Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1116

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: 35198
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:5052 original size:13 final size:13

Alignment explanation

Indices: 5034--5059 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 5024 AGCAGCATAA 5034 CTTTTTTGTATGC 1 CTTTTTTGTATGC 5047 CTTTTTTGTATGC 1 CTTTTTTGTATGC 5060 ATTGTTATAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62 Consensus pattern (13 bp): CTTTTTTGTATGC Found at i:5135 original size:2 final size:2 Alignment explanation

Indices: 5128--5166 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 5118 TTATAGACTG 5128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 5167 TGTGTAATAT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:7339 original size:2 final size:2 Alignment explanation

Indices: 7332--7358 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 7322 ACGAATTTAA 7332 AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT A 7359 ATTGTCTATG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:14127 original size:16 final size:15 Alignment explanation

Indices: 14089--14139 Score: 59 Period size: 16 Copynumber: 3.3 Consensus size: 15 14079 AAAATATTAA 14089 AAAATTTATATTTT-T 1 AAAA-TTATATTTTAT * 14104 ATAATTATATTTATAT 1 AAAATTATATTT-TAT 14120 AAAATTATTATTTTAT 1 AAAATTA-TATTTTAT 14136 AAAA 1 AAAA 14140 AAATAATTTA Statistics Matches: 31, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 14 8 0.26 15 4 0.13 16 14 0.45 17 5 0.16 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (15 bp): AAAATTATATTTTAT Found at i:14944 original size:18 final size:17 Alignment explanation

Indices: 14921--14955 Score: 52 Period size: 17 Copynumber: 2.0 Consensus size: 17 14911 TTTTTGAACA 14921 TTTAATATATTAAAATTT 1 TTTAATAT-TTAAAATTT * 14939 TTTAATATTTCAAATTT 1 TTTAATATTTAAAATTT 14956 GATTTTAATG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57 Consensus pattern (17 bp): TTTAATATTTAAAATTT Found at i:18657 original size:21 final size:20 Alignment explanation

Indices: 18617--18655 Score: 53 Period size: 22 Copynumber: 1.9 Consensus size: 20 18607 TTAAGTATAA 18617 ATATTTTTCAAGCATTAAATC 1 ATATTTTTCAA-CATTAAATC 18638 ATATGTTTTCAA-ATTAAA 1 ATAT-TTTTCAACATTAAA 18656 ATAATTCAAA Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 20 6 0.35 21 4 0.24 22 7 0.41 ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44 Consensus pattern (20 bp): ATATTTTTCAACATTAAATC Found at i:27273 original size:19 final size:19 Alignment explanation

Indices: 27249--27303 Score: 101 Period size: 19 Copynumber: 2.9 Consensus size: 19 27239 AATTCAACAA 27249 TTTGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT 27268 TTTGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT * 27287 ATTGTATCGATACATAA 1 TTTGTATCGATACATAA 27304 TTAGCTACTA Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 19 35 1.00 ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40 Consensus pattern (19 bp): TTTGTATCGATACATAAGT Found at i:27361 original size:13 final size:13 Alignment explanation

Indices: 27343--27401 Score: 67 Period size: 13 Copynumber: 5.0 Consensus size: 13 27333 CATTTTTCTG 27343 TGTATCGATACAT 1 TGTATCGATACAT 27356 TGTATCGATACA- 1 TGTATCGATACAT * 27368 TG----GAT-CTT 1 TGTATCGATACAT 27376 TGTATCGATACAT 1 TGTATCGATACAT 27389 TGTATCGATACAT 1 TGTATCGATACAT 27402 GGATCTTTGT Statistics Matches: 38, Mismatches: 2, Indels: 12 0.73 0.04 0.23 Matches are distributed among these distances: 7 1 0.03 8 5 0.13 12 5 0.13 13 27 0.71 ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39 Consensus pattern (13 bp): TGTATCGATACAT Found at i:27367 original size:33 final size:33 Alignment explanation

Indices: 27343--27422 Score: 160 Period size: 33 Copynumber: 2.4 Consensus size: 33 27333 CATTTTTCTG 27343 TGTATCGATACATTGTATCGATACATGGATCTT 1 TGTATCGATACATTGTATCGATACATGGATCTT 27376 TGTATCGATACATTGTATCGATACATGGATCTT 1 TGTATCGATACATTGTATCGATACATGGATCTT 27409 TGTATCGATACATT 1 TGTATCGATACATT 27423 TGGAAATTTT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 47 1.00 ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40 Consensus pattern (33 bp): TGTATCGATACATTGTATCGATACATGGATCTT Found at i:27380 original size:20 final size:20 Alignment explanation

