:97
Alignment explanation
Indices: 25423746--25424017 Score: 355
Period size: 98 Copynumber: 2.8 Consensus size: 97
25423736 AAGCTACCAG
* * * * * * * * *
25423746 TCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGT
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCA-CCAACCTTATTTCCCT-GCGTTGC
25423811 AGTGGAACAGATTAAAGCTACAAATTATGGCGGA
64 AGTGGAACAGATTAAAGCTACAAATTATGGCGGA
* ** *
25423845 TCTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTATTTCCCTAGCGTTGCA
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCT-GCGTTGCA
25423910 GTGGAACAGATTAAAGCTACAAATTATGGCGGA
65 GTGGAACAGATTAAAGCTACAAATTATGGCGGA
* * *
25423943 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTTAAGCCACCAACCTTATCTCCCTGAAGTTGCA
1 TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCTG-CGTTGCA
*
25424008 GTGGAGCAGA
65 GTGGAACAGA
25424018 ATGAAGATAG
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
97 1 0.01
98 118 0.78
99 33 0.22
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATTTCCCTGCGTTGCAG
TGGAACAGATTAAAGCTACAAATTATGGCGGA
Found at i:25424103 original size:143 final size:143
Alignment explanation
Indices: 25423846--25424584 Score: 815
Period size: 143 Copynumber: 5.2 Consensus size: 143
25423836 TATGGCGGAT
* * * * ** * ** *
25423846 CTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAAGCCA-CCAGCCTTATTTCCCTAGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
25423910 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
*
25423975 TTAAGCCACCAAC
131 TGAAGCCACCAAC
* * * * *
25423988 CTTATCTCCCTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATTTTATCTCCTTAGTGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * **
25424053 GTGGAACAAATTAAAGCTATAAATTATGGCGGATCTTATCTTCCTGAAGTTGTAGTGGAGCAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
* *
25424118 TGAAGCTACCATC
131 TGAAGCCACCAAC
* * * * ** *
25424131 CTTATCTCCCTGAAGATACAATGGAGCAGACTGAAGAAAATGAATCTTATCTCCCTGGCGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * * * * *
25424196 GTGGAACAAATTAAAGCTATAAGTTATGGCAGATCTTATATTCTTGAAGTTGA-AGTGGAGCAGA
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTT-ACAGTGGAGCAGA
*
25424260 TTGAAGCCACCAGC
130 TTGAAGCCACCAAC
* * * * * * * * *
25424274 CTTATCTCCCTGAAGTTGTA-TCAGAGTAGACTGAAGACT-GCAAATCTTATTTCTCTGGCATTA
1 CTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTGAAGA-TAGCGAATCTTATCTCCCTAGCGTTG
* * * * *
25424337 CAGTGGAACAGATTAAAGCTACAAGTTATGGCGAATCTTATCCTCCTGAAGTTGCAGTGGAGTAG
64 CAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAG
*
25424402 ATTGAAGCCACCAGC
129 ATTGAAGCCACCAAC
* * * * *
25424417 CTTATCTCTCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCGTTG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
* * * *
25424481 GTGGAACAGATTAAAACTACAAATCATGGAGGATCTTATCTTCCTGAAGTTACAGTGGAACAGAT
66 GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
** * *
25424546 CAAAGACA-TAATC
131 TGAAGCCACCAA-C
*
25424559 CTTATCTCTCTGAAGTTGCAGTGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
25424585 TAGGTTGAAA
Statistics
Matches: 500, Mismatches: 89, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
141 1 0.00
142 121 0.24
143 378 0.76
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (143 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAGCGTTGCA
GTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTACAGTGGAGCAGAT
TGAAGCCACCAAC
Found at i:25427580 original size:87 final size:86
Alignment explanation
Indices: 25427340--25427672 Score: 384
Period size: 86 Copynumber: 3.9 Consensus size: 86
25427330 TGGCGGCTAG
* * * * **
25427340 TCCACAAAACCCAGTAGCAATTTGTTTAATCTGCGAATATGTTATGCACCCACAGTAAGTGACAG
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
*
25427405 TAACTGCAAACATGTGGCTCA
66 TAACTGCAAATATGTGGCTCA
* * *
25427426 TCCACAAAACCTAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACATCAAGTGACAG
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
*
25427491 TAACTACAAATATGTGGCTCA
66 TAACTGCAAATATGTGGCTCA
* * ** * **
25427512 TCTACAAAACCCAGTGGCTAATTTGTATAATCTATAAATATGTTGTGCACTCATAACAAGTGGTA