Indices: 27355--27421 Score: 85 Period size: 20 Copynumber: 3.7 Consensus size: 20 27345 TATCGATACA 27355 TTGTATCGATACATGGATCT 1 TTGTATCGATACATGGATCT 27375 TTGTATCGATAC----A--- 1 TTGTATCGATACATGGATCT 27388 TTGTATCGATACATGGATCT 1 TTGTATCGATACATGGATCT 27408 TTGTATCGATACAT 1 TTGTATCGATACAT 27422 TTGGAAATTT Statistics Matches: 40, Mismatches: 0, Indels: 14 0.74 0.00 0.26 Matches are distributed among these distances: 13 12 0.30 16 1 0.03 17 1 0.03 20 26 0.65 ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40 Consensus pattern (20 bp): TTGTATCGATACATGGATCT Found at i:28977 original size:55 final size:55 Alignment explanation

Indices: 28893--29392 Score: 628 Period size: 55 Copynumber: 9.0 Consensus size: 55 28883 GATGCCTTCT 28893 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG 1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG 28948 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG 1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG * 29003 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACG 1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG * * * 29058 CCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTATTCTTCAAAGAGCAGGATG 1 ----C-C-TTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG * * * * * * 29119 CCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCCAGTCCTCAAAGAGTAGGACA 1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG * * * 29175 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACA 1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG * * * * * 29230 CCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA 1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG * * * * 29285 CCTCTTAAAGCCCACACAGGTTGGTGGCACCTTTC-AGTCCTCAAAGACCA-GACCG 1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA-CG * * * ** * * 29340 CCTTTCAAAGCCCACACGAGTTAGTGGCACTTTTTAGTCCTCAATGAGTAGGA 1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA 29393 TACACTTTAT Statistics Matches: 399, Mismatches: 34, Indels: 23 0.88 0.07 0.05 Matches are distributed among these distances: 54 10 0.03 55 277 0.69 56 60 0.15 57 1 0.00 59 1 0.00 60 1 0.00 61 49 0.12 ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23 Consensus pattern (55 bp): CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACG Found at i:32716 original size:51 final size:52 Alignment explanation

Indices: 32657--33046 Score: 208 Period size: 52 Copynumber: 7.4 Consensus size: 52 32647 CTCAATTCTC * * * * 32657 CACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAGACA-CTAATTTT 1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT * ** 32707 CTATAATCGGGGATACTCCAACTCTAATTTTATTTCCAAAAAAACACCAAATTTT 1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAAACACCAAATTTT * * *** * * * 32762 CACAATCGGGGATACTCCAACTCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT 1 CACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----AT-TTT * * * * * *** * 32820 C-CGA--GGGGATACTCCAACCCCGACTTTATTTTC-AAAATATTGATTTTT 1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT * * * * * * * 32868 CATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTT 1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT * * * * * 32919 CCACAATCGGGGATACTACAACCCCGGTTTTATTTTC-AAAACACCAATTTTT 1 -CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT * * 32971 C-CTTTAATCGGAGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT 1 CAC---AATCGG-GGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT * 33026 CACAATCGAGGATACTCCAAC 1 CACAATCGGGGATACTCCAAC 33047 CTCGTTATCT Statistics Matches: 264, Mismatches: 49, Indels: 52 0.72 0.13 0.14 Matches are distributed among these distances: 48 4 0.02 49 3 0.01 50 5 0.02 51 65 0.25 52 66 0.25 53 16 0.06 54 52 0.20 55 40 0.15 56 2 0.01 57 7 0.03 58 4 0.02 ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32 Consensus pattern (52 bp): CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAATTTT Found at i:32781 original size:54 final size:50 Alignment explanation

Indices: 32657--33046 Score: 153 Period size: 51 Copynumber: 7.4 Consensus size: 50 32647 CTCAATTCTC * * * * * 32657 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT 1 CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACAAATTTT * * 32707 CTATAATCGGGGATACTCCAACTCTAATTTTATTTCCAAAAAAACACCAAATTTT 1 C-ACAATCGGGGATACTCCAACTCCAATTTTATTTCC---AAAACA-CAAATTTT ** * * *** 32762 CACAATCGGGGATACTCCAACTCCGTTAATCATCGGGGATACTCC--AACCCCGTTATTT 1 CACAATCGGGGATACTCCAACTCC---AAT--T---TTAT-TTCCAAAACACAAAT-TTT * * * * * * ** * 32820 C-CGA--GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTT 1 CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACA-CAAATTTT * * ** * * * 32868 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT 1 CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACAC-AAATTTT * * ** * * 32919 CCACAATCGGGGATACTACAACCCCGGTTTTATTTTCAAAACACCAATTTTT 1 -CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACA-CAAATTTT * * * 32971 C-CTTTAATCGGAGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT 1 CAC---AATCGG-GGATACTCCAACTCCAATTTTATTTCC-AAAACA-CAAATTTT * 33026 CACAATCGAGGATACTCCAAC 1 CACAATCGGGGATACTCCAAC 33047 CTCGTTATCT Statistics Matches: 260, Mismatches: 50, Indels: 58 0.71 0.14 0.16 Matches are distributed among these distances: 46 2 0.01 47 2 0.01 48 6 0.02 49 3 0.01 50 3 0.01 51 66 0.25 52 57 0.22 53 12 0.05 54 49 0.19 55 39 0.15 56 1 0.00 57 7 0.03 58 7 0.03 59 1 0.00 62 2 0.01 63 3 0.01 ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32 Consensus pattern (50 bp): CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACAAATTTT Found at i:32836 original size:28 final size:27 Alignment explanation