1 TCCACAAAACCCAGTGGC-AATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACA
*
25427577 GTAACTGCAAATATGTGGCTCG
65 GTAACTGCAAATATGTGGCTCA
* * * * * **
25427599 TCC-CCAAACCTAGTGAC-TTTTGTTTAATTTGCAACCATGTTGTGCACTCACAACAAGTGGA-A
1 TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGT-GACA
*
25427661 GTAATTGCAAAT
65 GTAACTGCAAAT
25427673 GTTTTTTTTA
Statistics
Matches: 209, Mismatches: 36, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
84 45 0.22
85 1 0.00
86 103 0.49
87 60 0.29
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (86 bp):
TCCACAAAACCCAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGACAG
TAACTGCAAATATGTGGCTCA
Found at i:25429112 original size:26 final size:24
Alignment explanation
Indices: 25429029--25429118 Score: 85
Period size: 26 Copynumber: 3.6 Consensus size: 24
25429019 TCGAGCCATG
**
25429029 ATCGGTAAGCTCATTCTGAGCTGAA
1 ATCGGTAAGCTCA-TAAGAGCTGAA
*
25429054 GAACGGTAAGCTCTATAA-AGCTGAA
1 -ATCGGTAAGCTC-ATAAGAGCTGAA
25429079 AT-GGTAAGCTCATAAGAGCTGATA
1 ATCGGTAAGCTCATAAGAGCTGA-A
*
25429103 TATCGGTAAGCACATA
1 -ATCGGTAAGCTCATA
25429119 CGGGTTGTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
22 4 0.07
23 15 0.28
24 2 0.04
25 9 0.17
26 23 0.43
27 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (24 bp):
ATCGGTAAGCTCATAAGAGCTGAA
Found at i:25431058 original size:25 final size:26
Alignment explanation
Indices: 25431011--25431060 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
25431001 AAGAATAAAT
25431011 AAATTAACTAAGTTTTCAAAAATAGC
1 AAATTAACTAAGTTTTCAAAAATAGC
25431037 AAATTAACTAAG-TTTCAAAAATAG
1 AAATTAACTAAGTTTTCAAAAATAG
25431061 TTATCATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (26 bp):
AAATTAACTAAGTTTTCAAAAATAGC
Found at i:25432449 original size:29 final size:30
Alignment explanation
Indices: 25432403--25432461 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
25432393 TTTGGTCAAA
*
25432403 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
* *
25432432 TGTGCAATTTTATTCATGAAATTTTGATTT
1 TGTGCAATTTTATACATGAAACTTTGATTT
25432462 GATCCTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTTTATACATGAAACTTTGATTT
Found at i:25438935 original size:16 final size:17
Alignment explanation
Indices: 25438903--25438936 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25438893 CAATTCAGTC
25438903 CAAAATTCATACTTTTG
1 CAAAATTCATACTTTTG
*
25438920 CAAAATT-ATGCTTTTG
1 CAAAATTCATACTTTTG
25438936 C
1 C
25438937 CTCTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
CAAAATTCATACTTTTG
Found at i:25447593 original size:66 final size:66
Alignment explanation
Indices: 25447487--25447654 Score: 214
Period size: 66 Copynumber: 2.5 Consensus size: 66
25447477 AAAATTACAA
* * * *
25447487 AACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCT
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-
25447551 A-C
64 AGC
*
25447553 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAG
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAG
25447618 C
66 C
* * * * *
25447619 AGCTTAAAGTAGATGCGGCAGCAAGAGAAGCAGAGG
1 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
25447655 CGGCAGCTAG
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
65 1 0.01
66 85 0.94
67 4 0.04
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (66 bp):
AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAG
C
Found at i:25447682 original size:42 final size:42
Alignment explanation
Indices: 25447636--25447737 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
25447626 AGTAGATGCG
* * ** *
25447636 GCAGCAAGAGAAGCAGAGGCGGCAGCTAGAGAAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCT
* * *
25447678 GCAGCGAGGGAAGCAGAGGCTAAAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCT
25447720 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
25447738 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.06
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCT
Found at i:25447698 original size:21 final size:21
Alignment explanation
Indices: 25447636--25447737 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 21
25447626 AGTAGATGCG
* * *
25447636 GCAGCAAGAGAAGCAGAGGCG
1 GCAGCGAGGGAAGCAGAGGCT
* * * *
25447657 GCAGCTAGAGAAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
25447678 GCAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
** *
25447699 AAAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
25447720 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
25447738 CAGCGTCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.06
Consensus pattern (21 bp):
GCAGCGAGGGAAGCAGAGGCT
Found at i:25447920 original size:10 final size:9
Alignment explanation
Indices: 25447901--25447930 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
25447891 TAATACGAAT
25447901 TTTATTATA
1 TTTATTATA
25447910 TTTATTGATA
1 TTTATT-ATA
25447920 TTTATTATA
1 TTTATTATA
25447929 TT
1 TT
25447931 ATTTGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTATTATA
Found at i:25448178 original size:43 final size:43
Alignment explanation
Indices: 25448092--25448615 Score: 268
Period size: 43 Copynumber: 12.2 Consensus size: 43
25448082 TGTTGGTCTT
* * * ** *
25448092 TAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATCAGGGTCTA
1 TAGCGGCGTTTTTGGCAAAAGCGCCGCTAAAGACCCTGATCTA
* * *
25448135 TTGTGGCGTTTTTGGGAAAAGCGCCGCTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTGGCAAAAGCGCCGCTAAAGACCCTGATCTA
* * *
25448178 TAGCGGCG-CTTTGAGCAAAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTG-GCAAAAGCGCCGCTAAAGACCCTGATCTA
* ** * *
25448221 TAGCGGCG-CTTTAACTAAAAACGCCGCTAAAGACCC-CAGTCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGA-TCTA
* ** * * *
25448264 TAGCGGCGCTAAT-ACTAAAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGATCTA
* ** * *
25448307 TAGCGGCG-CTTTAACTAAAAACGCCGCTAAAGACCC-CAGTCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGA-TCTA
* ** * * *
25448350 TAGCGGCGCTAAT-ACTAAAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGATCTA
* ** * *
25448393 TAGCGGCG-CTTTAACTAAAAACGCCGCTAAAGACCC-CAGTCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGA-TCTA
* ** * * *
25448436 TAGCGGCGCTAAT-ACTAAAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGATCTA
* ** * *
25448479 TAGCGGCG-CTTTAACTAAAAACGCCGCTAAAGACCC-CAGTCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGA-TCTA
* ** * * *
25448522 TAGCGGCGCTAAT-ACTAAAAACGCCACTAAAGACCCTGATCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGATCTA
* * * *
25448565 TAGCGGCGCTTTT-ACTAAAAACGCCGCTAAAGACCC-CAGTCTA
1 TAGCGGCGTTTTTGGC-AAAAGCGCCGCTAAAGACCCTGA-TCTA
25448608 TAGCGGCG
1 TAGCGGCG
25448616 CTTATACTAA
Statistics
Matches: 406, Mismatches: 57, Indels: 36
0.81 0.11 0.07
Matches are distributed among these distances:
42 13 0.03
43 385 0.95
44 8 0.02
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGCAAAAGCGCCGCTAAAGACCCTGATCTA
Found at i:25448616 original size:43 final size:43
Alignment explanation
Indices: 25448151--25448639 Score: 657
Period size: 43 Copynumber: 11.4 Consensus size: 43
25448141 CGTTTTTGGG
* *
25448151 AAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTGAGC-
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTA-CT
* *
25448194 AAAAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTAACT
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
* **
25448237 AAAAACGCCGCTAAAGACCC-CAGTCTATAGCGGCGCTAATACT
1 AAAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTTTACT
* *
25448280 AAAAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTAACT
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
* **
25448323 AAAAACGCCGCTAAAGACCC-CAGTCTATAGCGGCGCTAATACT
1 AAAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTTTACT
* *
25448366 AAAAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTAACT
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
* **
25448409 AAAAACGCCGCTAAAGACCC-CAGTCTATAGCGGCGCTAATACT
1 AAAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTTTACT
* *
25448452 AAAAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTAACT
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
* **
25448495 AAAAACGCCGCTAAAGACCC-CAGTCTATAGCGGCGCTAATACT
1 AAAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTTTACT
*