Indices: 32769--32841 Score: 92 Period size: 27 Copynumber: 2.7 Consensus size: 27 32759 TTTCACAATC * ** 32769 GGGGATACTCCAACTCCGTTAATCATC 1 GGGGATACTCCAACCCCGTTAATCAGA * * 32796 GGGGATACTCCAACCCCGTTATTTCCGA 1 GGGGATACTCCAACCCCGTTA-ATCAGA 32824 GGGGATACTCCAACCCCG 1 GGGGATACTCCAACCCCG 32842 ACTTTATTTT Statistics Matches: 40, Mismatches: 5, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 27 20 0.50 28 20 0.50 ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22 Consensus pattern (27 bp): GGGGATACTCCAACCCCGTTAATCAGA Found at i:33039 original size:106 final size:103 Alignment explanation

Indices: 32826--33047 Score: 266 Period size: 106 Copynumber: 2.1 Consensus size: 103 32816 ATTTCCGAGG * *** 32826 GGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCC 1 GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC * * * * * 32891 CGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG 66 CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA * ** * 32929 GGATACTACAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGAGGATACTCCAA 1 GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTT-C-ATAATCGG-GGATACTCCAA * * 32994 CTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA 63 CCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA 33035 GGATACTCCAACC 1 GGATACTCCAACC 33048 TCGTTATCTC Statistics Matches: 99, Mismatches: 16, Indels: 5 0.82 0.13 0.04 Matches are distributed among these distances: 103 35 0.35 104 1 0.01 105 7 0.07 106 40 0.40 107 16 0.16 ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33 Consensus pattern (103 bp): GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA Found at i:33066 original size:28 final size:28 Alignment explanation

Indices: 33030--33104 Score: 89 Period size: 28 Copynumber: 2.7 Consensus size: 28 33020 ATTTTTCACA * * 33030 ATCGAGGATACTCCAACCTCGTTA-TCTC 1 ATCGGGGATACTCCAACCCCGTTACT-TC 33058 ATCGGGGATACTCCAACCCCGTTACTTC 1 ATCGGGGATACTCCAACCCCGTTACTTC *** 33086 CGAGGGGATACTCCAACCC 1 ATCGGGGATACTCCAACCC 33105 TGGCTTTATT Statistics Matches: 41, Mismatches: 5, Indels: 2 0.85 0.10 0.04 Matches are distributed among these distances: 28 40 0.98 29 1 0.02 ACGTcount: A:0.24, C:0.35, G:0.19, T:0.23 Consensus pattern (28 bp): ATCGGGGATACTCCAACCCCGTTACTTC Found at i:33126 original size:265 final size:262 Alignment explanation

Indices: 32655--33157 Score: 758 Period size: 265 Copynumber: 1.9 Consensus size: 262 32645 TTCTCAATTC * * * * * 32655 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA 1 TCCACAATCGGGGATACTACAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA * * 32720 TACTCCAACTCTAATTTTATTTCCAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACTC 66 TACTCCAACTCCAATTTTATTTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACTC * 32785 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT 130 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT ** * 32850 TTCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT 195 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT 32915 TTT 260 TTT * * 32918 TCCACAATCGGGGATACTACAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGA 1 TCCACAATCGGGGATACTACAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGG- * * * 32983 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAAC 63 GGATACTCCAACTCCAATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC * * * 33047 -CTCGTTATCTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGGCTT 128 TC-CGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTT * 33111 TATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG 191 TATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG 33158 TTATTTTTGA Statistics Matches: 215, Mismatches: 20, Indels: 8 0.88 0.08 0.03 Matches are distributed among these distances: 263 43 0.20 264 43 0.20 265 104 0.48 266 25 0.12 ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31 Consensus pattern (262 bp): TCCACAATCGGGGATACTACAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA TACTCCAACTCCAATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACTCC GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT TT Done.