25448538 AAAAACGCCACTAAAGACCCTGATCTATAGCGGCGCTTTTACT
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
* *
25448581 AAAAACGCCGCTAAAGACCC-CAGTCTATAGCGGCGCTTATACT
1 AAAAACGCCGCTAAAGACCCTGA-TCTATAGCGGCGCTTTTACT
25448624 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
25448640 GTATTAGTCT
Statistics
Matches: 391, Mismatches: 45, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
42 6 0.02
43 381 0.97
44 4 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTTACT
Found at i:25448669 original size:86 final size:86
Alignment explanation
Indices: 25448151--25448639 Score: 876
Period size: 86 Copynumber: 5.7 Consensus size: 86
25448141 CGTTTTTGGG
* * *
25448151 AAAAGCGCCGCTAAAGA-CCCTGATCTATAGCGGCGCT-TTGAGC-AAAAACGCCACTAAAGACC
1 AAAAACGCCGCTAAAGACCCCAG-TCTATAGCGGCGCTAAT-A-CTAAAAACGCCACTAAAGACC
25448213 CTGATCTATAGCGGCGCTTTAACT
63 CTGATCTATAGCGGCGCTTTAACT
25448237 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
1 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
25448302 ATCTATAGCGGCGCTTTAACT
66 ATCTATAGCGGCGCTTTAACT
25448323 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
1 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
25448388 ATCTATAGCGGCGCTTTAACT
66 ATCTATAGCGGCGCTTTAACT
25448409 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
1 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
25448474 ATCTATAGCGGCGCTTTAACT
66 ATCTATAGCGGCGCTTTAACT
25448495 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
1 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
*
25448560 ATCTATAGCGGCGCTTTTACT
66 ATCTATAGCGGCGCTTTAACT
* *
25448581 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTTATACTAAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAG
25448640 GTATTAGTCT
Statistics
Matches: 394, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
85 1 0.00
86 388 0.98
87 5 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (86 bp):
AAAAACGCCGCTAAAGACCCCAGTCTATAGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTG
ATCTATAGCGGCGCTTTAACT
Found at i:25448693 original size:42 final size:43
Alignment explanation
Indices: 25448265--25448705 Score: 175
Period size: 43 Copynumber: 10.3 Consensus size: 43
25448255 CCCAGTCTAT
* ** *
25448265 AGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGA-TCTAT-
1 AGCGGCGCTTATACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* *** *
25448308 AGCGGCGCTT-TAACTAAAAACGCCGCTAAAGAC-CCCAGTCTAT-
1 AGCGGCGCTTAT-ACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* ** *
25448351 AGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGA-TCTAT-
1 AGCGGCGCTTATACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* *** *
25448394 AGCGGCGCTT-TAACTAAAAACGCCGCTAAAGAC-CCCAGTCTAT-
1 AGCGGCGCTTAT-ACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* ** *
25448437 AGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGA-TCTAT-
1 AGCGGCGCTTATACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* *** *
25448480 AGCGGCGCTT-TAACTAAAAACGCCGCTAAAGAC-CCCAGTCTAT-
1 AGCGGCGCTTAT-ACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* ** *
25448523 AGCGGCGCTAATACTAAAAACGCCACTAAAGACCCTGA-TCTAT-
1 AGCGGCGCTTATACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* * *** *
25448566 AGCGGCGCTTTTACTAAAAACGCCGCTAAAGAC-CCCAGTCTAT-
1 AGCGGCGCTTATACTAAAAACGCCACTAAAG-CTATTACTCT-TC
* * *
25448609 AGCGGCGCTTATACTAAAAACGCCGCTAAAGGTATTAGTCTTC
1 AGCGGCGCTTATACTAAAAACGCCACTAAAGCTATTACTCTTC
* * *
25448652 AGCGGCGCTTCTACT-AAAGCGCCACTAAAGCTCTTACTCTTC
1 AGCGGCGCTTATACTAAAAACGCCACTAAAGCTATTACTCTTC
*
25448694 AGCGGCGTTTAT
1 AGCGGCGCTTAT
25448706 GATAGAAGCG
Statistics
Matches: 341, Mismatches: 42, Indels: 31
0.82 0.10 0.07
Matches are distributed among these distances:
42 44 0.13
43 288 0.84
44 9 0.03
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
AGCGGCGCTTATACTAAAAACGCCACTAAAGCTATTACTCTTC
Found at i:25448837 original size:22 final size:21
Alignment explanation
Indices: 25448804--25448848 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
25448794 TTCTGCGGCG
*
25448804 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
25448825 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
25448847 CT
1 CT
25448849 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:25449855 original size:27 final size:28
Alignment explanation
Indices: 25449802--25449861 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
25449792 CTTGGGAAAG
*
25449802 AAAAAATCATTTAAATACCACTTATGATA
1 AAAAAATCATTTAAATACCACTCATGA-A
*
25449831 AAAAAAT-ATTTAAGTACCAC-CATGAA
1 AAAAAATCATTTAAATACCACTCATGAA
25449857 AAAAA
1 AAAAA
25449862 GTTTATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 4 0.14
28 12 0.41
29 7 0.24
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAAATCATTTAAATACCACTCATGAA
Found at i:25454472 original size:30 final size:30
Alignment explanation
Indices: 25454438--25454539 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
25454428 AAGTAGGATC
25454438 ACACGACCGTGTAACTCTCTGACTTGCCAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
* * *
25454468 ACACGGCCGTATAACTCTCTGACTTACCAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
* * *
25454498 ACACGGCTGTGTAACTCTCTGACTTGCTAT
1 ACACGACCGTGTAACTCTCTGACTTGCCAT
25454528 ACAC-AGCCGTGT
1 ACACGA-CCGTGT
25454540 CGCAGGCCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (30 bp):
ACACGACCGTGTAACTCTCTGACTTGCCAT
Found at i:25454565 original size:42 final size:42
Alignment explanation
Indices: 25454506--25454593 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
25454496 ATACACGGCT
* * *
25454506 GTGTAACTCTCTGACTTGCTATACACAGCCGTGTCGCAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
*
25454548 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTGGCAGGCC
1 GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
25454590 GTGT
1 GTGT
25454594 GCTAGGCCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (42 bp):
GTGTAACTCTCTAACTTGCCACACACAGCCGTGTCGCAGGCC
Found at i:25457307 original size:37 final size:37
Alignment explanation
Indices: 25457249--25457319 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
25457239 ACTACATGTG
* *
25457249 AGCTGGGAACAGAAAGGTTGCGAACTGATGGAGTGCA
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
* * *
25457286 AGCTGCGAACAGAGAGCTTGCGCACTGGTGGAGT
1 AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGT
25457320 ACGAGTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.38, T:0.17
Consensus pattern (37 bp):
AGCTGCGAACAGAAAGCTTGCGAACTGATGGAGTGCA
Found at i:25459194 original size:21 final size:22
Alignment explanation
Indices: 25459165--25459255 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 22
25459155 CTTCTCTCTC
25459165 AAAA-AATTTC-ATTATATAAT
1 AAAATAATTTCAATTATATAAT
* * *
25459185 AAAATAATTT-TATTTTAAAAT
1 AAAATAATTTCAATTATATAAT
*
25459206 AAGATAATTTCAATTTAATATAAT
1 AAAATAATTTCAA-TT-ATATAAT
* *
25459230 -TAATAAGTTTACTATTATATAAT
1 AAAATAA-TTT-CAATTATATAAT
25459253 AAA
1 AAA
25459256 TTGTTAAACG
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.08
21 22 0.42
22 1 0.02
23 13 0.25
24 11 0.21
25 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATAATTTCAATTATATAAT
Found at i:25459940 original size:2 final size:2
Alignment explanation
Indices: 25459935--25459963 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25459925 TTTCCTCTCT
25459935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25459964 TCCCCAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25465291 original size:12 final size:12
Alignment explanation
Indices: 25465274--25465306 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25465264 AAATCGGCAG
25465274 AAAAAGAGAAAA-
1 AAAAAGA-AAAAC
25465286 AAAAAGAAAAAC
1 AAAAAGAAAAAC
25465298 AAAAAGAAA
1 AAAAAGAAA
25465307 TAGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:25478798 original size:44 final size:44
Alignment explanation
Indices: 25478743--25479064 Score: 163
Period size: 44 Copynumber: 7.3 Consensus size: 44
25478733 CAGTAAGGAT
* *
25478743 AGCAGATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* ** ** * *
25478787 GGCAAATCTTATCT-TTTCAAG-A-TAGTGGGAAGCAGATTTAGGCC
1 AGCAAATCTTATCTCCCT-AAGCAGTAGT-GG-AGCAGATCAAAGAC
* * * * * * * * ** **
25478831 ACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGGT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
*
25478875 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * ** *
25478919 GGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCC
1 AGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGAC
** * * * * * * * * *
25478963 TCCGAGTCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTC-AAGAT
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGAC
*
25479007 AGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
25479051 GGTAAATCTTATCT
1 AGCAAATCTTATCT
25479065 TTCTAGGATA
Statistics
Matches: 192, Mismatches: 72, Indels: 28
0.66 0.25 0.10
Matches are distributed among these distances:
42 8 0.04
43 13 0.07
44 155 0.81
45 12 0.06
46 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
AGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
Found at i:25478979 original size:132 final size:132
Alignment explanation
Indices: 25478737--25479135 Score: 663
Period size: 132 Copynumber: 3.0 Consensus size: 132
25478727 ACAGATCAGT
*
25478737 AAGGATAGCAGATCTTATCCCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTT
1 AAGG-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTT
* * * *
25478802 TTCAAGATAGTGGGAAGCAGATTTAGGCCACCAAACCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
65 TCCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGG
25478867 TTG
130 TTG
25478870 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* *
25478935 CCAAGATAGTGGGAAGCAGATTTAAGCCTCCGAGTCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
*
25479000 TC
131 TG
* *
25479002 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTT
1 AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* * * *
25479067 CTAGGATAGTGGGAAGCAGATTTAAGCCACAGAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
25479132 TG
131 TG
25479134 AA
1 AA
25479136 AATTAGAAGT
Statistics
Matches: 249, Mismatches: 17, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
132 245 0.98
133 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (132 bp):
AAGGTAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
TG
Found at i:25479816 original size:12 final size:12
Alignment explanation
Indices: 25479799--25479831 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25479789 AAATCGGCAG
25479799 AAAAAGAGAAAA-
1 AAAAAGA-AAAAC
25479811 AAAAAGAAAAAC
1 AAAAAGAAAAAC
25479823 AAAAAGAAA
1 AAAAAGAAA
25479832 TAGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:25481120 original size:43 final size:43
Alignment explanation
Indices: 25481059--25481287 Score: 431
Period size: 43 Copynumber: 5.3 Consensus size: 43
25481049 TTTTTAATAT
25481059 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
25481102 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
25481145 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
25481188 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
25481231 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
1 ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
* *
25481274 TCTATATTTTATAT
1 ACTAT-TATTATAT
25481288 ATTTTAACTT
Statistics
Matches: 183, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
43 176 0.96
44 7 0.04
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (43 bp):
ACTATTATTATATGTATGTACATAATTATTTTAATTACCCTCC
Found at i:25490862 original size:29 final size:29
Alignment explanation
Indices: 25490829--25490886 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
25490819 TCTTCTTCTC
*
25490829 CTTCTTTTTTTTTTTTTTTTTTAAATCTA
1 CTTCTTTTTTTTTTTTTTTTCTAAATCTA
25490858 CTTCTTTTTTTTTTTTTTTTCTAAATCTA
1 CTTCTTTTTTTTTTTTTTTTCTAAATCTA
25490887 GTTTAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (29 bp):
CTTCTTTTTTTTTTTTTTTTCTAAATCTA
Found at i:25490898 original size:29 final size:29
Alignment explanation
Indices: 25490837--25490902 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
25490827 TCCTTCTTTT
* * *
25490837 TTTTTTTTTTTTTTAAATCTACTTCTTTT
1 TTTTTTTTTTTTCTAAATCTACTTCTATA
*
25490866 TTTTTTTTTTTTCTAAATCTAGTT-TAATA
1 TTTTTTTTTTTTCTAAATCTACTTCT-ATA
25490895 TTTTTTTT
1 TTTTTTTT
25490903 GTCATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.74
Consensus pattern (29 bp):
TTTTTTTTTTTTCTAAATCTACTTCTATA
Found at i:25492233 original size:9 final size:9
Alignment explanation
Indices: 25492219--25492252 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
25492209 GTTTTCGAAG
*
25492219 TCGAATAAC
1 TCGAATAAT
25492228 TCGAATAAT
1 TCGAATAAT
25492237 TCGAATAAT
1 TCGAATAAT
25492246 TCGAATA
1 TCGAATA
25492253 TCAAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (9 bp):
TCGAATAAT
Found at i:25497521 original size:14 final size:14
Alignment explanation
Indices: 25497479--25497521 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
25497469 AAAATCGTCG
*
25497479 AATAAAATTGAAGAA
1 AATAAAATAGAA-AA
* *
25497494 AATAAAAAATAAAA
1 AATAAAATAGAAAA
25497508 AATAAAATAGAAAA
1 AATAAAATAGAAAA
25497522 TCCCCTTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
AATAAAATAGAAAA
Found at i:25497809 original size:30 final size:30
Alignment explanation
Indices: 25497773--25497836 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
25497763 TGGTTTTTGG
* *
25497773 GTTTAGGCTAGTTGGGTTTGGGTTAAAGCT
1 GTTTAGGCTAATTGGGTTTAGGTTAAAGCT
*
25497803 GTTTAGGCTAATTGGGTTTAGGTTAAAGTT
1 GTTTAGGCTAATTGGGTTTAGGTTAAAGCT
25497833 GTTT
1 GTTT
25497837 TTTTTTTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.44
Consensus pattern (30 bp):
GTTTAGGCTAATTGGGTTTAGGTTAAAGCT
Found at i:25497821 original size:15 final size:15
Alignment explanation
Indices: 25497769--25497824 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
25497759 GGCTTGGTTT
*
25497769 TTGGGTTTAGGCTAG
1 TTGGGTTTAGGCTAA
* *
25497784 TTGGGTTTGGGTTAA
1 TTGGGTTTAGGCTAA
* *
25497799 -AGCTGTTTAGGCTAA
1 TTG-GGTTTAGGCTAA
25497814 TTGGGTTTAGG
1 TTGGGTTTAGG
25497825 TTAAAGTTGT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.38, T:0.41
Consensus pattern (15 bp):
TTGGGTTTAGGCTAA
Found at i:25498314 original size:44 final size:44
Alignment explanation
Indices: 25498265--25498646 Score: 147
Period size: 44 Copynumber: 8.2 Consensus size: 44
25498255 TAACTTTAGA
* * *
25498265 GAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * * *
25498309 GAGATAGGATTAC-TAGCTTCAATCTGCT-TAGCTGTAATATCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCA-CTGTAATCTCAGG
* *
25498353 GAGATAAGAT--TTCTGGCTTCAATATGATGCGATCTACTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-GCTTC---A--ATCCG--CT-C-C-ACTGTAATC-TCAGG
* ** *
25498407 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGG
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * * *
25498451 GAGATAGGATTAC-TAGCTTCAATCTGCT-TAGCTGTAATATCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCA-CTGTAATCTCAGG
*
25498495 GAGATAAGAT--TTCTGGCTTCAATCCGGTGCGATCTATTCTACTGTAA-CTTCAGA
1 GAGATAAGATACTT-T-GCTTCAATCC---GC--TC----C-ACTGTAATC-TCAGG
* ** * *
25498549 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGA
1 GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
* * * *
25498593 GAGATAGGATTAC-TAGCTTCAATCTGCTCCGCTGTAATCTCAGG
1 GAGATAAGA-TACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
25498637 GAGATAAGAT
1 GAGATAAGAT
25498647 TTCTGGCTTT
Statistics
Matches: 249, Mismatches: 48, Indels: 83
0.66 0.13 0.22
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
44 154 0.62
45 10 0.04
46 1 0.00
47 5 0.02
49 10 0.04
51 5 0.02
54 49 0.20
55 4 0.02
56 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
GAGATAAGATACTTTGCTTCAATCCGCTCCACTGTAATCTCAGG
Found at i:25498395 original size:142 final size:142
Alignment explanation
Indices: 25498226--25498746 Score: 907
Period size: 142 Copynumber: 3.7 Consensus size: 142
25498216 TGCTGTTGTA
* *
25498226 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTGTTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
25498291 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
25498356 ATAAGATTTCTG
131 ATAAGATTTCTG
*
25498368 GCTTCAATATGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
25498433 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
25498498 ATAAGATTTCTG
131 ATAAGATTTCTG
* * *
25498510 GCTTCAATCCGGTGCGATCTATTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
* ** *
25498575 CTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
25498640 ATAAGATTTCTG
131 ATAAGATTTCTG
* * * *
25498652 GCTTTAATCTGATGCAATCTACTCTACTATAACTTTAGAGAGATAAGATCCTTTTATTTTAATCC
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC-TTTATTTTAATCC
25498717 GCTCCACTGTAATCTCAGGGAGATAGGATT
65 GCTCCACTGTAATCTCAGGGAGATAGGATT
25498747 TCTTCTATCT
Statistics
Matches: 359, Mismatches: 19, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
142 317 0.88
143 42 0.12
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (142 bp):
GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTTAGCTGTAATATCAGGGAG
ATAAGATTTCTG
Found at i:25498661 original size:44 final size:44
Alignment explanation
Indices: 25498566--25498662 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
25498556 GATCCTTTAT
* *
25498566 TTTAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGC
1 TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
* * * * *
25498610 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGC
1 TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
25498654 TTTAATCTG
1 TTTAATCTG
25498663 ATGCAATCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGC
Found at i:25512641 original size:30 final size:30
Alignment explanation
Indices: 25512607--25512670 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
25512597 TGGTTTTTGG
* *
25512607 GTTTAGGCT-AGCTAGGTTTGGGTTAAAGCT
1 GTTTAGGCTAATC-AGGTTTGAGTTAAAGCT
*
25512637 GTTTAGGCTAATCGGGTTTGAGTTAAAGCT
1 GTTTAGGCTAATCAGGTTTGAGTTAAAGCT
25512667 GTTT
1 GTTT
25512671 TTTTTTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.39
Consensus pattern (30 bp):
GTTTAGGCTAATCAGGTTTGAGTTAAAGCT
Found at i:25515232 original size:18 final size:18
Alignment explanation
Indices: 25515205--25515241 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25515195 TGATTTTTCG
*
25515205 AATTCAAATAACTCGAAT
1 AATTCAAATAAATCGAAT
*
25515223 AATTCGAATAAATCGAAT
1 AATTCAAATAAATCGAAT
25515241 A
1 A
25515242 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:25520737 original size:1 final size:1
Alignment explanation
Indices: 25520731--25520760 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
25520721 CTAAGCAAGC
25520731 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25520761 GAAGAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25528224 original size:85 final size:85
Alignment explanation
Indices: 25528081--25528250 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
25528071 TCACTTTTGG
25528081 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTATAAAATTCCCATTTTTATCGAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTATAAAATTCCCATTTTTATCGAGAAA
*
25528146 AGAGCCAAAGTGAGATTTTA
66 AGAGCCAAACTGAGATTTTA
* *
25528166 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTGTAAAATTCCCATTTTTATCTAGAAA
1 GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTATAAAATTCCCATTTTTATCGAGAAA
*
25528231 ATAGCCAAACTGAGATTTTA
66 AGAGCCAAACTGAGATTTTA
25528251 ATTACTCATG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (85 bp):
GACTAAATTAGAAAATTTGAATAGTACAATGATTAAATTATAAAATTCCCATTTTTATCGAGAAA
AGAGCCAAACTGAGATTTTA
Found at i:25533874 original size:16 final size:16
Alignment explanation
Indices: 25533835--25533874 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
25533825 TCTTCAACTG
*
25533835 AAGAAAGAATATGCCT
1 AAGAAAGAATACGCCT
*
25533851 AATAAAGAATACGCCT
1 AAGAAAGAATACGCCT
*
25533867 AAGGAAGA
1 AAGAAAGA
25533875 GTATGCCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (16 bp):
AAGAAAGAATACGCCT
Found at i:25535169 original size:25 final size:25
Alignment explanation
Indices: 25535126--25535179 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
25535116 TTGTAGCGAG
* **
25535126 TTATTTGTAAGGCTTTTATGAAAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
**
25535151 TTATTTGTAAAGCCCTTATGGTAAA
1 TTATTTGTAAAGCCCTTATGAAAAA
25535176 TTAT
1 TTAT
25535180 CTAAAAGGCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGTAAAGCCCTTATGAAAAA
Done.